Test case 1
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
3: Feature feature0 = new Feature(blastStreamFeature0);
4: feature0.removeFromEntry();
Test case 2
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
4: Range range0 = new Range(0, 5);
5: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
6: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
7: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
8: Entry entry0 = filteredEntryGroup0.createEntry();
9: Feature feature0 = filteredEntryGroup0.createFeature();
10: EntryChangeEvent entryChangeEvent0 = new EntryChangeEvent(entry0, feature0, 5);
11: feature0.entryChanged(entryChangeEvent0);
Test case 3
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
4: Range range0 = new Range(0, 5);
5: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
6: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
7: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
8: filteredEntryGroup0.createEntry();
9: Feature feature0 = filteredEntryGroup0.createFeature();
10: boolean boolean0 = feature0.trimStart(false, true);
11: assertFalse(boolean0);
Test case 4
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
4: Range range0 = new Range(0, 5);
5: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
6: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
7: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
8: filteredEntryGroup0.createEntry();
9: Feature feature0 = filteredEntryGroup0.createFeature();
10: String string0 = feature0.getNote();
11: assertNull(string0);
Test case 5
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
4: Range range0 = new Range(0, 5);
5: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
6: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
7: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "");
8: filteredEntryGroup0.createEntry();
9: Feature feature0 = filteredEntryGroup0.createFeature();
10: OptionChangeEvent optionChangeEvent0 = new OptionChangeEvent(simpleEntryGroup1, "");
11: feature0.optionChanged(optionChangeEvent0);
12: assertEquals("", optionChangeEvent0.getOptionName());
Test case 6
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: StringReader stringReader0 = (StringReader)feature0.toReader();
9: assertNotNull(stringReader0);
10: assertFalse(feature0.isReadOnly());
Test case 7
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.length());
4: assertEquals(0, genbankStreamSequence0.getCCount());
5: assertEquals(0, genbankStreamSequence0.getACount());
6: assertNull(genbankStreamSequence0.getHeader());
7: assertEquals(0, genbankStreamSequence0.getGCount());
8: assertEquals(2, genbankStreamSequence0.getFormatType());
9: assertEquals(0, genbankStreamSequence0.getOtherCount());
10: assertEquals(0, genbankStreamSequence0.getTCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.length());
15: assertEquals(0, genbankStreamSequence0.getCCount());
16: assertEquals(0, genbankStreamSequence0.getACount());
17: assertNull(genbankStreamSequence0.getHeader());
18: assertEquals(0, genbankStreamSequence0.getGCount());
19: assertEquals(2, genbankStreamSequence0.getFormatType());
20: assertEquals(0, genbankStreamSequence0.getOtherCount());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals(2, Bases.REVERSE);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.length());
32: assertEquals(0, genbankStreamSequence0.getCCount());
33: assertEquals(0, genbankStreamSequence0.getACount());
34: assertNull(genbankStreamSequence0.getHeader());
35: assertEquals(0, genbankStreamSequence0.getGCount());
36: assertEquals(2, genbankStreamSequence0.getFormatType());
37: assertEquals(0, genbankStreamSequence0.getOtherCount());
38: assertEquals(0, genbankStreamSequence0.getTCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals(2, Bases.REVERSE);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(5, range0.getEnd());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.length());
61: assertEquals(0, genbankStreamSequence0.getCCount());
62: assertEquals(0, genbankStreamSequence0.getACount());
63: assertNull(genbankStreamSequence0.getHeader());
64: assertEquals(0, genbankStreamSequence0.getGCount());
65: assertEquals(2, genbankStreamSequence0.getFormatType());
66: assertEquals(0, genbankStreamSequence0.getOtherCount());
67: assertEquals(0, genbankStreamSequence0.getTCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(0, range0.getStart());
73: assertEquals(5, range0.getEnd());
74: assertEquals(6, range0.getCount());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals(2, Bases.REVERSE);
82: assertEquals(5, Bases.MAX_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.length());
89: assertEquals(0, genbankStreamSequence0.getCCount());
90: assertEquals(0, genbankStreamSequence0.getACount());
91: assertNull(genbankStreamSequence0.getHeader());
92: assertEquals(0, genbankStreamSequence0.getGCount());
93: assertEquals(2, genbankStreamSequence0.getFormatType());
94: assertEquals(0, genbankStreamSequence0.getOtherCount());
95: assertEquals(0, genbankStreamSequence0.getTCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals(2, Bases.REVERSE);
104: assertEquals(5, Bases.MAX_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.length());
111: assertEquals(0, genbankStreamSequence0.getCCount());
112: assertEquals(0, genbankStreamSequence0.getACount());
113: assertNull(genbankStreamSequence0.getHeader());
114: assertEquals(0, genbankStreamSequence0.getGCount());
115: assertEquals(2, genbankStreamSequence0.getFormatType());
116: assertEquals(0, genbankStreamSequence0.getOtherCount());
117: assertEquals(0, genbankStreamSequence0.getTCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(0, range0.getStart());
123: assertEquals(5, range0.getEnd());
124: assertEquals(6, range0.getCount());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals(2, Bases.REVERSE);
136: assertEquals(5, Bases.MAX_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.length());
145: assertEquals(0, genbankStreamSequence0.getCCount());
146: assertEquals(0, genbankStreamSequence0.getACount());
147: assertNull(genbankStreamSequence0.getHeader());
148: assertEquals(0, genbankStreamSequence0.getGCount());
149: assertEquals(2, genbankStreamSequence0.getFormatType());
150: assertEquals(0, genbankStreamSequence0.getOtherCount());
151: assertEquals(0, genbankStreamSequence0.getTCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(0, range0.getStart());
157: assertEquals(5, range0.getEnd());
158: assertEquals(6, range0.getCount());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals(1, filteredEntryGroup0.size());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals(2, Bases.REVERSE);
171: assertEquals(5, Bases.MAX_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.length());
180: assertEquals(0, genbankStreamSequence0.getCCount());
181: assertEquals(0, genbankStreamSequence0.getACount());
182: assertNull(genbankStreamSequence0.getHeader());
183: assertEquals(0, genbankStreamSequence0.getGCount());
184: assertEquals(2, genbankStreamSequence0.getFormatType());
185: assertEquals(0, genbankStreamSequence0.getOtherCount());
186: assertEquals(0, genbankStreamSequence0.getTCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(0, range0.getStart());
192: assertEquals(5, range0.getEnd());
193: assertEquals(6, range0.getCount());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals(1, filteredEntryGroup0.size());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals(2, Bases.REVERSE);
206: assertEquals(5, Bases.MAX_PRIORITY);
207:
208: double double0 = feature0.get12CorrelationScore();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertEquals(0.5, double0, 0.01);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.length());
215: assertEquals(0, genbankStreamSequence0.getCCount());
216: assertEquals(0, genbankStreamSequence0.getACount());
217: assertNull(genbankStreamSequence0.getHeader());
218: assertEquals(0, genbankStreamSequence0.getGCount());
219: assertEquals(2, genbankStreamSequence0.getFormatType());
220: assertEquals(0, genbankStreamSequence0.getOtherCount());
221: assertEquals(0, genbankStreamSequence0.getTCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.getSequenceLength());
224: assertEquals(0, simpleEntryGroup0.refCount());
225: assertEquals(0, simpleEntryGroup0.size());
226: assertEquals(0, range0.getStart());
227: assertEquals(5, range0.getEnd());
228: assertEquals(6, range0.getCount());
229: assertEquals(6, simpleEntryGroup1.getSequenceLength());
230: assertEquals(1, simpleEntryGroup1.size());
231: assertEquals(0, simpleEntryGroup1.refCount());
232: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
233: assertEquals(0, filteredEntryGroup0.refCount());
234: assertEquals(1, filteredEntryGroup0.size());
235: assertEquals(6, filteredEntryGroup0.getSequenceLength());
236: assertFalse(feature0.isReadOnly());
237: assertEquals((-5), Bases.MIN_PRIORITY);
238: assertEquals(0, Bases.MEDIUM_PRIORITY);
239: assertEquals(1, Bases.FORWARD);
240: assertEquals(2, Bases.REVERSE);
241: assertEquals(5, Bases.MAX_PRIORITY);
Test case 8
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertNull(genbankStreamSequence0.getHeader());
4: assertEquals(0, genbankStreamSequence0.getACount());
5: assertEquals(0, genbankStreamSequence0.getCCount());
6: assertEquals(0, genbankStreamSequence0.getOtherCount());
7: assertEquals(0, genbankStreamSequence0.getGCount());
8: assertEquals(2, genbankStreamSequence0.getFormatType());
9: assertEquals(0, genbankStreamSequence0.length());
10: assertEquals(0, genbankStreamSequence0.getTCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertNull(genbankStreamSequence0.getHeader());
15: assertEquals(0, genbankStreamSequence0.getACount());
16: assertEquals(0, genbankStreamSequence0.getCCount());
17: assertEquals(0, genbankStreamSequence0.getOtherCount());
18: assertEquals(0, genbankStreamSequence0.getGCount());
19: assertEquals(2, genbankStreamSequence0.getFormatType());
20: assertEquals(0, genbankStreamSequence0.length());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(2, Bases.REVERSE);
27: assertEquals(1, Bases.FORWARD);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertNull(genbankStreamSequence0.getHeader());
32: assertEquals(0, genbankStreamSequence0.getACount());
33: assertEquals(0, genbankStreamSequence0.getCCount());
34: assertEquals(0, genbankStreamSequence0.getOtherCount());
35: assertEquals(0, genbankStreamSequence0.getGCount());
36: assertEquals(2, genbankStreamSequence0.getFormatType());
37: assertEquals(0, genbankStreamSequence0.length());
38: assertEquals(0, genbankStreamSequence0.getTCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.refCount());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(2, Bases.REVERSE);
47: assertEquals(1, Bases.FORWARD);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(5, range0.getEnd());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertNull(genbankStreamSequence0.getHeader());
61: assertEquals(0, genbankStreamSequence0.getACount());
62: assertEquals(0, genbankStreamSequence0.getCCount());
63: assertEquals(0, genbankStreamSequence0.getOtherCount());
64: assertEquals(0, genbankStreamSequence0.getGCount());
65: assertEquals(2, genbankStreamSequence0.getFormatType());
66: assertEquals(0, genbankStreamSequence0.length());
67: assertEquals(0, genbankStreamSequence0.getTCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.refCount());
72: assertEquals(6, range0.getCount());
73: assertEquals(5, range0.getEnd());
74: assertEquals(0, range0.getStart());
75: assertEquals(0, simpleEntryGroup1.refCount());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(5, Bases.MAX_PRIORITY);
81: assertEquals(2, Bases.REVERSE);
82: assertEquals(1, Bases.FORWARD);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertNull(genbankStreamSequence0.getHeader());
89: assertEquals(0, genbankStreamSequence0.getACount());
90: assertEquals(0, genbankStreamSequence0.getCCount());
91: assertEquals(0, genbankStreamSequence0.getOtherCount());
92: assertEquals(0, genbankStreamSequence0.getGCount());
93: assertEquals(2, genbankStreamSequence0.getFormatType());
94: assertEquals(0, genbankStreamSequence0.length());
95: assertEquals(0, genbankStreamSequence0.getTCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.refCount());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(5, Bases.MAX_PRIORITY);
103: assertEquals(2, Bases.REVERSE);
104: assertEquals(1, Bases.FORWARD);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertNull(genbankStreamSequence0.getHeader());
111: assertEquals(0, genbankStreamSequence0.getACount());
112: assertEquals(0, genbankStreamSequence0.getCCount());
113: assertEquals(0, genbankStreamSequence0.getOtherCount());
114: assertEquals(0, genbankStreamSequence0.getGCount());
115: assertEquals(2, genbankStreamSequence0.getFormatType());
116: assertEquals(0, genbankStreamSequence0.length());
117: assertEquals(0, genbankStreamSequence0.getTCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.refCount());
122: assertEquals(6, range0.getCount());
123: assertEquals(5, range0.getEnd());
124: assertEquals(0, range0.getStart());
125: assertEquals(0, simpleEntryGroup1.refCount());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals(6, filteredEntryGroup0.getSequenceLength());
129: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals(0, filteredEntryGroup0.refCount());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(5, Bases.MAX_PRIORITY);
135: assertEquals(2, Bases.REVERSE);
136: assertEquals(1, Bases.FORWARD);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertNull(genbankStreamSequence0.getHeader());
145: assertEquals(0, genbankStreamSequence0.getACount());
146: assertEquals(0, genbankStreamSequence0.getCCount());
147: assertEquals(0, genbankStreamSequence0.getOtherCount());
148: assertEquals(0, genbankStreamSequence0.getGCount());
149: assertEquals(2, genbankStreamSequence0.getFormatType());
150: assertEquals(0, genbankStreamSequence0.length());
151: assertEquals(0, genbankStreamSequence0.getTCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.refCount());
156: assertEquals(6, range0.getCount());
157: assertEquals(5, range0.getEnd());
158: assertEquals(0, range0.getStart());
159: assertEquals(0, simpleEntryGroup1.refCount());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(1, simpleEntryGroup1.size());
162: assertEquals(6, filteredEntryGroup0.getSequenceLength());
163: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
164: assertEquals(1, filteredEntryGroup0.size());
165: assertEquals(0, filteredEntryGroup0.refCount());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(5, Bases.MAX_PRIORITY);
170: assertEquals(2, Bases.REVERSE);
171: assertEquals(1, Bases.FORWARD);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertNull(genbankStreamSequence0.getHeader());
180: assertEquals(0, genbankStreamSequence0.getACount());
181: assertEquals(0, genbankStreamSequence0.getCCount());
182: assertEquals(0, genbankStreamSequence0.getOtherCount());
183: assertEquals(0, genbankStreamSequence0.getGCount());
184: assertEquals(2, genbankStreamSequence0.getFormatType());
185: assertEquals(0, genbankStreamSequence0.length());
186: assertEquals(0, genbankStreamSequence0.getTCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.size());
190: assertEquals(0, simpleEntryGroup0.refCount());
191: assertEquals(6, range0.getCount());
192: assertEquals(5, range0.getEnd());
193: assertEquals(0, range0.getStart());
194: assertEquals(0, simpleEntryGroup1.refCount());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(1, simpleEntryGroup1.size());
197: assertEquals(6, filteredEntryGroup0.getSequenceLength());
198: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
199: assertEquals(1, filteredEntryGroup0.size());
200: assertEquals(0, filteredEntryGroup0.refCount());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(5, Bases.MAX_PRIORITY);
205: assertEquals(2, Bases.REVERSE);
206: assertEquals(1, Bases.FORWARD);
207:
208: Marker marker0 = feature0.getFirstCodingBaseMarker();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(marker0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertNull(genbankStreamSequence0.getHeader());
215: assertEquals(0, genbankStreamSequence0.getACount());
216: assertEquals(0, genbankStreamSequence0.getCCount());
217: assertEquals(0, genbankStreamSequence0.getOtherCount());
218: assertEquals(0, genbankStreamSequence0.getGCount());
219: assertEquals(2, genbankStreamSequence0.getFormatType());
220: assertEquals(0, genbankStreamSequence0.length());
221: assertEquals(0, genbankStreamSequence0.getTCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.getSequenceLength());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(0, simpleEntryGroup0.refCount());
226: assertEquals(6, range0.getCount());
227: assertEquals(5, range0.getEnd());
228: assertEquals(0, range0.getStart());
229: assertEquals(0, simpleEntryGroup1.refCount());
230: assertEquals(6, simpleEntryGroup1.getSequenceLength());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals(6, filteredEntryGroup0.getSequenceLength());
233: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
234: assertEquals(1, filteredEntryGroup0.size());
235: assertEquals(0, filteredEntryGroup0.refCount());
236: assertFalse(feature0.isReadOnly());
237: assertEquals((-5), Bases.MIN_PRIORITY);
238: assertEquals(0, Bases.MEDIUM_PRIORITY);
239: assertEquals(5, Bases.MAX_PRIORITY);
240: assertEquals(2, Bases.REVERSE);
241: assertEquals(1, Bases.FORWARD);
242: assertEquals(0, Marker.LISTENER_PRIORITY);
243:
244: int int0 = feature0.getFeaturePositionFromMarker(marker0);
245: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
246: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
247: assertEquals(0, int0);
248: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
249: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
250: assertNull(genbankStreamSequence0.getHeader());
251: assertEquals(0, genbankStreamSequence0.getACount());
252: assertEquals(0, genbankStreamSequence0.getCCount());
253: assertEquals(0, genbankStreamSequence0.getOtherCount());
254: assertEquals(0, genbankStreamSequence0.getGCount());
255: assertEquals(2, genbankStreamSequence0.getFormatType());
256: assertEquals(0, genbankStreamSequence0.length());
257: assertEquals(0, genbankStreamSequence0.getTCount());
258: assertEquals(0, bases0.getLength());
259: assertEquals(0, simpleEntryGroup0.getSequenceLength());
260: assertEquals(0, simpleEntryGroup0.size());
261: assertEquals(0, simpleEntryGroup0.refCount());
262: assertEquals(6, range0.getCount());
263: assertEquals(5, range0.getEnd());
264: assertEquals(0, range0.getStart());
265: assertEquals(0, simpleEntryGroup1.refCount());
266: assertEquals(6, simpleEntryGroup1.getSequenceLength());
267: assertEquals(1, simpleEntryGroup1.size());
268: assertEquals(6, filteredEntryGroup0.getSequenceLength());
269: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
270: assertEquals(1, filteredEntryGroup0.size());
271: assertEquals(0, filteredEntryGroup0.refCount());
272: assertFalse(feature0.isReadOnly());
273: assertEquals((-5), Bases.MIN_PRIORITY);
274: assertEquals(0, Bases.MEDIUM_PRIORITY);
275: assertEquals(5, Bases.MAX_PRIORITY);
276: assertEquals(2, Bases.REVERSE);
277: assertEquals(1, Bases.FORWARD);
278: assertEquals(0, Marker.LISTENER_PRIORITY);
Test case 9
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getACount());
4: assertEquals(0, genbankStreamSequence0.getOtherCount());
5: assertNull(genbankStreamSequence0.getHeader());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertEquals(0, genbankStreamSequence0.getTCount());
8: assertEquals(0, genbankStreamSequence0.length());
9: assertEquals(0, genbankStreamSequence0.getGCount());
10: assertEquals(2, genbankStreamSequence0.getFormatType());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getACount());
15: assertEquals(0, genbankStreamSequence0.getOtherCount());
16: assertNull(genbankStreamSequence0.getHeader());
17: assertEquals(0, genbankStreamSequence0.getCCount());
18: assertEquals(0, genbankStreamSequence0.getTCount());
19: assertEquals(0, genbankStreamSequence0.length());
20: assertEquals(0, genbankStreamSequence0.getGCount());
21: assertEquals(2, genbankStreamSequence0.getFormatType());
22: assertEquals(0, bases0.getLength());
23: assertEquals(5, Bases.MAX_PRIORITY);
24: assertEquals(1, Bases.FORWARD);
25: assertEquals(2, Bases.REVERSE);
26: assertEquals((-5), Bases.MIN_PRIORITY);
27: assertEquals(0, Bases.MEDIUM_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getACount());
32: assertEquals(0, genbankStreamSequence0.getOtherCount());
33: assertNull(genbankStreamSequence0.getHeader());
34: assertEquals(0, genbankStreamSequence0.getCCount());
35: assertEquals(0, genbankStreamSequence0.getTCount());
36: assertEquals(0, genbankStreamSequence0.length());
37: assertEquals(0, genbankStreamSequence0.getGCount());
38: assertEquals(2, genbankStreamSequence0.getFormatType());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals(5, Bases.MAX_PRIORITY);
44: assertEquals(1, Bases.FORWARD);
45: assertEquals(2, Bases.REVERSE);
46: assertEquals((-5), Bases.MIN_PRIORITY);
47: assertEquals(0, Bases.MEDIUM_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(6, range0.getCount());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getACount());
61: assertEquals(0, genbankStreamSequence0.getOtherCount());
62: assertNull(genbankStreamSequence0.getHeader());
63: assertEquals(0, genbankStreamSequence0.getCCount());
64: assertEquals(0, genbankStreamSequence0.getTCount());
65: assertEquals(0, genbankStreamSequence0.length());
66: assertEquals(0, genbankStreamSequence0.getGCount());
67: assertEquals(2, genbankStreamSequence0.getFormatType());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(0, range0.getStart());
73: assertEquals(6, range0.getCount());
74: assertEquals(5, range0.getEnd());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(5, Bases.MAX_PRIORITY);
79: assertEquals(1, Bases.FORWARD);
80: assertEquals(2, Bases.REVERSE);
81: assertEquals((-5), Bases.MIN_PRIORITY);
82: assertEquals(0, Bases.MEDIUM_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getACount());
89: assertEquals(0, genbankStreamSequence0.getOtherCount());
90: assertNull(genbankStreamSequence0.getHeader());
91: assertEquals(0, genbankStreamSequence0.getCCount());
92: assertEquals(0, genbankStreamSequence0.getTCount());
93: assertEquals(0, genbankStreamSequence0.length());
94: assertEquals(0, genbankStreamSequence0.getGCount());
95: assertEquals(2, genbankStreamSequence0.getFormatType());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals(5, Bases.MAX_PRIORITY);
101: assertEquals(1, Bases.FORWARD);
102: assertEquals(2, Bases.REVERSE);
103: assertEquals((-5), Bases.MIN_PRIORITY);
104: assertEquals(0, Bases.MEDIUM_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getACount());
111: assertEquals(0, genbankStreamSequence0.getOtherCount());
112: assertNull(genbankStreamSequence0.getHeader());
113: assertEquals(0, genbankStreamSequence0.getCCount());
114: assertEquals(0, genbankStreamSequence0.getTCount());
115: assertEquals(0, genbankStreamSequence0.length());
116: assertEquals(0, genbankStreamSequence0.getGCount());
117: assertEquals(2, genbankStreamSequence0.getFormatType());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(0, range0.getStart());
123: assertEquals(6, range0.getCount());
124: assertEquals(5, range0.getEnd());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(0, filteredEntryGroup0.refCount());
129: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals(5, Bases.MAX_PRIORITY);
133: assertEquals(1, Bases.FORWARD);
134: assertEquals(2, Bases.REVERSE);
135: assertEquals((-5), Bases.MIN_PRIORITY);
136: assertEquals(0, Bases.MEDIUM_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getACount());
145: assertEquals(0, genbankStreamSequence0.getOtherCount());
146: assertNull(genbankStreamSequence0.getHeader());
147: assertEquals(0, genbankStreamSequence0.getCCount());
148: assertEquals(0, genbankStreamSequence0.getTCount());
149: assertEquals(0, genbankStreamSequence0.length());
150: assertEquals(0, genbankStreamSequence0.getGCount());
151: assertEquals(2, genbankStreamSequence0.getFormatType());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(0, range0.getStart());
157: assertEquals(6, range0.getCount());
158: assertEquals(5, range0.getEnd());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(0, filteredEntryGroup0.refCount());
163: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
164: assertEquals(1, filteredEntryGroup0.size());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(5, Bases.MAX_PRIORITY);
168: assertEquals(1, Bases.FORWARD);
169: assertEquals(2, Bases.REVERSE);
170: assertEquals((-5), Bases.MIN_PRIORITY);
171: assertEquals(0, Bases.MEDIUM_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getACount());
180: assertEquals(0, genbankStreamSequence0.getOtherCount());
181: assertNull(genbankStreamSequence0.getHeader());
182: assertEquals(0, genbankStreamSequence0.getCCount());
183: assertEquals(0, genbankStreamSequence0.getTCount());
184: assertEquals(0, genbankStreamSequence0.length());
185: assertEquals(0, genbankStreamSequence0.getGCount());
186: assertEquals(2, genbankStreamSequence0.getFormatType());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(0, range0.getStart());
192: assertEquals(6, range0.getCount());
193: assertEquals(5, range0.getEnd());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(0, filteredEntryGroup0.refCount());
198: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
199: assertEquals(1, filteredEntryGroup0.size());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(5, Bases.MAX_PRIORITY);
203: assertEquals(1, Bases.FORWARD);
204: assertEquals(2, Bases.REVERSE);
205: assertEquals((-5), Bases.MIN_PRIORITY);
206: assertEquals(0, Bases.MEDIUM_PRIORITY);
207:
208: boolean boolean0 = feature0.hasValidStartCodon();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertTrue(boolean0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.getACount());
215: assertEquals(0, genbankStreamSequence0.getOtherCount());
216: assertNull(genbankStreamSequence0.getHeader());
217: assertEquals(0, genbankStreamSequence0.getCCount());
218: assertEquals(0, genbankStreamSequence0.getTCount());
219: assertEquals(0, genbankStreamSequence0.length());
220: assertEquals(0, genbankStreamSequence0.getGCount());
221: assertEquals(2, genbankStreamSequence0.getFormatType());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.getSequenceLength());
224: assertEquals(0, simpleEntryGroup0.refCount());
225: assertEquals(0, simpleEntryGroup0.size());
226: assertEquals(0, range0.getStart());
227: assertEquals(6, range0.getCount());
228: assertEquals(5, range0.getEnd());
229: assertEquals(1, simpleEntryGroup1.size());
230: assertEquals(6, simpleEntryGroup1.getSequenceLength());
231: assertEquals(0, simpleEntryGroup1.refCount());
232: assertEquals(0, filteredEntryGroup0.refCount());
233: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
234: assertEquals(1, filteredEntryGroup0.size());
235: assertEquals(6, filteredEntryGroup0.getSequenceLength());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(5, Bases.MAX_PRIORITY);
238: assertEquals(1, Bases.FORWARD);
239: assertEquals(2, Bases.REVERSE);
240: assertEquals((-5), Bases.MIN_PRIORITY);
241: assertEquals(0, Bases.MEDIUM_PRIORITY);
Test case 10
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(2, genbankStreamSequence0.getFormatType());
4: assertEquals(0, genbankStreamSequence0.getTCount());
5: assertEquals(0, genbankStreamSequence0.length());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertEquals(0, genbankStreamSequence0.getOtherCount());
8: assertEquals(0, genbankStreamSequence0.getGCount());
9: assertNull(genbankStreamSequence0.getHeader());
10: assertEquals(0, genbankStreamSequence0.getACount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, genbankStreamSequence0.getFormatType());
15: assertEquals(0, genbankStreamSequence0.getTCount());
16: assertEquals(0, genbankStreamSequence0.length());
17: assertEquals(0, genbankStreamSequence0.getCCount());
18: assertEquals(0, genbankStreamSequence0.getOtherCount());
19: assertEquals(0, genbankStreamSequence0.getGCount());
20: assertNull(genbankStreamSequence0.getHeader());
21: assertEquals(0, genbankStreamSequence0.getACount());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(2, Bases.REVERSE);
27: assertEquals(1, Bases.FORWARD);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(2, genbankStreamSequence0.getFormatType());
32: assertEquals(0, genbankStreamSequence0.getTCount());
33: assertEquals(0, genbankStreamSequence0.length());
34: assertEquals(0, genbankStreamSequence0.getCCount());
35: assertEquals(0, genbankStreamSequence0.getOtherCount());
36: assertEquals(0, genbankStreamSequence0.getGCount());
37: assertNull(genbankStreamSequence0.getHeader());
38: assertEquals(0, genbankStreamSequence0.getACount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(2, Bases.REVERSE);
47: assertEquals(1, Bases.FORWARD);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(0, range0.getStart());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(2, genbankStreamSequence0.getFormatType());
61: assertEquals(0, genbankStreamSequence0.getTCount());
62: assertEquals(0, genbankStreamSequence0.length());
63: assertEquals(0, genbankStreamSequence0.getCCount());
64: assertEquals(0, genbankStreamSequence0.getOtherCount());
65: assertEquals(0, genbankStreamSequence0.getGCount());
66: assertNull(genbankStreamSequence0.getHeader());
67: assertEquals(0, genbankStreamSequence0.getACount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(6, range0.getCount());
73: assertEquals(0, range0.getStart());
74: assertEquals(5, range0.getEnd());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(5, Bases.MAX_PRIORITY);
81: assertEquals(2, Bases.REVERSE);
82: assertEquals(1, Bases.FORWARD);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(2, genbankStreamSequence0.getFormatType());
89: assertEquals(0, genbankStreamSequence0.getTCount());
90: assertEquals(0, genbankStreamSequence0.length());
91: assertEquals(0, genbankStreamSequence0.getCCount());
92: assertEquals(0, genbankStreamSequence0.getOtherCount());
93: assertEquals(0, genbankStreamSequence0.getGCount());
94: assertNull(genbankStreamSequence0.getHeader());
95: assertEquals(0, genbankStreamSequence0.getACount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(5, Bases.MAX_PRIORITY);
103: assertEquals(2, Bases.REVERSE);
104: assertEquals(1, Bases.FORWARD);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(2, genbankStreamSequence0.getFormatType());
111: assertEquals(0, genbankStreamSequence0.getTCount());
112: assertEquals(0, genbankStreamSequence0.length());
113: assertEquals(0, genbankStreamSequence0.getCCount());
114: assertEquals(0, genbankStreamSequence0.getOtherCount());
115: assertEquals(0, genbankStreamSequence0.getGCount());
116: assertNull(genbankStreamSequence0.getHeader());
117: assertEquals(0, genbankStreamSequence0.getACount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(6, range0.getCount());
123: assertEquals(0, range0.getStart());
124: assertEquals(5, range0.getEnd());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(0, filteredEntryGroup0.size());
129: assertEquals("", filteredEntryGroup0.getFilterName());
130: assertEquals(0, filteredEntryGroup0.refCount());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(5, Bases.MAX_PRIORITY);
135: assertEquals(2, Bases.REVERSE);
136: assertEquals(1, Bases.FORWARD);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(2, genbankStreamSequence0.getFormatType());
145: assertEquals(0, genbankStreamSequence0.getTCount());
146: assertEquals(0, genbankStreamSequence0.length());
147: assertEquals(0, genbankStreamSequence0.getCCount());
148: assertEquals(0, genbankStreamSequence0.getOtherCount());
149: assertEquals(0, genbankStreamSequence0.getGCount());
150: assertNull(genbankStreamSequence0.getHeader());
151: assertEquals(0, genbankStreamSequence0.getACount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(6, range0.getCount());
157: assertEquals(0, range0.getStart());
158: assertEquals(5, range0.getEnd());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals("", filteredEntryGroup0.getFilterName());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals(6, filteredEntryGroup0.getSequenceLength());
165: assertEquals(1, filteredEntryGroup0.size());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(5, Bases.MAX_PRIORITY);
170: assertEquals(2, Bases.REVERSE);
171: assertEquals(1, Bases.FORWARD);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(2, genbankStreamSequence0.getFormatType());
180: assertEquals(0, genbankStreamSequence0.getTCount());
181: assertEquals(0, genbankStreamSequence0.length());
182: assertEquals(0, genbankStreamSequence0.getCCount());
183: assertEquals(0, genbankStreamSequence0.getOtherCount());
184: assertEquals(0, genbankStreamSequence0.getGCount());
185: assertNull(genbankStreamSequence0.getHeader());
186: assertEquals(0, genbankStreamSequence0.getACount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(6, range0.getCount());
192: assertEquals(0, range0.getStart());
193: assertEquals(5, range0.getEnd());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals("", filteredEntryGroup0.getFilterName());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals(6, filteredEntryGroup0.getSequenceLength());
200: assertEquals(1, filteredEntryGroup0.size());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(5, Bases.MAX_PRIORITY);
205: assertEquals(2, Bases.REVERSE);
206: assertEquals(1, Bases.FORWARD);
207:
208: feature0.moveTo(entry0, false);
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
212: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
213: assertEquals(2, genbankStreamSequence0.getFormatType());
214: assertEquals(0, genbankStreamSequence0.getTCount());
215: assertEquals(0, genbankStreamSequence0.length());
216: assertEquals(0, genbankStreamSequence0.getCCount());
217: assertEquals(0, genbankStreamSequence0.getOtherCount());
218: assertEquals(0, genbankStreamSequence0.getGCount());
219: assertNull(genbankStreamSequence0.getHeader());
220: assertEquals(0, genbankStreamSequence0.getACount());
221: assertEquals(0, bases0.getLength());
222: assertEquals(0, simpleEntryGroup0.getSequenceLength());
223: assertEquals(0, simpleEntryGroup0.refCount());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(6, range0.getCount());
226: assertEquals(0, range0.getStart());
227: assertEquals(5, range0.getEnd());
228: assertEquals(6, simpleEntryGroup1.getSequenceLength());
229: assertEquals(1, simpleEntryGroup1.size());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals("", filteredEntryGroup0.getFilterName());
232: assertEquals(0, filteredEntryGroup0.refCount());
233: assertEquals(6, filteredEntryGroup0.getSequenceLength());
234: assertEquals(1, filteredEntryGroup0.size());
235: assertFalse(entry0.isReadOnly());
236: assertFalse(feature0.isReadOnly());
237: assertEquals((-5), Bases.MIN_PRIORITY);
238: assertEquals(0, Bases.MEDIUM_PRIORITY);
239: assertEquals(5, Bases.MAX_PRIORITY);
240: assertEquals(2, Bases.REVERSE);
241: assertEquals(1, Bases.FORWARD);
Test case 11
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getCCount());
4: assertNull(genbankStreamSequence0.getHeader());
5: assertEquals(0, genbankStreamSequence0.length());
6: assertEquals(0, genbankStreamSequence0.getOtherCount());
7: assertEquals(0, genbankStreamSequence0.getACount());
8: assertEquals(2, genbankStreamSequence0.getFormatType());
9: assertEquals(0, genbankStreamSequence0.getGCount());
10: assertEquals(0, genbankStreamSequence0.getTCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getCCount());
15: assertNull(genbankStreamSequence0.getHeader());
16: assertEquals(0, genbankStreamSequence0.length());
17: assertEquals(0, genbankStreamSequence0.getOtherCount());
18: assertEquals(0, genbankStreamSequence0.getACount());
19: assertEquals(2, genbankStreamSequence0.getFormatType());
20: assertEquals(0, genbankStreamSequence0.getGCount());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(2, Bases.REVERSE);
24: assertEquals(1, Bases.FORWARD);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals((-5), Bases.MIN_PRIORITY);
27: assertEquals(0, Bases.MEDIUM_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getCCount());
32: assertNull(genbankStreamSequence0.getHeader());
33: assertEquals(0, genbankStreamSequence0.length());
34: assertEquals(0, genbankStreamSequence0.getOtherCount());
35: assertEquals(0, genbankStreamSequence0.getACount());
36: assertEquals(2, genbankStreamSequence0.getFormatType());
37: assertEquals(0, genbankStreamSequence0.getGCount());
38: assertEquals(0, genbankStreamSequence0.getTCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals(2, Bases.REVERSE);
44: assertEquals(1, Bases.FORWARD);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals((-5), Bases.MIN_PRIORITY);
47: assertEquals(0, Bases.MEDIUM_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(5, range0.getEnd());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getCCount());
61: assertNull(genbankStreamSequence0.getHeader());
62: assertEquals(0, genbankStreamSequence0.length());
63: assertEquals(0, genbankStreamSequence0.getOtherCount());
64: assertEquals(0, genbankStreamSequence0.getACount());
65: assertEquals(2, genbankStreamSequence0.getFormatType());
66: assertEquals(0, genbankStreamSequence0.getGCount());
67: assertEquals(0, genbankStreamSequence0.getTCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(6, range0.getCount());
73: assertEquals(5, range0.getEnd());
74: assertEquals(0, range0.getStart());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(2, Bases.REVERSE);
79: assertEquals(1, Bases.FORWARD);
80: assertEquals(5, Bases.MAX_PRIORITY);
81: assertEquals((-5), Bases.MIN_PRIORITY);
82: assertEquals(0, Bases.MEDIUM_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getCCount());
89: assertNull(genbankStreamSequence0.getHeader());
