Test case 1
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = bases0.getReverseStrand();
3: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
4: aGWindowAlgorithm0.getValueCount();
Test case 2
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("Joz- ^$d](\"INZS+");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
5: Float float0 = aGWindowAlgorithm0.getMaximumInternal();
6: assertEquals(100.0F, (float)float0, 0.01F);
7: assertTrue(aGWindowAlgorithm0.scalingFlag());
Test case 3
1: Short short0 = new Short((short)2953);
2: Integer integer0 = new Integer(103);
3: PartialSequence partialSequence0 = new PartialSequence((char[]) null, 0, 0, short0, integer0);
4: Bases bases0 = new Bases(partialSequence0);
5: Strand strand0 = bases0.getReverseStrand();
6: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
7: Float float0 = aGWindowAlgorithm0.getMinimumInternal();
8: assertTrue(aGWindowAlgorithm0.scalingFlag());
9: assertEquals(0.0F, (float)float0, 0.01F);
Test case 4
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("Joz- ^$d](\"INZS+");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
5: aGWindowAlgorithm0.getAverage();
6: assertTrue(aGWindowAlgorithm0.scalingFlag());
Test case 5
1: RawStreamSequence rawStreamSequence0 = new RawStreamSequence("Reverse GC Frame Plot");
2: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence(rawStreamSequence0);
3: Bases bases0 = new Bases(emblStreamSequence0);
4: Strand strand0 = bases0.getForwardStrand();
5: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
6: float[] floatArray0 = new float[3];
7: aGWindowAlgorithm0.getValues(2, 3294, floatArray0);
8: assertArrayEquals(new float[] {0.030367445F, 0.0F, 0.0F}, floatArray0, 0.01F);
9: assertTrue(aGWindowAlgorithm0.scalingFlag());
Test case 6
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("");
2: assertEquals(0, emblStreamSequence0.getGCount());
3: assertEquals(0, emblStreamSequence0.getOtherCount());
4: assertEquals(0, emblStreamSequence0.getACount());
5: assertEquals(0, emblStreamSequence0.getCCount());
6: assertEquals(0, emblStreamSequence0.length());
7: assertNull(emblStreamSequence0.getHeader());
8: assertEquals(1, emblStreamSequence0.getFormatType());
9: assertEquals(0, emblStreamSequence0.getTCount());
10: assertNotNull(emblStreamSequence0);
11:
12: Bases bases0 = new Bases(emblStreamSequence0);
13: assertEquals(0, emblStreamSequence0.getGCount());
14: assertEquals(0, emblStreamSequence0.getOtherCount());
15: assertEquals(0, emblStreamSequence0.getACount());
16: assertEquals(0, emblStreamSequence0.getCCount());
17: assertEquals(0, emblStreamSequence0.length());
18: assertNull(emblStreamSequence0.getHeader());
19: assertEquals(1, emblStreamSequence0.getFormatType());
20: assertEquals(0, emblStreamSequence0.getTCount());
21: assertNotNull(bases0);
22: assertEquals((-5), Bases.MIN_PRIORITY);
23: assertEquals(0, Bases.MEDIUM_PRIORITY);
24: assertEquals(2, Bases.REVERSE);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27:
28: Strand strand0 = bases0.getReverseStrand();
29: assertEquals(0, emblStreamSequence0.getGCount());
30: assertEquals(0, emblStreamSequence0.getOtherCount());
31: assertEquals(0, emblStreamSequence0.getACount());
32: assertEquals(0, emblStreamSequence0.getCCount());
33: assertEquals(0, emblStreamSequence0.length());
34: assertNull(emblStreamSequence0.getHeader());
35: assertEquals(1, emblStreamSequence0.getFormatType());
36: assertEquals(0, emblStreamSequence0.getTCount());
37: assertFalse(strand0.isForwardStrand());
38: assertEquals(2, strand0.getDirection());
39: assertNotNull(strand0);
40: assertEquals((-5), Bases.MIN_PRIORITY);
41: assertEquals(0, Bases.MEDIUM_PRIORITY);
42: assertEquals(2, Bases.REVERSE);
43: assertEquals(5, Bases.MAX_PRIORITY);
44: assertEquals(1, Bases.FORWARD);
45: assertEquals(2, Strand.REVERSE);
46: assertEquals(1, Strand.FORWARD);
47:
48: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
49: assertEquals(0, emblStreamSequence0.getGCount());
50: assertEquals(0, emblStreamSequence0.getOtherCount());
51: assertEquals(0, emblStreamSequence0.getACount());
52: assertEquals(0, emblStreamSequence0.getCCount());
53: assertEquals(0, emblStreamSequence0.length());
54: assertNull(emblStreamSequence0.getHeader());
55: assertEquals(1, emblStreamSequence0.getFormatType());
56: assertEquals(0, emblStreamSequence0.getTCount());
57: assertFalse(strand0.isForwardStrand());
58: assertEquals(2, strand0.getDirection());
59: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