90: assertEquals(0, genbankStreamSequence0.length());
91: assertEquals(0, genbankStreamSequence0.getOtherCount());
92: assertEquals(0, genbankStreamSequence0.getACount());
93: assertEquals(2, genbankStreamSequence0.getFormatType());
94: assertEquals(0, genbankStreamSequence0.getGCount());
95: assertEquals(0, genbankStreamSequence0.getTCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals(2, Bases.REVERSE);
101: assertEquals(1, Bases.FORWARD);
102: assertEquals(5, Bases.MAX_PRIORITY);
103: assertEquals((-5), Bases.MIN_PRIORITY);
104: assertEquals(0, Bases.MEDIUM_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getCCount());
111: assertNull(genbankStreamSequence0.getHeader());
112: assertEquals(0, genbankStreamSequence0.length());
113: assertEquals(0, genbankStreamSequence0.getOtherCount());
114: assertEquals(0, genbankStreamSequence0.getACount());
115: assertEquals(2, genbankStreamSequence0.getFormatType());
116: assertEquals(0, genbankStreamSequence0.getGCount());
117: assertEquals(0, genbankStreamSequence0.getTCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(6, range0.getCount());
123: assertEquals(5, range0.getEnd());
124: assertEquals(0, range0.getStart());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(6, filteredEntryGroup0.getSequenceLength());
129: assertEquals(0, filteredEntryGroup0.size());
130: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
131: assertEquals(0, filteredEntryGroup0.refCount());
132: assertEquals(2, Bases.REVERSE);
133: assertEquals(1, Bases.FORWARD);
134: assertEquals(5, Bases.MAX_PRIORITY);
135: assertEquals((-5), Bases.MIN_PRIORITY);
136: assertEquals(0, Bases.MEDIUM_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getCCount());
145: assertNull(genbankStreamSequence0.getHeader());
146: assertEquals(0, genbankStreamSequence0.length());
147: assertEquals(0, genbankStreamSequence0.getOtherCount());
148: assertEquals(0, genbankStreamSequence0.getACount());
149: assertEquals(2, genbankStreamSequence0.getFormatType());
150: assertEquals(0, genbankStreamSequence0.getGCount());
151: assertEquals(0, genbankStreamSequence0.getTCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(6, range0.getCount());
157: assertEquals(5, range0.getEnd());
158: assertEquals(0, range0.getStart());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(6, filteredEntryGroup0.getSequenceLength());
163: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
164: assertEquals(1, filteredEntryGroup0.size());
165: assertEquals(0, filteredEntryGroup0.refCount());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(2, Bases.REVERSE);
168: assertEquals(1, Bases.FORWARD);
169: assertEquals(5, Bases.MAX_PRIORITY);
170: assertEquals((-5), Bases.MIN_PRIORITY);
171: assertEquals(0, Bases.MEDIUM_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getCCount());
180: assertNull(genbankStreamSequence0.getHeader());
181: assertEquals(0, genbankStreamSequence0.length());
182: assertEquals(0, genbankStreamSequence0.getOtherCount());
183: assertEquals(0, genbankStreamSequence0.getACount());
184: assertEquals(2, genbankStreamSequence0.getFormatType());
185: assertEquals(0, genbankStreamSequence0.getGCount());
186: assertEquals(0, genbankStreamSequence0.getTCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.size());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(6, range0.getCount());
192: assertEquals(5, range0.getEnd());
193: assertEquals(0, range0.getStart());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(6, filteredEntryGroup0.getSequenceLength());
198: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
199: assertEquals(1, filteredEntryGroup0.size());
200: assertEquals(0, filteredEntryGroup0.refCount());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(2, Bases.REVERSE);
203: assertEquals(1, Bases.FORWARD);
204: assertEquals(5, Bases.MAX_PRIORITY);
205: assertEquals((-5), Bases.MIN_PRIORITY);
206: assertEquals(0, Bases.MEDIUM_PRIORITY);
207:
208: PipedWriter pipedWriter0 = new PipedWriter();
209: assertNotNull(pipedWriter0);
210:
211: MockPrintWriter mockPrintWriter0 = new MockPrintWriter(pipedWriter0, false);
212: assertNotNull(mockPrintWriter0);
213:
214: feature0.writeAminoAcidsOfFeature(mockPrintWriter0);
215: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
216: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
217: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
218: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
219: assertEquals(0, genbankStreamSequence0.getCCount());
220: assertNull(genbankStreamSequence0.getHeader());
221: assertEquals(0, genbankStreamSequence0.length());
222: assertEquals(0, genbankStreamSequence0.getOtherCount());
223: assertEquals(0, genbankStreamSequence0.getACount());
224: assertEquals(2, genbankStreamSequence0.getFormatType());
225: assertEquals(0, genbankStreamSequence0.getGCount());
226: assertEquals(0, genbankStreamSequence0.getTCount());
227: assertEquals(0, bases0.getLength());
228: assertEquals(0, simpleEntryGroup0.refCount());
229: assertEquals(0, simpleEntryGroup0.size());
230: assertEquals(0, simpleEntryGroup0.getSequenceLength());
231: assertEquals(6, range0.getCount());
232: assertEquals(5, range0.getEnd());
233: assertEquals(0, range0.getStart());
234: assertEquals(1, simpleEntryGroup1.size());
235: assertEquals(6, simpleEntryGroup1.getSequenceLength());
236: assertEquals(0, simpleEntryGroup1.refCount());
237: assertEquals(6, filteredEntryGroup0.getSequenceLength());
238: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
239: assertEquals(1, filteredEntryGroup0.size());
240: assertEquals(0, filteredEntryGroup0.refCount());
241: assertFalse(feature0.isReadOnly());
242: assertEquals(2, Bases.REVERSE);
243: assertEquals(1, Bases.FORWARD);
244: assertEquals(5, Bases.MAX_PRIORITY);
245: assertEquals((-5), Bases.MIN_PRIORITY);
246: assertEquals(0, Bases.MEDIUM_PRIORITY);
Test case 12
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getGCount());
4: assertEquals(0, genbankStreamSequence0.getACount());
5: assertEquals(2, genbankStreamSequence0.getFormatType());
6: assertEquals(0, genbankStreamSequence0.length());
7: assertNull(genbankStreamSequence0.getHeader());
8: assertEquals(0, genbankStreamSequence0.getCCount());
9: assertEquals(0, genbankStreamSequence0.getTCount());
10: assertEquals(0, genbankStreamSequence0.getOtherCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getGCount());
15: assertEquals(0, genbankStreamSequence0.getACount());
16: assertEquals(2, genbankStreamSequence0.getFormatType());
17: assertEquals(0, genbankStreamSequence0.length());
18: assertNull(genbankStreamSequence0.getHeader());
19: assertEquals(0, genbankStreamSequence0.getCCount());
20: assertEquals(0, genbankStreamSequence0.getTCount());
21: assertEquals(0, genbankStreamSequence0.getOtherCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(1, Bases.FORWARD);
24: assertEquals((-5), Bases.MIN_PRIORITY);
25: assertEquals(0, Bases.MEDIUM_PRIORITY);
26: assertEquals(5, Bases.MAX_PRIORITY);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getGCount());
32: assertEquals(0, genbankStreamSequence0.getACount());
33: assertEquals(2, genbankStreamSequence0.getFormatType());
34: assertEquals(0, genbankStreamSequence0.length());
35: assertNull(genbankStreamSequence0.getHeader());
36: assertEquals(0, genbankStreamSequence0.getCCount());
37: assertEquals(0, genbankStreamSequence0.getTCount());
38: assertEquals(0, genbankStreamSequence0.getOtherCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals(1, Bases.FORWARD);
44: assertEquals((-5), Bases.MIN_PRIORITY);
45: assertEquals(0, Bases.MEDIUM_PRIORITY);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(0, range0.getStart());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getGCount());
61: assertEquals(0, genbankStreamSequence0.getACount());
62: assertEquals(2, genbankStreamSequence0.getFormatType());
63: assertEquals(0, genbankStreamSequence0.length());
64: assertNull(genbankStreamSequence0.getHeader());
65: assertEquals(0, genbankStreamSequence0.getCCount());
66: assertEquals(0, genbankStreamSequence0.getTCount());
67: assertEquals(0, genbankStreamSequence0.getOtherCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(6, range0.getCount());
73: assertEquals(0, range0.getStart());
74: assertEquals(5, range0.getEnd());
75: assertEquals(0, simpleEntryGroup1.refCount());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(6, simpleEntryGroup1.getSequenceLength());
78: assertEquals(1, Bases.FORWARD);
79: assertEquals((-5), Bases.MIN_PRIORITY);
80: assertEquals(0, Bases.MEDIUM_PRIORITY);
81: assertEquals(5, Bases.MAX_PRIORITY);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getGCount());
89: assertEquals(0, genbankStreamSequence0.getACount());
90: assertEquals(2, genbankStreamSequence0.getFormatType());
91: assertEquals(0, genbankStreamSequence0.length());
92: assertNull(genbankStreamSequence0.getHeader());
93: assertEquals(0, genbankStreamSequence0.getCCount());
94: assertEquals(0, genbankStreamSequence0.getTCount());
95: assertEquals(0, genbankStreamSequence0.getOtherCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals(1, Bases.FORWARD);
101: assertEquals((-5), Bases.MIN_PRIORITY);
102: assertEquals(0, Bases.MEDIUM_PRIORITY);
103: assertEquals(5, Bases.MAX_PRIORITY);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getGCount());
111: assertEquals(0, genbankStreamSequence0.getACount());
112: assertEquals(2, genbankStreamSequence0.getFormatType());
113: assertEquals(0, genbankStreamSequence0.length());
114: assertNull(genbankStreamSequence0.getHeader());
115: assertEquals(0, genbankStreamSequence0.getCCount());
116: assertEquals(0, genbankStreamSequence0.getTCount());
117: assertEquals(0, genbankStreamSequence0.getOtherCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(6, range0.getCount());
123: assertEquals(0, range0.getStart());
124: assertEquals(5, range0.getEnd());
125: assertEquals(0, simpleEntryGroup1.refCount());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(6, simpleEntryGroup1.getSequenceLength());
128: assertEquals(0, filteredEntryGroup0.refCount());
129: assertEquals(0, filteredEntryGroup0.size());
130: assertEquals(6, filteredEntryGroup0.getSequenceLength());
131: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
132: assertEquals(1, Bases.FORWARD);
133: assertEquals((-5), Bases.MIN_PRIORITY);
134: assertEquals(0, Bases.MEDIUM_PRIORITY);
135: assertEquals(5, Bases.MAX_PRIORITY);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getGCount());
145: assertEquals(0, genbankStreamSequence0.getACount());
146: assertEquals(2, genbankStreamSequence0.getFormatType());
147: assertEquals(0, genbankStreamSequence0.length());
148: assertNull(genbankStreamSequence0.getHeader());
149: assertEquals(0, genbankStreamSequence0.getCCount());
150: assertEquals(0, genbankStreamSequence0.getTCount());
151: assertEquals(0, genbankStreamSequence0.getOtherCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(6, range0.getCount());
157: assertEquals(0, range0.getStart());
158: assertEquals(5, range0.getEnd());
159: assertEquals(0, simpleEntryGroup1.refCount());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(6, simpleEntryGroup1.getSequenceLength());
162: assertEquals(0, filteredEntryGroup0.refCount());
163: assertEquals(6, filteredEntryGroup0.getSequenceLength());
164: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
165: assertEquals(1, filteredEntryGroup0.size());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(1, Bases.FORWARD);
168: assertEquals((-5), Bases.MIN_PRIORITY);
169: assertEquals(0, Bases.MEDIUM_PRIORITY);
170: assertEquals(5, Bases.MAX_PRIORITY);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getGCount());
180: assertEquals(0, genbankStreamSequence0.getACount());
181: assertEquals(2, genbankStreamSequence0.getFormatType());
182: assertEquals(0, genbankStreamSequence0.length());
183: assertNull(genbankStreamSequence0.getHeader());
184: assertEquals(0, genbankStreamSequence0.getCCount());
185: assertEquals(0, genbankStreamSequence0.getTCount());
186: assertEquals(0, genbankStreamSequence0.getOtherCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(6, range0.getCount());
192: assertEquals(0, range0.getStart());
193: assertEquals(5, range0.getEnd());
194: assertEquals(0, simpleEntryGroup1.refCount());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(6, simpleEntryGroup1.getSequenceLength());
197: assertEquals(0, filteredEntryGroup0.refCount());
198: assertEquals(6, filteredEntryGroup0.getSequenceLength());
199: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
200: assertEquals(1, filteredEntryGroup0.size());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(1, Bases.FORWARD);
203: assertEquals((-5), Bases.MIN_PRIORITY);
204: assertEquals(0, Bases.MEDIUM_PRIORITY);
205: assertEquals(5, Bases.MAX_PRIORITY);
206: assertEquals(2, Bases.REVERSE);
207:
208: String string0 = feature0.getDownstreamBases(2);
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(string0);
212: assertEquals("", string0);
213: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
214: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
215: assertEquals(0, genbankStreamSequence0.getGCount());
216: assertEquals(0, genbankStreamSequence0.getACount());
217: assertEquals(2, genbankStreamSequence0.getFormatType());
218: assertEquals(0, genbankStreamSequence0.length());
219: assertNull(genbankStreamSequence0.getHeader());
220: assertEquals(0, genbankStreamSequence0.getCCount());
221: assertEquals(0, genbankStreamSequence0.getTCount());
222: assertEquals(0, genbankStreamSequence0.getOtherCount());
223: assertEquals(0, bases0.getLength());
224: assertEquals(0, simpleEntryGroup0.refCount());
225: assertEquals(0, simpleEntryGroup0.getSequenceLength());
226: assertEquals(0, simpleEntryGroup0.size());
227: assertEquals(6, range0.getCount());
228: assertEquals(0, range0.getStart());
229: assertEquals(5, range0.getEnd());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals(6, simpleEntryGroup1.getSequenceLength());
233: assertEquals(0, filteredEntryGroup0.refCount());
234: assertEquals(6, filteredEntryGroup0.getSequenceLength());
235: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
236: assertEquals(1, filteredEntryGroup0.size());
237: assertFalse(feature0.isReadOnly());
238: assertEquals(1, Bases.FORWARD);
239: assertEquals((-5), Bases.MIN_PRIORITY);
240: assertEquals(0, Bases.MEDIUM_PRIORITY);
241: assertEquals(5, Bases.MAX_PRIORITY);
242: assertEquals(2, Bases.REVERSE);
Test case 13
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.markerChanged((MarkerChangeEvent) null);
Test case 14
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.resetColour();
12: assertFalse(feature0.isReadOnly());
Test case 15
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: boolean boolean0 = feature0.isReadOnly();
12: assertFalse(boolean0);
13: assertFalse(feature0.isReadOnly());
Test case 16
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence(" ~psW,9{eMZ?#");
2: assertNotNull(emblStreamSequence0);
3: assertEquals(0, emblStreamSequence0.getGCount());
4: assertEquals(0, emblStreamSequence0.getACount());
5: assertEquals(0, emblStreamSequence0.getCCount());
6: assertEquals(13, emblStreamSequence0.getOtherCount());
7: assertNull(emblStreamSequence0.getHeader());
8: assertEquals(1, emblStreamSequence0.getFormatType());
9: assertEquals(13, emblStreamSequence0.length());
10: assertEquals(0, emblStreamSequence0.getTCount());
11:
12: Bases bases0 = new Bases(emblStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, emblStreamSequence0.getGCount());
15: assertEquals(0, emblStreamSequence0.getACount());
16: assertEquals(0, emblStreamSequence0.getCCount());
17: assertEquals(13, emblStreamSequence0.getOtherCount());
18: assertNull(emblStreamSequence0.getHeader());
19: assertEquals(1, emblStreamSequence0.getFormatType());
20: assertEquals(13, emblStreamSequence0.length());
21: assertEquals(0, emblStreamSequence0.getTCount());
22: assertEquals(13, bases0.getLength());
23: assertEquals(1, Bases.FORWARD);
24: assertEquals((-5), Bases.MIN_PRIORITY);
25: assertEquals(0, Bases.MEDIUM_PRIORITY);
26: assertEquals(5, Bases.MAX_PRIORITY);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, emblStreamSequence0.getGCount());
32: assertEquals(0, emblStreamSequence0.getACount());
33: assertEquals(0, emblStreamSequence0.getCCount());
34: assertEquals(13, emblStreamSequence0.getOtherCount());
35: assertNull(emblStreamSequence0.getHeader());
36: assertEquals(1, emblStreamSequence0.getFormatType());
37: assertEquals(13, emblStreamSequence0.length());
38: assertEquals(0, emblStreamSequence0.getTCount());
39: assertEquals(13, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(13, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals(1, Bases.FORWARD);
44: assertEquals((-5), Bases.MIN_PRIORITY);
45: assertEquals(0, Bases.MEDIUM_PRIORITY);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48:
49: Entry entry0 = simpleEntryGroup0.createEntry(" ~psW,9{eMZ?#");
50: assertNotNull(entry0);
51: assertEquals(0, emblStreamSequence0.getGCount());
52: assertEquals(0, emblStreamSequence0.getACount());
53: assertEquals(0, emblStreamSequence0.getCCount());
54: assertEquals(13, emblStreamSequence0.getOtherCount());
55: assertNull(emblStreamSequence0.getHeader());
56: assertEquals(1, emblStreamSequence0.getFormatType());
57: assertEquals(13, emblStreamSequence0.length());
58: assertEquals(0, emblStreamSequence0.getTCount());
59: assertEquals(13, bases0.getLength());
60: assertEquals(0, simpleEntryGroup0.refCount());
61: assertEquals(13, simpleEntryGroup0.getSequenceLength());
62: assertEquals(1, simpleEntryGroup0.size());
63: assertFalse(entry0.isReadOnly());
64: assertEquals(1, Bases.FORWARD);
65: assertEquals((-5), Bases.MIN_PRIORITY);
66: assertEquals(0, Bases.MEDIUM_PRIORITY);
67: assertEquals(5, Bases.MAX_PRIORITY);
68: assertEquals(2, Bases.REVERSE);
69:
70: Range range0 = new Range((-1069), 1);
71: assertNotNull(range0);
72: assertEquals(1, range0.getEnd());
73: assertEquals((-1069), range0.getStart());
74: assertEquals(1071, range0.getCount());
75:
76: FeatureVector featureVector0 = entry0.getFeaturesInRange(range0);
77: assertNotNull(featureVector0);
78: assertEquals(0, emblStreamSequence0.getGCount());
79: assertEquals(0, emblStreamSequence0.getACount());
80: assertEquals(0, emblStreamSequence0.getCCount());
81: assertEquals(13, emblStreamSequence0.getOtherCount());
82: assertNull(emblStreamSequence0.getHeader());
83: assertEquals(1, emblStreamSequence0.getFormatType());
84: assertEquals(13, emblStreamSequence0.length());
85: assertEquals(0, emblStreamSequence0.getTCount());
86: assertEquals(13, bases0.getLength());
87: assertEquals(0, simpleEntryGroup0.refCount());
88: assertEquals(13, simpleEntryGroup0.getSequenceLength());
89: assertEquals(1, simpleEntryGroup0.size());
90: assertFalse(entry0.isReadOnly());
91: assertEquals(1, range0.getEnd());
92: assertEquals((-1069), range0.getStart());
93: assertEquals(1071, range0.getCount());
94: assertEquals(1, Bases.FORWARD);
95: assertEquals((-5), Bases.MIN_PRIORITY);
96: assertEquals(0, Bases.MEDIUM_PRIORITY);
97: assertEquals(5, Bases.MAX_PRIORITY);
98: assertEquals(2, Bases.REVERSE);
99:
100: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup0, featureVector0, "product");
101: assertNotNull(filteredEntryGroup0);
102: assertEquals(0, emblStreamSequence0.getGCount());
103: assertEquals(0, emblStreamSequence0.getACount());
104: assertEquals(0, emblStreamSequence0.getCCount());
105: assertEquals(13, emblStreamSequence0.getOtherCount());
106: assertNull(emblStreamSequence0.getHeader());
107: assertEquals(1, emblStreamSequence0.getFormatType());
108: assertEquals(13, emblStreamSequence0.length());
109: assertEquals(0, emblStreamSequence0.getTCount());
110: assertEquals(13, bases0.getLength());
111: assertEquals(0, simpleEntryGroup0.refCount());
112: assertEquals(13, simpleEntryGroup0.getSequenceLength());
113: assertEquals(1, simpleEntryGroup0.size());
114: assertFalse(entry0.isReadOnly());
115: assertEquals(1, range0.getEnd());
116: assertEquals((-1069), range0.getStart());
117: assertEquals(1071, range0.getCount());
118: assertEquals(1, filteredEntryGroup0.size());
119: assertEquals("product", filteredEntryGroup0.getFilterName());
120: assertEquals(13, filteredEntryGroup0.getSequenceLength());
121: assertEquals(0, filteredEntryGroup0.refCount());
122: assertEquals(1, Bases.FORWARD);
123: assertEquals((-5), Bases.MIN_PRIORITY);
124: assertEquals(0, Bases.MEDIUM_PRIORITY);
125: assertEquals(5, Bases.MAX_PRIORITY);
126: assertEquals(2, Bases.REVERSE);
127:
128: Feature feature0 = filteredEntryGroup0.createFeature();
129: assertNotNull(feature0);
130: assertEquals(0, emblStreamSequence0.getGCount());
131: assertEquals(0, emblStreamSequence0.getACount());
132: assertEquals(0, emblStreamSequence0.getCCount());
133: assertEquals(13, emblStreamSequence0.getOtherCount());
134: assertNull(emblStreamSequence0.getHeader());
135: assertEquals(1, emblStreamSequence0.getFormatType());
136: assertEquals(13, emblStreamSequence0.length());
137: assertEquals(0, emblStreamSequence0.getTCount());
138: assertEquals(13, bases0.getLength());
139: assertEquals(0, simpleEntryGroup0.refCount());
140: assertEquals(13, simpleEntryGroup0.getSequenceLength());
141: assertEquals(1, simpleEntryGroup0.size());
142: assertFalse(entry0.isReadOnly());
143: assertEquals(1, range0.getEnd());
144: assertEquals((-1069), range0.getStart());
145: assertEquals(1071, range0.getCount());
146: assertEquals(1, filteredEntryGroup0.size());
147: assertEquals("product", filteredEntryGroup0.getFilterName());
148: assertEquals(13, filteredEntryGroup0.getSequenceLength());
149: assertEquals(0, filteredEntryGroup0.refCount());
150: assertFalse(feature0.isReadOnly());
151: assertEquals(1, Bases.FORWARD);
152: assertEquals((-5), Bases.MIN_PRIORITY);
153: assertEquals(0, Bases.MEDIUM_PRIORITY);
154: assertEquals(5, Bases.MAX_PRIORITY);
155: assertEquals(2, Bases.REVERSE);
156:
157: Range range1 = feature0.getMaxRawRange();
158: assertFalse(range1.equals((Object)range0));
159: assertNotNull(range1);
160: assertNotSame(range0, range1);
161: assertNotSame(range1, range0);
162: assertEquals(0, emblStreamSequence0.getGCount());
163: assertEquals(0, emblStreamSequence0.getACount());
164: assertEquals(0, emblStreamSequence0.getCCount());
165: assertEquals(13, emblStreamSequence0.getOtherCount());
166: assertNull(emblStreamSequence0.getHeader());
167: assertEquals(1, emblStreamSequence0.getFormatType());
168: assertEquals(13, emblStreamSequence0.length());
169: assertEquals(0, emblStreamSequence0.getTCount());
170: assertEquals(13, bases0.getLength());
171: assertEquals(0, simpleEntryGroup0.refCount());
172: assertEquals(13, simpleEntryGroup0.getSequenceLength());
173: assertEquals(1, simpleEntryGroup0.size());
174: assertFalse(entry0.isReadOnly());
175: assertEquals(1, range0.getEnd());
176: assertEquals((-1069), range0.getStart());
177: assertEquals(1071, range0.getCount());
178: assertEquals(1, filteredEntryGroup0.size());
179: assertEquals("product", filteredEntryGroup0.getFilterName());
180: assertEquals(13, filteredEntryGroup0.getSequenceLength());
181: assertEquals(0, filteredEntryGroup0.refCount());
182: assertFalse(feature0.isReadOnly());
183: assertEquals(13, range1.getCount());
184: assertEquals(1, range1.getStart());
185: assertEquals(13, range1.getEnd());
186: assertEquals(1, Bases.FORWARD);
187: assertEquals((-5), Bases.MIN_PRIORITY);
188: assertEquals(0, Bases.MEDIUM_PRIORITY);
189: assertEquals(5, Bases.MAX_PRIORITY);
190: assertEquals(2, Bases.REVERSE);
Test case 17
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.length());
4: assertEquals(0, genbankStreamSequence0.getCCount());
5: assertNull(genbankStreamSequence0.getHeader());
6: assertEquals(2, genbankStreamSequence0.getFormatType());
7: assertEquals(0, genbankStreamSequence0.getOtherCount());
8: assertEquals(0, genbankStreamSequence0.getGCount());
9: assertEquals(0, genbankStreamSequence0.getACount());
10: assertEquals(0, genbankStreamSequence0.getTCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.length());
15: assertEquals(0, genbankStreamSequence0.getCCount());
16: assertNull(genbankStreamSequence0.getHeader());
17: assertEquals(2, genbankStreamSequence0.getFormatType());
18: assertEquals(0, genbankStreamSequence0.getOtherCount());
19: assertEquals(0, genbankStreamSequence0.getGCount());
20: assertEquals(0, genbankStreamSequence0.getACount());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals(2, Bases.REVERSE);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.length());
32: assertEquals(0, genbankStreamSequence0.getCCount());
33: assertNull(genbankStreamSequence0.getHeader());
34: assertEquals(2, genbankStreamSequence0.getFormatType());
35: assertEquals(0, genbankStreamSequence0.getOtherCount());
36: assertEquals(0, genbankStreamSequence0.getGCount());
37: assertEquals(0, genbankStreamSequence0.getACount());
38: assertEquals(0, genbankStreamSequence0.getTCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals(2, Bases.REVERSE);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(5, range0.getEnd());
52: assertEquals(0, range0.getStart());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.length());
61: assertEquals(0, genbankStreamSequence0.getCCount());
62: assertNull(genbankStreamSequence0.getHeader());
63: assertEquals(2, genbankStreamSequence0.getFormatType());
64: assertEquals(0, genbankStreamSequence0.getOtherCount());
65: assertEquals(0, genbankStreamSequence0.getGCount());
66: assertEquals(0, genbankStreamSequence0.getACount());
67: assertEquals(0, genbankStreamSequence0.getTCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(5, range0.getEnd());
73: assertEquals(0, range0.getStart());
74: assertEquals(6, range0.getCount());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals(2, Bases.REVERSE);
82: assertEquals(5, Bases.MAX_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.length());
89: assertEquals(0, genbankStreamSequence0.getCCount());
90: assertNull(genbankStreamSequence0.getHeader());
91: assertEquals(2, genbankStreamSequence0.getFormatType());
92: assertEquals(0, genbankStreamSequence0.getOtherCount());
93: assertEquals(0, genbankStreamSequence0.getGCount());
94: assertEquals(0, genbankStreamSequence0.getACount());
95: assertEquals(0, genbankStreamSequence0.getTCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals(2, Bases.REVERSE);
104: assertEquals(5, Bases.MAX_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.length());
111: assertEquals(0, genbankStreamSequence0.getCCount());
112: assertNull(genbankStreamSequence0.getHeader());
113: assertEquals(2, genbankStreamSequence0.getFormatType());
114: assertEquals(0, genbankStreamSequence0.getOtherCount());
115: assertEquals(0, genbankStreamSequence0.getGCount());
116: assertEquals(0, genbankStreamSequence0.getACount());
117: assertEquals(0, genbankStreamSequence0.getTCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(5, range0.getEnd());
123: assertEquals(0, range0.getStart());
124: assertEquals(6, range0.getCount());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(0, filteredEntryGroup0.size());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals(2, Bases.REVERSE);
136: assertEquals(5, Bases.MAX_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.length());
145: assertEquals(0, genbankStreamSequence0.getCCount());
146: assertNull(genbankStreamSequence0.getHeader());
147: assertEquals(2, genbankStreamSequence0.getFormatType());
148: assertEquals(0, genbankStreamSequence0.getOtherCount());
149: assertEquals(0, genbankStreamSequence0.getGCount());
150: assertEquals(0, genbankStreamSequence0.getACount());
151: assertEquals(0, genbankStreamSequence0.getTCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(5, range0.getEnd());
157: assertEquals(0, range0.getStart());
158: assertEquals(6, range0.getCount());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(1, filteredEntryGroup0.size());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals(2, Bases.REVERSE);
171: assertEquals(5, Bases.MAX_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.length());
180: assertEquals(0, genbankStreamSequence0.getCCount());
181: assertNull(genbankStreamSequence0.getHeader());
182: assertEquals(2, genbankStreamSequence0.getFormatType());
183: assertEquals(0, genbankStreamSequence0.getOtherCount());
184: assertEquals(0, genbankStreamSequence0.getGCount());
185: assertEquals(0, genbankStreamSequence0.getACount());
186: assertEquals(0, genbankStreamSequence0.getTCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(5, range0.getEnd());
192: assertEquals(0, range0.getStart());
193: assertEquals(6, range0.getCount());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(1, filteredEntryGroup0.size());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals(2, Bases.REVERSE);
206: assertEquals(5, Bases.MAX_PRIORITY);
207:
208: SequenceChangeEvent sequenceChangeEvent0 = new SequenceChangeEvent(bases0, (-2));
209: assertNotNull(sequenceChangeEvent0);
210: assertEquals(0, genbankStreamSequence0.length());
211: assertEquals(0, genbankStreamSequence0.getCCount());
212: assertNull(genbankStreamSequence0.getHeader());
213: assertEquals(2, genbankStreamSequence0.getFormatType());
214: assertEquals(0, genbankStreamSequence0.getOtherCount());
215: assertEquals(0, genbankStreamSequence0.getGCount());
216: assertEquals(0, genbankStreamSequence0.getACount());
217: assertEquals(0, genbankStreamSequence0.getTCount());
218: assertEquals(0, bases0.getLength());
219: assertNull(sequenceChangeEvent0.getSubSequence());
220: assertEquals((-2), sequenceChangeEvent0.getType());
221: assertEquals(0, sequenceChangeEvent0.getPosition());
222: assertEquals(0, sequenceChangeEvent0.getLength());
223: assertEquals((-5), Bases.MIN_PRIORITY);
224: assertEquals(0, Bases.MEDIUM_PRIORITY);
225: assertEquals(1, Bases.FORWARD);
226: assertEquals(2, Bases.REVERSE);
227: assertEquals(5, Bases.MAX_PRIORITY);
228: assertEquals(3, SequenceChangeEvent.REVERSE_COMPLEMENT);
229: assertEquals(1, SequenceChangeEvent.DELETION);
230: assertEquals(5, SequenceChangeEvent.CONTIG_REORDER);
231: assertEquals(2, SequenceChangeEvent.INSERTION);
232: assertEquals(4, SequenceChangeEvent.CONTIG_REVERSE_COMPLEMENT);
233:
234: feature0.sequenceChanged(sequenceChangeEvent0);
235: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
236: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
237: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
238: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
239: assertEquals(0, genbankStreamSequence0.length());
240: assertEquals(0, genbankStreamSequence0.getCCount());
241: assertNull(genbankStreamSequence0.getHeader());
242: assertEquals(2, genbankStreamSequence0.getFormatType());
243: assertEquals(0, genbankStreamSequence0.getOtherCount());
244: assertEquals(0, genbankStreamSequence0.getGCount());
245: assertEquals(0, genbankStreamSequence0.getACount());
246: assertEquals(0, genbankStreamSequence0.getTCount());
247: assertEquals(0, bases0.getLength());
248: assertEquals(0, simpleEntryGroup0.refCount());
249: assertEquals(0, simpleEntryGroup0.getSequenceLength());
250: assertEquals(0, simpleEntryGroup0.size());
251: assertEquals(5, range0.getEnd());
252: assertEquals(0, range0.getStart());
253: assertEquals(6, range0.getCount());
254: assertEquals(1, simpleEntryGroup1.size());
255: assertEquals(6, simpleEntryGroup1.getSequenceLength());
256: assertEquals(0, simpleEntryGroup1.refCount());
257: assertEquals(1, filteredEntryGroup0.size());
258: assertEquals(0, filteredEntryGroup0.refCount());
259: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
260: assertEquals(6, filteredEntryGroup0.getSequenceLength());
261: assertFalse(feature0.isReadOnly());
262: assertNull(sequenceChangeEvent0.getSubSequence());
263: assertEquals((-2), sequenceChangeEvent0.getType());
264: assertEquals(0, sequenceChangeEvent0.getPosition());
265: assertEquals(0, sequenceChangeEvent0.getLength());
266: assertEquals((-5), Bases.MIN_PRIORITY);
267: assertEquals(0, Bases.MEDIUM_PRIORITY);
268: assertEquals(1, Bases.FORWARD);
269: assertEquals(2, Bases.REVERSE);
270: assertEquals(5, Bases.MAX_PRIORITY);
271: assertEquals(3, SequenceChangeEvent.REVERSE_COMPLEMENT);
272: assertEquals(1, SequenceChangeEvent.DELETION);
273: assertEquals(5, SequenceChangeEvent.CONTIG_REORDER);
274: assertEquals(2, SequenceChangeEvent.INSERTION);
275: assertEquals(4, SequenceChangeEvent.CONTIG_REVERSE_COMPLEMENT);
Test case 18
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getACount());
4: assertEquals(0, genbankStreamSequence0.getGCount());
5: assertNull(genbankStreamSequence0.getHeader());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertEquals(0, genbankStreamSequence0.getOtherCount());
8: assertEquals(0, genbankStreamSequence0.length());
9: assertEquals(0, genbankStreamSequence0.getTCount());
10: assertEquals(2, genbankStreamSequence0.getFormatType());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getACount());
15: assertEquals(0, genbankStreamSequence0.getGCount());
16: assertNull(genbankStreamSequence0.getHeader());
17: assertEquals(0, genbankStreamSequence0.getCCount());
18: assertEquals(0, genbankStreamSequence0.getOtherCount());
19: assertEquals(0, genbankStreamSequence0.length());
20: assertEquals(0, genbankStreamSequence0.getTCount());
21: assertEquals(2, genbankStreamSequence0.getFormatType());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(2, Bases.REVERSE);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getACount());
32: assertEquals(0, genbankStreamSequence0.getGCount());
33: assertNull(genbankStreamSequence0.getHeader());
34: assertEquals(0, genbankStreamSequence0.getCCount());
35: assertEquals(0, genbankStreamSequence0.getOtherCount());
36: assertEquals(0, genbankStreamSequence0.length());
37: assertEquals(0, genbankStreamSequence0.getTCount());
38: assertEquals(2, genbankStreamSequence0.getFormatType());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(2, Bases.REVERSE);
46: assertEquals(1, Bases.FORWARD);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(5, range0.getEnd());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getACount());
61: assertEquals(0, genbankStreamSequence0.getGCount());
62: assertNull(genbankStreamSequence0.getHeader());
63: assertEquals(0, genbankStreamSequence0.getCCount());
64: assertEquals(0, genbankStreamSequence0.getOtherCount());
65: assertEquals(0, genbankStreamSequence0.length());
66: assertEquals(0, genbankStreamSequence0.getTCount());
67: assertEquals(2, genbankStreamSequence0.getFormatType());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(0, range0.getStart());
73: assertEquals(5, range0.getEnd());
74: assertEquals(6, range0.getCount());
75: assertEquals(0, simpleEntryGroup1.refCount());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(2, Bases.REVERSE);
81: assertEquals(1, Bases.FORWARD);
82: assertEquals(5, Bases.MAX_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getACount());
89: assertEquals(0, genbankStreamSequence0.getGCount());
90: assertNull(genbankStreamSequence0.getHeader());
91: assertEquals(0, genbankStreamSequence0.getCCount());
92: assertEquals(0, genbankStreamSequence0.getOtherCount());
93: assertEquals(0, genbankStreamSequence0.length());
94: assertEquals(0, genbankStreamSequence0.getTCount());
95: assertEquals(2, genbankStreamSequence0.getFormatType());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(2, Bases.REVERSE);
103: assertEquals(1, Bases.FORWARD);
104: assertEquals(5, Bases.MAX_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getACount());
111: assertEquals(0, genbankStreamSequence0.getGCount());
112: assertNull(genbankStreamSequence0.getHeader());
113: assertEquals(0, genbankStreamSequence0.getCCount());
114: assertEquals(0, genbankStreamSequence0.getOtherCount());
115: assertEquals(0, genbankStreamSequence0.length());
116: assertEquals(0, genbankStreamSequence0.getTCount());
117: assertEquals(2, genbankStreamSequence0.getFormatType());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(0, range0.getStart());
123: assertEquals(5, range0.getEnd());
124: assertEquals(6, range0.getCount());
125: assertEquals(0, simpleEntryGroup1.refCount());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
129: assertEquals(6, filteredEntryGroup0.getSequenceLength());
130: assertEquals(0, filteredEntryGroup0.refCount());
131: assertEquals(0, filteredEntryGroup0.size());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(2, Bases.REVERSE);
135: assertEquals(1, Bases.FORWARD);
136: assertEquals(5, Bases.MAX_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getACount());
145: assertEquals(0, genbankStreamSequence0.getGCount());
146: assertNull(genbankStreamSequence0.getHeader());
147: assertEquals(0, genbankStreamSequence0.getCCount());
148: assertEquals(0, genbankStreamSequence0.getOtherCount());
149: assertEquals(0, genbankStreamSequence0.length());
150: assertEquals(0, genbankStreamSequence0.getTCount());
151: assertEquals(2, genbankStreamSequence0.getFormatType());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(0, range0.getStart());
157: assertEquals(5, range0.getEnd());
158: assertEquals(6, range0.getCount());
159: assertEquals(0, simpleEntryGroup1.refCount());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(6, simpleEntryGroup1.getSequenceLength());
162: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
163: assertEquals(6, filteredEntryGroup0.getSequenceLength());
164: assertEquals(0, filteredEntryGroup0.refCount());
165: assertEquals(1, filteredEntryGroup0.size());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(2, Bases.REVERSE);
170: assertEquals(1, Bases.FORWARD);
171: assertEquals(5, Bases.MAX_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getACount());
180: assertEquals(0, genbankStreamSequence0.getGCount());
181: assertNull(genbankStreamSequence0.getHeader());
182: assertEquals(0, genbankStreamSequence0.getCCount());
183: assertEquals(0, genbankStreamSequence0.getOtherCount());
184: assertEquals(0, genbankStreamSequence0.length());
185: assertEquals(0, genbankStreamSequence0.getTCount());
186: assertEquals(2, genbankStreamSequence0.getFormatType());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(0, range0.getStart());
192: assertEquals(5, range0.getEnd());
193: assertEquals(6, range0.getCount());
194: assertEquals(0, simpleEntryGroup1.refCount());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(6, simpleEntryGroup1.getSequenceLength());
197: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
198: assertEquals(6, filteredEntryGroup0.getSequenceLength());
199: assertEquals(0, filteredEntryGroup0.refCount());
200: assertEquals(1, filteredEntryGroup0.size());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(2, Bases.REVERSE);
205: assertEquals(1, Bases.FORWARD);
206: assertEquals(5, Bases.MAX_PRIORITY);
207:
208: String string0 = feature0.getUpstreamBases(2);
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(string0);
212: assertEquals("", string0);
213: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
214: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
215: assertEquals(0, genbankStreamSequence0.getACount());
216: assertEquals(0, genbankStreamSequence0.getGCount());
217: assertNull(genbankStreamSequence0.getHeader());
218: assertEquals(0, genbankStreamSequence0.getCCount());
219: assertEquals(0, genbankStreamSequence0.getOtherCount());
220: assertEquals(0, genbankStreamSequence0.length());
221: assertEquals(0, genbankStreamSequence0.getTCount());
222: assertEquals(2, genbankStreamSequence0.getFormatType());
223: assertEquals(0, bases0.getLength());
224: assertEquals(0, simpleEntryGroup0.getSequenceLength());
225: assertEquals(0, simpleEntryGroup0.refCount());
226: assertEquals(0, simpleEntryGroup0.size());
227: assertEquals(0, range0.getStart());
228: assertEquals(5, range0.getEnd());
229: assertEquals(6, range0.getCount());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals(6, simpleEntryGroup1.getSequenceLength());
233: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
234: assertEquals(6, filteredEntryGroup0.getSequenceLength());
235: assertEquals(0, filteredEntryGroup0.refCount());
236: assertEquals(1, filteredEntryGroup0.size());
237: assertFalse(feature0.isReadOnly());
238: assertEquals((-5), Bases.MIN_PRIORITY);
239: assertEquals(0, Bases.MEDIUM_PRIORITY);
240: assertEquals(2, Bases.REVERSE);
241: assertEquals(1, Bases.FORWARD);
242: assertEquals(5, Bases.MAX_PRIORITY);
Test case 19
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: boolean boolean0 = feature0.isProteinFeature();
9: assertTrue(boolean0);
10: assertFalse(feature0.isReadOnly());
Test case 20
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("TimeZone");
2: assertNotNull(genbankStreamSequence0);
3: assertNull(genbankStreamSequence0.getHeader());
4: assertEquals(0, genbankStreamSequence0.getCCount());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(8, genbankStreamSequence0.getOtherCount());
7: assertEquals(2, genbankStreamSequence0.getFormatType());
8: assertEquals(8, genbankStreamSequence0.length());
9: assertEquals(0, genbankStreamSequence0.getGCount());
10: assertEquals(0, genbankStreamSequence0.getACount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertNull(genbankStreamSequence0.getHeader());
15: assertEquals(0, genbankStreamSequence0.getCCount());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertEquals(8, genbankStreamSequence0.getOtherCount());
18: assertEquals(2, genbankStreamSequence0.getFormatType());
19: assertEquals(8, genbankStreamSequence0.length());
20: assertEquals(0, genbankStreamSequence0.getGCount());
21: assertEquals(0, genbankStreamSequence0.getACount());
22: assertEquals(8, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertNull(genbankStreamSequence0.getHeader());
32: assertEquals(0, genbankStreamSequence0.getCCount());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertEquals(8, genbankStreamSequence0.getOtherCount());
35: assertEquals(2, genbankStreamSequence0.getFormatType());
36: assertEquals(8, genbankStreamSequence0.length());
37: assertEquals(0, genbankStreamSequence0.getGCount());
38: assertEquals(0, genbankStreamSequence0.getACount());
39: assertEquals(8, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(8, simpleEntryGroup0.getSequenceLength());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(1, Bases.FORWARD);
47: assertEquals(2, Bases.REVERSE);
48:
49: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
50: assertNotNull(featureVector0);
51: assertNull(genbankStreamSequence0.getHeader());
52: assertEquals(0, genbankStreamSequence0.getCCount());
53: assertEquals(0, genbankStreamSequence0.getTCount());
54: assertEquals(8, genbankStreamSequence0.getOtherCount());
55: assertEquals(2, genbankStreamSequence0.getFormatType());
56: assertEquals(8, genbankStreamSequence0.length());
57: assertEquals(0, genbankStreamSequence0.getGCount());
58: assertEquals(0, genbankStreamSequence0.getACount());
59: assertEquals(8, bases0.getLength());
60: assertEquals(0, simpleEntryGroup0.refCount());
61: assertEquals(0, simpleEntryGroup0.size());
62: assertEquals(8, simpleEntryGroup0.getSequenceLength());
63: assertEquals((-5), Bases.MIN_PRIORITY);
64: assertEquals(0, Bases.MEDIUM_PRIORITY);
65: assertEquals(5, Bases.MAX_PRIORITY);
66: assertEquals(1, Bases.FORWARD);
67: assertEquals(2, Bases.REVERSE);
68:
69: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup0, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
70: assertNotNull(filteredEntryGroup0);
71: assertNull(genbankStreamSequence0.getHeader());
72: assertEquals(0, genbankStreamSequence0.getCCount());
73: assertEquals(0, genbankStreamSequence0.getTCount());
74: assertEquals(8, genbankStreamSequence0.getOtherCount());
75: assertEquals(2, genbankStreamSequence0.getFormatType());
76: assertEquals(8, genbankStreamSequence0.length());
77: assertEquals(0, genbankStreamSequence0.getGCount());
78: assertEquals(0, genbankStreamSequence0.getACount());
79: assertEquals(8, bases0.getLength());
80: assertEquals(0, simpleEntryGroup0.refCount());
81: assertEquals(0, simpleEntryGroup0.size());
82: assertEquals(8, simpleEntryGroup0.getSequenceLength());
83: assertEquals(0, filteredEntryGroup0.refCount());
84: assertEquals(8, filteredEntryGroup0.getSequenceLength());
85: assertEquals(0, filteredEntryGroup0.size());
86: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
87: assertEquals((-5), Bases.MIN_PRIORITY);
88: assertEquals(0, Bases.MEDIUM_PRIORITY);
89: assertEquals(5, Bases.MAX_PRIORITY);
90: assertEquals(1, Bases.FORWARD);
91: assertEquals(2, Bases.REVERSE);
92:
93: Entry entry0 = filteredEntryGroup0.createEntry();
94: assertNotNull(entry0);
95: assertNull(genbankStreamSequence0.getHeader());
96: assertEquals(0, genbankStreamSequence0.getCCount());
97: assertEquals(0, genbankStreamSequence0.getTCount());
98: assertEquals(8, genbankStreamSequence0.getOtherCount());
99: assertEquals(2, genbankStreamSequence0.getFormatType());
100: assertEquals(8, genbankStreamSequence0.length());
101: assertEquals(0, genbankStreamSequence0.getGCount());
102: assertEquals(0, genbankStreamSequence0.getACount());
103: assertEquals(8, bases0.getLength());
104: assertEquals(1, simpleEntryGroup0.size());
105: assertEquals(0, simpleEntryGroup0.refCount());
106: assertEquals(8, simpleEntryGroup0.getSequenceLength());
107: assertEquals(0, filteredEntryGroup0.refCount());
108: assertEquals(8, filteredEntryGroup0.getSequenceLength());
109: assertEquals(1, filteredEntryGroup0.size());
110: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
111: assertFalse(entry0.isReadOnly());
112: assertEquals((-5), Bases.MIN_PRIORITY);
113: assertEquals(0, Bases.MEDIUM_PRIORITY);
114: assertEquals(5, Bases.MAX_PRIORITY);
115: assertEquals(1, Bases.FORWARD);
116: assertEquals(2, Bases.REVERSE);
117:
118: Feature feature0 = filteredEntryGroup0.createFeature();
119: assertNotNull(feature0);
120: assertNull(genbankStreamSequence0.getHeader());
121: assertEquals(0, genbankStreamSequence0.getCCount());
122: assertEquals(0, genbankStreamSequence0.getTCount());
123: assertEquals(8, genbankStreamSequence0.getOtherCount());
124: assertEquals(2, genbankStreamSequence0.getFormatType());
125: assertEquals(8, genbankStreamSequence0.length());
126: assertEquals(0, genbankStreamSequence0.getGCount());
127: assertEquals(0, genbankStreamSequence0.getACount());
128: assertEquals(8, bases0.getLength());
129: assertEquals(1, simpleEntryGroup0.size());
130: assertEquals(0, simpleEntryGroup0.refCount());
131: assertEquals(8, simpleEntryGroup0.getSequenceLength());
132: assertEquals(0, filteredEntryGroup0.refCount());
133: assertEquals(8, filteredEntryGroup0.getSequenceLength());
134: assertEquals(1, filteredEntryGroup0.size());
135: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
136: assertFalse(feature0.isReadOnly());
137: assertEquals((-5), Bases.MIN_PRIORITY);
138: assertEquals(0, Bases.MEDIUM_PRIORITY);
139: assertEquals(5, Bases.MAX_PRIORITY);
140: assertEquals(1, Bases.FORWARD);
141: assertEquals(2, Bases.REVERSE);
142:
143: boolean boolean0 = feature0.isProteinFeature();
144: assertFalse(boolean0);
145: assertNull(genbankStreamSequence0.getHeader());
146: assertEquals(0, genbankStreamSequence0.getCCount());
147: assertEquals(0, genbankStreamSequence0.getTCount());
148: assertEquals(8, genbankStreamSequence0.getOtherCount());
149: assertEquals(2, genbankStreamSequence0.getFormatType());
150: assertEquals(8, genbankStreamSequence0.length());
151: assertEquals(0, genbankStreamSequence0.getGCount());
152: assertEquals(0, genbankStreamSequence0.getACount());
153: assertEquals(8, bases0.getLength());
154: assertEquals(1, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.refCount());
156: assertEquals(8, simpleEntryGroup0.getSequenceLength());
157: assertEquals(0, filteredEntryGroup0.refCount());
158: assertEquals(8, filteredEntryGroup0.getSequenceLength());
159: assertEquals(1, filteredEntryGroup0.size());
160: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
161: assertFalse(feature0.isReadOnly());
162: assertEquals((-5), Bases.MIN_PRIORITY);
163: assertEquals(0, Bases.MEDIUM_PRIORITY);
164: assertEquals(5, Bases.MAX_PRIORITY);
165: assertEquals(1, Bases.FORWARD);
166: assertEquals(2, Bases.REVERSE);
Test case 21
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.hasValidStartCodon(false);
Test case 22
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: int int0 = feature0.getScore();
9: assertEquals((-1), int0);
10: assertFalse(feature0.isReadOnly());
Test case 23
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getTCount());
4: assertEquals(0, genbankStreamSequence0.getOtherCount());
5: assertEquals(0, genbankStreamSequence0.length());
6: assertEquals(2, genbankStreamSequence0.getFormatType());
7: assertEquals(0, genbankStreamSequence0.getGCount());
8: assertEquals(0, genbankStreamSequence0.getCCount());
9: assertNull(genbankStreamSequence0.getHeader());
10: assertEquals(0, genbankStreamSequence0.getACount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getTCount());
15: assertEquals(0, genbankStreamSequence0.getOtherCount());
16: assertEquals(0, genbankStreamSequence0.length());
17: assertEquals(2, genbankStreamSequence0.getFormatType());
18: assertEquals(0, genbankStreamSequence0.getGCount());
19: assertEquals(0, genbankStreamSequence0.getCCount());
20: assertNull(genbankStreamSequence0.getHeader());
21: assertEquals(0, genbankStreamSequence0.getACount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(5, Bases.MAX_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals((-5), Bases.MIN_PRIORITY);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getTCount());
32: assertEquals(0, genbankStreamSequence0.getOtherCount());
33: assertEquals(0, genbankStreamSequence0.length());
34: assertEquals(2, genbankStreamSequence0.getFormatType());
35: assertEquals(0, genbankStreamSequence0.getGCount());
36: assertEquals(0, genbankStreamSequence0.getCCount());
37: assertNull(genbankStreamSequence0.getHeader());
38: assertEquals(0, genbankStreamSequence0.getACount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals(5, Bases.MAX_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals((-5), Bases.MIN_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(5, range0.getEnd());
52: assertEquals(6, range0.getCount());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getTCount());
61: assertEquals(0, genbankStreamSequence0.getOtherCount());
62: assertEquals(0, genbankStreamSequence0.length());
63: assertEquals(2, genbankStreamSequence0.getFormatType());
64: assertEquals(0, genbankStreamSequence0.getGCount());
65: assertEquals(0, genbankStreamSequence0.getCCount());
66: assertNull(genbankStreamSequence0.getHeader());
67: assertEquals(0, genbankStreamSequence0.getACount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(5, range0.getEnd());
73: assertEquals(6, range0.getCount());
74: assertEquals(0, range0.getStart());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(5, Bases.MAX_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals((-5), Bases.MIN_PRIORITY);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getTCount());
89: assertEquals(0, genbankStreamSequence0.getOtherCount());
90: assertEquals(0, genbankStreamSequence0.length());
91: assertEquals(2, genbankStreamSequence0.getFormatType());
92: assertEquals(0, genbankStreamSequence0.getGCount());
93: assertEquals(0, genbankStreamSequence0.getCCount());
94: assertNull(genbankStreamSequence0.getHeader());
95: assertEquals(0, genbankStreamSequence0.getACount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals(5, Bases.MAX_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals((-5), Bases.MIN_PRIORITY);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getTCount());
111: assertEquals(0, genbankStreamSequence0.getOtherCount());
112: assertEquals(0, genbankStreamSequence0.length());
113: assertEquals(2, genbankStreamSequence0.getFormatType());
114: assertEquals(0, genbankStreamSequence0.getGCount());
115: assertEquals(0, genbankStreamSequence0.getCCount());
116: assertNull(genbankStreamSequence0.getHeader());
117: assertEquals(0, genbankStreamSequence0.getACount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(5, range0.getEnd());
123: assertEquals(6, range0.getCount());
124: assertEquals(0, range0.getStart());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(0, filteredEntryGroup0.size());
129: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
130: assertEquals(0, filteredEntryGroup0.refCount());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals(5, Bases.MAX_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals((-5), Bases.MIN_PRIORITY);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getTCount());
145: assertEquals(0, genbankStreamSequence0.getOtherCount());
146: assertEquals(0, genbankStreamSequence0.length());
147: assertEquals(2, genbankStreamSequence0.getFormatType());
148: assertEquals(0, genbankStreamSequence0.getGCount());
149: assertEquals(0, genbankStreamSequence0.getCCount());
150: assertNull(genbankStreamSequence0.getHeader());
151: assertEquals(0, genbankStreamSequence0.getACount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(5, range0.getEnd());
157: assertEquals(6, range0.getCount());
158: assertEquals(0, range0.getStart());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(1, filteredEntryGroup0.size());
163: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
164: assertEquals(0, filteredEntryGroup0.refCount());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(5, Bases.MAX_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals((-5), Bases.MIN_PRIORITY);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getTCount());
180: assertEquals(0, genbankStreamSequence0.getOtherCount());
181: assertEquals(0, genbankStreamSequence0.length());
182: assertEquals(2, genbankStreamSequence0.getFormatType());
183: assertEquals(0, genbankStreamSequence0.getGCount());
184: assertEquals(0, genbankStreamSequence0.getCCount());
185: assertNull(genbankStreamSequence0.getHeader());
186: assertEquals(0, genbankStreamSequence0.getACount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(5, range0.getEnd());
192: assertEquals(6, range0.getCount());
193: assertEquals(0, range0.getStart());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(1, filteredEntryGroup0.size());
198: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
199: assertEquals(0, filteredEntryGroup0.refCount());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(5, Bases.MAX_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals((-5), Bases.MIN_PRIORITY);
206: assertEquals(2, Bases.REVERSE);
207:
208: feature0.setEntry(entry0);
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
212: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
213: assertEquals(0, genbankStreamSequence0.getTCount());
214: assertEquals(0, genbankStreamSequence0.getOtherCount());
215: assertEquals(0, genbankStreamSequence0.length());
216: assertEquals(2, genbankStreamSequence0.getFormatType());
217: assertEquals(0, genbankStreamSequence0.getGCount());
218: assertEquals(0, genbankStreamSequence0.getCCount());
219: assertNull(genbankStreamSequence0.getHeader());
220: assertEquals(0, genbankStreamSequence0.getACount());
221: assertEquals(0, bases0.getLength());
222: assertEquals(0, simpleEntryGroup0.refCount());
223: assertEquals(0, simpleEntryGroup0.getSequenceLength());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(5, range0.getEnd());
226: assertEquals(6, range0.getCount());
227: assertEquals(0, range0.getStart());
228: assertEquals(6, simpleEntryGroup1.getSequenceLength());
229: assertEquals(1, simpleEntryGroup1.size());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(1, filteredEntryGroup0.size());
232: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
233: assertEquals(0, filteredEntryGroup0.refCount());
234: assertEquals(6, filteredEntryGroup0.getSequenceLength());
235: assertFalse(entry0.isReadOnly());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(5, Bases.MAX_PRIORITY);
238: assertEquals(0, Bases.MEDIUM_PRIORITY);
239: assertEquals(1, Bases.FORWARD);
240: assertEquals((-5), Bases.MIN_PRIORITY);
241: assertEquals(2, Bases.REVERSE);
Test case 24
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: Qualifier qualifier0 = new Qualifier((String) null);
9: assertNotNull(qualifier0);
10: assertNull(qualifier0.getName());
11:
12: feature0.addQualifierValues(qualifier0);
Test case 25
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.removeQualifierByName("4'Yj6#V");
9: assertFalse(feature0.isReadOnly());
Test case 26
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: boolean boolean0 = feature0.findOrReplaceText("exon", false, true, false, (StringVector) null, "");
12: assertFalse(boolean0);
13: assertFalse(feature0.isReadOnly());
Test case 27
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.findOrReplaceText((String) null, true, true, true, (StringVector) null, "");
Test case 28
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getGCount());
4: assertEquals(2, genbankStreamSequence0.getFormatType());
5: assertNull(genbankStreamSequence0.getHeader());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertEquals(0, genbankStreamSequence0.getTCount());
8: assertEquals(0, genbankStreamSequence0.getACount());
9: assertEquals(0, genbankStreamSequence0.length());
10: assertEquals(0, genbankStreamSequence0.getOtherCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getGCount());
15: assertEquals(2, genbankStreamSequence0.getFormatType());
16: assertNull(genbankStreamSequence0.getHeader());
17: assertEquals(0, genbankStreamSequence0.getCCount());
18: assertEquals(0, genbankStreamSequence0.getTCount());
19: assertEquals(0, genbankStreamSequence0.getACount());
20: assertEquals(0, genbankStreamSequence0.length());
21: assertEquals(0, genbankStreamSequence0.getOtherCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(1, Bases.FORWARD);
24: assertEquals((-5), Bases.MIN_PRIORITY);
25: assertEquals(0, Bases.MEDIUM_PRIORITY);
26: assertEquals(5, Bases.MAX_PRIORITY);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getGCount());
32: assertEquals(2, genbankStreamSequence0.getFormatType());
33: assertNull(genbankStreamSequence0.getHeader());
34: assertEquals(0, genbankStreamSequence0.getCCount());
35: assertEquals(0, genbankStreamSequence0.getTCount());
36: assertEquals(0, genbankStreamSequence0.getACount());
37: assertEquals(0, genbankStreamSequence0.length());
38: assertEquals(0, genbankStreamSequence0.getOtherCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals(1, Bases.FORWARD);
44: assertEquals((-5), Bases.MIN_PRIORITY);
45: assertEquals(0, Bases.MEDIUM_PRIORITY);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(6, range0.getCount());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getGCount());
61: assertEquals(2, genbankStreamSequence0.getFormatType());
62: assertNull(genbankStreamSequence0.getHeader());
63: assertEquals(0, genbankStreamSequence0.getCCount());
64: assertEquals(0, genbankStreamSequence0.getTCount());
65: assertEquals(0, genbankStreamSequence0.getACount());
66: assertEquals(0, genbankStreamSequence0.length());
67: assertEquals(0, genbankStreamSequence0.getOtherCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(0, range0.getStart());
73: assertEquals(6, range0.getCount());
74: assertEquals(5, range0.getEnd());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(0, simpleEntryGroup1.refCount());
77: assertEquals(6, simpleEntryGroup1.getSequenceLength());
78: assertEquals(1, Bases.FORWARD);
79: assertEquals((-5), Bases.MIN_PRIORITY);
80: assertEquals(0, Bases.MEDIUM_PRIORITY);
81: assertEquals(5, Bases.MAX_PRIORITY);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getGCount());
89: assertEquals(2, genbankStreamSequence0.getFormatType());
90: assertNull(genbankStreamSequence0.getHeader());
91: assertEquals(0, genbankStreamSequence0.getCCount());
92: assertEquals(0, genbankStreamSequence0.getTCount());
93: assertEquals(0, genbankStreamSequence0.getACount());
94: assertEquals(0, genbankStreamSequence0.length());
95: assertEquals(0, genbankStreamSequence0.getOtherCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals(1, Bases.FORWARD);
101: assertEquals((-5), Bases.MIN_PRIORITY);
102: assertEquals(0, Bases.MEDIUM_PRIORITY);
103: assertEquals(5, Bases.MAX_PRIORITY);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getGCount());
111: assertEquals(2, genbankStreamSequence0.getFormatType());
112: assertNull(genbankStreamSequence0.getHeader());
113: assertEquals(0, genbankStreamSequence0.getCCount());
114: assertEquals(0, genbankStreamSequence0.getTCount());
115: assertEquals(0, genbankStreamSequence0.getACount());
116: assertEquals(0, genbankStreamSequence0.length());
117: assertEquals(0, genbankStreamSequence0.getOtherCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(0, range0.getStart());
123: assertEquals(6, range0.getCount());
124: assertEquals(5, range0.getEnd());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(0, simpleEntryGroup1.refCount());
127: assertEquals(6, simpleEntryGroup1.getSequenceLength());
128: assertEquals(6, filteredEntryGroup0.getSequenceLength());
129: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
130: assertEquals(0, filteredEntryGroup0.refCount());
131: assertEquals(0, filteredEntryGroup0.size());
132: assertEquals(1, Bases.FORWARD);
133: assertEquals((-5), Bases.MIN_PRIORITY);
134: assertEquals(0, Bases.MEDIUM_PRIORITY);
135: assertEquals(5, Bases.MAX_PRIORITY);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getGCount());
145: assertEquals(2, genbankStreamSequence0.getFormatType());
146: assertNull(genbankStreamSequence0.getHeader());
147: assertEquals(0, genbankStreamSequence0.getCCount());
148: assertEquals(0, genbankStreamSequence0.getTCount());
149: assertEquals(0, genbankStreamSequence0.getACount());
150: assertEquals(0, genbankStreamSequence0.length());
151: assertEquals(0, genbankStreamSequence0.getOtherCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(0, range0.getStart());
157: assertEquals(6, range0.getCount());
158: assertEquals(5, range0.getEnd());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(0, simpleEntryGroup1.refCount());
161: assertEquals(6, simpleEntryGroup1.getSequenceLength());
162: assertEquals(6, filteredEntryGroup0.getSequenceLength());
163: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
164: assertEquals(0, filteredEntryGroup0.refCount());
165: assertEquals(1, filteredEntryGroup0.size());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(1, Bases.FORWARD);
168: assertEquals((-5), Bases.MIN_PRIORITY);
169: assertEquals(0, Bases.MEDIUM_PRIORITY);
170: assertEquals(5, Bases.MAX_PRIORITY);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getGCount());
180: assertEquals(2, genbankStreamSequence0.getFormatType());
181: assertNull(genbankStreamSequence0.getHeader());
182: assertEquals(0, genbankStreamSequence0.getCCount());
183: assertEquals(0, genbankStreamSequence0.getTCount());
184: assertEquals(0, genbankStreamSequence0.getACount());
185: assertEquals(0, genbankStreamSequence0.length());
186: assertEquals(0, genbankStreamSequence0.getOtherCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(0, range0.getStart());
192: assertEquals(6, range0.getCount());
193: assertEquals(5, range0.getEnd());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(0, simpleEntryGroup1.refCount());
196: assertEquals(6, simpleEntryGroup1.getSequenceLength());
197: assertEquals(6, filteredEntryGroup0.getSequenceLength());
198: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
199: assertEquals(0, filteredEntryGroup0.refCount());
200: assertEquals(1, filteredEntryGroup0.size());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(1, Bases.FORWARD);
203: assertEquals((-5), Bases.MIN_PRIORITY);
204: assertEquals(0, Bases.MEDIUM_PRIORITY);
205: assertEquals(5, Bases.MAX_PRIORITY);
206: assertEquals(2, Bases.REVERSE);
207:
208: boolean boolean0 = feature0.hasValidStartCodon(true);
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertFalse(boolean0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.getGCount());
215: assertEquals(2, genbankStreamSequence0.getFormatType());
216: assertNull(genbankStreamSequence0.getHeader());
217: assertEquals(0, genbankStreamSequence0.getCCount());
218: assertEquals(0, genbankStreamSequence0.getTCount());
219: assertEquals(0, genbankStreamSequence0.getACount());
220: assertEquals(0, genbankStreamSequence0.length());
221: assertEquals(0, genbankStreamSequence0.getOtherCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.getSequenceLength());
224: assertEquals(0, simpleEntryGroup0.refCount());
225: assertEquals(0, simpleEntryGroup0.size());
226: assertEquals(0, range0.getStart());
227: assertEquals(6, range0.getCount());
228: assertEquals(5, range0.getEnd());
229: assertEquals(1, simpleEntryGroup1.size());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(6, simpleEntryGroup1.getSequenceLength());
232: assertEquals(6, filteredEntryGroup0.getSequenceLength());
233: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
234: assertEquals(0, filteredEntryGroup0.refCount());
235: assertEquals(1, filteredEntryGroup0.size());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(1, Bases.FORWARD);
238: assertEquals((-5), Bases.MIN_PRIORITY);
239: assertEquals(0, Bases.MEDIUM_PRIORITY);
240: assertEquals(5, Bases.MAX_PRIORITY);
241: assertEquals(2, Bases.REVERSE);
Test case 29
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.fixStopCodon();
Test case 30
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(2, genbankStreamSequence0.getFormatType());
4: assertEquals(0, genbankStreamSequence0.getOtherCount());
5: assertEquals(0, genbankStreamSequence0.getGCount());
6: assertNull(genbankStreamSequence0.getHeader());
7: assertEquals(0, genbankStreamSequence0.getACount());
8: assertEquals(0, genbankStreamSequence0.getCCount());
9: assertEquals(0, genbankStreamSequence0.getTCount());
10: assertEquals(0, genbankStreamSequence0.length());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, genbankStreamSequence0.getFormatType());
15: assertEquals(0, genbankStreamSequence0.getOtherCount());
16: assertEquals(0, genbankStreamSequence0.getGCount());
17: assertNull(genbankStreamSequence0.getHeader());
18: assertEquals(0, genbankStreamSequence0.getACount());
19: assertEquals(0, genbankStreamSequence0.getCCount());
20: assertEquals(0, genbankStreamSequence0.getTCount());
21: assertEquals(0, genbankStreamSequence0.length());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals(5, Bases.MAX_PRIORITY);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(2, genbankStreamSequence0.getFormatType());
32: assertEquals(0, genbankStreamSequence0.getOtherCount());
33: assertEquals(0, genbankStreamSequence0.getGCount());
34: assertNull(genbankStreamSequence0.getHeader());
35: assertEquals(0, genbankStreamSequence0.getACount());
36: assertEquals(0, genbankStreamSequence0.getCCount());
37: assertEquals(0, genbankStreamSequence0.getTCount());
38: assertEquals(0, genbankStreamSequence0.length());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(5, range0.getEnd());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(2, genbankStreamSequence0.getFormatType());
61: assertEquals(0, genbankStreamSequence0.getOtherCount());
62: assertEquals(0, genbankStreamSequence0.getGCount());
63: assertNull(genbankStreamSequence0.getHeader());
64: assertEquals(0, genbankStreamSequence0.getACount());
65: assertEquals(0, genbankStreamSequence0.getCCount());
66: assertEquals(0, genbankStreamSequence0.getTCount());
67: assertEquals(0, genbankStreamSequence0.length());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(6, range0.getCount());
73: assertEquals(5, range0.getEnd());
74: assertEquals(0, range0.getStart());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals(5, Bases.MAX_PRIORITY);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(2, genbankStreamSequence0.getFormatType());
89: assertEquals(0, genbankStreamSequence0.getOtherCount());
90: assertEquals(0, genbankStreamSequence0.getGCount());
91: assertNull(genbankStreamSequence0.getHeader());
92: assertEquals(0, genbankStreamSequence0.getACount());
93: assertEquals(0, genbankStreamSequence0.getCCount());
94: assertEquals(0, genbankStreamSequence0.getTCount());
95: assertEquals(0, genbankStreamSequence0.length());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals(5, Bases.MAX_PRIORITY);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(2, genbankStreamSequence0.getFormatType());
111: assertEquals(0, genbankStreamSequence0.getOtherCount());
112: assertEquals(0, genbankStreamSequence0.getGCount());
113: assertNull(genbankStreamSequence0.getHeader());
114: assertEquals(0, genbankStreamSequence0.getACount());
115: assertEquals(0, genbankStreamSequence0.getCCount());
116: assertEquals(0, genbankStreamSequence0.getTCount());
117: assertEquals(0, genbankStreamSequence0.length());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(6, range0.getCount());
123: assertEquals(5, range0.getEnd());
124: assertEquals(0, range0.getStart());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals(5, Bases.MAX_PRIORITY);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(2, genbankStreamSequence0.getFormatType());
145: assertEquals(0, genbankStreamSequence0.getOtherCount());
146: assertEquals(0, genbankStreamSequence0.getGCount());
147: assertNull(genbankStreamSequence0.getHeader());
148: assertEquals(0, genbankStreamSequence0.getACount());
149: assertEquals(0, genbankStreamSequence0.getCCount());
150: assertEquals(0, genbankStreamSequence0.getTCount());
151: assertEquals(0, genbankStreamSequence0.length());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(6, range0.getCount());
157: assertEquals(5, range0.getEnd());
158: assertEquals(0, range0.getStart());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals(1, filteredEntryGroup0.size());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals(5, Bases.MAX_PRIORITY);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(2, genbankStreamSequence0.getFormatType());
180: assertEquals(0, genbankStreamSequence0.getOtherCount());
181: assertEquals(0, genbankStreamSequence0.getGCount());
182: assertNull(genbankStreamSequence0.getHeader());
183: assertEquals(0, genbankStreamSequence0.getACount());
184: assertEquals(0, genbankStreamSequence0.getCCount());
185: assertEquals(0, genbankStreamSequence0.getTCount());
186: assertEquals(0, genbankStreamSequence0.length());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.size());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(6, range0.getCount());
192: assertEquals(5, range0.getEnd());
193: assertEquals(0, range0.getStart());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals(1, filteredEntryGroup0.size());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals(5, Bases.MAX_PRIORITY);
206: assertEquals(2, Bases.REVERSE);
207:
208: int int0 = feature0.getBaseCount();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertEquals(6, int0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(2, genbankStreamSequence0.getFormatType());
215: assertEquals(0, genbankStreamSequence0.getOtherCount());
216: assertEquals(0, genbankStreamSequence0.getGCount());
217: assertNull(genbankStreamSequence0.getHeader());
218: assertEquals(0, genbankStreamSequence0.getACount());
219: assertEquals(0, genbankStreamSequence0.getCCount());
220: assertEquals(0, genbankStreamSequence0.getTCount());
221: assertEquals(0, genbankStreamSequence0.length());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.refCount());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(0, simpleEntryGroup0.getSequenceLength());
226: assertEquals(6, range0.getCount());
227: assertEquals(5, range0.getEnd());
228: assertEquals(0, range0.getStart());
229: assertEquals(6, simpleEntryGroup1.getSequenceLength());
230: assertEquals(1, simpleEntryGroup1.size());
231: assertEquals(0, simpleEntryGroup1.refCount());
232: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
233: assertEquals(0, filteredEntryGroup0.refCount());
234: assertEquals(1, filteredEntryGroup0.size());
235: assertEquals(6, filteredEntryGroup0.getSequenceLength());
236: assertFalse(feature0.isReadOnly());
237: assertEquals((-5), Bases.MIN_PRIORITY);
238: assertEquals(0, Bases.MEDIUM_PRIORITY);
239: assertEquals(1, Bases.FORWARD);
240: assertEquals(5, Bases.MAX_PRIORITY);
241: assertEquals(2, Bases.REVERSE);
Test case 31
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.getAACount();
Test case 32
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.getCodonCount(46, 2147483645, (-1002));
Test case 33
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.getResidueCount(180);
Test case 34
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.getBaseCount(634);
Test case 35
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getCCount());
4: assertEquals(0, genbankStreamSequence0.length());
5: assertEquals(0, genbankStreamSequence0.getACount());
6: assertEquals(0, genbankStreamSequence0.getOtherCount());
7: assertNull(genbankStreamSequence0.getHeader());
8: assertEquals(2, genbankStreamSequence0.getFormatType());
9: assertEquals(0, genbankStreamSequence0.getGCount());
10: assertEquals(0, genbankStreamSequence0.getTCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getCCount());
15: assertEquals(0, genbankStreamSequence0.length());
16: assertEquals(0, genbankStreamSequence0.getACount());
17: assertEquals(0, genbankStreamSequence0.getOtherCount());
18: assertNull(genbankStreamSequence0.getHeader());
19: assertEquals(2, genbankStreamSequence0.getFormatType());
20: assertEquals(0, genbankStreamSequence0.getGCount());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(5, Bases.MAX_PRIORITY);
24: assertEquals((-5), Bases.MIN_PRIORITY);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals(2, Bases.REVERSE);
27: assertEquals(0, Bases.MEDIUM_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getCCount());
32: assertEquals(0, genbankStreamSequence0.length());
33: assertEquals(0, genbankStreamSequence0.getACount());
34: assertEquals(0, genbankStreamSequence0.getOtherCount());
35: assertNull(genbankStreamSequence0.getHeader());
36: assertEquals(2, genbankStreamSequence0.getFormatType());
37: assertEquals(0, genbankStreamSequence0.getGCount());
38: assertEquals(0, genbankStreamSequence0.getTCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals(5, Bases.MAX_PRIORITY);
44: assertEquals((-5), Bases.MIN_PRIORITY);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals(2, Bases.REVERSE);
47: assertEquals(0, Bases.MEDIUM_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(5, range0.getEnd());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getCCount());
61: assertEquals(0, genbankStreamSequence0.length());
62: assertEquals(0, genbankStreamSequence0.getACount());
63: assertEquals(0, genbankStreamSequence0.getOtherCount());
64: assertNull(genbankStreamSequence0.getHeader());
65: assertEquals(2, genbankStreamSequence0.getFormatType());
66: assertEquals(0, genbankStreamSequence0.getGCount());
67: assertEquals(0, genbankStreamSequence0.getTCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.size());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(0, range0.getStart());
73: assertEquals(5, range0.getEnd());
74: assertEquals(6, range0.getCount());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(5, Bases.MAX_PRIORITY);
79: assertEquals((-5), Bases.MIN_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals(2, Bases.REVERSE);
82: assertEquals(0, Bases.MEDIUM_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getCCount());
89: assertEquals(0, genbankStreamSequence0.length());
90: assertEquals(0, genbankStreamSequence0.getACount());
91: assertEquals(0, genbankStreamSequence0.getOtherCount());
92: assertNull(genbankStreamSequence0.getHeader());
93: assertEquals(2, genbankStreamSequence0.getFormatType());
94: assertEquals(0, genbankStreamSequence0.getGCount());
95: assertEquals(0, genbankStreamSequence0.getTCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.size());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals(5, Bases.MAX_PRIORITY);