60: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
61: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
62: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
63: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
64: assertTrue(aGWindowAlgorithm0.scalingFlag());
65: assertEquals(1, aGWindowAlgorithm0.getValueCount());
66: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
67: assertNotNull(aGWindowAlgorithm0);
68: assertEquals((-5), Bases.MIN_PRIORITY);
69: assertEquals(0, Bases.MEDIUM_PRIORITY);
70: assertEquals(2, Bases.REVERSE);
71: assertEquals(5, Bases.MAX_PRIORITY);
72: assertEquals(1, Bases.FORWARD);
73: assertEquals(2, Strand.REVERSE);
74: assertEquals(1, Strand.FORWARD);
75:
76: Integer integer0 = aGWindowAlgorithm0.getDefaultWindowSize();
77: assertEquals(0, emblStreamSequence0.getGCount());
78: assertEquals(0, emblStreamSequence0.getOtherCount());
79: assertEquals(0, emblStreamSequence0.getACount());
80: assertEquals(0, emblStreamSequence0.getCCount());
81: assertEquals(0, emblStreamSequence0.length());
82: assertNull(emblStreamSequence0.getHeader());
83: assertEquals(1, emblStreamSequence0.getFormatType());
84: assertEquals(0, emblStreamSequence0.getTCount());
85: assertFalse(strand0.isForwardStrand());
86: assertEquals(2, strand0.getDirection());
87: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
88: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
89: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
90: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
91: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
92: assertTrue(aGWindowAlgorithm0.scalingFlag());
93: assertEquals(1, aGWindowAlgorithm0.getValueCount());
94: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
95: assertNotNull(integer0);
96: assertEquals(120, (int)integer0);
97: assertEquals((-5), Bases.MIN_PRIORITY);
98: assertEquals(0, Bases.MEDIUM_PRIORITY);
99: assertEquals(2, Bases.REVERSE);
100: assertEquals(5, Bases.MAX_PRIORITY);
101: assertEquals(1, Bases.FORWARD);
102: assertEquals(2, Strand.REVERSE);
103: assertEquals(1, Strand.FORWARD);
Test case 7
1: RawStreamSequence rawStreamSequence0 = new RawStreamSequence("Cannot find the 'token' Tokenization for RNA!?");
2: assertEquals(4, rawStreamSequence0.getTCount());
3: assertEquals(46, rawStreamSequence0.length());
4: assertEquals(40, rawStreamSequence0.getOtherCount());
5: assertEquals(2, rawStreamSequence0.getACount());
6: assertEquals(0, rawStreamSequence0.getGCount());
7: assertEquals(0, rawStreamSequence0.getCCount());
8: assertEquals(3, rawStreamSequence0.getFormatType());
9: assertNotNull(rawStreamSequence0);
10:
11: Bases bases0 = new Bases(rawStreamSequence0);
12: assertEquals(4, rawStreamSequence0.getTCount());
13: assertEquals(46, rawStreamSequence0.length());
14: assertEquals(40, rawStreamSequence0.getOtherCount());
15: assertEquals(2, rawStreamSequence0.getACount());
16: assertEquals(0, rawStreamSequence0.getGCount());
17: assertEquals(0, rawStreamSequence0.getCCount());
18: assertEquals(3, rawStreamSequence0.getFormatType());
19: assertNotNull(bases0);
20: assertEquals((-5), Bases.MIN_PRIORITY);
21: assertEquals(0, Bases.MEDIUM_PRIORITY);
22: assertEquals(2, Bases.REVERSE);
23: assertEquals(1, Bases.FORWARD);
24: assertEquals(5, Bases.MAX_PRIORITY);
25:
26: Strand strand0 = bases0.getReverseStrand();
27: assertEquals(4, rawStreamSequence0.getTCount());
28: assertEquals(46, rawStreamSequence0.length());
29: assertEquals(40, rawStreamSequence0.getOtherCount());
30: assertEquals(2, rawStreamSequence0.getACount());
31: assertEquals(0, rawStreamSequence0.getGCount());
32: assertEquals(0, rawStreamSequence0.getCCount());
33: assertEquals(3, rawStreamSequence0.getFormatType());
34: assertEquals(2, strand0.getDirection());
35: assertFalse(strand0.isForwardStrand());
36: assertNotNull(strand0);
37: assertEquals((-5), Bases.MIN_PRIORITY);
38: assertEquals(0, Bases.MEDIUM_PRIORITY);
39: assertEquals(2, Bases.REVERSE);
40: assertEquals(1, Bases.FORWARD);
41: assertEquals(5, Bases.MAX_PRIORITY);
42: assertEquals(2, Strand.REVERSE);
43: assertEquals(1, Strand.FORWARD);
44:
45: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
46: assertEquals(4, rawStreamSequence0.getTCount());
47: assertEquals(46, rawStreamSequence0.length());
48: assertEquals(40, rawStreamSequence0.getOtherCount());
49: assertEquals(2, rawStreamSequence0.getACount());
50: assertEquals(0, rawStreamSequence0.getGCount());
51: assertEquals(0, rawStreamSequence0.getCCount());