101: assertEquals((-5), Bases.MIN_PRIORITY);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals(2, Bases.REVERSE);
104: assertEquals(0, Bases.MEDIUM_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getCCount());
111: assertEquals(0, genbankStreamSequence0.length());
112: assertEquals(0, genbankStreamSequence0.getACount());
113: assertEquals(0, genbankStreamSequence0.getOtherCount());
114: assertNull(genbankStreamSequence0.getHeader());
115: assertEquals(2, genbankStreamSequence0.getFormatType());
116: assertEquals(0, genbankStreamSequence0.getGCount());
117: assertEquals(0, genbankStreamSequence0.getTCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.size());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(0, range0.getStart());
123: assertEquals(5, range0.getEnd());
124: assertEquals(6, range0.getCount());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(6, filteredEntryGroup0.getSequenceLength());
129: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
130: assertEquals(0, filteredEntryGroup0.refCount());
131: assertEquals(0, filteredEntryGroup0.size());
132: assertEquals(5, Bases.MAX_PRIORITY);
133: assertEquals((-5), Bases.MIN_PRIORITY);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals(2, Bases.REVERSE);
136: assertEquals(0, Bases.MEDIUM_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getCCount());
145: assertEquals(0, genbankStreamSequence0.length());
146: assertEquals(0, genbankStreamSequence0.getACount());
147: assertEquals(0, genbankStreamSequence0.getOtherCount());
148: assertNull(genbankStreamSequence0.getHeader());
149: assertEquals(2, genbankStreamSequence0.getFormatType());
150: assertEquals(0, genbankStreamSequence0.getGCount());
151: assertEquals(0, genbankStreamSequence0.getTCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.size());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(0, range0.getStart());
157: assertEquals(5, range0.getEnd());
158: assertEquals(6, range0.getCount());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(6, filteredEntryGroup0.getSequenceLength());
163: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
164: assertEquals(0, filteredEntryGroup0.refCount());
165: assertEquals(1, filteredEntryGroup0.size());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(5, Bases.MAX_PRIORITY);
168: assertEquals((-5), Bases.MIN_PRIORITY);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals(2, Bases.REVERSE);
171: assertEquals(0, Bases.MEDIUM_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getCCount());
180: assertEquals(0, genbankStreamSequence0.length());
181: assertEquals(0, genbankStreamSequence0.getACount());
182: assertEquals(0, genbankStreamSequence0.getOtherCount());
183: assertNull(genbankStreamSequence0.getHeader());
184: assertEquals(2, genbankStreamSequence0.getFormatType());
185: assertEquals(0, genbankStreamSequence0.getGCount());
186: assertEquals(0, genbankStreamSequence0.getTCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.size());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(0, range0.getStart());
192: assertEquals(5, range0.getEnd());
193: assertEquals(6, range0.getCount());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(6, filteredEntryGroup0.getSequenceLength());
198: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
199: assertEquals(0, filteredEntryGroup0.refCount());
200: assertEquals(1, filteredEntryGroup0.size());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(5, Bases.MAX_PRIORITY);
203: assertEquals((-5), Bases.MIN_PRIORITY);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals(2, Bases.REVERSE);
206: assertEquals(0, Bases.MEDIUM_PRIORITY);
207:
208: double double0 = feature0.getPercentGC();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertEquals(0.0, double0, 0.01);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.getCCount());
215: assertEquals(0, genbankStreamSequence0.length());
216: assertEquals(0, genbankStreamSequence0.getACount());
217: assertEquals(0, genbankStreamSequence0.getOtherCount());
218: assertNull(genbankStreamSequence0.getHeader());
219: assertEquals(2, genbankStreamSequence0.getFormatType());
220: assertEquals(0, genbankStreamSequence0.getGCount());
221: assertEquals(0, genbankStreamSequence0.getTCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.size());
224: assertEquals(0, simpleEntryGroup0.refCount());
225: assertEquals(0, simpleEntryGroup0.getSequenceLength());
226: assertEquals(0, range0.getStart());
227: assertEquals(5, range0.getEnd());
228: assertEquals(6, range0.getCount());
229: assertEquals(1, simpleEntryGroup1.size());
230: assertEquals(6, simpleEntryGroup1.getSequenceLength());
231: assertEquals(0, simpleEntryGroup1.refCount());
232: assertEquals(6, filteredEntryGroup0.getSequenceLength());
233: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
234: assertEquals(0, filteredEntryGroup0.refCount());
235: assertEquals(1, filteredEntryGroup0.size());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(5, Bases.MAX_PRIORITY);
238: assertEquals((-5), Bases.MIN_PRIORITY);
239: assertEquals(1, Bases.FORWARD);
240: assertEquals(2, Bases.REVERSE);
241: assertEquals(0, Bases.MEDIUM_PRIORITY);
Test case 36
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.getPositionInSequence(5);
Test case 37
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(2, genbankStreamSequence0.getFormatType());
4: assertEquals(0, genbankStreamSequence0.getOtherCount());
5: assertEquals(0, genbankStreamSequence0.getGCount());
6: assertNull(genbankStreamSequence0.getHeader());
7: assertEquals(0, genbankStreamSequence0.getACount());
8: assertEquals(0, genbankStreamSequence0.getCCount());
9: assertEquals(0, genbankStreamSequence0.length());
10: assertEquals(0, genbankStreamSequence0.getTCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, genbankStreamSequence0.getFormatType());
15: assertEquals(0, genbankStreamSequence0.getOtherCount());
16: assertEquals(0, genbankStreamSequence0.getGCount());
17: assertNull(genbankStreamSequence0.getHeader());
18: assertEquals(0, genbankStreamSequence0.getACount());
19: assertEquals(0, genbankStreamSequence0.getCCount());
20: assertEquals(0, genbankStreamSequence0.length());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(2, Bases.REVERSE);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(2, genbankStreamSequence0.getFormatType());
32: assertEquals(0, genbankStreamSequence0.getOtherCount());
33: assertEquals(0, genbankStreamSequence0.getGCount());
34: assertNull(genbankStreamSequence0.getHeader());
35: assertEquals(0, genbankStreamSequence0.getACount());
36: assertEquals(0, genbankStreamSequence0.getCCount());
37: assertEquals(0, genbankStreamSequence0.length());
38: assertEquals(0, genbankStreamSequence0.getTCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(2, Bases.REVERSE);
46: assertEquals(1, Bases.FORWARD);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(1);
50: assertNotNull(range0);
51: assertEquals(1, range0.getEnd());
52: assertEquals(1, range0.getCount());
53: assertEquals(1, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(2, genbankStreamSequence0.getFormatType());
61: assertEquals(0, genbankStreamSequence0.getOtherCount());
62: assertEquals(0, genbankStreamSequence0.getGCount());
63: assertNull(genbankStreamSequence0.getHeader());
64: assertEquals(0, genbankStreamSequence0.getACount());
65: assertEquals(0, genbankStreamSequence0.getCCount());
66: assertEquals(0, genbankStreamSequence0.length());
67: assertEquals(0, genbankStreamSequence0.getTCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(1, range0.getEnd());
73: assertEquals(1, range0.getCount());
74: assertEquals(1, range0.getStart());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(1, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(2, Bases.REVERSE);
81: assertEquals(1, Bases.FORWARD);
82: assertEquals(5, Bases.MAX_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(2, genbankStreamSequence0.getFormatType());
89: assertEquals(0, genbankStreamSequence0.getOtherCount());
90: assertEquals(0, genbankStreamSequence0.getGCount());
91: assertNull(genbankStreamSequence0.getHeader());
92: assertEquals(0, genbankStreamSequence0.getACount());
93: assertEquals(0, genbankStreamSequence0.getCCount());
94: assertEquals(0, genbankStreamSequence0.length());
95: assertEquals(0, genbankStreamSequence0.getTCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(2, Bases.REVERSE);
103: assertEquals(1, Bases.FORWARD);
104: assertEquals(5, Bases.MAX_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(2, genbankStreamSequence0.getFormatType());
111: assertEquals(0, genbankStreamSequence0.getOtherCount());
112: assertEquals(0, genbankStreamSequence0.getGCount());
113: assertNull(genbankStreamSequence0.getHeader());
114: assertEquals(0, genbankStreamSequence0.getACount());
115: assertEquals(0, genbankStreamSequence0.getCCount());
116: assertEquals(0, genbankStreamSequence0.length());
117: assertEquals(0, genbankStreamSequence0.getTCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(1, range0.getEnd());
123: assertEquals(1, range0.getCount());
124: assertEquals(1, range0.getStart());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(1, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(1, filteredEntryGroup0.getSequenceLength());
129: assertEquals(0, filteredEntryGroup0.size());
130: assertEquals(0, filteredEntryGroup0.refCount());
131: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(2, Bases.REVERSE);
135: assertEquals(1, Bases.FORWARD);
136: assertEquals(5, Bases.MAX_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(2, genbankStreamSequence0.getFormatType());
145: assertEquals(0, genbankStreamSequence0.getOtherCount());
146: assertEquals(0, genbankStreamSequence0.getGCount());
147: assertNull(genbankStreamSequence0.getHeader());
148: assertEquals(0, genbankStreamSequence0.getACount());
149: assertEquals(0, genbankStreamSequence0.getCCount());
150: assertEquals(0, genbankStreamSequence0.length());
151: assertEquals(0, genbankStreamSequence0.getTCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(1, range0.getEnd());
157: assertEquals(1, range0.getCount());
158: assertEquals(1, range0.getStart());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(1, simpleEntryGroup1.getSequenceLength());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(1, filteredEntryGroup0.getSequenceLength());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals(1, filteredEntryGroup0.size());
165: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(2, Bases.REVERSE);
170: assertEquals(1, Bases.FORWARD);
171: assertEquals(5, Bases.MAX_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(2, genbankStreamSequence0.getFormatType());
180: assertEquals(0, genbankStreamSequence0.getOtherCount());
181: assertEquals(0, genbankStreamSequence0.getGCount());
182: assertNull(genbankStreamSequence0.getHeader());
183: assertEquals(0, genbankStreamSequence0.getACount());
184: assertEquals(0, genbankStreamSequence0.getCCount());
185: assertEquals(0, genbankStreamSequence0.length());
186: assertEquals(0, genbankStreamSequence0.getTCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(1, range0.getEnd());
192: assertEquals(1, range0.getCount());
193: assertEquals(1, range0.getStart());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(1, simpleEntryGroup1.getSequenceLength());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(1, filteredEntryGroup0.getSequenceLength());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals(1, filteredEntryGroup0.size());
200: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(2, Bases.REVERSE);
205: assertEquals(1, Bases.FORWARD);
206: assertEquals(5, Bases.MAX_PRIORITY);
207:
208: feature0.getPositionInSequence((-5));
Test case 38
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.duplicate(false);
Test case 39
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getOtherCount());
4: assertEquals(0, genbankStreamSequence0.getGCount());
5: assertEquals(0, genbankStreamSequence0.getACount());
6: assertEquals(0, genbankStreamSequence0.getTCount());
7: assertNull(genbankStreamSequence0.getHeader());
8: assertEquals(2, genbankStreamSequence0.getFormatType());
9: assertEquals(0, genbankStreamSequence0.length());
10: assertEquals(0, genbankStreamSequence0.getCCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getOtherCount());
15: assertEquals(0, genbankStreamSequence0.getGCount());
16: assertEquals(0, genbankStreamSequence0.getACount());
17: assertEquals(0, genbankStreamSequence0.getTCount());
18: assertNull(genbankStreamSequence0.getHeader());
19: assertEquals(2, genbankStreamSequence0.getFormatType());
20: assertEquals(0, genbankStreamSequence0.length());
21: assertEquals(0, genbankStreamSequence0.getCCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals(2, Bases.REVERSE);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getOtherCount());
32: assertEquals(0, genbankStreamSequence0.getGCount());
33: assertEquals(0, genbankStreamSequence0.getACount());
34: assertEquals(0, genbankStreamSequence0.getTCount());
35: assertNull(genbankStreamSequence0.getHeader());
36: assertEquals(2, genbankStreamSequence0.getFormatType());
37: assertEquals(0, genbankStreamSequence0.length());
38: assertEquals(0, genbankStreamSequence0.getCCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals(2, Bases.REVERSE);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(5, range0.getEnd());
52: assertEquals(0, range0.getStart());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getOtherCount());
61: assertEquals(0, genbankStreamSequence0.getGCount());
62: assertEquals(0, genbankStreamSequence0.getACount());
63: assertEquals(0, genbankStreamSequence0.getTCount());
64: assertNull(genbankStreamSequence0.getHeader());
65: assertEquals(2, genbankStreamSequence0.getFormatType());
66: assertEquals(0, genbankStreamSequence0.length());
67: assertEquals(0, genbankStreamSequence0.getCCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(5, range0.getEnd());
73: assertEquals(0, range0.getStart());
74: assertEquals(6, range0.getCount());
75: assertEquals(0, simpleEntryGroup1.refCount());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(6, simpleEntryGroup1.getSequenceLength());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals(2, Bases.REVERSE);
82: assertEquals(5, Bases.MAX_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getOtherCount());
89: assertEquals(0, genbankStreamSequence0.getGCount());
90: assertEquals(0, genbankStreamSequence0.getACount());
91: assertEquals(0, genbankStreamSequence0.getTCount());
92: assertNull(genbankStreamSequence0.getHeader());
93: assertEquals(2, genbankStreamSequence0.getFormatType());
94: assertEquals(0, genbankStreamSequence0.length());
95: assertEquals(0, genbankStreamSequence0.getCCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals(2, Bases.REVERSE);
104: assertEquals(5, Bases.MAX_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getOtherCount());
111: assertEquals(0, genbankStreamSequence0.getGCount());
112: assertEquals(0, genbankStreamSequence0.getACount());
113: assertEquals(0, genbankStreamSequence0.getTCount());
114: assertNull(genbankStreamSequence0.getHeader());
115: assertEquals(2, genbankStreamSequence0.getFormatType());
116: assertEquals(0, genbankStreamSequence0.length());
117: assertEquals(0, genbankStreamSequence0.getCCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(5, range0.getEnd());
123: assertEquals(0, range0.getStart());
124: assertEquals(6, range0.getCount());
125: assertEquals(0, simpleEntryGroup1.refCount());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(6, simpleEntryGroup1.getSequenceLength());
128: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
129: assertEquals(6, filteredEntryGroup0.getSequenceLength());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals(0, filteredEntryGroup0.refCount());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals(2, Bases.REVERSE);
136: assertEquals(5, Bases.MAX_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getOtherCount());
145: assertEquals(0, genbankStreamSequence0.getGCount());
146: assertEquals(0, genbankStreamSequence0.getACount());
147: assertEquals(0, genbankStreamSequence0.getTCount());
148: assertNull(genbankStreamSequence0.getHeader());
149: assertEquals(2, genbankStreamSequence0.getFormatType());
150: assertEquals(0, genbankStreamSequence0.length());
151: assertEquals(0, genbankStreamSequence0.getCCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(5, range0.getEnd());
157: assertEquals(0, range0.getStart());
158: assertEquals(6, range0.getCount());
159: assertEquals(0, simpleEntryGroup1.refCount());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(6, simpleEntryGroup1.getSequenceLength());
162: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
163: assertEquals(6, filteredEntryGroup0.getSequenceLength());
164: assertEquals(1, filteredEntryGroup0.size());
165: assertEquals(0, filteredEntryGroup0.refCount());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals(2, Bases.REVERSE);
171: assertEquals(5, Bases.MAX_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getOtherCount());
180: assertEquals(0, genbankStreamSequence0.getGCount());
181: assertEquals(0, genbankStreamSequence0.getACount());
182: assertEquals(0, genbankStreamSequence0.getTCount());
183: assertNull(genbankStreamSequence0.getHeader());
184: assertEquals(2, genbankStreamSequence0.getFormatType());
185: assertEquals(0, genbankStreamSequence0.length());
186: assertEquals(0, genbankStreamSequence0.getCCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(5, range0.getEnd());
192: assertEquals(0, range0.getStart());
193: assertEquals(6, range0.getCount());
194: assertEquals(0, simpleEntryGroup1.refCount());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(6, simpleEntryGroup1.getSequenceLength());
197: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
198: assertEquals(6, filteredEntryGroup0.getSequenceLength());
199: assertEquals(1, filteredEntryGroup0.size());
200: assertEquals(0, filteredEntryGroup0.refCount());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals(2, Bases.REVERSE);
206: assertEquals(5, Bases.MAX_PRIORITY);
207:
208: Feature feature1 = feature0.copyTo(entry0);
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertFalse(feature1.equals((Object)feature0));
212: assertNotNull(feature1);
213: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
214: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
215: assertNotSame(feature0, feature1);
216: assertNotSame(feature1, feature0);
217: assertEquals(0, genbankStreamSequence0.getOtherCount());
218: assertEquals(0, genbankStreamSequence0.getGCount());
219: assertEquals(0, genbankStreamSequence0.getACount());
220: assertEquals(0, genbankStreamSequence0.getTCount());
221: assertNull(genbankStreamSequence0.getHeader());
222: assertEquals(2, genbankStreamSequence0.getFormatType());
223: assertEquals(0, genbankStreamSequence0.length());
224: assertEquals(0, genbankStreamSequence0.getCCount());
225: assertEquals(0, bases0.getLength());
226: assertEquals(0, simpleEntryGroup0.refCount());
227: assertEquals(0, simpleEntryGroup0.getSequenceLength());
228: assertEquals(0, simpleEntryGroup0.size());
229: assertEquals(5, range0.getEnd());
230: assertEquals(0, range0.getStart());
231: assertEquals(6, range0.getCount());
232: assertEquals(0, simpleEntryGroup1.refCount());
233: assertEquals(1, simpleEntryGroup1.size());
234: assertEquals(6, simpleEntryGroup1.getSequenceLength());
235: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
236: assertEquals(6, filteredEntryGroup0.getSequenceLength());
237: assertEquals(1, filteredEntryGroup0.size());
238: assertEquals(0, filteredEntryGroup0.refCount());
239: assertFalse(entry0.isReadOnly());
240: assertFalse(feature0.isReadOnly());
241: assertFalse(feature1.isReadOnly());
242: assertEquals((-5), Bases.MIN_PRIORITY);
243: assertEquals(0, Bases.MEDIUM_PRIORITY);
244: assertEquals(1, Bases.FORWARD);
245: assertEquals(2, Bases.REVERSE);
246: assertEquals(5, Bases.MAX_PRIORITY);
Test case 40
1: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup();
2: assertNotNull(simpleEntryGroup0);
3: assertEquals(0, simpleEntryGroup0.size());
4: assertEquals(0, simpleEntryGroup0.refCount());
5:
6: Key key0 = Key.CDS;
7: assertNotNull(key0);
8: assertEquals(3, key0.length());
9: assertEquals("CDS", key0.getKeyString());
10: assertEquals("CDS", key0.toString());
11:
12: FeatureKeyQualifierPredicate featureKeyQualifierPredicate0 = new FeatureKeyQualifierPredicate(key0, "", "", false, false);
13: assertNotNull(featureKeyQualifierPredicate0);
14: assertEquals(3, key0.length());
15: assertEquals("CDS", key0.getKeyString());
16: assertEquals("CDS", key0.toString());
17:
18: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup0, featureKeyQualifierPredicate0, "");
19: assertNotNull(filteredEntryGroup0);
20: assertEquals(0, simpleEntryGroup0.size());
21: assertEquals(0, simpleEntryGroup0.refCount());
22: assertEquals(3, key0.length());
23: assertEquals("CDS", key0.getKeyString());
24: assertEquals("CDS", key0.toString());
25: assertEquals(0, filteredEntryGroup0.size());
26: assertEquals(0, filteredEntryGroup0.refCount());
27: assertEquals("", filteredEntryGroup0.getFilterName());
28:
29: Entry entry0 = filteredEntryGroup0.createEntry("partial 3' ");
30: FeatureVector featureVector0 = entry0.checkForOverlappingCDSs();
31: Feature.getAllQualifierNames(featureVector0);
Test case 41
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup();
12: assertNotNull(simpleEntryGroup0);
13: assertEquals(0, simpleEntryGroup0.refCount());
14: assertEquals(0, simpleEntryGroup0.size());
15:
16: feature0.addFeatureChangeListener(simpleEntryGroup0);
17: assertFalse(feature0.isReadOnly());
18: assertEquals(0, simpleEntryGroup0.refCount());
19: assertEquals(0, simpleEntryGroup0.size());
Test case 42
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: String string0 = feature0.toString();
9: assertNotNull(string0);
10: assertFalse(feature0.isReadOnly());
Test case 43
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getOtherCount());
4: assertEquals(0, genbankStreamSequence0.getGCount());
5: assertNull(genbankStreamSequence0.getHeader());
6: assertEquals(0, genbankStreamSequence0.getACount());
7: assertEquals(0, genbankStreamSequence0.getTCount());
8: assertEquals(0, genbankStreamSequence0.length());
9: assertEquals(0, genbankStreamSequence0.getCCount());
10: assertEquals(2, genbankStreamSequence0.getFormatType());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getOtherCount());
15: assertEquals(0, genbankStreamSequence0.getGCount());
16: assertNull(genbankStreamSequence0.getHeader());
17: assertEquals(0, genbankStreamSequence0.getACount());
18: assertEquals(0, genbankStreamSequence0.getTCount());
19: assertEquals(0, genbankStreamSequence0.length());
20: assertEquals(0, genbankStreamSequence0.getCCount());
21: assertEquals(2, genbankStreamSequence0.getFormatType());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals(5, Bases.MAX_PRIORITY);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getOtherCount());
32: assertEquals(0, genbankStreamSequence0.getGCount());
33: assertNull(genbankStreamSequence0.getHeader());
34: assertEquals(0, genbankStreamSequence0.getACount());
35: assertEquals(0, genbankStreamSequence0.getTCount());
36: assertEquals(0, genbankStreamSequence0.length());
37: assertEquals(0, genbankStreamSequence0.getCCount());
38: assertEquals(2, genbankStreamSequence0.getFormatType());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(5, range0.getEnd());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getOtherCount());
61: assertEquals(0, genbankStreamSequence0.getGCount());
62: assertNull(genbankStreamSequence0.getHeader());
63: assertEquals(0, genbankStreamSequence0.getACount());
64: assertEquals(0, genbankStreamSequence0.getTCount());
65: assertEquals(0, genbankStreamSequence0.length());
66: assertEquals(0, genbankStreamSequence0.getCCount());
67: assertEquals(2, genbankStreamSequence0.getFormatType());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(0, range0.getStart());
73: assertEquals(5, range0.getEnd());
74: assertEquals(6, range0.getCount());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.refCount());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals(5, Bases.MAX_PRIORITY);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getOtherCount());
89: assertEquals(0, genbankStreamSequence0.getGCount());
90: assertNull(genbankStreamSequence0.getHeader());
91: assertEquals(0, genbankStreamSequence0.getACount());
92: assertEquals(0, genbankStreamSequence0.getTCount());
93: assertEquals(0, genbankStreamSequence0.length());
94: assertEquals(0, genbankStreamSequence0.getCCount());
95: assertEquals(2, genbankStreamSequence0.getFormatType());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals(5, Bases.MAX_PRIORITY);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getOtherCount());
111: assertEquals(0, genbankStreamSequence0.getGCount());
112: assertNull(genbankStreamSequence0.getHeader());
113: assertEquals(0, genbankStreamSequence0.getACount());
114: assertEquals(0, genbankStreamSequence0.getTCount());
115: assertEquals(0, genbankStreamSequence0.length());
116: assertEquals(0, genbankStreamSequence0.getCCount());
117: assertEquals(2, genbankStreamSequence0.getFormatType());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(0, range0.getStart());
123: assertEquals(5, range0.getEnd());
124: assertEquals(6, range0.getCount());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.refCount());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals(0, filteredEntryGroup0.refCount());
129: assertEquals(6, filteredEntryGroup0.getSequenceLength());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals(5, Bases.MAX_PRIORITY);
136: assertEquals(2, Bases.REVERSE);
137:
138: filteredEntryGroup0.createEntry();
139: Feature feature0 = filteredEntryGroup0.createFeature();
140: feature0.getTranslationBases();
Test case 44
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(2, genbankStreamSequence0.getFormatType());
4: assertEquals(0, genbankStreamSequence0.length());
5: assertNull(genbankStreamSequence0.getHeader());
6: assertEquals(0, genbankStreamSequence0.getTCount());
7: assertEquals(0, genbankStreamSequence0.getOtherCount());
8: assertEquals(0, genbankStreamSequence0.getGCount());
9: assertEquals(0, genbankStreamSequence0.getACount());
10: assertEquals(0, genbankStreamSequence0.getCCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, genbankStreamSequence0.getFormatType());
15: assertEquals(0, genbankStreamSequence0.length());
16: assertNull(genbankStreamSequence0.getHeader());
17: assertEquals(0, genbankStreamSequence0.getTCount());
18: assertEquals(0, genbankStreamSequence0.getOtherCount());
19: assertEquals(0, genbankStreamSequence0.getGCount());
20: assertEquals(0, genbankStreamSequence0.getACount());
21: assertEquals(0, genbankStreamSequence0.getCCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(2, Bases.REVERSE);
24: assertEquals(1, Bases.FORWARD);
25: assertEquals((-5), Bases.MIN_PRIORITY);
26: assertEquals(0, Bases.MEDIUM_PRIORITY);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(2, genbankStreamSequence0.getFormatType());
32: assertEquals(0, genbankStreamSequence0.length());
33: assertNull(genbankStreamSequence0.getHeader());
34: assertEquals(0, genbankStreamSequence0.getTCount());
35: assertEquals(0, genbankStreamSequence0.getOtherCount());
36: assertEquals(0, genbankStreamSequence0.getGCount());
37: assertEquals(0, genbankStreamSequence0.getACount());
38: assertEquals(0, genbankStreamSequence0.getCCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.refCount());
43: assertEquals(2, Bases.REVERSE);
44: assertEquals(1, Bases.FORWARD);
45: assertEquals((-5), Bases.MIN_PRIORITY);
46: assertEquals(0, Bases.MEDIUM_PRIORITY);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(5, range0.getEnd());
52: assertEquals(0, range0.getStart());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
57: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
58: filteredEntryGroup0.createEntry();
59: Feature feature0 = filteredEntryGroup0.createFeature();
60: feature0.getKey();
Test case 45
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: Entry entry0 = feature0.getEntry();
12: assertNull(entry0);
13: assertFalse(feature0.isReadOnly());
Test case 46
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertNull(genbankStreamSequence0.getHeader());
4: assertEquals(0, genbankStreamSequence0.getTCount());
5: assertEquals(0, genbankStreamSequence0.getACount());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertEquals(0, genbankStreamSequence0.length());
8: assertEquals(0, genbankStreamSequence0.getOtherCount());
9: assertEquals(0, genbankStreamSequence0.getGCount());
10: assertEquals(2, genbankStreamSequence0.getFormatType());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertNull(genbankStreamSequence0.getHeader());
15: assertEquals(0, genbankStreamSequence0.getTCount());
16: assertEquals(0, genbankStreamSequence0.getACount());
17: assertEquals(0, genbankStreamSequence0.getCCount());
18: assertEquals(0, genbankStreamSequence0.length());
19: assertEquals(0, genbankStreamSequence0.getOtherCount());
20: assertEquals(0, genbankStreamSequence0.getGCount());
21: assertEquals(2, genbankStreamSequence0.getFormatType());
22: assertEquals(0, bases0.getLength());
23: assertEquals(2, Bases.REVERSE);
24: assertEquals(1, Bases.FORWARD);
25: assertEquals((-5), Bases.MIN_PRIORITY);
26: assertEquals(0, Bases.MEDIUM_PRIORITY);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertNull(genbankStreamSequence0.getHeader());
32: assertEquals(0, genbankStreamSequence0.getTCount());
33: assertEquals(0, genbankStreamSequence0.getACount());
34: assertEquals(0, genbankStreamSequence0.getCCount());
35: assertEquals(0, genbankStreamSequence0.length());
36: assertEquals(0, genbankStreamSequence0.getOtherCount());
37: assertEquals(0, genbankStreamSequence0.getGCount());
38: assertEquals(2, genbankStreamSequence0.getFormatType());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.refCount());
43: assertEquals(2, Bases.REVERSE);
44: assertEquals(1, Bases.FORWARD);
45: assertEquals((-5), Bases.MIN_PRIORITY);
46: assertEquals(0, Bases.MEDIUM_PRIORITY);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(5, range0.getEnd());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertNull(genbankStreamSequence0.getHeader());
61: assertEquals(0, genbankStreamSequence0.getTCount());
62: assertEquals(0, genbankStreamSequence0.getACount());
63: assertEquals(0, genbankStreamSequence0.getCCount());
64: assertEquals(0, genbankStreamSequence0.length());
65: assertEquals(0, genbankStreamSequence0.getOtherCount());
66: assertEquals(0, genbankStreamSequence0.getGCount());
67: assertEquals(2, genbankStreamSequence0.getFormatType());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.size());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.refCount());
72: assertEquals(6, range0.getCount());
73: assertEquals(5, range0.getEnd());
74: assertEquals(0, range0.getStart());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(2, Bases.REVERSE);
79: assertEquals(1, Bases.FORWARD);
80: assertEquals((-5), Bases.MIN_PRIORITY);
81: assertEquals(0, Bases.MEDIUM_PRIORITY);
82: assertEquals(5, Bases.MAX_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertNull(genbankStreamSequence0.getHeader());
89: assertEquals(0, genbankStreamSequence0.getTCount());
90: assertEquals(0, genbankStreamSequence0.getACount());
91: assertEquals(0, genbankStreamSequence0.getCCount());
92: assertEquals(0, genbankStreamSequence0.length());
93: assertEquals(0, genbankStreamSequence0.getOtherCount());
94: assertEquals(0, genbankStreamSequence0.getGCount());
95: assertEquals(2, genbankStreamSequence0.getFormatType());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.size());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.refCount());
100: assertEquals(2, Bases.REVERSE);
101: assertEquals(1, Bases.FORWARD);
102: assertEquals((-5), Bases.MIN_PRIORITY);
103: assertEquals(0, Bases.MEDIUM_PRIORITY);
104: assertEquals(5, Bases.MAX_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertNull(genbankStreamSequence0.getHeader());
111: assertEquals(0, genbankStreamSequence0.getTCount());
112: assertEquals(0, genbankStreamSequence0.getACount());
113: assertEquals(0, genbankStreamSequence0.getCCount());
114: assertEquals(0, genbankStreamSequence0.length());
115: assertEquals(0, genbankStreamSequence0.getOtherCount());
116: assertEquals(0, genbankStreamSequence0.getGCount());
117: assertEquals(2, genbankStreamSequence0.getFormatType());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.size());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.refCount());
122: assertEquals(6, range0.getCount());
123: assertEquals(5, range0.getEnd());
124: assertEquals(0, range0.getStart());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(0, filteredEntryGroup0.size());
129: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
130: assertEquals(6, filteredEntryGroup0.getSequenceLength());
131: assertEquals(0, filteredEntryGroup0.refCount());
132: assertEquals(2, Bases.REVERSE);
133: assertEquals(1, Bases.FORWARD);
134: assertEquals((-5), Bases.MIN_PRIORITY);
135: assertEquals(0, Bases.MEDIUM_PRIORITY);
136: assertEquals(5, Bases.MAX_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertNull(genbankStreamSequence0.getHeader());
145: assertEquals(0, genbankStreamSequence0.getTCount());
146: assertEquals(0, genbankStreamSequence0.getACount());
147: assertEquals(0, genbankStreamSequence0.getCCount());
148: assertEquals(0, genbankStreamSequence0.length());
149: assertEquals(0, genbankStreamSequence0.getOtherCount());
150: assertEquals(0, genbankStreamSequence0.getGCount());
151: assertEquals(2, genbankStreamSequence0.getFormatType());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.size());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.refCount());
156: assertEquals(6, range0.getCount());
157: assertEquals(5, range0.getEnd());
158: assertEquals(0, range0.getStart());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
163: assertEquals(1, filteredEntryGroup0.size());
164: assertEquals(6, filteredEntryGroup0.getSequenceLength());
165: assertEquals(0, filteredEntryGroup0.refCount());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(2, Bases.REVERSE);
168: assertEquals(1, Bases.FORWARD);
169: assertEquals((-5), Bases.MIN_PRIORITY);
170: assertEquals(0, Bases.MEDIUM_PRIORITY);
171: assertEquals(5, Bases.MAX_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertNull(genbankStreamSequence0.getHeader());
180: assertEquals(0, genbankStreamSequence0.getTCount());
181: assertEquals(0, genbankStreamSequence0.getACount());
182: assertEquals(0, genbankStreamSequence0.getCCount());
183: assertEquals(0, genbankStreamSequence0.length());
184: assertEquals(0, genbankStreamSequence0.getOtherCount());
185: assertEquals(0, genbankStreamSequence0.getGCount());
186: assertEquals(2, genbankStreamSequence0.getFormatType());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.size());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.refCount());
191: assertEquals(6, range0.getCount());
192: assertEquals(5, range0.getEnd());
193: assertEquals(0, range0.getStart());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
198: assertEquals(1, filteredEntryGroup0.size());
199: assertEquals(6, filteredEntryGroup0.getSequenceLength());
200: assertEquals(0, filteredEntryGroup0.refCount());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(2, Bases.REVERSE);
203: assertEquals(1, Bases.FORWARD);
204: assertEquals((-5), Bases.MIN_PRIORITY);
205: assertEquals(0, Bases.MEDIUM_PRIORITY);
206: assertEquals(5, Bases.MAX_PRIORITY);
207:
208: Location location0 = feature0.getLocation();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(location0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertNull(genbankStreamSequence0.getHeader());
215: assertEquals(0, genbankStreamSequence0.getTCount());
216: assertEquals(0, genbankStreamSequence0.getACount());
217: assertEquals(0, genbankStreamSequence0.getCCount());
218: assertEquals(0, genbankStreamSequence0.length());
219: assertEquals(0, genbankStreamSequence0.getOtherCount());
220: assertEquals(0, genbankStreamSequence0.getGCount());
221: assertEquals(2, genbankStreamSequence0.getFormatType());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.size());
224: assertEquals(0, simpleEntryGroup0.getSequenceLength());
225: assertEquals(0, simpleEntryGroup0.refCount());
226: assertEquals(6, range0.getCount());
227: assertEquals(5, range0.getEnd());
228: assertEquals(0, range0.getStart());
229: assertEquals(1, simpleEntryGroup1.size());
230: assertEquals(6, simpleEntryGroup1.getSequenceLength());
231: assertEquals(0, simpleEntryGroup1.refCount());
232: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
233: assertEquals(1, filteredEntryGroup0.size());
234: assertEquals(6, filteredEntryGroup0.getSequenceLength());
235: assertEquals(0, filteredEntryGroup0.refCount());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(2, Bases.REVERSE);
238: assertEquals(1, Bases.FORWARD);
239: assertEquals((-5), Bases.MIN_PRIORITY);
240: assertEquals(0, Bases.MEDIUM_PRIORITY);
241: assertEquals(5, Bases.MAX_PRIORITY);
Test case 47
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: Qualifier qualifier0 = feature0.getQualifierByName((String) null);
12: assertNull(qualifier0);
13: assertFalse(feature0.isReadOnly());
Test case 48
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: MockPrintStream mockPrintStream0 = new MockPrintStream("label");
9: assertNotNull(mockPrintStream0);
10:
11: Charset charset0 = Charset.defaultCharset();
12: assertNotNull(charset0);
13: assertTrue(charset0.isRegistered());
14: assertEquals("UTF-8", charset0.displayName());
15: assertTrue(charset0.canEncode());
16: assertEquals("UTF-8", charset0.name());
17: assertEquals("UTF-8", charset0.toString());
18:
19: OutputStreamWriter outputStreamWriter0 = new OutputStreamWriter(mockPrintStream0, charset0);
20: assertNotNull(outputStreamWriter0);
21: assertTrue(charset0.isRegistered());
22: assertEquals("UTF-8", charset0.displayName());
23: assertTrue(charset0.canEncode());
24: assertEquals("UTF-8", charset0.name());
25: assertEquals("UTF-8", charset0.toString());
26:
27: feature0.writeNative(outputStreamWriter0);
28: assertFalse(feature0.isReadOnly());
29: assertTrue(charset0.isRegistered());
30: assertEquals("UTF-8", charset0.displayName());
31: assertTrue(charset0.canEncode());
32: assertEquals("UTF-8", charset0.name());
33: assertEquals("UTF-8", charset0.toString());
Test case 49
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.getWriteRange();
Test case 50
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: boolean boolean0 = feature0.isForwardFeature();
12: assertTrue(boolean0);
13: assertFalse(feature0.isReadOnly());
Test case 51
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getGCount());
4: assertEquals(2, genbankStreamSequence0.getFormatType());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertNull(genbankStreamSequence0.getHeader());
8: assertEquals(0, genbankStreamSequence0.getACount());
9: assertEquals(0, genbankStreamSequence0.length());
10: assertEquals(0, genbankStreamSequence0.getOtherCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getGCount());
15: assertEquals(2, genbankStreamSequence0.getFormatType());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertEquals(0, genbankStreamSequence0.getCCount());
18: assertNull(genbankStreamSequence0.getHeader());
19: assertEquals(0, genbankStreamSequence0.getACount());
20: assertEquals(0, genbankStreamSequence0.length());
21: assertEquals(0, genbankStreamSequence0.getOtherCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(1, Bases.FORWARD);
24: assertEquals((-5), Bases.MIN_PRIORITY);
25: assertEquals(0, Bases.MEDIUM_PRIORITY);
26: assertEquals(2, Bases.REVERSE);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getGCount());
32: assertEquals(2, genbankStreamSequence0.getFormatType());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertEquals(0, genbankStreamSequence0.getCCount());
35: assertNull(genbankStreamSequence0.getHeader());
36: assertEquals(0, genbankStreamSequence0.getACount());
37: assertEquals(0, genbankStreamSequence0.length());
38: assertEquals(0, genbankStreamSequence0.getOtherCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals(1, Bases.FORWARD);
44: assertEquals((-5), Bases.MIN_PRIORITY);
45: assertEquals(0, Bases.MEDIUM_PRIORITY);
46: assertEquals(2, Bases.REVERSE);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(5, range0.getEnd());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getGCount());
61: assertEquals(2, genbankStreamSequence0.getFormatType());
62: assertEquals(0, genbankStreamSequence0.getTCount());
63: assertEquals(0, genbankStreamSequence0.getCCount());
64: assertNull(genbankStreamSequence0.getHeader());
65: assertEquals(0, genbankStreamSequence0.getACount());
66: assertEquals(0, genbankStreamSequence0.length());
67: assertEquals(0, genbankStreamSequence0.getOtherCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.size());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(6, range0.getCount());
73: assertEquals(5, range0.getEnd());
74: assertEquals(0, range0.getStart());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(1, Bases.FORWARD);
79: assertEquals((-5), Bases.MIN_PRIORITY);
80: assertEquals(0, Bases.MEDIUM_PRIORITY);
81: assertEquals(2, Bases.REVERSE);
82: assertEquals(5, Bases.MAX_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getGCount());
89: assertEquals(2, genbankStreamSequence0.getFormatType());
90: assertEquals(0, genbankStreamSequence0.getTCount());
91: assertEquals(0, genbankStreamSequence0.getCCount());
92: assertNull(genbankStreamSequence0.getHeader());
93: assertEquals(0, genbankStreamSequence0.getACount());
94: assertEquals(0, genbankStreamSequence0.length());
95: assertEquals(0, genbankStreamSequence0.getOtherCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.size());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals(1, Bases.FORWARD);
101: assertEquals((-5), Bases.MIN_PRIORITY);
102: assertEquals(0, Bases.MEDIUM_PRIORITY);
103: assertEquals(2, Bases.REVERSE);
104: assertEquals(5, Bases.MAX_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getGCount());
111: assertEquals(2, genbankStreamSequence0.getFormatType());
112: assertEquals(0, genbankStreamSequence0.getTCount());
113: assertEquals(0, genbankStreamSequence0.getCCount());
114: assertNull(genbankStreamSequence0.getHeader());
115: assertEquals(0, genbankStreamSequence0.getACount());
116: assertEquals(0, genbankStreamSequence0.length());
117: assertEquals(0, genbankStreamSequence0.getOtherCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.size());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(6, range0.getCount());
123: assertEquals(5, range0.getEnd());
124: assertEquals(0, range0.getStart());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals(1, Bases.FORWARD);
133: assertEquals((-5), Bases.MIN_PRIORITY);
134: assertEquals(0, Bases.MEDIUM_PRIORITY);
135: assertEquals(2, Bases.REVERSE);
136: assertEquals(5, Bases.MAX_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getGCount());
145: assertEquals(2, genbankStreamSequence0.getFormatType());
146: assertEquals(0, genbankStreamSequence0.getTCount());
147: assertEquals(0, genbankStreamSequence0.getCCount());
148: assertNull(genbankStreamSequence0.getHeader());
149: assertEquals(0, genbankStreamSequence0.getACount());
150: assertEquals(0, genbankStreamSequence0.length());
151: assertEquals(0, genbankStreamSequence0.getOtherCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.size());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(6, range0.getCount());
157: assertEquals(5, range0.getEnd());
158: assertEquals(0, range0.getStart());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(1, filteredEntryGroup0.size());
163: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
164: assertEquals(0, filteredEntryGroup0.refCount());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(1, Bases.FORWARD);
168: assertEquals((-5), Bases.MIN_PRIORITY);
169: assertEquals(0, Bases.MEDIUM_PRIORITY);
170: assertEquals(2, Bases.REVERSE);
171: assertEquals(5, Bases.MAX_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getGCount());
180: assertEquals(2, genbankStreamSequence0.getFormatType());
181: assertEquals(0, genbankStreamSequence0.getTCount());
182: assertEquals(0, genbankStreamSequence0.getCCount());
183: assertNull(genbankStreamSequence0.getHeader());
184: assertEquals(0, genbankStreamSequence0.getACount());
185: assertEquals(0, genbankStreamSequence0.length());
186: assertEquals(0, genbankStreamSequence0.getOtherCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.size());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(6, range0.getCount());
192: assertEquals(5, range0.getEnd());
193: assertEquals(0, range0.getStart());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(1, filteredEntryGroup0.size());
198: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
199: assertEquals(0, filteredEntryGroup0.refCount());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(1, Bases.FORWARD);
203: assertEquals((-5), Bases.MIN_PRIORITY);
204: assertEquals(0, Bases.MEDIUM_PRIORITY);
205: assertEquals(2, Bases.REVERSE);
206: assertEquals(5, Bases.MAX_PRIORITY);
207:
208: boolean boolean0 = feature0.isCDS();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertFalse(boolean0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.getGCount());
215: assertEquals(2, genbankStreamSequence0.getFormatType());
216: assertEquals(0, genbankStreamSequence0.getTCount());
217: assertEquals(0, genbankStreamSequence0.getCCount());
218: assertNull(genbankStreamSequence0.getHeader());
219: assertEquals(0, genbankStreamSequence0.getACount());
220: assertEquals(0, genbankStreamSequence0.length());
221: assertEquals(0, genbankStreamSequence0.getOtherCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.size());
224: assertEquals(0, simpleEntryGroup0.refCount());
225: assertEquals(0, simpleEntryGroup0.getSequenceLength());
226: assertEquals(6, range0.getCount());
227: assertEquals(5, range0.getEnd());
228: assertEquals(0, range0.getStart());
229: assertEquals(6, simpleEntryGroup1.getSequenceLength());
230: assertEquals(1, simpleEntryGroup1.size());
231: assertEquals(0, simpleEntryGroup1.refCount());
232: assertEquals(1, filteredEntryGroup0.size());
233: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
234: assertEquals(0, filteredEntryGroup0.refCount());
235: assertEquals(6, filteredEntryGroup0.getSequenceLength());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(1, Bases.FORWARD);
238: assertEquals((-5), Bases.MIN_PRIORITY);
239: assertEquals(0, Bases.MEDIUM_PRIORITY);
240: assertEquals(2, Bases.REVERSE);
241: assertEquals(5, Bases.MAX_PRIORITY);
Test case 52
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getOtherCount());
4: assertNull(genbankStreamSequence0.getHeader());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(0, genbankStreamSequence0.getACount());
7: assertEquals(0, genbankStreamSequence0.getCCount());
8: assertEquals(0, genbankStreamSequence0.length());
9: assertEquals(0, genbankStreamSequence0.getGCount());
10: assertEquals(2, genbankStreamSequence0.getFormatType());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getOtherCount());
15: assertNull(genbankStreamSequence0.getHeader());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertEquals(0, genbankStreamSequence0.getACount());
18: assertEquals(0, genbankStreamSequence0.getCCount());
19: assertEquals(0, genbankStreamSequence0.length());
20: assertEquals(0, genbankStreamSequence0.getGCount());
21: assertEquals(2, genbankStreamSequence0.getFormatType());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getOtherCount());
32: assertNull(genbankStreamSequence0.getHeader());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertEquals(0, genbankStreamSequence0.getACount());
35: assertEquals(0, genbankStreamSequence0.getCCount());
36: assertEquals(0, genbankStreamSequence0.length());
37: assertEquals(0, genbankStreamSequence0.getGCount());
38: assertEquals(2, genbankStreamSequence0.getFormatType());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(1, Bases.FORWARD);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(5, range0.getEnd());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getOtherCount());
61: assertNull(genbankStreamSequence0.getHeader());
62: assertEquals(0, genbankStreamSequence0.getTCount());
63: assertEquals(0, genbankStreamSequence0.getACount());
64: assertEquals(0, genbankStreamSequence0.getCCount());
65: assertEquals(0, genbankStreamSequence0.length());
66: assertEquals(0, genbankStreamSequence0.getGCount());
67: assertEquals(2, genbankStreamSequence0.getFormatType());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(6, range0.getCount());
73: assertEquals(5, range0.getEnd());
74: assertEquals(0, range0.getStart());
75: assertEquals(0, simpleEntryGroup1.refCount());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(5, Bases.MAX_PRIORITY);
81: assertEquals(1, Bases.FORWARD);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getOtherCount());
89: assertNull(genbankStreamSequence0.getHeader());
90: assertEquals(0, genbankStreamSequence0.getTCount());
91: assertEquals(0, genbankStreamSequence0.getACount());
92: assertEquals(0, genbankStreamSequence0.getCCount());
93: assertEquals(0, genbankStreamSequence0.length());
94: assertEquals(0, genbankStreamSequence0.getGCount());
95: assertEquals(2, genbankStreamSequence0.getFormatType());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(5, Bases.MAX_PRIORITY);
103: assertEquals(1, Bases.FORWARD);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getOtherCount());
111: assertNull(genbankStreamSequence0.getHeader());
112: assertEquals(0, genbankStreamSequence0.getTCount());
113: assertEquals(0, genbankStreamSequence0.getACount());
114: assertEquals(0, genbankStreamSequence0.getCCount());
115: assertEquals(0, genbankStreamSequence0.length());
116: assertEquals(0, genbankStreamSequence0.getGCount());
117: assertEquals(2, genbankStreamSequence0.getFormatType());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(6, range0.getCount());
123: assertEquals(5, range0.getEnd());
124: assertEquals(0, range0.getStart());
125: assertEquals(0, simpleEntryGroup1.refCount());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals(0, filteredEntryGroup0.size());
129: assertEquals(6, filteredEntryGroup0.getSequenceLength());
130: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
131: assertEquals(0, filteredEntryGroup0.refCount());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(5, Bases.MAX_PRIORITY);
135: assertEquals(1, Bases.FORWARD);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getOtherCount());
145: assertNull(genbankStreamSequence0.getHeader());
146: assertEquals(0, genbankStreamSequence0.getTCount());
147: assertEquals(0, genbankStreamSequence0.getACount());
148: assertEquals(0, genbankStreamSequence0.getCCount());
149: assertEquals(0, genbankStreamSequence0.length());
150: assertEquals(0, genbankStreamSequence0.getGCount());
151: assertEquals(2, genbankStreamSequence0.getFormatType());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(6, range0.getCount());
157: assertEquals(5, range0.getEnd());
158: assertEquals(0, range0.getStart());
159: assertEquals(0, simpleEntryGroup1.refCount());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(1, simpleEntryGroup1.size());
162: assertEquals(1, filteredEntryGroup0.size());
163: assertEquals(6, filteredEntryGroup0.getSequenceLength());
164: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
165: assertEquals(0, filteredEntryGroup0.refCount());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(5, Bases.MAX_PRIORITY);
170: assertEquals(1, Bases.FORWARD);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getOtherCount());
180: assertNull(genbankStreamSequence0.getHeader());
181: assertEquals(0, genbankStreamSequence0.getTCount());
182: assertEquals(0, genbankStreamSequence0.getACount());
183: assertEquals(0, genbankStreamSequence0.getCCount());
184: assertEquals(0, genbankStreamSequence0.length());
185: assertEquals(0, genbankStreamSequence0.getGCount());
186: assertEquals(2, genbankStreamSequence0.getFormatType());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.size());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(6, range0.getCount());
192: assertEquals(5, range0.getEnd());
193: assertEquals(0, range0.getStart());
194: assertEquals(0, simpleEntryGroup1.refCount());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(1, simpleEntryGroup1.size());
197: assertEquals(1, filteredEntryGroup0.size());
198: assertEquals(6, filteredEntryGroup0.getSequenceLength());
199: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
200: assertEquals(0, filteredEntryGroup0.refCount());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(5, Bases.MAX_PRIORITY);
205: assertEquals(1, Bases.FORWARD);
206: assertEquals(2, Bases.REVERSE);
207:
208: int int0 = feature0.getCodonStart();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertEquals(1, int0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.getOtherCount());
215: assertNull(genbankStreamSequence0.getHeader());
216: assertEquals(0, genbankStreamSequence0.getTCount());
217: assertEquals(0, genbankStreamSequence0.getACount());
218: assertEquals(0, genbankStreamSequence0.getCCount());
219: assertEquals(0, genbankStreamSequence0.length());
220: assertEquals(0, genbankStreamSequence0.getGCount());
221: assertEquals(2, genbankStreamSequence0.getFormatType());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.refCount());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(0, simpleEntryGroup0.getSequenceLength());
226: assertEquals(6, range0.getCount());
227: assertEquals(5, range0.getEnd());
228: assertEquals(0, range0.getStart());
229: assertEquals(0, simpleEntryGroup1.refCount());
230: assertEquals(6, simpleEntryGroup1.getSequenceLength());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals(1, filteredEntryGroup0.size());
233: assertEquals(6, filteredEntryGroup0.getSequenceLength());
234: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
235: assertEquals(0, filteredEntryGroup0.refCount());
236: assertFalse(feature0.isReadOnly());
237: assertEquals((-5), Bases.MIN_PRIORITY);
238: assertEquals(0, Bases.MEDIUM_PRIORITY);
239: assertEquals(5, Bases.MAX_PRIORITY);
240: assertEquals(1, Bases.FORWARD);
241: assertEquals(2, Bases.REVERSE);
Test case 53
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence(" -");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(2, genbankStreamSequence0.getOtherCount());
4: assertEquals(2, genbankStreamSequence0.length());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(2, genbankStreamSequence0.getFormatType());
7: assertNull(genbankStreamSequence0.getHeader());
8: assertEquals(0, genbankStreamSequence0.getCCount());
9: assertEquals(0, genbankStreamSequence0.getACount());
10: assertEquals(0, genbankStreamSequence0.getGCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, genbankStreamSequence0.getOtherCount());
15: assertEquals(2, genbankStreamSequence0.length());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertEquals(2, genbankStreamSequence0.getFormatType());
18: assertNull(genbankStreamSequence0.getHeader());
19: assertEquals(0, genbankStreamSequence0.getCCount());
20: assertEquals(0, genbankStreamSequence0.getACount());
21: assertEquals(0, genbankStreamSequence0.getGCount());
22: assertEquals(2, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(2, genbankStreamSequence0.getOtherCount());
32: assertEquals(2, genbankStreamSequence0.length());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertEquals(2, genbankStreamSequence0.getFormatType());
35: assertNull(genbankStreamSequence0.getHeader());
36: assertEquals(0, genbankStreamSequence0.getCCount());
37: assertEquals(0, genbankStreamSequence0.getACount());
38: assertEquals(0, genbankStreamSequence0.getGCount());
39: assertEquals(2, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(2, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.refCount());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(1, Bases.FORWARD);
47: assertEquals(2, Bases.REVERSE);
48:
49: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
50: assertNotNull(featureVector0);
51: assertEquals(2, genbankStreamSequence0.getOtherCount());
52: assertEquals(2, genbankStreamSequence0.length());
53: assertEquals(0, genbankStreamSequence0.getTCount());
54: assertEquals(2, genbankStreamSequence0.getFormatType());
55: assertNull(genbankStreamSequence0.getHeader());
56: assertEquals(0, genbankStreamSequence0.getCCount());
57: assertEquals(0, genbankStreamSequence0.getACount());
58: assertEquals(0, genbankStreamSequence0.getGCount());
59: assertEquals(2, bases0.getLength());
60: assertEquals(0, simpleEntryGroup0.size());
61: assertEquals(2, simpleEntryGroup0.getSequenceLength());
62: assertEquals(0, simpleEntryGroup0.refCount());
63: assertEquals((-5), Bases.MIN_PRIORITY);
64: assertEquals(0, Bases.MEDIUM_PRIORITY);
65: assertEquals(5, Bases.MAX_PRIORITY);
66: assertEquals(1, Bases.FORWARD);
67: assertEquals(2, Bases.REVERSE);
68:
69: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup0, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
70: assertNotNull(filteredEntryGroup0);
71: assertEquals(2, genbankStreamSequence0.getOtherCount());
72: assertEquals(2, genbankStreamSequence0.length());
73: assertEquals(0, genbankStreamSequence0.getTCount());
74: assertEquals(2, genbankStreamSequence0.getFormatType());
75: assertNull(genbankStreamSequence0.getHeader());
76: assertEquals(0, genbankStreamSequence0.getCCount());
77: assertEquals(0, genbankStreamSequence0.getACount());
78: assertEquals(0, genbankStreamSequence0.getGCount());
79: assertEquals(2, bases0.getLength());
80: assertEquals(0, simpleEntryGroup0.size());
81: assertEquals(2, simpleEntryGroup0.getSequenceLength());
82: assertEquals(0, simpleEntryGroup0.refCount());
83: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
84: assertEquals(0, filteredEntryGroup0.refCount());
85: assertEquals(2, filteredEntryGroup0.getSequenceLength());
86: assertEquals(0, filteredEntryGroup0.size());
87: assertEquals((-5), Bases.MIN_PRIORITY);
88: assertEquals(0, Bases.MEDIUM_PRIORITY);
89: assertEquals(5, Bases.MAX_PRIORITY);
90: assertEquals(1, Bases.FORWARD);
91: assertEquals(2, Bases.REVERSE);
92:
93: Entry entry0 = filteredEntryGroup0.createEntry();
94: assertNotNull(entry0);
95: assertEquals(2, genbankStreamSequence0.getOtherCount());
96: assertEquals(2, genbankStreamSequence0.length());
97: assertEquals(0, genbankStreamSequence0.getTCount());
98: assertEquals(2, genbankStreamSequence0.getFormatType());
99: assertNull(genbankStreamSequence0.getHeader());
100: assertEquals(0, genbankStreamSequence0.getCCount());
101: assertEquals(0, genbankStreamSequence0.getACount());
102: assertEquals(0, genbankStreamSequence0.getGCount());
103: assertEquals(2, bases0.getLength());
104: assertEquals(1, simpleEntryGroup0.size());
105: assertEquals(2, simpleEntryGroup0.getSequenceLength());
106: assertEquals(0, simpleEntryGroup0.refCount());
107: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
108: assertEquals(0, filteredEntryGroup0.refCount());
109: assertEquals(2, filteredEntryGroup0.getSequenceLength());
110: assertEquals(1, filteredEntryGroup0.size());
111: assertFalse(entry0.isReadOnly());
112: assertEquals((-5), Bases.MIN_PRIORITY);
113: assertEquals(0, Bases.MEDIUM_PRIORITY);
114: assertEquals(5, Bases.MAX_PRIORITY);
115: assertEquals(1, Bases.FORWARD);
116: assertEquals(2, Bases.REVERSE);
117:
118: Feature feature0 = filteredEntryGroup0.createFeature();
119: assertNotNull(feature0);
120: assertEquals(2, genbankStreamSequence0.getOtherCount());
121: assertEquals(2, genbankStreamSequence0.length());
122: assertEquals(0, genbankStreamSequence0.getTCount());
123: assertEquals(2, genbankStreamSequence0.getFormatType());
124: assertNull(genbankStreamSequence0.getHeader());
125: assertEquals(0, genbankStreamSequence0.getCCount());
126: assertEquals(0, genbankStreamSequence0.getACount());
127: assertEquals(0, genbankStreamSequence0.getGCount());
128: assertEquals(2, bases0.getLength());
129: assertEquals(1, simpleEntryGroup0.size());
130: assertEquals(2, simpleEntryGroup0.getSequenceLength());
131: assertEquals(0, simpleEntryGroup0.refCount());
132: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
133: assertEquals(0, filteredEntryGroup0.refCount());
134: assertEquals(2, filteredEntryGroup0.getSequenceLength());
135: assertEquals(1, filteredEntryGroup0.size());
136: assertFalse(feature0.isReadOnly());
137: assertEquals((-5), Bases.MIN_PRIORITY);
138: assertEquals(0, Bases.MEDIUM_PRIORITY);
139: assertEquals(5, Bases.MAX_PRIORITY);
140: assertEquals(1, Bases.FORWARD);
141: assertEquals(2, Bases.REVERSE);
142:
143: boolean boolean0 = feature0.hasValidStartCodon(false);
144: assertTrue(boolean0);
145: assertEquals(2, genbankStreamSequence0.getOtherCount());
146: assertEquals(2, genbankStreamSequence0.length());
147: assertEquals(0, genbankStreamSequence0.getTCount());
148: assertEquals(2, genbankStreamSequence0.getFormatType());
149: assertNull(genbankStreamSequence0.getHeader());
150: assertEquals(0, genbankStreamSequence0.getCCount());
151: assertEquals(0, genbankStreamSequence0.getACount());
152: assertEquals(0, genbankStreamSequence0.getGCount());
153: assertEquals(2, bases0.getLength());
154: assertEquals(1, simpleEntryGroup0.size());
155: assertEquals(2, simpleEntryGroup0.getSequenceLength());
156: assertEquals(0, simpleEntryGroup0.refCount());
157: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
158: assertEquals(0, filteredEntryGroup0.refCount());
159: assertEquals(2, filteredEntryGroup0.getSequenceLength());
160: assertEquals(1, filteredEntryGroup0.size());
161: assertFalse(feature0.isReadOnly());
162: assertEquals((-5), Bases.MIN_PRIORITY);
163: assertEquals(0, Bases.MEDIUM_PRIORITY);
164: assertEquals(5, Bases.MAX_PRIORITY);
165: assertEquals(1, Bases.FORWARD);
166: assertEquals(2, Bases.REVERSE);
Test case 54
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: String string0 = feature0.getIDString();
12: assertNotNull(string0);
13: assertEquals("CDS", string0);
14: assertFalse(feature0.isReadOnly());
Test case 55
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getCCount());
4: assertEquals(0, genbankStreamSequence0.getTCount());
5: assertEquals(0, genbankStreamSequence0.length());
6: assertNull(genbankStreamSequence0.getHeader());
7: assertEquals(0, genbankStreamSequence0.getACount());
8: assertEquals(0, genbankStreamSequence0.getOtherCount());
9: assertEquals(0, genbankStreamSequence0.getGCount());
10: assertEquals(2, genbankStreamSequence0.getFormatType());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getCCount());
15: assertEquals(0, genbankStreamSequence0.getTCount());
16: assertEquals(0, genbankStreamSequence0.length());
17: assertNull(genbankStreamSequence0.getHeader());
18: assertEquals(0, genbankStreamSequence0.getACount());
19: assertEquals(0, genbankStreamSequence0.getOtherCount());
20: assertEquals(0, genbankStreamSequence0.getGCount());
21: assertEquals(2, genbankStreamSequence0.getFormatType());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals(2, Bases.REVERSE);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getCCount());
32: assertEquals(0, genbankStreamSequence0.getTCount());
33: assertEquals(0, genbankStreamSequence0.length());
34: assertNull(genbankStreamSequence0.getHeader());
35: assertEquals(0, genbankStreamSequence0.getACount());
36: assertEquals(0, genbankStreamSequence0.getOtherCount());
37: assertEquals(0, genbankStreamSequence0.getGCount());
38: assertEquals(2, genbankStreamSequence0.getFormatType());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.refCount());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals(2, Bases.REVERSE);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(5, range0.getEnd());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getCCount());
61: assertEquals(0, genbankStreamSequence0.getTCount());
62: assertEquals(0, genbankStreamSequence0.length());
63: assertNull(genbankStreamSequence0.getHeader());
64: assertEquals(0, genbankStreamSequence0.getACount());
65: assertEquals(0, genbankStreamSequence0.getOtherCount());
66: assertEquals(0, genbankStreamSequence0.getGCount());
67: assertEquals(2, genbankStreamSequence0.getFormatType());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.size());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.refCount());
72: assertEquals(6, range0.getCount());
73: assertEquals(5, range0.getEnd());
74: assertEquals(0, range0.getStart());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.refCount());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals(2, Bases.REVERSE);
82: assertEquals(5, Bases.MAX_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getCCount());
89: assertEquals(0, genbankStreamSequence0.getTCount());
90: assertEquals(0, genbankStreamSequence0.length());
91: assertNull(genbankStreamSequence0.getHeader());
92: assertEquals(0, genbankStreamSequence0.getACount());
93: assertEquals(0, genbankStreamSequence0.getOtherCount());
94: assertEquals(0, genbankStreamSequence0.getGCount());
95: assertEquals(2, genbankStreamSequence0.getFormatType());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.size());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.refCount());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals(2, Bases.REVERSE);
104: assertEquals(5, Bases.MAX_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getCCount());
111: assertEquals(0, genbankStreamSequence0.getTCount());
112: assertEquals(0, genbankStreamSequence0.length());
113: assertNull(genbankStreamSequence0.getHeader());
114: assertEquals(0, genbankStreamSequence0.getACount());
115: assertEquals(0, genbankStreamSequence0.getOtherCount());
116: assertEquals(0, genbankStreamSequence0.getGCount());
117: assertEquals(2, genbankStreamSequence0.getFormatType());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.size());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.refCount());
122: assertEquals(6, range0.getCount());
123: assertEquals(5, range0.getEnd());
124: assertEquals(0, range0.getStart());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.refCount());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals(0, filteredEntryGroup0.size());
129: assertEquals(6, filteredEntryGroup0.getSequenceLength());
130: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
131: assertEquals(0, filteredEntryGroup0.refCount());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals(2, Bases.REVERSE);
136: assertEquals(5, Bases.MAX_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getCCount());
145: assertEquals(0, genbankStreamSequence0.getTCount());
146: assertEquals(0, genbankStreamSequence0.length());
147: assertNull(genbankStreamSequence0.getHeader());
148: assertEquals(0, genbankStreamSequence0.getACount());
149: assertEquals(0, genbankStreamSequence0.getOtherCount());
150: assertEquals(0, genbankStreamSequence0.getGCount());
151: assertEquals(2, genbankStreamSequence0.getFormatType());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.size());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.refCount());
156: assertEquals(6, range0.getCount());
157: assertEquals(5, range0.getEnd());
158: assertEquals(0, range0.getStart());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(1, filteredEntryGroup0.size());
163: assertEquals(6, filteredEntryGroup0.getSequenceLength());
164: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
165: assertEquals(0, filteredEntryGroup0.refCount());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals(2, Bases.REVERSE);
171: assertEquals(5, Bases.MAX_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getCCount());
180: assertEquals(0, genbankStreamSequence0.getTCount());
181: assertEquals(0, genbankStreamSequence0.length());
182: assertNull(genbankStreamSequence0.getHeader());
183: assertEquals(0, genbankStreamSequence0.getACount());
184: assertEquals(0, genbankStreamSequence0.getOtherCount());
185: assertEquals(0, genbankStreamSequence0.getGCount());
186: assertEquals(2, genbankStreamSequence0.getFormatType());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.size());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.refCount());
191: assertEquals(6, range0.getCount());
192: assertEquals(5, range0.getEnd());
193: assertEquals(0, range0.getStart());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(1, filteredEntryGroup0.size());
198: assertEquals(6, filteredEntryGroup0.getSequenceLength());
199: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
200: assertEquals(0, filteredEntryGroup0.refCount());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals(2, Bases.REVERSE);
206: assertEquals(5, Bases.MAX_PRIORITY);
207:
208: String string0 = feature0.getSystematicName();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(string0);
212: assertEquals("misc_feature", string0);
213: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
214: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
215: assertEquals(0, genbankStreamSequence0.getCCount());
216: assertEquals(0, genbankStreamSequence0.getTCount());
217: assertEquals(0, genbankStreamSequence0.length());
218: assertNull(genbankStreamSequence0.getHeader());
219: assertEquals(0, genbankStreamSequence0.getACount());
220: assertEquals(0, genbankStreamSequence0.getOtherCount());
221: assertEquals(0, genbankStreamSequence0.getGCount());
222: assertEquals(2, genbankStreamSequence0.getFormatType());
223: assertEquals(0, bases0.getLength());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(0, simpleEntryGroup0.getSequenceLength());
226: assertEquals(0, simpleEntryGroup0.refCount());
227: assertEquals(6, range0.getCount());
228: assertEquals(5, range0.getEnd());
229: assertEquals(0, range0.getStart());
230: assertEquals(6, simpleEntryGroup1.getSequenceLength());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals(0, simpleEntryGroup1.refCount());
233: assertEquals(1, filteredEntryGroup0.size());
234: assertEquals(6, filteredEntryGroup0.getSequenceLength());
235: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
236: assertEquals(0, filteredEntryGroup0.refCount());
237: assertFalse(feature0.isReadOnly());
238: assertEquals((-5), Bases.MIN_PRIORITY);
239: assertEquals(0, Bases.MEDIUM_PRIORITY);
240: assertEquals(1, Bases.FORWARD);
241: assertEquals(2, Bases.REVERSE);
242: assertEquals(5, Bases.MAX_PRIORITY);
Test case 56
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: String string0 = feature0.getProductString();
9: assertNull(string0);
10: assertFalse(feature0.isReadOnly());
Test case 57
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.getBases();
Test case 58
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getGCount());
4: assertEquals(0, genbankStreamSequence0.getACount());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(2, genbankStreamSequence0.getFormatType());
7: assertEquals(0, genbankStreamSequence0.length());
8: assertNull(genbankStreamSequence0.getHeader());
9: assertEquals(0, genbankStreamSequence0.getCCount());
10: assertEquals(0, genbankStreamSequence0.getOtherCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getGCount());
15: assertEquals(0, genbankStreamSequence0.getACount());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertEquals(2, genbankStreamSequence0.getFormatType());
18: assertEquals(0, genbankStreamSequence0.length());
19: assertNull(genbankStreamSequence0.getHeader());
20: assertEquals(0, genbankStreamSequence0.getCCount());
21: assertEquals(0, genbankStreamSequence0.getOtherCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(5, Bases.MAX_PRIORITY);
24: assertEquals(2, Bases.REVERSE);
25: assertEquals((-5), Bases.MIN_PRIORITY);
26: assertEquals(0, Bases.MEDIUM_PRIORITY);
27: assertEquals(1, Bases.FORWARD);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getGCount());
32: assertEquals(0, genbankStreamSequence0.getACount());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertEquals(2, genbankStreamSequence0.getFormatType());
35: assertEquals(0, genbankStreamSequence0.length());
36: assertNull(genbankStreamSequence0.getHeader());
37: assertEquals(0, genbankStreamSequence0.getCCount());
38: assertEquals(0, genbankStreamSequence0.getOtherCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals(5, Bases.MAX_PRIORITY);
44: assertEquals(2, Bases.REVERSE);
45: assertEquals((-5), Bases.MIN_PRIORITY);
46: assertEquals(0, Bases.MEDIUM_PRIORITY);
47: assertEquals(1, Bases.FORWARD);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(0, range0.getStart());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getGCount());
61: assertEquals(0, genbankStreamSequence0.getACount());
62: assertEquals(0, genbankStreamSequence0.getTCount());
63: assertEquals(2, genbankStreamSequence0.getFormatType());
64: assertEquals(0, genbankStreamSequence0.length());
65: assertNull(genbankStreamSequence0.getHeader());
66: assertEquals(0, genbankStreamSequence0.getCCount());
67: assertEquals(0, genbankStreamSequence0.getOtherCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(6, range0.getCount());
73: assertEquals(0, range0.getStart());
74: assertEquals(5, range0.getEnd());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(0, simpleEntryGroup1.refCount());
77: assertEquals(6, simpleEntryGroup1.getSequenceLength());
78: assertEquals(5, Bases.MAX_PRIORITY);
79: assertEquals(2, Bases.REVERSE);
80: assertEquals((-5), Bases.MIN_PRIORITY);
81: assertEquals(0, Bases.MEDIUM_PRIORITY);
82: assertEquals(1, Bases.FORWARD);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getGCount());
89: assertEquals(0, genbankStreamSequence0.getACount());
90: assertEquals(0, genbankStreamSequence0.getTCount());
91: assertEquals(2, genbankStreamSequence0.getFormatType());
92: assertEquals(0, genbankStreamSequence0.length());
93: assertNull(genbankStreamSequence0.getHeader());
94: assertEquals(0, genbankStreamSequence0.getCCount());
95: assertEquals(0, genbankStreamSequence0.getOtherCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals(5, Bases.MAX_PRIORITY);
101: assertEquals(2, Bases.REVERSE);
102: assertEquals((-5), Bases.MIN_PRIORITY);
103: assertEquals(0, Bases.MEDIUM_PRIORITY);
104: assertEquals(1, Bases.FORWARD);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getGCount());
111: assertEquals(0, genbankStreamSequence0.getACount());
112: assertEquals(0, genbankStreamSequence0.getTCount());
113: assertEquals(2, genbankStreamSequence0.getFormatType());
114: assertEquals(0, genbankStreamSequence0.length());
115: assertNull(genbankStreamSequence0.getHeader());
116: assertEquals(0, genbankStreamSequence0.getCCount());
117: assertEquals(0, genbankStreamSequence0.getOtherCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(6, range0.getCount());
123: assertEquals(0, range0.getStart());
124: assertEquals(5, range0.getEnd());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(0, simpleEntryGroup1.refCount());
127: assertEquals(6, simpleEntryGroup1.getSequenceLength());
128: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals(6, filteredEntryGroup0.getSequenceLength());
131: assertEquals(0, filteredEntryGroup0.size());
132: assertEquals(5, Bases.MAX_PRIORITY);
133: assertEquals(2, Bases.REVERSE);
134: assertEquals((-5), Bases.MIN_PRIORITY);
135: assertEquals(0, Bases.MEDIUM_PRIORITY);
136: assertEquals(1, Bases.FORWARD);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getGCount());
145: assertEquals(0, genbankStreamSequence0.getACount());
146: assertEquals(0, genbankStreamSequence0.getTCount());
147: assertEquals(2, genbankStreamSequence0.getFormatType());
148: assertEquals(0, genbankStreamSequence0.length());
149: assertNull(genbankStreamSequence0.getHeader());
150: assertEquals(0, genbankStreamSequence0.getCCount());
151: assertEquals(0, genbankStreamSequence0.getOtherCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(6, range0.getCount());
157: assertEquals(0, range0.getStart());
158: assertEquals(5, range0.getEnd());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(0, simpleEntryGroup1.refCount());
161: assertEquals(6, simpleEntryGroup1.getSequenceLength());
162: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals(6, filteredEntryGroup0.getSequenceLength());
165: assertEquals(1, filteredEntryGroup0.size());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(5, Bases.MAX_PRIORITY);
168: assertEquals(2, Bases.REVERSE);
169: assertEquals((-5), Bases.MIN_PRIORITY);
170: assertEquals(0, Bases.MEDIUM_PRIORITY);
171: assertEquals(1, Bases.FORWARD);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getGCount());
180: assertEquals(0, genbankStreamSequence0.getACount());
181: assertEquals(0, genbankStreamSequence0.getTCount());
182: assertEquals(2, genbankStreamSequence0.getFormatType());
183: assertEquals(0, genbankStreamSequence0.length());
184: assertNull(genbankStreamSequence0.getHeader());
185: assertEquals(0, genbankStreamSequence0.getCCount());
186: assertEquals(0, genbankStreamSequence0.getOtherCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.size());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(6, range0.getCount());
192: assertEquals(0, range0.getStart());
193: assertEquals(5, range0.getEnd());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(0, simpleEntryGroup1.refCount());
196: assertEquals(6, simpleEntryGroup1.getSequenceLength());
197: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals(6, filteredEntryGroup0.getSequenceLength());
200: assertEquals(1, filteredEntryGroup0.size());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(5, Bases.MAX_PRIORITY);
203: assertEquals(2, Bases.REVERSE);
204: assertEquals((-5), Bases.MIN_PRIORITY);
205: assertEquals(0, Bases.MEDIUM_PRIORITY);
206: assertEquals(1, Bases.FORWARD);
207:
208: String string0 = feature0.getBases();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(string0);
212: assertEquals("nnnnnn", string0);
213: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
214: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
215: assertEquals(0, genbankStreamSequence0.getGCount());
216: assertEquals(0, genbankStreamSequence0.getACount());
217: assertEquals(0, genbankStreamSequence0.getTCount());
218: assertEquals(2, genbankStreamSequence0.getFormatType());
219: assertEquals(0, genbankStreamSequence0.length());
220: assertNull(genbankStreamSequence0.getHeader());
221: assertEquals(0, genbankStreamSequence0.getCCount());
222: assertEquals(0, genbankStreamSequence0.getOtherCount());
223: assertEquals(0, bases0.getLength());
224: assertEquals(0, simpleEntryGroup0.refCount());
225: assertEquals(0, simpleEntryGroup0.size());
226: assertEquals(0, simpleEntryGroup0.getSequenceLength());
227: assertEquals(6, range0.getCount());
228: assertEquals(0, range0.getStart());
229: assertEquals(5, range0.getEnd());
230: assertEquals(1, simpleEntryGroup1.size());
231: assertEquals(0, simpleEntryGroup1.refCount());
232: assertEquals(6, simpleEntryGroup1.getSequenceLength());
233: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
234: assertEquals(0, filteredEntryGroup0.refCount());
235: assertEquals(6, filteredEntryGroup0.getSequenceLength());
236: assertEquals(1, filteredEntryGroup0.size());
237: assertFalse(feature0.isReadOnly());
238: assertEquals(5, Bases.MAX_PRIORITY);
239: assertEquals(2, Bases.REVERSE);
240: assertEquals((-5), Bases.MIN_PRIORITY);
241: assertEquals(0, Bases.MEDIUM_PRIORITY);
242: assertEquals(1, Bases.FORWARD);
Test case 59
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.getTranslation();
Test case 60
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.getPositionalBaseCount((-830), 31);
Test case 61
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getGCount());
4: assertEquals(0, genbankStreamSequence0.getOtherCount());
5: assertNull(genbankStreamSequence0.getHeader());
6: assertEquals(0, genbankStreamSequence0.getACount());
7: assertEquals(2, genbankStreamSequence0.getFormatType());
8: assertEquals(0, genbankStreamSequence0.length());
9: assertEquals(0, genbankStreamSequence0.getCCount());
10: assertEquals(0, genbankStreamSequence0.getTCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getGCount());
15: assertEquals(0, genbankStreamSequence0.getOtherCount());
16: assertNull(genbankStreamSequence0.getHeader());
17: assertEquals(0, genbankStreamSequence0.getACount());
18: assertEquals(2, genbankStreamSequence0.getFormatType());
19: assertEquals(0, genbankStreamSequence0.length());
20: assertEquals(0, genbankStreamSequence0.getCCount());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(0, Bases.MEDIUM_PRIORITY);
24: assertEquals(2, Bases.REVERSE);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals((-5), Bases.MIN_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getGCount());
32: assertEquals(0, genbankStreamSequence0.getOtherCount());
33: assertNull(genbankStreamSequence0.getHeader());
34: assertEquals(0, genbankStreamSequence0.getACount());
35: assertEquals(2, genbankStreamSequence0.getFormatType());
36: assertEquals(0, genbankStreamSequence0.length());
37: assertEquals(0, genbankStreamSequence0.getCCount());
38: assertEquals(0, genbankStreamSequence0.getTCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.refCount());
43: assertEquals(0, Bases.MEDIUM_PRIORITY);
44: assertEquals(2, Bases.REVERSE);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(1, Bases.FORWARD);
47: assertEquals((-5), Bases.MIN_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(5, range0.getEnd());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getGCount());
61: assertEquals(0, genbankStreamSequence0.getOtherCount());
62: assertNull(genbankStreamSequence0.getHeader());
63: assertEquals(0, genbankStreamSequence0.getACount());
64: assertEquals(2, genbankStreamSequence0.getFormatType());
65: assertEquals(0, genbankStreamSequence0.length());
66: assertEquals(0, genbankStreamSequence0.getCCount());
67: assertEquals(0, genbankStreamSequence0.getTCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.refCount());
72: assertEquals(6, range0.getCount());
73: assertEquals(5, range0.getEnd());
74: assertEquals(0, range0.getStart());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(0, Bases.MEDIUM_PRIORITY);
79: assertEquals(2, Bases.REVERSE);
80: assertEquals(5, Bases.MAX_PRIORITY);
81: assertEquals(1, Bases.FORWARD);
82: assertEquals((-5), Bases.MIN_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getGCount());
89: assertEquals(0, genbankStreamSequence0.getOtherCount());
90: assertNull(genbankStreamSequence0.getHeader());
91: assertEquals(0, genbankStreamSequence0.getACount());
92: assertEquals(2, genbankStreamSequence0.getFormatType());
93: assertEquals(0, genbankStreamSequence0.length());
94: assertEquals(0, genbankStreamSequence0.getCCount());
95: assertEquals(0, genbankStreamSequence0.getTCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.refCount());
100: assertEquals(0, Bases.MEDIUM_PRIORITY);
101: assertEquals(2, Bases.REVERSE);
102: assertEquals(5, Bases.MAX_PRIORITY);
103: assertEquals(1, Bases.FORWARD);
104: assertEquals((-5), Bases.MIN_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getGCount());
111: assertEquals(0, genbankStreamSequence0.getOtherCount());
112: assertNull(genbankStreamSequence0.getHeader());
113: assertEquals(0, genbankStreamSequence0.getACount());
114: assertEquals(2, genbankStreamSequence0.getFormatType());
115: assertEquals(0, genbankStreamSequence0.length());
116: assertEquals(0, genbankStreamSequence0.getCCount());
117: assertEquals(0, genbankStreamSequence0.getTCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.refCount());
122: assertEquals(6, range0.getCount());
123: assertEquals(5, range0.getEnd());
124: assertEquals(0, range0.getStart());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(0, filteredEntryGroup0.refCount());
129: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
130: assertEquals(6, filteredEntryGroup0.getSequenceLength());
131: assertEquals(0, filteredEntryGroup0.size());
132: assertEquals(0, Bases.MEDIUM_PRIORITY);
133: assertEquals(2, Bases.REVERSE);
134: assertEquals(5, Bases.MAX_PRIORITY);
135: assertEquals(1, Bases.FORWARD);
136: assertEquals((-5), Bases.MIN_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getGCount());
145: assertEquals(0, genbankStreamSequence0.getOtherCount());
146: assertNull(genbankStreamSequence0.getHeader());
147: assertEquals(0, genbankStreamSequence0.getACount());
148: assertEquals(2, genbankStreamSequence0.getFormatType());
149: assertEquals(0, genbankStreamSequence0.length());
150: assertEquals(0, genbankStreamSequence0.getCCount());
151: assertEquals(0, genbankStreamSequence0.getTCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.refCount());
156: assertEquals(6, range0.getCount());
157: assertEquals(5, range0.getEnd());
158: assertEquals(0, range0.getStart());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(0, filteredEntryGroup0.refCount());
163: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
164: assertEquals(6, filteredEntryGroup0.getSequenceLength());
165: assertEquals(1, filteredEntryGroup0.size());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(0, Bases.MEDIUM_PRIORITY);
168: assertEquals(2, Bases.REVERSE);
169: assertEquals(5, Bases.MAX_PRIORITY);
170: assertEquals(1, Bases.FORWARD);
171: assertEquals((-5), Bases.MIN_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getGCount());
180: assertEquals(0, genbankStreamSequence0.getOtherCount());
181: assertNull(genbankStreamSequence0.getHeader());
182: assertEquals(0, genbankStreamSequence0.getACount());
183: assertEquals(2, genbankStreamSequence0.getFormatType());
184: assertEquals(0, genbankStreamSequence0.length());
185: assertEquals(0, genbankStreamSequence0.getCCount());
186: assertEquals(0, genbankStreamSequence0.getTCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.size());
190: assertEquals(0, simpleEntryGroup0.refCount());
191: assertEquals(6, range0.getCount());
192: assertEquals(5, range0.getEnd());
193: assertEquals(0, range0.getStart());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(0, filteredEntryGroup0.refCount());
198: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
199: assertEquals(6, filteredEntryGroup0.getSequenceLength());
200: assertEquals(1, filteredEntryGroup0.size());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(0, Bases.MEDIUM_PRIORITY);
203: assertEquals(2, Bases.REVERSE);
204: assertEquals(5, Bases.MAX_PRIORITY);
205: assertEquals(1, Bases.FORWARD);
206: assertEquals((-5), Bases.MIN_PRIORITY);
207:
208: int int0 = feature0.getFirstBase();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertEquals(1, int0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.getGCount());
215: assertEquals(0, genbankStreamSequence0.getOtherCount());
216: assertNull(genbankStreamSequence0.getHeader());
217: assertEquals(0, genbankStreamSequence0.getACount());
218: assertEquals(2, genbankStreamSequence0.getFormatType());
219: assertEquals(0, genbankStreamSequence0.length());
220: assertEquals(0, genbankStreamSequence0.getCCount());
221: assertEquals(0, genbankStreamSequence0.getTCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.getSequenceLength());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(0, simpleEntryGroup0.refCount());
226: assertEquals(6, range0.getCount());
227: assertEquals(5, range0.getEnd());
228: assertEquals(0, range0.getStart());
229: assertEquals(6, simpleEntryGroup1.getSequenceLength());
230: assertEquals(1, simpleEntryGroup1.size());
231: assertEquals(0, simpleEntryGroup1.refCount());
232: assertEquals(0, filteredEntryGroup0.refCount());
233: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
234: assertEquals(6, filteredEntryGroup0.getSequenceLength());
235: assertEquals(1, filteredEntryGroup0.size());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(0, Bases.MEDIUM_PRIORITY);
238: assertEquals(2, Bases.REVERSE);
239: assertEquals(5, Bases.MAX_PRIORITY);
240: assertEquals(1, Bases.FORWARD);
241: assertEquals((-5), Bases.MIN_PRIORITY);
Test case 62
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(2, genbankStreamSequence0.getFormatType());
4: assertEquals(0, genbankStreamSequence0.getGCount());
5: assertEquals(0, genbankStreamSequence0.getACount());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertNull(genbankStreamSequence0.getHeader());
8: assertEquals(0, genbankStreamSequence0.getTCount());
9: assertEquals(0, genbankStreamSequence0.getOtherCount());
10: assertEquals(0, genbankStreamSequence0.length());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, genbankStreamSequence0.getFormatType());
15: assertEquals(0, genbankStreamSequence0.getGCount());
16: assertEquals(0, genbankStreamSequence0.getACount());
17: assertEquals(0, genbankStreamSequence0.getCCount());
18: assertNull(genbankStreamSequence0.getHeader());
19: assertEquals(0, genbankStreamSequence0.getTCount());
20: assertEquals(0, genbankStreamSequence0.getOtherCount());
21: assertEquals(0, genbankStreamSequence0.length());
22: assertEquals(0, bases0.getLength());
23: assertEquals(2, Bases.REVERSE);
24: assertEquals(5, Bases.MAX_PRIORITY);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals((-5), Bases.MIN_PRIORITY);
27: assertEquals(0, Bases.MEDIUM_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(2, genbankStreamSequence0.getFormatType());
32: assertEquals(0, genbankStreamSequence0.getGCount());
33: assertEquals(0, genbankStreamSequence0.getACount());
34: assertEquals(0, genbankStreamSequence0.getCCount());
35: assertNull(genbankStreamSequence0.getHeader());
36: assertEquals(0, genbankStreamSequence0.getTCount());
37: assertEquals(0, genbankStreamSequence0.getOtherCount());
38: assertEquals(0, genbankStreamSequence0.length());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals(2, Bases.REVERSE);
44: assertEquals(5, Bases.MAX_PRIORITY);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals((-5), Bases.MIN_PRIORITY);
47: assertEquals(0, Bases.MEDIUM_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(6, range0.getCount());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(2, genbankStreamSequence0.getFormatType());
61: assertEquals(0, genbankStreamSequence0.getGCount());
62: assertEquals(0, genbankStreamSequence0.getACount());
63: assertEquals(0, genbankStreamSequence0.getCCount());
64: assertNull(genbankStreamSequence0.getHeader());
65: assertEquals(0, genbankStreamSequence0.getTCount());
66: assertEquals(0, genbankStreamSequence0.getOtherCount());
67: assertEquals(0, genbankStreamSequence0.length());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(0, range0.getStart());
73: assertEquals(6, range0.getCount());
74: assertEquals(5, range0.getEnd());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.refCount());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals(2, Bases.REVERSE);
79: assertEquals(5, Bases.MAX_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals((-5), Bases.MIN_PRIORITY);
82: assertEquals(0, Bases.MEDIUM_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(2, genbankStreamSequence0.getFormatType());
89: assertEquals(0, genbankStreamSequence0.getGCount());
90: assertEquals(0, genbankStreamSequence0.getACount());
91: assertEquals(0, genbankStreamSequence0.getCCount());
92: assertNull(genbankStreamSequence0.getHeader());
93: assertEquals(0, genbankStreamSequence0.getTCount());
94: assertEquals(0, genbankStreamSequence0.getOtherCount());
95: assertEquals(0, genbankStreamSequence0.length());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals(2, Bases.REVERSE);
101: assertEquals(5, Bases.MAX_PRIORITY);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals((-5), Bases.MIN_PRIORITY);
104: assertEquals(0, Bases.MEDIUM_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(2, genbankStreamSequence0.getFormatType());
111: assertEquals(0, genbankStreamSequence0.getGCount());
112: assertEquals(0, genbankStreamSequence0.getACount());
113: assertEquals(0, genbankStreamSequence0.getCCount());
114: assertNull(genbankStreamSequence0.getHeader());
115: assertEquals(0, genbankStreamSequence0.getTCount());
116: assertEquals(0, genbankStreamSequence0.getOtherCount());
117: assertEquals(0, genbankStreamSequence0.length());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(0, range0.getStart());
123: assertEquals(6, range0.getCount());
124: assertEquals(5, range0.getEnd());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.refCount());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals(6, filteredEntryGroup0.getSequenceLength());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
132: assertEquals(2, Bases.REVERSE);
133: assertEquals(5, Bases.MAX_PRIORITY);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals((-5), Bases.MIN_PRIORITY);
136: assertEquals(0, Bases.MEDIUM_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(2, genbankStreamSequence0.getFormatType());
145: assertEquals(0, genbankStreamSequence0.getGCount());
146: assertEquals(0, genbankStreamSequence0.getACount());
147: assertEquals(0, genbankStreamSequence0.getCCount());
148: assertNull(genbankStreamSequence0.getHeader());
149: assertEquals(0, genbankStreamSequence0.getTCount());
150: assertEquals(0, genbankStreamSequence0.getOtherCount());
151: assertEquals(0, genbankStreamSequence0.length());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(0, range0.getStart());
157: assertEquals(6, range0.getCount());
158: assertEquals(5, range0.getEnd());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(0, simpleEntryGroup1.refCount());
161: assertEquals(1, simpleEntryGroup1.size());
162: assertEquals(6, filteredEntryGroup0.getSequenceLength());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
165: assertEquals(1, filteredEntryGroup0.size());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(2, Bases.REVERSE);
168: assertEquals(5, Bases.MAX_PRIORITY);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals((-5), Bases.MIN_PRIORITY);
171: assertEquals(0, Bases.MEDIUM_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(2, genbankStreamSequence0.getFormatType());
180: assertEquals(0, genbankStreamSequence0.getGCount());
181: assertEquals(0, genbankStreamSequence0.getACount());
182: assertEquals(0, genbankStreamSequence0.getCCount());
183: assertNull(genbankStreamSequence0.getHeader());
184: assertEquals(0, genbankStreamSequence0.getTCount());
185: assertEquals(0, genbankStreamSequence0.getOtherCount());
186: assertEquals(0, genbankStreamSequence0.length());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.size());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(0, range0.getStart());
192: assertEquals(6, range0.getCount());
193: assertEquals(5, range0.getEnd());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(0, simpleEntryGroup1.refCount());
196: assertEquals(1, simpleEntryGroup1.size());
197: assertEquals(6, filteredEntryGroup0.getSequenceLength());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
200: assertEquals(1, filteredEntryGroup0.size());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(2, Bases.REVERSE);
203: assertEquals(5, Bases.MAX_PRIORITY);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals((-5), Bases.MIN_PRIORITY);
206: assertEquals(0, Bases.MEDIUM_PRIORITY);
207:
208: int int0 = feature0.getRawFirstBase();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertEquals(1, int0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(2, genbankStreamSequence0.getFormatType());
215: assertEquals(0, genbankStreamSequence0.getGCount());
216: assertEquals(0, genbankStreamSequence0.getACount());
217: assertEquals(0, genbankStreamSequence0.getCCount());
218: assertNull(genbankStreamSequence0.getHeader());
219: assertEquals(0, genbankStreamSequence0.getTCount());
220: assertEquals(0, genbankStreamSequence0.getOtherCount());
221: assertEquals(0, genbankStreamSequence0.length());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.refCount());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(0, simpleEntryGroup0.getSequenceLength());
226: assertEquals(0, range0.getStart());
227: assertEquals(6, range0.getCount());
228: assertEquals(5, range0.getEnd());
229: assertEquals(6, simpleEntryGroup1.getSequenceLength());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals(6, filteredEntryGroup0.getSequenceLength());
233: assertEquals(0, filteredEntryGroup0.refCount());
234: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
235: assertEquals(1, filteredEntryGroup0.size());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(2, Bases.REVERSE);
238: assertEquals(5, Bases.MAX_PRIORITY);
239: assertEquals(1, Bases.FORWARD);
240: assertEquals((-5), Bases.MIN_PRIORITY);
241: assertEquals(0, Bases.MEDIUM_PRIORITY);
Test case 63
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getOtherCount());
4: assertEquals(0, genbankStreamSequence0.getACount());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(2, genbankStreamSequence0.getFormatType());
7: assertNull(genbankStreamSequence0.getHeader());
8: assertEquals(0, genbankStreamSequence0.getCCount());
9: assertEquals(0, genbankStreamSequence0.getGCount());
10: assertEquals(0, genbankStreamSequence0.length());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getOtherCount());
15: assertEquals(0, genbankStreamSequence0.getACount());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertEquals(2, genbankStreamSequence0.getFormatType());
18: assertNull(genbankStreamSequence0.getHeader());
19: assertEquals(0, genbankStreamSequence0.getCCount());
20: assertEquals(0, genbankStreamSequence0.getGCount());
21: assertEquals(0, genbankStreamSequence0.length());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getOtherCount());
32: assertEquals(0, genbankStreamSequence0.getACount());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertEquals(2, genbankStreamSequence0.getFormatType());
35: assertNull(genbankStreamSequence0.getHeader());
36: assertEquals(0, genbankStreamSequence0.getCCount());
37: assertEquals(0, genbankStreamSequence0.getGCount());
38: assertEquals(0, genbankStreamSequence0.length());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(1, Bases.FORWARD);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(5, range0.getEnd());
52: assertEquals(6, range0.getCount());
53: assertEquals(0, range0.getStart());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getOtherCount());
61: assertEquals(0, genbankStreamSequence0.getACount());
62: assertEquals(0, genbankStreamSequence0.getTCount());
63: assertEquals(2, genbankStreamSequence0.getFormatType());
64: assertNull(genbankStreamSequence0.getHeader());
65: assertEquals(0, genbankStreamSequence0.getCCount());
66: assertEquals(0, genbankStreamSequence0.getGCount());
67: assertEquals(0, genbankStreamSequence0.length());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(5, range0.getEnd());
73: assertEquals(6, range0.getCount());
74: assertEquals(0, range0.getStart());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.refCount());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(5, Bases.MAX_PRIORITY);
81: assertEquals(1, Bases.FORWARD);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getOtherCount());
89: assertEquals(0, genbankStreamSequence0.getACount());
90: assertEquals(0, genbankStreamSequence0.getTCount());
91: assertEquals(2, genbankStreamSequence0.getFormatType());
92: assertNull(genbankStreamSequence0.getHeader());
93: assertEquals(0, genbankStreamSequence0.getCCount());
94: assertEquals(0, genbankStreamSequence0.getGCount());
95: assertEquals(0, genbankStreamSequence0.length());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(5, Bases.MAX_PRIORITY);
103: assertEquals(1, Bases.FORWARD);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getOtherCount());
111: assertEquals(0, genbankStreamSequence0.getACount());
112: assertEquals(0, genbankStreamSequence0.getTCount());
113: assertEquals(2, genbankStreamSequence0.getFormatType());
114: assertNull(genbankStreamSequence0.getHeader());
115: assertEquals(0, genbankStreamSequence0.getCCount());
116: assertEquals(0, genbankStreamSequence0.getGCount());
117: assertEquals(0, genbankStreamSequence0.length());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(5, range0.getEnd());
123: assertEquals(6, range0.getCount());
124: assertEquals(0, range0.getStart());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.refCount());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(5, Bases.MAX_PRIORITY);
135: assertEquals(1, Bases.FORWARD);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getOtherCount());
145: assertEquals(0, genbankStreamSequence0.getACount());
146: assertEquals(0, genbankStreamSequence0.getTCount());
147: assertEquals(2, genbankStreamSequence0.getFormatType());
148: assertNull(genbankStreamSequence0.getHeader());
149: assertEquals(0, genbankStreamSequence0.getCCount());
150: assertEquals(0, genbankStreamSequence0.getGCount());
151: assertEquals(0, genbankStreamSequence0.length());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(5, range0.getEnd());
157: assertEquals(6, range0.getCount());
158: assertEquals(0, range0.getStart());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(0, simpleEntryGroup1.refCount());
161: assertEquals(1, simpleEntryGroup1.size());
162: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals(1, filteredEntryGroup0.size());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(5, Bases.MAX_PRIORITY);
170: assertEquals(1, Bases.FORWARD);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getOtherCount());
180: assertEquals(0, genbankStreamSequence0.getACount());
181: assertEquals(0, genbankStreamSequence0.getTCount());
182: assertEquals(2, genbankStreamSequence0.getFormatType());
183: assertNull(genbankStreamSequence0.getHeader());
184: assertEquals(0, genbankStreamSequence0.getCCount());
185: assertEquals(0, genbankStreamSequence0.getGCount());
186: assertEquals(0, genbankStreamSequence0.length());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(5, range0.getEnd());
192: assertEquals(6, range0.getCount());
193: assertEquals(0, range0.getStart());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(0, simpleEntryGroup1.refCount());
196: assertEquals(1, simpleEntryGroup1.size());
197: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals(1, filteredEntryGroup0.size());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(5, Bases.MAX_PRIORITY);
205: assertEquals(1, Bases.FORWARD);
206: assertEquals(2, Bases.REVERSE);
207:
208: int int0 = feature0.getRawLastBase();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertEquals(6, int0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.getOtherCount());
215: assertEquals(0, genbankStreamSequence0.getACount());
216: assertEquals(0, genbankStreamSequence0.getTCount());
217: assertEquals(2, genbankStreamSequence0.getFormatType());
218: assertNull(genbankStreamSequence0.getHeader());
219: assertEquals(0, genbankStreamSequence0.getCCount());
220: assertEquals(0, genbankStreamSequence0.getGCount());
221: assertEquals(0, genbankStreamSequence0.length());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.getSequenceLength());
224: assertEquals(0, simpleEntryGroup0.refCount());
225: assertEquals(0, simpleEntryGroup0.size());
226: assertEquals(5, range0.getEnd());
227: assertEquals(6, range0.getCount());
228: assertEquals(0, range0.getStart());
229: assertEquals(6, simpleEntryGroup1.getSequenceLength());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
233: assertEquals(0, filteredEntryGroup0.refCount());
234: assertEquals(1, filteredEntryGroup0.size());
235: assertEquals(6, filteredEntryGroup0.getSequenceLength());
236: assertFalse(feature0.isReadOnly());
237: assertEquals((-5), Bases.MIN_PRIORITY);
238: assertEquals(0, Bases.MEDIUM_PRIORITY);
239: assertEquals(5, Bases.MAX_PRIORITY);
240: assertEquals(1, Bases.FORWARD);
241: assertEquals(2, Bases.REVERSE);
Test case 64
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(2, genbankStreamSequence0.getFormatType());
4: assertEquals(0, genbankStreamSequence0.length());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(0, genbankStreamSequence0.getOtherCount());
7: assertEquals(0, genbankStreamSequence0.getGCount());
8: assertNull(genbankStreamSequence0.getHeader());
9: assertEquals(0, genbankStreamSequence0.getACount());
10: assertEquals(0, genbankStreamSequence0.getCCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, genbankStreamSequence0.getFormatType());
15: assertEquals(0, genbankStreamSequence0.length());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertEquals(0, genbankStreamSequence0.getOtherCount());
18: assertEquals(0, genbankStreamSequence0.getGCount());
19: assertNull(genbankStreamSequence0.getHeader());
20: assertEquals(0, genbankStreamSequence0.getACount());
21: assertEquals(0, genbankStreamSequence0.getCCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(5, Bases.MAX_PRIORITY);
24: assertEquals(2, Bases.REVERSE);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals((-5), Bases.MIN_PRIORITY);
27: assertEquals(0, Bases.MEDIUM_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(2, genbankStreamSequence0.getFormatType());
32: assertEquals(0, genbankStreamSequence0.length());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertEquals(0, genbankStreamSequence0.getOtherCount());
35: assertEquals(0, genbankStreamSequence0.getGCount());
36: assertNull(genbankStreamSequence0.getHeader());
37: assertEquals(0, genbankStreamSequence0.getACount());
38: assertEquals(0, genbankStreamSequence0.getCCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals(5, Bases.MAX_PRIORITY);
44: assertEquals(2, Bases.REVERSE);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals((-5), Bases.MIN_PRIORITY);
47: assertEquals(0, Bases.MEDIUM_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(6, range0.getCount());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(2, genbankStreamSequence0.getFormatType());
61: assertEquals(0, genbankStreamSequence0.length());
62: assertEquals(0, genbankStreamSequence0.getTCount());
63: assertEquals(0, genbankStreamSequence0.getOtherCount());
64: assertEquals(0, genbankStreamSequence0.getGCount());
65: assertNull(genbankStreamSequence0.getHeader());
66: assertEquals(0, genbankStreamSequence0.getACount());
67: assertEquals(0, genbankStreamSequence0.getCCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.size());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(0, range0.getStart());
73: assertEquals(6, range0.getCount());
74: assertEquals(5, range0.getEnd());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.refCount());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals(5, Bases.MAX_PRIORITY);
79: assertEquals(2, Bases.REVERSE);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals((-5), Bases.MIN_PRIORITY);
82: assertEquals(0, Bases.MEDIUM_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(2, genbankStreamSequence0.getFormatType());
89: assertEquals(0, genbankStreamSequence0.length());
90: assertEquals(0, genbankStreamSequence0.getTCount());
91: assertEquals(0, genbankStreamSequence0.getOtherCount());
92: assertEquals(0, genbankStreamSequence0.getGCount());
93: assertNull(genbankStreamSequence0.getHeader());
94: assertEquals(0, genbankStreamSequence0.getACount());
95: assertEquals(0, genbankStreamSequence0.getCCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.size());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals(5, Bases.MAX_PRIORITY);
101: assertEquals(2, Bases.REVERSE);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals((-5), Bases.MIN_PRIORITY);
104: assertEquals(0, Bases.MEDIUM_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(2, genbankStreamSequence0.getFormatType());
111: assertEquals(0, genbankStreamSequence0.length());
112: assertEquals(0, genbankStreamSequence0.getTCount());
113: assertEquals(0, genbankStreamSequence0.getOtherCount());
114: assertEquals(0, genbankStreamSequence0.getGCount());
115: assertNull(genbankStreamSequence0.getHeader());
116: assertEquals(0, genbankStreamSequence0.getACount());
117: assertEquals(0, genbankStreamSequence0.getCCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.size());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(0, range0.getStart());
123: assertEquals(6, range0.getCount());
124: assertEquals(5, range0.getEnd());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.refCount());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals(0, filteredEntryGroup0.refCount());
129: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals(5, Bases.MAX_PRIORITY);
133: assertEquals(2, Bases.REVERSE);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals((-5), Bases.MIN_PRIORITY);
136: assertEquals(0, Bases.MEDIUM_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(2, genbankStreamSequence0.getFormatType());
145: assertEquals(0, genbankStreamSequence0.length());
146: assertEquals(0, genbankStreamSequence0.getTCount());
147: assertEquals(0, genbankStreamSequence0.getOtherCount());
148: assertEquals(0, genbankStreamSequence0.getGCount());
149: assertNull(genbankStreamSequence0.getHeader());
150: assertEquals(0, genbankStreamSequence0.getACount());
151: assertEquals(0, genbankStreamSequence0.getCCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.size());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(0, range0.getStart());
157: assertEquals(6, range0.getCount());
158: assertEquals(5, range0.getEnd());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(0, simpleEntryGroup1.refCount());
161: assertEquals(1, simpleEntryGroup1.size());
162: assertEquals(0, filteredEntryGroup0.refCount());
163: assertEquals(1, filteredEntryGroup0.size());
164: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(5, Bases.MAX_PRIORITY);
168: assertEquals(2, Bases.REVERSE);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals((-5), Bases.MIN_PRIORITY);
171: assertEquals(0, Bases.MEDIUM_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(2, genbankStreamSequence0.getFormatType());
180: assertEquals(0, genbankStreamSequence0.length());
181: assertEquals(0, genbankStreamSequence0.getTCount());
182: assertEquals(0, genbankStreamSequence0.getOtherCount());
183: assertEquals(0, genbankStreamSequence0.getGCount());
184: assertNull(genbankStreamSequence0.getHeader());
185: assertEquals(0, genbankStreamSequence0.getACount());
186: assertEquals(0, genbankStreamSequence0.getCCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.size());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(0, range0.getStart());
192: assertEquals(6, range0.getCount());
193: assertEquals(5, range0.getEnd());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(0, simpleEntryGroup1.refCount());
196: assertEquals(1, simpleEntryGroup1.size());
197: assertEquals(0, filteredEntryGroup0.refCount());
198: assertEquals(1, filteredEntryGroup0.size());
199: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(5, Bases.MAX_PRIORITY);
203: assertEquals(2, Bases.REVERSE);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals((-5), Bases.MIN_PRIORITY);
206: assertEquals(0, Bases.MEDIUM_PRIORITY);
207:
208: Marker marker0 = feature0.getFirstBaseMarker();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(marker0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(2, genbankStreamSequence0.getFormatType());
215: assertEquals(0, genbankStreamSequence0.length());
216: assertEquals(0, genbankStreamSequence0.getTCount());
217: assertEquals(0, genbankStreamSequence0.getOtherCount());
218: assertEquals(0, genbankStreamSequence0.getGCount());
219: assertNull(genbankStreamSequence0.getHeader());
220: assertEquals(0, genbankStreamSequence0.getACount());
221: assertEquals(0, genbankStreamSequence0.getCCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.size());
224: assertEquals(0, simpleEntryGroup0.refCount());
225: assertEquals(0, simpleEntryGroup0.getSequenceLength());
226: assertEquals(0, range0.getStart());
227: assertEquals(6, range0.getCount());
228: assertEquals(5, range0.getEnd());
229: assertEquals(6, simpleEntryGroup1.getSequenceLength());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals(0, filteredEntryGroup0.refCount());
233: assertEquals(1, filteredEntryGroup0.size());
234: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
235: assertEquals(6, filteredEntryGroup0.getSequenceLength());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(5, Bases.MAX_PRIORITY);
238: assertEquals(2, Bases.REVERSE);
239: assertEquals(1, Bases.FORWARD);
240: assertEquals((-5), Bases.MIN_PRIORITY);
241: assertEquals(0, Bases.MEDIUM_PRIORITY);
242: assertEquals(0, Marker.LISTENER_PRIORITY);
243:
244: Strand strand0 = feature0.getStrand();
245: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
246: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
247: assertNotNull(strand0);
248: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
249: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
250: assertEquals(2, genbankStreamSequence0.getFormatType());
251: assertEquals(0, genbankStreamSequence0.length());
252: assertEquals(0, genbankStreamSequence0.getTCount());
253: assertEquals(0, genbankStreamSequence0.getOtherCount());
254: assertEquals(0, genbankStreamSequence0.getGCount());
255: assertNull(genbankStreamSequence0.getHeader());
256: assertEquals(0, genbankStreamSequence0.getACount());
257: assertEquals(0, genbankStreamSequence0.getCCount());
258: assertEquals(0, bases0.getLength());
259: assertEquals(0, simpleEntryGroup0.size());
260: assertEquals(0, simpleEntryGroup0.refCount());
261: assertEquals(0, simpleEntryGroup0.getSequenceLength());
262: assertEquals(0, range0.getStart());
263: assertEquals(6, range0.getCount());
264: assertEquals(5, range0.getEnd());
265: assertEquals(6, simpleEntryGroup1.getSequenceLength());
266: assertEquals(0, simpleEntryGroup1.refCount());
267: assertEquals(1, simpleEntryGroup1.size());
268: assertEquals(0, filteredEntryGroup0.refCount());
269: assertEquals(1, filteredEntryGroup0.size());
270: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
271: assertEquals(6, filteredEntryGroup0.getSequenceLength());
272: assertFalse(feature0.isReadOnly());
273: assertEquals(1, strand0.getDirection());
274: assertTrue(strand0.isForwardStrand());
275: assertEquals(6, strand0.getSequenceLength());
276: assertEquals(5, Bases.MAX_PRIORITY);
277: assertEquals(2, Bases.REVERSE);
278: assertEquals(1, Bases.FORWARD);
279: assertEquals((-5), Bases.MIN_PRIORITY);
280: assertEquals(0, Bases.MEDIUM_PRIORITY);
281: assertEquals(2, Strand.REVERSE);
282: assertEquals(1, Strand.FORWARD);
283:
284: MarkerChangeEvent markerChangeEvent0 = new MarkerChangeEvent(marker0, strand0, 0);
285: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
286: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
287: assertNotNull(markerChangeEvent0);
288: assertEquals(2, genbankStreamSequence0.getFormatType());
289: assertEquals(0, genbankStreamSequence0.length());
290: assertEquals(0, genbankStreamSequence0.getTCount());
291: assertEquals(0, genbankStreamSequence0.getOtherCount());
292: assertEquals(0, genbankStreamSequence0.getGCount());
293: assertNull(genbankStreamSequence0.getHeader());
294: assertEquals(0, genbankStreamSequence0.getACount());
295: assertEquals(0, genbankStreamSequence0.getCCount());
296: assertEquals(0, bases0.getLength());
297: assertEquals(0, simpleEntryGroup0.size());
298: assertEquals(0, simpleEntryGroup0.refCount());
299: assertEquals(0, simpleEntryGroup0.getSequenceLength());
300: assertEquals(0, range0.getStart());
301: assertEquals(6, range0.getCount());
302: assertEquals(5, range0.getEnd());
303: assertEquals(6, simpleEntryGroup1.getSequenceLength());
304: assertEquals(0, simpleEntryGroup1.refCount());
305: assertEquals(1, simpleEntryGroup1.size());
306: assertEquals(0, filteredEntryGroup0.refCount());
307: assertEquals(1, filteredEntryGroup0.size());
308: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
309: assertEquals(6, filteredEntryGroup0.getSequenceLength());
310: assertFalse(feature0.isReadOnly());
311: assertEquals(1, strand0.getDirection());
312: assertTrue(strand0.isForwardStrand());
313: assertEquals(6, strand0.getSequenceLength());
314: assertEquals(5, Bases.MAX_PRIORITY);
315: assertEquals(2, Bases.REVERSE);
316: assertEquals(1, Bases.FORWARD);
317: assertEquals((-5), Bases.MIN_PRIORITY);
318: assertEquals(0, Bases.MEDIUM_PRIORITY);
319: assertEquals(0, Marker.LISTENER_PRIORITY);
320: assertEquals(2, Strand.REVERSE);
321: assertEquals(1, Strand.FORWARD);
322:
323: feature0.markerChanged(markerChangeEvent0);
324: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
325: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
326: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
327: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
328: assertEquals(2, genbankStreamSequence0.getFormatType());
329: assertEquals(0, genbankStreamSequence0.length());
330: assertEquals(0, genbankStreamSequence0.getTCount());
331: assertEquals(0, genbankStreamSequence0.getOtherCount());
332: assertEquals(0, genbankStreamSequence0.getGCount());
333: assertNull(genbankStreamSequence0.getHeader());
334: assertEquals(0, genbankStreamSequence0.getACount());
335: assertEquals(0, genbankStreamSequence0.getCCount());
336: assertEquals(0, bases0.getLength());
337: assertEquals(0, simpleEntryGroup0.size());
338: assertEquals(0, simpleEntryGroup0.refCount());
339: assertEquals(0, simpleEntryGroup0.getSequenceLength());
340: assertEquals(0, range0.getStart());
341: assertEquals(6, range0.getCount());
342: assertEquals(5, range0.getEnd());
343: assertEquals(6, simpleEntryGroup1.getSequenceLength());
344: assertEquals(0, simpleEntryGroup1.refCount());
345: assertEquals(1, simpleEntryGroup1.size());
346: assertEquals(0, filteredEntryGroup0.refCount());
347: assertEquals(1, filteredEntryGroup0.size());
348: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
349: assertEquals(6, filteredEntryGroup0.getSequenceLength());
350: assertFalse(feature0.isReadOnly());
351: assertEquals(1, strand0.getDirection());
352: assertTrue(strand0.isForwardStrand());
353: assertEquals(6, strand0.getSequenceLength());
354: assertEquals(5, Bases.MAX_PRIORITY);
355: assertEquals(2, Bases.REVERSE);
356: assertEquals(1, Bases.FORWARD);
357: assertEquals((-5), Bases.MIN_PRIORITY);
358: assertEquals(0, Bases.MEDIUM_PRIORITY);
359: assertEquals(0, Marker.LISTENER_PRIORITY);
360: assertEquals(2, Strand.REVERSE);
361: assertEquals(1, Strand.FORWARD);
Test case 65
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.length());
4: assertEquals(0, genbankStreamSequence0.getTCount());
5: assertEquals(2, genbankStreamSequence0.getFormatType());
6: assertEquals(0, genbankStreamSequence0.getGCount());
7: assertNull(genbankStreamSequence0.getHeader());
8: assertEquals(0, genbankStreamSequence0.getACount());
9: assertEquals(0, genbankStreamSequence0.getCCount());
10: assertEquals(0, genbankStreamSequence0.getOtherCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.length());
15: assertEquals(0, genbankStreamSequence0.getTCount());
16: assertEquals(2, genbankStreamSequence0.getFormatType());
17: assertEquals(0, genbankStreamSequence0.getGCount());
18: assertNull(genbankStreamSequence0.getHeader());
19: assertEquals(0, genbankStreamSequence0.getACount());
20: assertEquals(0, genbankStreamSequence0.getCCount());
21: assertEquals(0, genbankStreamSequence0.getOtherCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.length());
32: assertEquals(0, genbankStreamSequence0.getTCount());
33: assertEquals(2, genbankStreamSequence0.getFormatType());
34: assertEquals(0, genbankStreamSequence0.getGCount());
35: assertNull(genbankStreamSequence0.getHeader());
36: assertEquals(0, genbankStreamSequence0.getACount());
37: assertEquals(0, genbankStreamSequence0.getCCount());
38: assertEquals(0, genbankStreamSequence0.getOtherCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(1, Bases.FORWARD);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(5, range0.getEnd());
52: assertEquals(0, range0.getStart());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.length());
61: assertEquals(0, genbankStreamSequence0.getTCount());
62: assertEquals(2, genbankStreamSequence0.getFormatType());
63: assertEquals(0, genbankStreamSequence0.getGCount());
64: assertNull(genbankStreamSequence0.getHeader());
65: assertEquals(0, genbankStreamSequence0.getACount());
66: assertEquals(0, genbankStreamSequence0.getCCount());
67: assertEquals(0, genbankStreamSequence0.getOtherCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(5, range0.getEnd());
73: assertEquals(0, range0.getStart());
74: assertEquals(6, range0.getCount());
75: assertEquals(0, simpleEntryGroup1.refCount());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(6, simpleEntryGroup1.getSequenceLength());
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(5, Bases.MAX_PRIORITY);
81: assertEquals(1, Bases.FORWARD);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.length());
89: assertEquals(0, genbankStreamSequence0.getTCount());
90: assertEquals(2, genbankStreamSequence0.getFormatType());
91: assertEquals(0, genbankStreamSequence0.getGCount());
92: assertNull(genbankStreamSequence0.getHeader());
93: assertEquals(0, genbankStreamSequence0.getACount());
94: assertEquals(0, genbankStreamSequence0.getCCount());
95: assertEquals(0, genbankStreamSequence0.getOtherCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals((-5), Bases.MIN_PRIORITY);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(5, Bases.MAX_PRIORITY);
103: assertEquals(1, Bases.FORWARD);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.length());
111: assertEquals(0, genbankStreamSequence0.getTCount());
112: assertEquals(2, genbankStreamSequence0.getFormatType());
113: assertEquals(0, genbankStreamSequence0.getGCount());
114: assertNull(genbankStreamSequence0.getHeader());
115: assertEquals(0, genbankStreamSequence0.getACount());
116: assertEquals(0, genbankStreamSequence0.getCCount());
117: assertEquals(0, genbankStreamSequence0.getOtherCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(5, range0.getEnd());
123: assertEquals(0, range0.getStart());
124: assertEquals(6, range0.getCount());
125: assertEquals(0, simpleEntryGroup1.refCount());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(6, simpleEntryGroup1.getSequenceLength());
128: assertEquals(0, filteredEntryGroup0.size());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals(6, filteredEntryGroup0.getSequenceLength());
131: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
132: assertEquals((-5), Bases.MIN_PRIORITY);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(5, Bases.MAX_PRIORITY);
135: assertEquals(1, Bases.FORWARD);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.length());
145: assertEquals(0, genbankStreamSequence0.getTCount());
146: assertEquals(2, genbankStreamSequence0.getFormatType());
147: assertEquals(0, genbankStreamSequence0.getGCount());
148: assertNull(genbankStreamSequence0.getHeader());
149: assertEquals(0, genbankStreamSequence0.getACount());
150: assertEquals(0, genbankStreamSequence0.getCCount());
151: assertEquals(0, genbankStreamSequence0.getOtherCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(5, range0.getEnd());
157: assertEquals(0, range0.getStart());
158: assertEquals(6, range0.getCount());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(0, simpleEntryGroup1.refCount());
161: assertEquals(6, simpleEntryGroup1.getSequenceLength());
162: assertEquals(1, filteredEntryGroup0.size());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals(6, filteredEntryGroup0.getSequenceLength());
165: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
166: assertFalse(entry0.isReadOnly());
167: assertEquals((-5), Bases.MIN_PRIORITY);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(5, Bases.MAX_PRIORITY);
170: assertEquals(1, Bases.FORWARD);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.length());
180: assertEquals(0, genbankStreamSequence0.getTCount());
181: assertEquals(2, genbankStreamSequence0.getFormatType());
182: assertEquals(0, genbankStreamSequence0.getGCount());
183: assertNull(genbankStreamSequence0.getHeader());
184: assertEquals(0, genbankStreamSequence0.getACount());
185: assertEquals(0, genbankStreamSequence0.getCCount());
186: assertEquals(0, genbankStreamSequence0.getOtherCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(5, range0.getEnd());
192: assertEquals(0, range0.getStart());
193: assertEquals(6, range0.getCount());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(0, simpleEntryGroup1.refCount());
196: assertEquals(6, simpleEntryGroup1.getSequenceLength());
197: assertEquals(1, filteredEntryGroup0.size());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals(6, filteredEntryGroup0.getSequenceLength());
200: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
201: assertFalse(feature0.isReadOnly());
202: assertEquals((-5), Bases.MIN_PRIORITY);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(5, Bases.MAX_PRIORITY);
205: assertEquals(1, Bases.FORWARD);
206: assertEquals(2, Bases.REVERSE);
207:
208: Marker marker0 = feature0.getLastBaseMarker();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(marker0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.length());
215: assertEquals(0, genbankStreamSequence0.getTCount());
216: assertEquals(2, genbankStreamSequence0.getFormatType());
217: assertEquals(0, genbankStreamSequence0.getGCount());
218: assertNull(genbankStreamSequence0.getHeader());
219: assertEquals(0, genbankStreamSequence0.getACount());
220: assertEquals(0, genbankStreamSequence0.getCCount());
221: assertEquals(0, genbankStreamSequence0.getOtherCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.refCount());
224: assertEquals(0, simpleEntryGroup0.getSequenceLength());
225: assertEquals(0, simpleEntryGroup0.size());
226: assertEquals(5, range0.getEnd());
227: assertEquals(0, range0.getStart());
228: assertEquals(6, range0.getCount());
229: assertEquals(1, simpleEntryGroup1.size());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(6, simpleEntryGroup1.getSequenceLength());
232: assertEquals(1, filteredEntryGroup0.size());
233: assertEquals(0, filteredEntryGroup0.refCount());
234: assertEquals(6, filteredEntryGroup0.getSequenceLength());
235: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
236: assertFalse(feature0.isReadOnly());
237: assertEquals((-5), Bases.MIN_PRIORITY);
238: assertEquals(0, Bases.MEDIUM_PRIORITY);
239: assertEquals(5, Bases.MAX_PRIORITY);
240: assertEquals(1, Bases.FORWARD);
241: assertEquals(2, Bases.REVERSE);
242: assertEquals(0, Marker.LISTENER_PRIORITY);
Test case 66
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: StringVector stringVector0 = feature0.getValuesOfQualifier("");
9: assertNull(stringVector0);
10: assertFalse(feature0.isReadOnly());
Test case 67
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: String string0 = feature0.getValueOfQualifier("CDS");
12: assertNull(string0);
13: assertFalse(feature0.isReadOnly());
Test case 68
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getTCount());
4: assertNull(genbankStreamSequence0.getHeader());
5: assertEquals(0, genbankStreamSequence0.getACount());
6: assertEquals(0, genbankStreamSequence0.length());
7: assertEquals(2, genbankStreamSequence0.getFormatType());
8: assertEquals(0, genbankStreamSequence0.getGCount());
9: assertEquals(0, genbankStreamSequence0.getCCount());
10: assertEquals(0, genbankStreamSequence0.getOtherCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getTCount());
15: assertNull(genbankStreamSequence0.getHeader());
16: assertEquals(0, genbankStreamSequence0.getACount());
17: assertEquals(0, genbankStreamSequence0.length());
18: assertEquals(2, genbankStreamSequence0.getFormatType());
19: assertEquals(0, genbankStreamSequence0.getGCount());
20: assertEquals(0, genbankStreamSequence0.getCCount());
21: assertEquals(0, genbankStreamSequence0.getOtherCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(0, Bases.MEDIUM_PRIORITY);
24: assertEquals(1, Bases.FORWARD);
25: assertEquals((-5), Bases.MIN_PRIORITY);
26: assertEquals(5, Bases.MAX_PRIORITY);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getTCount());
32: assertNull(genbankStreamSequence0.getHeader());
33: assertEquals(0, genbankStreamSequence0.getACount());
34: assertEquals(0, genbankStreamSequence0.length());
35: assertEquals(2, genbankStreamSequence0.getFormatType());
36: assertEquals(0, genbankStreamSequence0.getGCount());
37: assertEquals(0, genbankStreamSequence0.getCCount());
38: assertEquals(0, genbankStreamSequence0.getOtherCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.getSequenceLength());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.refCount());
43: assertEquals(0, Bases.MEDIUM_PRIORITY);
44: assertEquals(1, Bases.FORWARD);
45: assertEquals((-5), Bases.MIN_PRIORITY);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(6, range0.getCount());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getTCount());
61: assertNull(genbankStreamSequence0.getHeader());
62: assertEquals(0, genbankStreamSequence0.getACount());
63: assertEquals(0, genbankStreamSequence0.length());
64: assertEquals(2, genbankStreamSequence0.getFormatType());
65: assertEquals(0, genbankStreamSequence0.getGCount());
66: assertEquals(0, genbankStreamSequence0.getCCount());
67: assertEquals(0, genbankStreamSequence0.getOtherCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.getSequenceLength());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.refCount());
72: assertEquals(0, range0.getStart());
73: assertEquals(6, range0.getCount());
74: assertEquals(5, range0.getEnd());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(0, Bases.MEDIUM_PRIORITY);
79: assertEquals(1, Bases.FORWARD);
80: assertEquals((-5), Bases.MIN_PRIORITY);
81: assertEquals(5, Bases.MAX_PRIORITY);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getTCount());
89: assertNull(genbankStreamSequence0.getHeader());
90: assertEquals(0, genbankStreamSequence0.getACount());
91: assertEquals(0, genbankStreamSequence0.length());
92: assertEquals(2, genbankStreamSequence0.getFormatType());
93: assertEquals(0, genbankStreamSequence0.getGCount());
94: assertEquals(0, genbankStreamSequence0.getCCount());
95: assertEquals(0, genbankStreamSequence0.getOtherCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.getSequenceLength());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.refCount());
100: assertEquals(0, Bases.MEDIUM_PRIORITY);
101: assertEquals(1, Bases.FORWARD);
102: assertEquals((-5), Bases.MIN_PRIORITY);
103: assertEquals(5, Bases.MAX_PRIORITY);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getTCount());
111: assertNull(genbankStreamSequence0.getHeader());
112: assertEquals(0, genbankStreamSequence0.getACount());
113: assertEquals(0, genbankStreamSequence0.length());
114: assertEquals(2, genbankStreamSequence0.getFormatType());
115: assertEquals(0, genbankStreamSequence0.getGCount());
116: assertEquals(0, genbankStreamSequence0.getCCount());
117: assertEquals(0, genbankStreamSequence0.getOtherCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.getSequenceLength());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.refCount());
122: assertEquals(0, range0.getStart());
123: assertEquals(6, range0.getCount());
124: assertEquals(5, range0.getEnd());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(0, filteredEntryGroup0.refCount());
129: assertEquals(0, filteredEntryGroup0.size());
130: assertEquals(6, filteredEntryGroup0.getSequenceLength());
131: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
132: assertEquals(0, Bases.MEDIUM_PRIORITY);
133: assertEquals(1, Bases.FORWARD);
134: assertEquals((-5), Bases.MIN_PRIORITY);
135: assertEquals(5, Bases.MAX_PRIORITY);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getTCount());
145: assertNull(genbankStreamSequence0.getHeader());
146: assertEquals(0, genbankStreamSequence0.getACount());
147: assertEquals(0, genbankStreamSequence0.length());
148: assertEquals(2, genbankStreamSequence0.getFormatType());
149: assertEquals(0, genbankStreamSequence0.getGCount());
150: assertEquals(0, genbankStreamSequence0.getCCount());
151: assertEquals(0, genbankStreamSequence0.getOtherCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.getSequenceLength());
154: assertEquals(0, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.refCount());
156: assertEquals(0, range0.getStart());
157: assertEquals(6, range0.getCount());
158: assertEquals(5, range0.getEnd());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(0, filteredEntryGroup0.refCount());
163: assertEquals(1, filteredEntryGroup0.size());
164: assertEquals(6, filteredEntryGroup0.getSequenceLength());
165: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(0, Bases.MEDIUM_PRIORITY);
168: assertEquals(1, Bases.FORWARD);
169: assertEquals((-5), Bases.MIN_PRIORITY);
170: assertEquals(5, Bases.MAX_PRIORITY);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getTCount());
180: assertNull(genbankStreamSequence0.getHeader());
181: assertEquals(0, genbankStreamSequence0.getACount());
182: assertEquals(0, genbankStreamSequence0.length());
183: assertEquals(2, genbankStreamSequence0.getFormatType());
184: assertEquals(0, genbankStreamSequence0.getGCount());
185: assertEquals(0, genbankStreamSequence0.getCCount());
186: assertEquals(0, genbankStreamSequence0.getOtherCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.getSequenceLength());
189: assertEquals(0, simpleEntryGroup0.size());
190: assertEquals(0, simpleEntryGroup0.refCount());
191: assertEquals(0, range0.getStart());
192: assertEquals(6, range0.getCount());
193: assertEquals(5, range0.getEnd());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(0, filteredEntryGroup0.refCount());
198: assertEquals(1, filteredEntryGroup0.size());
199: assertEquals(6, filteredEntryGroup0.getSequenceLength());
200: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(0, Bases.MEDIUM_PRIORITY);
203: assertEquals(1, Bases.FORWARD);
204: assertEquals((-5), Bases.MIN_PRIORITY);
205: assertEquals(5, Bases.MAX_PRIORITY);
206: assertEquals(2, Bases.REVERSE);
207:
208: Strand strand0 = feature0.getStrand();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(strand0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.getTCount());
215: assertNull(genbankStreamSequence0.getHeader());
216: assertEquals(0, genbankStreamSequence0.getACount());
217: assertEquals(0, genbankStreamSequence0.length());
218: assertEquals(2, genbankStreamSequence0.getFormatType());
219: assertEquals(0, genbankStreamSequence0.getGCount());
220: assertEquals(0, genbankStreamSequence0.getCCount());
221: assertEquals(0, genbankStreamSequence0.getOtherCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.getSequenceLength());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(0, simpleEntryGroup0.refCount());
226: assertEquals(0, range0.getStart());
227: assertEquals(6, range0.getCount());
228: assertEquals(5, range0.getEnd());
229: assertEquals(1, simpleEntryGroup1.size());
230: assertEquals(6, simpleEntryGroup1.getSequenceLength());
231: assertEquals(0, simpleEntryGroup1.refCount());
232: assertEquals(0, filteredEntryGroup0.refCount());
233: assertEquals(1, filteredEntryGroup0.size());
234: assertEquals(6, filteredEntryGroup0.getSequenceLength());
235: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(1, strand0.getDirection());
238: assertTrue(strand0.isForwardStrand());
239: assertEquals(6, strand0.getSequenceLength());
240: assertEquals(0, Bases.MEDIUM_PRIORITY);
241: assertEquals(1, Bases.FORWARD);
242: assertEquals((-5), Bases.MIN_PRIORITY);
243: assertEquals(5, Bases.MAX_PRIORITY);
244: assertEquals(2, Bases.REVERSE);
245: assertEquals(2, Strand.REVERSE);
246: assertEquals(1, Strand.FORWARD);
Test case 69
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("r");
2: assertNotNull(fastaStreamSequence0);
3: assertEquals(0, fastaStreamSequence0.getCCount());
4: assertEquals(4, fastaStreamSequence0.getFormatType());
5: assertEquals(0, fastaStreamSequence0.getGCount());
6: assertEquals(0, fastaStreamSequence0.getACount());
7: assertEquals(0, fastaStreamSequence0.getTCount());
8: assertEquals(1, fastaStreamSequence0.getOtherCount());
9: assertEquals(1, fastaStreamSequence0.length());
10:
11: Bases bases0 = new Bases(fastaStreamSequence0);
12: assertNotNull(bases0);
13: assertEquals(0, fastaStreamSequence0.getCCount());
14: assertEquals(4, fastaStreamSequence0.getFormatType());
15: assertEquals(0, fastaStreamSequence0.getGCount());
16: assertEquals(0, fastaStreamSequence0.getACount());
17: assertEquals(0, fastaStreamSequence0.getTCount());
18: assertEquals(1, fastaStreamSequence0.getOtherCount());
19: assertEquals(1, fastaStreamSequence0.length());
20: assertEquals(1, bases0.getLength());
21: assertEquals(5, Bases.MAX_PRIORITY);
22: assertEquals(1, Bases.FORWARD);
23: assertEquals((-5), Bases.MIN_PRIORITY);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(2, Bases.REVERSE);
26:
27: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
28: assertNotNull(simpleEntryGroup0);
29: assertEquals(0, fastaStreamSequence0.getCCount());
30: assertEquals(4, fastaStreamSequence0.getFormatType());
31: assertEquals(0, fastaStreamSequence0.getGCount());
32: assertEquals(0, fastaStreamSequence0.getACount());
33: assertEquals(0, fastaStreamSequence0.getTCount());
34: assertEquals(1, fastaStreamSequence0.getOtherCount());
35: assertEquals(1, fastaStreamSequence0.length());
36: assertEquals(1, bases0.getLength());
37: assertEquals(1, simpleEntryGroup0.getSequenceLength());
38: assertEquals(0, simpleEntryGroup0.refCount());
39: assertEquals(0, simpleEntryGroup0.size());
40: assertEquals(5, Bases.MAX_PRIORITY);
41: assertEquals(1, Bases.FORWARD);
42: assertEquals((-5), Bases.MIN_PRIORITY);
43: assertEquals(0, Bases.MEDIUM_PRIORITY);
44: assertEquals(2, Bases.REVERSE);
45:
46: Entry entry0 = simpleEntryGroup0.createEntry();
47: assertNotNull(entry0);
48: assertEquals(0, fastaStreamSequence0.getCCount());
49: assertEquals(4, fastaStreamSequence0.getFormatType());
50: assertEquals(0, fastaStreamSequence0.getGCount());
51: assertEquals(0, fastaStreamSequence0.getACount());
52: assertEquals(0, fastaStreamSequence0.getTCount());
53: assertEquals(1, fastaStreamSequence0.getOtherCount());
54: assertEquals(1, fastaStreamSequence0.length());
55: assertEquals(1, bases0.getLength());
56: assertEquals(1, simpleEntryGroup0.getSequenceLength());
57: assertEquals(0, simpleEntryGroup0.refCount());
58: assertEquals(1, simpleEntryGroup0.size());
59: assertFalse(entry0.isReadOnly());
60: assertEquals(5, Bases.MAX_PRIORITY);
61: assertEquals(1, Bases.FORWARD);
62: assertEquals((-5), Bases.MIN_PRIORITY);
63: assertEquals(0, Bases.MEDIUM_PRIORITY);
64: assertEquals(2, Bases.REVERSE);
65:
66: Feature feature0 = entry0.createFeature();
67: assertNotNull(feature0);
68: assertEquals(0, fastaStreamSequence0.getCCount());
69: assertEquals(4, fastaStreamSequence0.getFormatType());
70: assertEquals(0, fastaStreamSequence0.getGCount());
71: assertEquals(0, fastaStreamSequence0.getACount());
72: assertEquals(0, fastaStreamSequence0.getTCount());
73: assertEquals(1, fastaStreamSequence0.getOtherCount());
74: assertEquals(1, fastaStreamSequence0.length());
75: assertEquals(1, bases0.getLength());
76: assertEquals(1, simpleEntryGroup0.getSequenceLength());
77: assertEquals(0, simpleEntryGroup0.refCount());
78: assertEquals(1, simpleEntryGroup0.size());
79: assertFalse(entry0.isReadOnly());
80: assertFalse(feature0.isReadOnly());
81: assertEquals(5, Bases.MAX_PRIORITY);
82: assertEquals(1, Bases.FORWARD);
83: assertEquals((-5), Bases.MIN_PRIORITY);
84: assertEquals(0, Bases.MEDIUM_PRIORITY);
85: assertEquals(2, Bases.REVERSE);
Test case 70
1: uk.ac.sanger.artemis.Feature feature0 = new uk.ac.sanger.artemis.Feature((Feature) null);
Test case 71
1: Key key0 = Key.CDS;
2: assertNotNull(key0);
3: assertEquals("CDS", key0.toString());
4: assertEquals(3, key0.length());
5: assertEquals("CDS", key0.getKeyString());
6:
7: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(key0, (Location) null, (QualifierVector) null);
8: assertNotNull(blastStreamFeature0);
9: assertEquals("CDS", key0.toString());
10: assertEquals(3, key0.length());
11: assertEquals("CDS", key0.getKeyString());
12:
13: Feature feature0 = new Feature(blastStreamFeature0);
14: assertNotNull(feature0);
15: assertEquals("CDS", key0.toString());
16: assertEquals(3, key0.length());
17: assertEquals("CDS", key0.getKeyString());
18: assertFalse(feature0.isReadOnly());
19:
20: feature0.copyTo((Entry) null);
Test case 72
1: Feature.getAllQualifierNames((FeatureVector) null);
Test case 73
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.getDownstreamBases(46);
Test case 74
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.getFirstBase();
Test case 75
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.getFirstBaseMarker();
Test case 76
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.getLastBase();
Test case 77
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.getLastBaseMarker();
Test case 78
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.getMaxRawRange();
Test case 79
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.getPercentGC();
Test case 80
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.getRawLastBase();
Test case 81
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertNull(genbankStreamSequence0.getHeader());
4: assertEquals(0, genbankStreamSequence0.length());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(2, genbankStreamSequence0.getFormatType());
7: assertEquals(0, genbankStreamSequence0.getOtherCount());
8: assertEquals(0, genbankStreamSequence0.getGCount());
9: assertEquals(0, genbankStreamSequence0.getACount());
10: assertEquals(0, genbankStreamSequence0.getCCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertNull(genbankStreamSequence0.getHeader());
15: assertEquals(0, genbankStreamSequence0.length());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertEquals(2, genbankStreamSequence0.getFormatType());
18: assertEquals(0, genbankStreamSequence0.getOtherCount());
19: assertEquals(0, genbankStreamSequence0.getGCount());
20: assertEquals(0, genbankStreamSequence0.getACount());
21: assertEquals(0, genbankStreamSequence0.getCCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(5, Bases.MAX_PRIORITY);
24: assertEquals(2, Bases.REVERSE);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals((-5), Bases.MIN_PRIORITY);
27: assertEquals(0, Bases.MEDIUM_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertNull(genbankStreamSequence0.getHeader());
32: assertEquals(0, genbankStreamSequence0.length());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertEquals(2, genbankStreamSequence0.getFormatType());
35: assertEquals(0, genbankStreamSequence0.getOtherCount());
36: assertEquals(0, genbankStreamSequence0.getGCount());
37: assertEquals(0, genbankStreamSequence0.getACount());
38: assertEquals(0, genbankStreamSequence0.getCCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.size());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals(5, Bases.MAX_PRIORITY);
44: assertEquals(2, Bases.REVERSE);
45: assertEquals(1, Bases.FORWARD);
46: assertEquals((-5), Bases.MIN_PRIORITY);
47: assertEquals(0, Bases.MEDIUM_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(0, range0.getStart());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertNull(genbankStreamSequence0.getHeader());
61: assertEquals(0, genbankStreamSequence0.length());
62: assertEquals(0, genbankStreamSequence0.getTCount());
63: assertEquals(2, genbankStreamSequence0.getFormatType());
64: assertEquals(0, genbankStreamSequence0.getOtherCount());
65: assertEquals(0, genbankStreamSequence0.getGCount());
66: assertEquals(0, genbankStreamSequence0.getACount());
67: assertEquals(0, genbankStreamSequence0.getCCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.size());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(6, range0.getCount());
73: assertEquals(0, range0.getStart());
74: assertEquals(5, range0.getEnd());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(5, Bases.MAX_PRIORITY);
79: assertEquals(2, Bases.REVERSE);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals((-5), Bases.MIN_PRIORITY);
82: assertEquals(0, Bases.MEDIUM_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertNull(genbankStreamSequence0.getHeader());
89: assertEquals(0, genbankStreamSequence0.length());
90: assertEquals(0, genbankStreamSequence0.getTCount());
91: assertEquals(2, genbankStreamSequence0.getFormatType());
92: assertEquals(0, genbankStreamSequence0.getOtherCount());
93: assertEquals(0, genbankStreamSequence0.getGCount());
94: assertEquals(0, genbankStreamSequence0.getACount());
95: assertEquals(0, genbankStreamSequence0.getCCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.size());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals(5, Bases.MAX_PRIORITY);
101: assertEquals(2, Bases.REVERSE);
102: assertEquals(1, Bases.FORWARD);
103: assertEquals((-5), Bases.MIN_PRIORITY);
104: assertEquals(0, Bases.MEDIUM_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertNull(genbankStreamSequence0.getHeader());
111: assertEquals(0, genbankStreamSequence0.length());
112: assertEquals(0, genbankStreamSequence0.getTCount());
113: assertEquals(2, genbankStreamSequence0.getFormatType());
114: assertEquals(0, genbankStreamSequence0.getOtherCount());
115: assertEquals(0, genbankStreamSequence0.getGCount());
116: assertEquals(0, genbankStreamSequence0.getACount());
117: assertEquals(0, genbankStreamSequence0.getCCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.size());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(6, range0.getCount());
123: assertEquals(0, range0.getStart());
124: assertEquals(5, range0.getEnd());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(0, filteredEntryGroup0.refCount());
129: assertEquals(0, filteredEntryGroup0.size());
130: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals(5, Bases.MAX_PRIORITY);
133: assertEquals(2, Bases.REVERSE);
134: assertEquals(1, Bases.FORWARD);
135: assertEquals((-5), Bases.MIN_PRIORITY);
136: assertEquals(0, Bases.MEDIUM_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertNull(genbankStreamSequence0.getHeader());
145: assertEquals(0, genbankStreamSequence0.length());
146: assertEquals(0, genbankStreamSequence0.getTCount());
147: assertEquals(2, genbankStreamSequence0.getFormatType());
148: assertEquals(0, genbankStreamSequence0.getOtherCount());
149: assertEquals(0, genbankStreamSequence0.getGCount());
150: assertEquals(0, genbankStreamSequence0.getACount());
151: assertEquals(0, genbankStreamSequence0.getCCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.size());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(6, range0.getCount());
157: assertEquals(0, range0.getStart());
158: assertEquals(5, range0.getEnd());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(0, filteredEntryGroup0.refCount());
163: assertEquals(1, filteredEntryGroup0.size());
164: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(5, Bases.MAX_PRIORITY);
168: assertEquals(2, Bases.REVERSE);
169: assertEquals(1, Bases.FORWARD);
170: assertEquals((-5), Bases.MIN_PRIORITY);
171: assertEquals(0, Bases.MEDIUM_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertNull(genbankStreamSequence0.getHeader());
180: assertEquals(0, genbankStreamSequence0.length());
181: assertEquals(0, genbankStreamSequence0.getTCount());
182: assertEquals(2, genbankStreamSequence0.getFormatType());
183: assertEquals(0, genbankStreamSequence0.getOtherCount());
184: assertEquals(0, genbankStreamSequence0.getGCount());
185: assertEquals(0, genbankStreamSequence0.getACount());
186: assertEquals(0, genbankStreamSequence0.getCCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.size());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(6, range0.getCount());
192: assertEquals(0, range0.getStart());
193: assertEquals(5, range0.getEnd());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(0, filteredEntryGroup0.refCount());
198: assertEquals(1, filteredEntryGroup0.size());
199: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(5, Bases.MAX_PRIORITY);
203: assertEquals(2, Bases.REVERSE);
204: assertEquals(1, Bases.FORWARD);
205: assertEquals((-5), Bases.MIN_PRIORITY);
206: assertEquals(0, Bases.MEDIUM_PRIORITY);
207:
208: feature0.getResidueCount((-5));
Test case 82
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.getStrand();
Test case 83
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.hasValidEMBLKey();
Test case 84
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.moveTo((Entry) null, false);
Test case 85
1: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
2: assertNotNull(emblStreamFeature0);
3:
4: Feature feature0 = new Feature(emblStreamFeature0);
5: assertNotNull(feature0);
6: assertFalse(feature0.isReadOnly());
7:
8: feature0.removeSegment((FeatureSegment) null);
Test case 86
1: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
2: assertNotNull(genbankStreamFeature0);
3:
4: BlastStreamFeature blastStreamFeature0 = new BlastStreamFeature(genbankStreamFeature0);
5: assertNotNull(blastStreamFeature0);
6:
7: Feature feature0 = new Feature(blastStreamFeature0);
8: assertNotNull(feature0);
9: assertFalse(feature0.isReadOnly());
10:
11: feature0.writeAminoAcidsOfFeature((Writer) null);
Test case 87
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(2, genbankStreamSequence0.getFormatType());
4: assertEquals(0, genbankStreamSequence0.getGCount());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertNull(genbankStreamSequence0.getHeader());
7: assertEquals(0, genbankStreamSequence0.getACount());
8: assertEquals(0, genbankStreamSequence0.getCCount());
9: assertEquals(0, genbankStreamSequence0.getOtherCount());
10: assertEquals(0, genbankStreamSequence0.length());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, genbankStreamSequence0.getFormatType());
15: assertEquals(0, genbankStreamSequence0.getGCount());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertNull(genbankStreamSequence0.getHeader());
18: assertEquals(0, genbankStreamSequence0.getACount());
19: assertEquals(0, genbankStreamSequence0.getCCount());
20: assertEquals(0, genbankStreamSequence0.getOtherCount());
21: assertEquals(0, genbankStreamSequence0.length());
22: assertEquals(0, bases0.getLength());
23: assertEquals(1, Bases.FORWARD);
24: assertEquals((-5), Bases.MIN_PRIORITY);
25: assertEquals(0, Bases.MEDIUM_PRIORITY);
26: assertEquals(5, Bases.MAX_PRIORITY);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(2, genbankStreamSequence0.getFormatType());
32: assertEquals(0, genbankStreamSequence0.getGCount());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertNull(genbankStreamSequence0.getHeader());
35: assertEquals(0, genbankStreamSequence0.getACount());
36: assertEquals(0, genbankStreamSequence0.getCCount());
37: assertEquals(0, genbankStreamSequence0.getOtherCount());
38: assertEquals(0, genbankStreamSequence0.length());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.refCount());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.size());
43: assertEquals(1, Bases.FORWARD);
44: assertEquals((-5), Bases.MIN_PRIORITY);
45: assertEquals(0, Bases.MEDIUM_PRIORITY);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(6, range0.getCount());
52: assertEquals(0, range0.getStart());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(2, genbankStreamSequence0.getFormatType());
61: assertEquals(0, genbankStreamSequence0.getGCount());
62: assertEquals(0, genbankStreamSequence0.getTCount());
63: assertNull(genbankStreamSequence0.getHeader());
64: assertEquals(0, genbankStreamSequence0.getACount());
65: assertEquals(0, genbankStreamSequence0.getCCount());
66: assertEquals(0, genbankStreamSequence0.getOtherCount());
67: assertEquals(0, genbankStreamSequence0.length());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.refCount());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.size());
72: assertEquals(6, range0.getCount());
73: assertEquals(0, range0.getStart());
74: assertEquals(5, range0.getEnd());
75: assertEquals(0, simpleEntryGroup1.size());
76: assertEquals(0, simpleEntryGroup1.refCount());
77: assertEquals(6, simpleEntryGroup1.getSequenceLength());
78: assertEquals(1, Bases.FORWARD);
79: assertEquals((-5), Bases.MIN_PRIORITY);
80: assertEquals(0, Bases.MEDIUM_PRIORITY);
81: assertEquals(5, Bases.MAX_PRIORITY);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(2, genbankStreamSequence0.getFormatType());
89: assertEquals(0, genbankStreamSequence0.getGCount());
90: assertEquals(0, genbankStreamSequence0.getTCount());
91: assertNull(genbankStreamSequence0.getHeader());
92: assertEquals(0, genbankStreamSequence0.getACount());
93: assertEquals(0, genbankStreamSequence0.getCCount());
94: assertEquals(0, genbankStreamSequence0.getOtherCount());
95: assertEquals(0, genbankStreamSequence0.length());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.refCount());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.size());
100: assertEquals(1, Bases.FORWARD);
101: assertEquals((-5), Bases.MIN_PRIORITY);
102: assertEquals(0, Bases.MEDIUM_PRIORITY);
103: assertEquals(5, Bases.MAX_PRIORITY);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(2, genbankStreamSequence0.getFormatType());
111: assertEquals(0, genbankStreamSequence0.getGCount());
112: assertEquals(0, genbankStreamSequence0.getTCount());
113: assertNull(genbankStreamSequence0.getHeader());
114: assertEquals(0, genbankStreamSequence0.getACount());
115: assertEquals(0, genbankStreamSequence0.getCCount());
116: assertEquals(0, genbankStreamSequence0.getOtherCount());
117: assertEquals(0, genbankStreamSequence0.length());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.refCount());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.size());
122: assertEquals(6, range0.getCount());
123: assertEquals(0, range0.getStart());
124: assertEquals(5, range0.getEnd());
125: assertEquals(0, simpleEntryGroup1.size());
126: assertEquals(0, simpleEntryGroup1.refCount());
127: assertEquals(6, simpleEntryGroup1.getSequenceLength());
128: assertEquals(6, filteredEntryGroup0.getSequenceLength());
129: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
130: assertEquals(0, filteredEntryGroup0.refCount());
131: assertEquals(0, filteredEntryGroup0.size());
132: assertEquals(1, Bases.FORWARD);
133: assertEquals((-5), Bases.MIN_PRIORITY);
134: assertEquals(0, Bases.MEDIUM_PRIORITY);
135: assertEquals(5, Bases.MAX_PRIORITY);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(2, genbankStreamSequence0.getFormatType());
145: assertEquals(0, genbankStreamSequence0.getGCount());
146: assertEquals(0, genbankStreamSequence0.getTCount());
147: assertNull(genbankStreamSequence0.getHeader());
148: assertEquals(0, genbankStreamSequence0.getACount());
149: assertEquals(0, genbankStreamSequence0.getCCount());
150: assertEquals(0, genbankStreamSequence0.getOtherCount());
151: assertEquals(0, genbankStreamSequence0.length());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.refCount());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.size());
156: assertEquals(6, range0.getCount());
157: assertEquals(0, range0.getStart());
158: assertEquals(5, range0.getEnd());
159: assertEquals(1, simpleEntryGroup1.size());
160: assertEquals(0, simpleEntryGroup1.refCount());
161: assertEquals(6, simpleEntryGroup1.getSequenceLength());
162: assertEquals(6, filteredEntryGroup0.getSequenceLength());
163: assertEquals(1, filteredEntryGroup0.size());
164: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
165: assertEquals(0, filteredEntryGroup0.refCount());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(1, Bases.FORWARD);
168: assertEquals((-5), Bases.MIN_PRIORITY);
169: assertEquals(0, Bases.MEDIUM_PRIORITY);
170: assertEquals(5, Bases.MAX_PRIORITY);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(2, genbankStreamSequence0.getFormatType());
180: assertEquals(0, genbankStreamSequence0.getGCount());
181: assertEquals(0, genbankStreamSequence0.getTCount());
182: assertNull(genbankStreamSequence0.getHeader());
183: assertEquals(0, genbankStreamSequence0.getACount());
184: assertEquals(0, genbankStreamSequence0.getCCount());
185: assertEquals(0, genbankStreamSequence0.getOtherCount());
186: assertEquals(0, genbankStreamSequence0.length());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.refCount());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.size());
191: assertEquals(6, range0.getCount());
192: assertEquals(0, range0.getStart());
193: assertEquals(5, range0.getEnd());
194: assertEquals(1, simpleEntryGroup1.size());
195: assertEquals(0, simpleEntryGroup1.refCount());
196: assertEquals(6, simpleEntryGroup1.getSequenceLength());
197: assertEquals(6, filteredEntryGroup0.getSequenceLength());
198: assertEquals(1, filteredEntryGroup0.size());
199: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
200: assertEquals(0, filteredEntryGroup0.refCount());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(1, Bases.FORWARD);
203: assertEquals((-5), Bases.MIN_PRIORITY);
204: assertEquals(0, Bases.MEDIUM_PRIORITY);
205: assertEquals(5, Bases.MAX_PRIORITY);
206: assertEquals(2, Bases.REVERSE);
207:
208: int int0 = feature0.getCodonCount(2, 0, 1);
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertEquals(0, int0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(2, genbankStreamSequence0.getFormatType());
215: assertEquals(0, genbankStreamSequence0.getGCount());
216: assertEquals(0, genbankStreamSequence0.getTCount());
217: assertNull(genbankStreamSequence0.getHeader());
218: assertEquals(0, genbankStreamSequence0.getACount());
219: assertEquals(0, genbankStreamSequence0.getCCount());
220: assertEquals(0, genbankStreamSequence0.getOtherCount());
221: assertEquals(0, genbankStreamSequence0.length());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.refCount());
224: assertEquals(0, simpleEntryGroup0.getSequenceLength());
225: assertEquals(0, simpleEntryGroup0.size());
226: assertEquals(6, range0.getCount());
227: assertEquals(0, range0.getStart());
228: assertEquals(5, range0.getEnd());
229: assertEquals(1, simpleEntryGroup1.size());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(6, simpleEntryGroup1.getSequenceLength());
232: assertEquals(6, filteredEntryGroup0.getSequenceLength());
233: assertEquals(1, filteredEntryGroup0.size());
234: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
235: assertEquals(0, filteredEntryGroup0.refCount());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(1, Bases.FORWARD);
238: assertEquals((-5), Bases.MIN_PRIORITY);
239: assertEquals(0, Bases.MEDIUM_PRIORITY);
240: assertEquals(5, Bases.MAX_PRIORITY);
241: assertEquals(2, Bases.REVERSE);
Test case 88
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(2, genbankStreamSequence0.getFormatType());
4: assertEquals(0, genbankStreamSequence0.getGCount());
5: assertNull(genbankStreamSequence0.getHeader());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertEquals(0, genbankStreamSequence0.getACount());
8: assertEquals(0, genbankStreamSequence0.getOtherCount());
9: assertEquals(0, genbankStreamSequence0.length());
10: assertEquals(0, genbankStreamSequence0.getTCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, genbankStreamSequence0.getFormatType());
15: assertEquals(0, genbankStreamSequence0.getGCount());
16: assertNull(genbankStreamSequence0.getHeader());
17: assertEquals(0, genbankStreamSequence0.getCCount());
18: assertEquals(0, genbankStreamSequence0.getACount());
19: assertEquals(0, genbankStreamSequence0.getOtherCount());
20: assertEquals(0, genbankStreamSequence0.length());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(5, Bases.MAX_PRIORITY);
24: assertEquals(1, Bases.FORWARD);
25: assertEquals(0, Bases.MEDIUM_PRIORITY);
26: assertEquals((-5), Bases.MIN_PRIORITY);
27: assertEquals(2, Bases.REVERSE);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(2, genbankStreamSequence0.getFormatType());
32: assertEquals(0, genbankStreamSequence0.getGCount());
33: assertNull(genbankStreamSequence0.getHeader());
34: assertEquals(0, genbankStreamSequence0.getCCount());
35: assertEquals(0, genbankStreamSequence0.getACount());
36: assertEquals(0, genbankStreamSequence0.getOtherCount());
37: assertEquals(0, genbankStreamSequence0.length());
38: assertEquals(0, genbankStreamSequence0.getTCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.refCount());
43: assertEquals(5, Bases.MAX_PRIORITY);
44: assertEquals(1, Bases.FORWARD);
45: assertEquals(0, Bases.MEDIUM_PRIORITY);
46: assertEquals((-5), Bases.MIN_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(6, range0.getCount());
53: assertEquals(5, range0.getEnd());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(2, genbankStreamSequence0.getFormatType());
61: assertEquals(0, genbankStreamSequence0.getGCount());
62: assertNull(genbankStreamSequence0.getHeader());
63: assertEquals(0, genbankStreamSequence0.getCCount());
64: assertEquals(0, genbankStreamSequence0.getACount());
65: assertEquals(0, genbankStreamSequence0.getOtherCount());
66: assertEquals(0, genbankStreamSequence0.length());
67: assertEquals(0, genbankStreamSequence0.getTCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.size());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.refCount());
72: assertEquals(0, range0.getStart());
73: assertEquals(6, range0.getCount());
74: assertEquals(5, range0.getEnd());
75: assertEquals(6, simpleEntryGroup1.getSequenceLength());
76: assertEquals(0, simpleEntryGroup1.size());
77: assertEquals(0, simpleEntryGroup1.refCount());
78: assertEquals(5, Bases.MAX_PRIORITY);
79: assertEquals(1, Bases.FORWARD);
80: assertEquals(0, Bases.MEDIUM_PRIORITY);
81: assertEquals((-5), Bases.MIN_PRIORITY);
82: assertEquals(2, Bases.REVERSE);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(2, genbankStreamSequence0.getFormatType());
89: assertEquals(0, genbankStreamSequence0.getGCount());
90: assertNull(genbankStreamSequence0.getHeader());
91: assertEquals(0, genbankStreamSequence0.getCCount());
92: assertEquals(0, genbankStreamSequence0.getACount());
93: assertEquals(0, genbankStreamSequence0.getOtherCount());
94: assertEquals(0, genbankStreamSequence0.length());
95: assertEquals(0, genbankStreamSequence0.getTCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.size());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.refCount());
100: assertEquals(5, Bases.MAX_PRIORITY);
101: assertEquals(1, Bases.FORWARD);
102: assertEquals(0, Bases.MEDIUM_PRIORITY);
103: assertEquals((-5), Bases.MIN_PRIORITY);
104: assertEquals(2, Bases.REVERSE);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(2, genbankStreamSequence0.getFormatType());
111: assertEquals(0, genbankStreamSequence0.getGCount());
112: assertNull(genbankStreamSequence0.getHeader());
113: assertEquals(0, genbankStreamSequence0.getCCount());
114: assertEquals(0, genbankStreamSequence0.getACount());
115: assertEquals(0, genbankStreamSequence0.getOtherCount());
116: assertEquals(0, genbankStreamSequence0.length());
117: assertEquals(0, genbankStreamSequence0.getTCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.size());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.refCount());
122: assertEquals(0, range0.getStart());
123: assertEquals(6, range0.getCount());
124: assertEquals(5, range0.getEnd());
125: assertEquals(6, simpleEntryGroup1.getSequenceLength());
126: assertEquals(0, simpleEntryGroup1.size());
127: assertEquals(0, simpleEntryGroup1.refCount());
128: assertEquals(6, filteredEntryGroup0.getSequenceLength());
129: assertEquals(0, filteredEntryGroup0.size());
130: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
131: assertEquals(0, filteredEntryGroup0.refCount());
132: assertEquals(5, Bases.MAX_PRIORITY);
133: assertEquals(1, Bases.FORWARD);
134: assertEquals(0, Bases.MEDIUM_PRIORITY);
135: assertEquals((-5), Bases.MIN_PRIORITY);
136: assertEquals(2, Bases.REVERSE);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(2, genbankStreamSequence0.getFormatType());
145: assertEquals(0, genbankStreamSequence0.getGCount());
146: assertNull(genbankStreamSequence0.getHeader());
147: assertEquals(0, genbankStreamSequence0.getCCount());
148: assertEquals(0, genbankStreamSequence0.getACount());
149: assertEquals(0, genbankStreamSequence0.getOtherCount());
150: assertEquals(0, genbankStreamSequence0.length());
151: assertEquals(0, genbankStreamSequence0.getTCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.size());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.refCount());
156: assertEquals(0, range0.getStart());
157: assertEquals(6, range0.getCount());
158: assertEquals(5, range0.getEnd());
159: assertEquals(6, simpleEntryGroup1.getSequenceLength());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(0, simpleEntryGroup1.refCount());
162: assertEquals(6, filteredEntryGroup0.getSequenceLength());
163: assertEquals(1, filteredEntryGroup0.size());
164: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
165: assertEquals(0, filteredEntryGroup0.refCount());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(5, Bases.MAX_PRIORITY);
168: assertEquals(1, Bases.FORWARD);
169: assertEquals(0, Bases.MEDIUM_PRIORITY);
170: assertEquals((-5), Bases.MIN_PRIORITY);
171: assertEquals(2, Bases.REVERSE);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(2, genbankStreamSequence0.getFormatType());
180: assertEquals(0, genbankStreamSequence0.getGCount());
181: assertNull(genbankStreamSequence0.getHeader());
182: assertEquals(0, genbankStreamSequence0.getCCount());
183: assertEquals(0, genbankStreamSequence0.getACount());
184: assertEquals(0, genbankStreamSequence0.getOtherCount());
185: assertEquals(0, genbankStreamSequence0.length());
186: assertEquals(0, genbankStreamSequence0.getTCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.size());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.refCount());
191: assertEquals(0, range0.getStart());
192: assertEquals(6, range0.getCount());
193: assertEquals(5, range0.getEnd());
194: assertEquals(6, simpleEntryGroup1.getSequenceLength());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(0, simpleEntryGroup1.refCount());
197: assertEquals(6, filteredEntryGroup0.getSequenceLength());
198: assertEquals(1, filteredEntryGroup0.size());
199: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
200: assertEquals(0, filteredEntryGroup0.refCount());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(5, Bases.MAX_PRIORITY);
203: assertEquals(1, Bases.FORWARD);
204: assertEquals(0, Bases.MEDIUM_PRIORITY);
205: assertEquals((-5), Bases.MIN_PRIORITY);
206: assertEquals(2, Bases.REVERSE);
207:
208: Entry entry1 = feature0.getEntry();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(entry1);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertSame(entry1, entry0);
215: assertEquals(2, genbankStreamSequence0.getFormatType());
216: assertEquals(0, genbankStreamSequence0.getGCount());
217: assertNull(genbankStreamSequence0.getHeader());
218: assertEquals(0, genbankStreamSequence0.getCCount());
219: assertEquals(0, genbankStreamSequence0.getACount());
220: assertEquals(0, genbankStreamSequence0.getOtherCount());
221: assertEquals(0, genbankStreamSequence0.length());
222: assertEquals(0, genbankStreamSequence0.getTCount());
223: assertEquals(0, bases0.getLength());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(0, simpleEntryGroup0.getSequenceLength());
226: assertEquals(0, simpleEntryGroup0.refCount());
227: assertEquals(0, range0.getStart());
228: assertEquals(6, range0.getCount());
229: assertEquals(5, range0.getEnd());
230: assertEquals(6, simpleEntryGroup1.getSequenceLength());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals(0, simpleEntryGroup1.refCount());
233: assertEquals(6, filteredEntryGroup0.getSequenceLength());
234: assertEquals(1, filteredEntryGroup0.size());
235: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
236: assertEquals(0, filteredEntryGroup0.refCount());
237: assertFalse(feature0.isReadOnly());
238: assertFalse(entry1.isReadOnly());
239: assertEquals(5, Bases.MAX_PRIORITY);
240: assertEquals(1, Bases.FORWARD);
241: assertEquals(0, Bases.MEDIUM_PRIORITY);
242: assertEquals((-5), Bases.MIN_PRIORITY);
243: assertEquals(2, Bases.REVERSE);
Test case 89
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getOtherCount());
4: assertEquals(0, genbankStreamSequence0.getTCount());
5: assertEquals(0, genbankStreamSequence0.length());
6: assertNull(genbankStreamSequence0.getHeader());
7: assertEquals(2, genbankStreamSequence0.getFormatType());
8: assertEquals(0, genbankStreamSequence0.getCCount());
9: assertEquals(0, genbankStreamSequence0.getACount());
10: assertEquals(0, genbankStreamSequence0.getGCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, genbankStreamSequence0.getOtherCount());
15: assertEquals(0, genbankStreamSequence0.getTCount());
16: assertEquals(0, genbankStreamSequence0.length());
17: assertNull(genbankStreamSequence0.getHeader());
18: assertEquals(2, genbankStreamSequence0.getFormatType());
19: assertEquals(0, genbankStreamSequence0.getCCount());
20: assertEquals(0, genbankStreamSequence0.getACount());
21: assertEquals(0, genbankStreamSequence0.getGCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(1, Bases.FORWARD);
24: assertEquals(2, Bases.REVERSE);
25: assertEquals((-5), Bases.MIN_PRIORITY);
26: assertEquals(0, Bases.MEDIUM_PRIORITY);
27: assertEquals(5, Bases.MAX_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertEquals(0, genbankStreamSequence0.getOtherCount());
32: assertEquals(0, genbankStreamSequence0.getTCount());
33: assertEquals(0, genbankStreamSequence0.length());
34: assertNull(genbankStreamSequence0.getHeader());
35: assertEquals(2, genbankStreamSequence0.getFormatType());
36: assertEquals(0, genbankStreamSequence0.getCCount());
37: assertEquals(0, genbankStreamSequence0.getACount());
38: assertEquals(0, genbankStreamSequence0.getGCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(0, simpleEntryGroup0.getSequenceLength());
42: assertEquals(0, simpleEntryGroup0.refCount());
43: assertEquals(1, Bases.FORWARD);
44: assertEquals(2, Bases.REVERSE);
45: assertEquals((-5), Bases.MIN_PRIORITY);
46: assertEquals(0, Bases.MEDIUM_PRIORITY);
47: assertEquals(5, Bases.MAX_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(5, range0.getEnd());
52: assertEquals(0, range0.getStart());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertEquals(0, genbankStreamSequence0.getOtherCount());
61: assertEquals(0, genbankStreamSequence0.getTCount());
62: assertEquals(0, genbankStreamSequence0.length());
63: assertNull(genbankStreamSequence0.getHeader());
64: assertEquals(2, genbankStreamSequence0.getFormatType());
65: assertEquals(0, genbankStreamSequence0.getCCount());
66: assertEquals(0, genbankStreamSequence0.getACount());
67: assertEquals(0, genbankStreamSequence0.getGCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.size());
70: assertEquals(0, simpleEntryGroup0.getSequenceLength());
71: assertEquals(0, simpleEntryGroup0.refCount());
72: assertEquals(5, range0.getEnd());
73: assertEquals(0, range0.getStart());
74: assertEquals(6, range0.getCount());
75: assertEquals(0, simpleEntryGroup1.refCount());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals(1, Bases.FORWARD);
79: assertEquals(2, Bases.REVERSE);
80: assertEquals((-5), Bases.MIN_PRIORITY);
81: assertEquals(0, Bases.MEDIUM_PRIORITY);
82: assertEquals(5, Bases.MAX_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertEquals(0, genbankStreamSequence0.getOtherCount());
89: assertEquals(0, genbankStreamSequence0.getTCount());
90: assertEquals(0, genbankStreamSequence0.length());
91: assertNull(genbankStreamSequence0.getHeader());
92: assertEquals(2, genbankStreamSequence0.getFormatType());
93: assertEquals(0, genbankStreamSequence0.getCCount());
94: assertEquals(0, genbankStreamSequence0.getACount());
95: assertEquals(0, genbankStreamSequence0.getGCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.size());
98: assertEquals(0, simpleEntryGroup0.getSequenceLength());
99: assertEquals(0, simpleEntryGroup0.refCount());
100: assertEquals(1, Bases.FORWARD);
101: assertEquals(2, Bases.REVERSE);
102: assertEquals((-5), Bases.MIN_PRIORITY);
103: assertEquals(0, Bases.MEDIUM_PRIORITY);
104: assertEquals(5, Bases.MAX_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertEquals(0, genbankStreamSequence0.getOtherCount());
111: assertEquals(0, genbankStreamSequence0.getTCount());
112: assertEquals(0, genbankStreamSequence0.length());
113: assertNull(genbankStreamSequence0.getHeader());
114: assertEquals(2, genbankStreamSequence0.getFormatType());
115: assertEquals(0, genbankStreamSequence0.getCCount());
116: assertEquals(0, genbankStreamSequence0.getACount());
117: assertEquals(0, genbankStreamSequence0.getGCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.size());
120: assertEquals(0, simpleEntryGroup0.getSequenceLength());
121: assertEquals(0, simpleEntryGroup0.refCount());
122: assertEquals(5, range0.getEnd());
123: assertEquals(0, range0.getStart());
124: assertEquals(6, range0.getCount());
125: assertEquals(0, simpleEntryGroup1.refCount());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals("", filteredEntryGroup0.getFilterName());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals(0, filteredEntryGroup0.size());
131: assertEquals(6, filteredEntryGroup0.getSequenceLength());
132: assertEquals(1, Bases.FORWARD);
133: assertEquals(2, Bases.REVERSE);
134: assertEquals((-5), Bases.MIN_PRIORITY);
135: assertEquals(0, Bases.MEDIUM_PRIORITY);
136: assertEquals(5, Bases.MAX_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertEquals(0, genbankStreamSequence0.getOtherCount());
145: assertEquals(0, genbankStreamSequence0.getTCount());
146: assertEquals(0, genbankStreamSequence0.length());
147: assertNull(genbankStreamSequence0.getHeader());
148: assertEquals(2, genbankStreamSequence0.getFormatType());
149: assertEquals(0, genbankStreamSequence0.getCCount());
150: assertEquals(0, genbankStreamSequence0.getACount());
151: assertEquals(0, genbankStreamSequence0.getGCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.size());
154: assertEquals(0, simpleEntryGroup0.getSequenceLength());
155: assertEquals(0, simpleEntryGroup0.refCount());
156: assertEquals(5, range0.getEnd());
157: assertEquals(0, range0.getStart());
158: assertEquals(6, range0.getCount());
159: assertEquals(0, simpleEntryGroup1.refCount());
160: assertEquals(6, simpleEntryGroup1.getSequenceLength());
161: assertEquals(1, simpleEntryGroup1.size());
162: assertEquals("", filteredEntryGroup0.getFilterName());
163: assertEquals(0, filteredEntryGroup0.refCount());
164: assertEquals(1, filteredEntryGroup0.size());
165: assertEquals(6, filteredEntryGroup0.getSequenceLength());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(1, Bases.FORWARD);
168: assertEquals(2, Bases.REVERSE);
169: assertEquals((-5), Bases.MIN_PRIORITY);
170: assertEquals(0, Bases.MEDIUM_PRIORITY);
171: assertEquals(5, Bases.MAX_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertEquals(0, genbankStreamSequence0.getOtherCount());
180: assertEquals(0, genbankStreamSequence0.getTCount());
181: assertEquals(0, genbankStreamSequence0.length());
182: assertNull(genbankStreamSequence0.getHeader());
183: assertEquals(2, genbankStreamSequence0.getFormatType());
184: assertEquals(0, genbankStreamSequence0.getCCount());
185: assertEquals(0, genbankStreamSequence0.getACount());
186: assertEquals(0, genbankStreamSequence0.getGCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.size());
189: assertEquals(0, simpleEntryGroup0.getSequenceLength());
190: assertEquals(0, simpleEntryGroup0.refCount());
191: assertEquals(5, range0.getEnd());
192: assertEquals(0, range0.getStart());
193: assertEquals(6, range0.getCount());
194: assertEquals(0, simpleEntryGroup1.refCount());
195: assertEquals(6, simpleEntryGroup1.getSequenceLength());
196: assertEquals(1, simpleEntryGroup1.size());
197: assertEquals("", filteredEntryGroup0.getFilterName());
198: assertEquals(0, filteredEntryGroup0.refCount());
199: assertEquals(1, filteredEntryGroup0.size());
200: assertEquals(6, filteredEntryGroup0.getSequenceLength());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(1, Bases.FORWARD);
203: assertEquals(2, Bases.REVERSE);
204: assertEquals((-5), Bases.MIN_PRIORITY);
205: assertEquals(0, Bases.MEDIUM_PRIORITY);
206: assertEquals(5, Bases.MAX_PRIORITY);
207:
208: int int0 = feature0.getResidueCount(5);
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertEquals(0, int0);
212: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
213: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
214: assertEquals(0, genbankStreamSequence0.getOtherCount());
215: assertEquals(0, genbankStreamSequence0.getTCount());
216: assertEquals(0, genbankStreamSequence0.length());
217: assertNull(genbankStreamSequence0.getHeader());
218: assertEquals(2, genbankStreamSequence0.getFormatType());
219: assertEquals(0, genbankStreamSequence0.getCCount());
220: assertEquals(0, genbankStreamSequence0.getACount());
221: assertEquals(0, genbankStreamSequence0.getGCount());
222: assertEquals(0, bases0.getLength());
223: assertEquals(0, simpleEntryGroup0.size());
224: assertEquals(0, simpleEntryGroup0.getSequenceLength());
225: assertEquals(0, simpleEntryGroup0.refCount());
226: assertEquals(5, range0.getEnd());
227: assertEquals(0, range0.getStart());
228: assertEquals(6, range0.getCount());
229: assertEquals(0, simpleEntryGroup1.refCount());
230: assertEquals(6, simpleEntryGroup1.getSequenceLength());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals("", filteredEntryGroup0.getFilterName());
233: assertEquals(0, filteredEntryGroup0.refCount());
234: assertEquals(1, filteredEntryGroup0.size());
235: assertEquals(6, filteredEntryGroup0.getSequenceLength());
236: assertFalse(feature0.isReadOnly());
237: assertEquals(1, Bases.FORWARD);
238: assertEquals(2, Bases.REVERSE);
239: assertEquals((-5), Bases.MIN_PRIORITY);
240: assertEquals(0, Bases.MEDIUM_PRIORITY);
241: assertEquals(5, Bases.MAX_PRIORITY);
Test case 90
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("");
2: assertNotNull(genbankStreamSequence0);
3: assertNull(genbankStreamSequence0.getHeader());
4: assertEquals(0, genbankStreamSequence0.length());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(2, genbankStreamSequence0.getFormatType());
7: assertEquals(0, genbankStreamSequence0.getOtherCount());
8: assertEquals(0, genbankStreamSequence0.getGCount());
9: assertEquals(0, genbankStreamSequence0.getACount());
10: assertEquals(0, genbankStreamSequence0.getCCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertNull(genbankStreamSequence0.getHeader());
15: assertEquals(0, genbankStreamSequence0.length());
16: assertEquals(0, genbankStreamSequence0.getTCount());
17: assertEquals(2, genbankStreamSequence0.getFormatType());
18: assertEquals(0, genbankStreamSequence0.getOtherCount());
19: assertEquals(0, genbankStreamSequence0.getGCount());
20: assertEquals(0, genbankStreamSequence0.getACount());
21: assertEquals(0, genbankStreamSequence0.getCCount());
22: assertEquals(0, bases0.getLength());
23: assertEquals(2, Bases.REVERSE);
24: assertEquals(0, Bases.MEDIUM_PRIORITY);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals((-5), Bases.MIN_PRIORITY);
28:
29: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
30: assertNotNull(simpleEntryGroup0);
31: assertNull(genbankStreamSequence0.getHeader());
32: assertEquals(0, genbankStreamSequence0.length());
33: assertEquals(0, genbankStreamSequence0.getTCount());
34: assertEquals(2, genbankStreamSequence0.getFormatType());
35: assertEquals(0, genbankStreamSequence0.getOtherCount());
36: assertEquals(0, genbankStreamSequence0.getGCount());
37: assertEquals(0, genbankStreamSequence0.getACount());
38: assertEquals(0, genbankStreamSequence0.getCCount());
39: assertEquals(0, bases0.getLength());
40: assertEquals(0, simpleEntryGroup0.size());
41: assertEquals(0, simpleEntryGroup0.refCount());
42: assertEquals(0, simpleEntryGroup0.getSequenceLength());
43: assertEquals(2, Bases.REVERSE);
44: assertEquals(0, Bases.MEDIUM_PRIORITY);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(1, Bases.FORWARD);
47: assertEquals((-5), Bases.MIN_PRIORITY);
48:
49: Range range0 = new Range(0, 5);
50: assertNotNull(range0);
51: assertEquals(0, range0.getStart());
52: assertEquals(5, range0.getEnd());
53: assertEquals(6, range0.getCount());
54:
55: SimpleEntryGroup simpleEntryGroup1 = (SimpleEntryGroup)simpleEntryGroup0.truncate(range0);
56: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
57: assertNotNull(simpleEntryGroup1);
58: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
59: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
60: assertNull(genbankStreamSequence0.getHeader());
61: assertEquals(0, genbankStreamSequence0.length());
62: assertEquals(0, genbankStreamSequence0.getTCount());
63: assertEquals(2, genbankStreamSequence0.getFormatType());
64: assertEquals(0, genbankStreamSequence0.getOtherCount());
65: assertEquals(0, genbankStreamSequence0.getGCount());
66: assertEquals(0, genbankStreamSequence0.getACount());
67: assertEquals(0, genbankStreamSequence0.getCCount());
68: assertEquals(0, bases0.getLength());
69: assertEquals(0, simpleEntryGroup0.size());
70: assertEquals(0, simpleEntryGroup0.refCount());
71: assertEquals(0, simpleEntryGroup0.getSequenceLength());
72: assertEquals(0, range0.getStart());
73: assertEquals(5, range0.getEnd());
74: assertEquals(6, range0.getCount());
75: assertEquals(0, simpleEntryGroup1.refCount());
76: assertEquals(6, simpleEntryGroup1.getSequenceLength());
77: assertEquals(0, simpleEntryGroup1.size());
78: assertEquals(2, Bases.REVERSE);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(5, Bases.MAX_PRIORITY);
81: assertEquals(1, Bases.FORWARD);
82: assertEquals((-5), Bases.MIN_PRIORITY);
83:
84: FeatureVector featureVector0 = simpleEntryGroup0.getAllFeatures();
85: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
86: assertNotNull(featureVector0);
87: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
88: assertNull(genbankStreamSequence0.getHeader());
89: assertEquals(0, genbankStreamSequence0.length());
90: assertEquals(0, genbankStreamSequence0.getTCount());
91: assertEquals(2, genbankStreamSequence0.getFormatType());
92: assertEquals(0, genbankStreamSequence0.getOtherCount());
93: assertEquals(0, genbankStreamSequence0.getGCount());
94: assertEquals(0, genbankStreamSequence0.getACount());
95: assertEquals(0, genbankStreamSequence0.getCCount());
96: assertEquals(0, bases0.getLength());
97: assertEquals(0, simpleEntryGroup0.size());
98: assertEquals(0, simpleEntryGroup0.refCount());
99: assertEquals(0, simpleEntryGroup0.getSequenceLength());
100: assertEquals(2, Bases.REVERSE);
101: assertEquals(0, Bases.MEDIUM_PRIORITY);
102: assertEquals(5, Bases.MAX_PRIORITY);
103: assertEquals(1, Bases.FORWARD);
104: assertEquals((-5), Bases.MIN_PRIORITY);
105:
106: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup1, featureVector0, "aJ$ihh/1|\"DH{1#<J.4");
107: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
108: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
109: assertNotNull(filteredEntryGroup0);
110: assertNull(genbankStreamSequence0.getHeader());
111: assertEquals(0, genbankStreamSequence0.length());
112: assertEquals(0, genbankStreamSequence0.getTCount());
113: assertEquals(2, genbankStreamSequence0.getFormatType());
114: assertEquals(0, genbankStreamSequence0.getOtherCount());
115: assertEquals(0, genbankStreamSequence0.getGCount());
116: assertEquals(0, genbankStreamSequence0.getACount());
117: assertEquals(0, genbankStreamSequence0.getCCount());
118: assertEquals(0, bases0.getLength());
119: assertEquals(0, simpleEntryGroup0.size());
120: assertEquals(0, simpleEntryGroup0.refCount());
121: assertEquals(0, simpleEntryGroup0.getSequenceLength());
122: assertEquals(0, range0.getStart());
123: assertEquals(5, range0.getEnd());
124: assertEquals(6, range0.getCount());
125: assertEquals(0, simpleEntryGroup1.refCount());
126: assertEquals(6, simpleEntryGroup1.getSequenceLength());
127: assertEquals(0, simpleEntryGroup1.size());
128: assertEquals(0, filteredEntryGroup0.size());
129: assertEquals(0, filteredEntryGroup0.refCount());
130: assertEquals(6, filteredEntryGroup0.getSequenceLength());
131: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
132: assertEquals(2, Bases.REVERSE);
133: assertEquals(0, Bases.MEDIUM_PRIORITY);
134: assertEquals(5, Bases.MAX_PRIORITY);
135: assertEquals(1, Bases.FORWARD);
136: assertEquals((-5), Bases.MIN_PRIORITY);
137:
138: Entry entry0 = filteredEntryGroup0.createEntry();
139: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
140: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
141: assertNotNull(entry0);
142: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
143: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
144: assertNull(genbankStreamSequence0.getHeader());
145: assertEquals(0, genbankStreamSequence0.length());
146: assertEquals(0, genbankStreamSequence0.getTCount());
147: assertEquals(2, genbankStreamSequence0.getFormatType());
148: assertEquals(0, genbankStreamSequence0.getOtherCount());
149: assertEquals(0, genbankStreamSequence0.getGCount());
150: assertEquals(0, genbankStreamSequence0.getACount());
151: assertEquals(0, genbankStreamSequence0.getCCount());
152: assertEquals(0, bases0.getLength());
153: assertEquals(0, simpleEntryGroup0.size());
154: assertEquals(0, simpleEntryGroup0.refCount());
155: assertEquals(0, simpleEntryGroup0.getSequenceLength());
156: assertEquals(0, range0.getStart());
157: assertEquals(5, range0.getEnd());
158: assertEquals(6, range0.getCount());
159: assertEquals(0, simpleEntryGroup1.refCount());
160: assertEquals(1, simpleEntryGroup1.size());
161: assertEquals(6, simpleEntryGroup1.getSequenceLength());
162: assertEquals(0, filteredEntryGroup0.refCount());
163: assertEquals(1, filteredEntryGroup0.size());
164: assertEquals(6, filteredEntryGroup0.getSequenceLength());
165: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
166: assertFalse(entry0.isReadOnly());
167: assertEquals(2, Bases.REVERSE);
168: assertEquals(0, Bases.MEDIUM_PRIORITY);
169: assertEquals(5, Bases.MAX_PRIORITY);
170: assertEquals(1, Bases.FORWARD);
171: assertEquals((-5), Bases.MIN_PRIORITY);
172:
173: Feature feature0 = filteredEntryGroup0.createFeature();
174: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
175: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
176: assertNotNull(feature0);
177: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
178: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
179: assertNull(genbankStreamSequence0.getHeader());
180: assertEquals(0, genbankStreamSequence0.length());
181: assertEquals(0, genbankStreamSequence0.getTCount());
182: assertEquals(2, genbankStreamSequence0.getFormatType());
183: assertEquals(0, genbankStreamSequence0.getOtherCount());
184: assertEquals(0, genbankStreamSequence0.getGCount());
185: assertEquals(0, genbankStreamSequence0.getACount());
186: assertEquals(0, genbankStreamSequence0.getCCount());
187: assertEquals(0, bases0.getLength());
188: assertEquals(0, simpleEntryGroup0.size());
189: assertEquals(0, simpleEntryGroup0.refCount());
190: assertEquals(0, simpleEntryGroup0.getSequenceLength());
191: assertEquals(0, range0.getStart());
192: assertEquals(5, range0.getEnd());
193: assertEquals(6, range0.getCount());
194: assertEquals(0, simpleEntryGroup1.refCount());
195: assertEquals(1, simpleEntryGroup1.size());
196: assertEquals(6, simpleEntryGroup1.getSequenceLength());
197: assertEquals(0, filteredEntryGroup0.refCount());
198: assertEquals(1, filteredEntryGroup0.size());
199: assertEquals(6, filteredEntryGroup0.getSequenceLength());
200: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
201: assertFalse(feature0.isReadOnly());
202: assertEquals(2, Bases.REVERSE);
203: assertEquals(0, Bases.MEDIUM_PRIORITY);
204: assertEquals(5, Bases.MAX_PRIORITY);
205: assertEquals(1, Bases.FORWARD);
206: assertEquals((-5), Bases.MIN_PRIORITY);
207:
208: String string0 = feature0.getWriteRange();
209: assertFalse(simpleEntryGroup0.equals((Object)simpleEntryGroup1));
210: assertFalse(simpleEntryGroup1.equals((Object)simpleEntryGroup0));
211: assertNotNull(string0);
212: assertEquals("1:6 forward", string0);
213: assertNotSame(simpleEntryGroup0, simpleEntryGroup1);
214: assertNotSame(simpleEntryGroup1, simpleEntryGroup0);
215: assertNull(genbankStreamSequence0.getHeader());
216: assertEquals(0, genbankStreamSequence0.length());
217: assertEquals(0, genbankStreamSequence0.getTCount());
218: assertEquals(2, genbankStreamSequence0.getFormatType());
219: assertEquals(0, genbankStreamSequence0.getOtherCount());
220: assertEquals(0, genbankStreamSequence0.getGCount());
221: assertEquals(0, genbankStreamSequence0.getACount());
222: assertEquals(0, genbankStreamSequence0.getCCount());
223: assertEquals(0, bases0.getLength());
224: assertEquals(0, simpleEntryGroup0.size());
225: assertEquals(0, simpleEntryGroup0.refCount());
226: assertEquals(0, simpleEntryGroup0.getSequenceLength());
227: assertEquals(0, range0.getStart());
228: assertEquals(5, range0.getEnd());
229: assertEquals(6, range0.getCount());
230: assertEquals(0, simpleEntryGroup1.refCount());
231: assertEquals(1, simpleEntryGroup1.size());
232: assertEquals(6, simpleEntryGroup1.getSequenceLength());
233: assertEquals(0, filteredEntryGroup0.refCount());
234: assertEquals(1, filteredEntryGroup0.size());
235: assertEquals(6, filteredEntryGroup0.getSequenceLength());
236: assertEquals("aJ$ihh/1|\"DH{1#<J.4", filteredEntryGroup0.getFilterName());
237: assertFalse(feature0.isReadOnly());
238: assertEquals(2, Bases.REVERSE);
239: assertEquals(0, Bases.MEDIUM_PRIORITY);
240: assertEquals(5, Bases.MAX_PRIORITY);
241: assertEquals(1, Bases.FORWARD);
242: assertEquals((-5), Bases.MIN_PRIORITY);