52: assertEquals(3, rawStreamSequence0.getFormatType());
53: assertEquals(2, strand0.getDirection());
54: assertFalse(strand0.isForwardStrand());
55: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
56: assertEquals(1, aGWindowAlgorithm0.getValueCount());
57: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
58: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
59: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
60: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
61: assertTrue(aGWindowAlgorithm0.scalingFlag());
62: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
63: assertNotNull(aGWindowAlgorithm0);
64: assertEquals((-5), Bases.MIN_PRIORITY);
65: assertEquals(0, Bases.MEDIUM_PRIORITY);
66: assertEquals(2, Bases.REVERSE);
67: assertEquals(1, Bases.FORWARD);
68: assertEquals(5, Bases.MAX_PRIORITY);
69: assertEquals(2, Strand.REVERSE);
70: assertEquals(1, Strand.FORWARD);
71:
72: Integer integer0 = aGWindowAlgorithm0.getDefaultMaxWindowSize();
73: assertEquals(4, rawStreamSequence0.getTCount());
74: assertEquals(46, rawStreamSequence0.length());
75: assertEquals(40, rawStreamSequence0.getOtherCount());
76: assertEquals(2, rawStreamSequence0.getACount());
77: assertEquals(0, rawStreamSequence0.getGCount());
78: assertEquals(0, rawStreamSequence0.getCCount());
79: assertEquals(3, rawStreamSequence0.getFormatType());
80: assertEquals(2, strand0.getDirection());
81: assertFalse(strand0.isForwardStrand());
82: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
83: assertEquals(1, aGWindowAlgorithm0.getValueCount());
84: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
85: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
86: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
87: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
88: assertTrue(aGWindowAlgorithm0.scalingFlag());
89: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
90: assertNotNull(integer0);
91: assertEquals(500, (int)integer0);
92: assertEquals((-5), Bases.MIN_PRIORITY);
93: assertEquals(0, Bases.MEDIUM_PRIORITY);
94: assertEquals(2, Bases.REVERSE);
95: assertEquals(1, Bases.FORWARD);
96: assertEquals(5, Bases.MAX_PRIORITY);
97: assertEquals(2, Strand.REVERSE);
98: assertEquals(1, Strand.FORWARD);
Test case 8
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("Joz- ^$d](\"INZS+");
2: assertEquals(0, fastaStreamSequence0.getCCount());
3: assertEquals(4, fastaStreamSequence0.getFormatType());
4: assertEquals(0, fastaStreamSequence0.getGCount());
5: assertEquals(0, fastaStreamSequence0.getACount());
6: assertEquals(16, fastaStreamSequence0.getOtherCount());
7: assertEquals(0, fastaStreamSequence0.getTCount());
8: assertEquals(16, fastaStreamSequence0.length());
9: assertNotNull(fastaStreamSequence0);
10:
11: Bases bases0 = new Bases(fastaStreamSequence0);
12: assertEquals(0, fastaStreamSequence0.getCCount());
13: assertEquals(4, fastaStreamSequence0.getFormatType());
14: assertEquals(0, fastaStreamSequence0.getGCount());
15: assertEquals(0, fastaStreamSequence0.getACount());
16: assertEquals(16, fastaStreamSequence0.getOtherCount());
17: assertEquals(0, fastaStreamSequence0.getTCount());
18: assertEquals(16, fastaStreamSequence0.length());
19: assertNotNull(bases0);
20: assertEquals((-5), Bases.MIN_PRIORITY);
21: assertEquals(0, Bases.MEDIUM_PRIORITY);
22: assertEquals(1, Bases.FORWARD);
23: assertEquals(5, Bases.MAX_PRIORITY);
24: assertEquals(2, Bases.REVERSE);
25:
26: Strand strand0 = bases0.getForwardStrand();
27: assertEquals(0, fastaStreamSequence0.getCCount());
28: assertEquals(4, fastaStreamSequence0.getFormatType());
29: assertEquals(0, fastaStreamSequence0.getGCount());
30: assertEquals(0, fastaStreamSequence0.getACount());
31: assertEquals(16, fastaStreamSequence0.getOtherCount());
32: assertEquals(0, fastaStreamSequence0.getTCount());
33: assertEquals(16, fastaStreamSequence0.length());
34: assertTrue(strand0.isForwardStrand());
35: assertEquals(1, strand0.getDirection());
36: assertNotNull(strand0);
37: assertEquals((-5), Bases.MIN_PRIORITY);
38: assertEquals(0, Bases.MEDIUM_PRIORITY);
39: assertEquals(1, Bases.FORWARD);
40: assertEquals(5, Bases.MAX_PRIORITY);
41: assertEquals(2, Bases.REVERSE);
42: assertEquals(1, Strand.FORWARD);
43: assertEquals(2, Strand.REVERSE);
44:
45: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
46: assertEquals(0, fastaStreamSequence0.getCCount());
47: assertEquals(4, fastaStreamSequence0.getFormatType());
48: assertEquals(0, fastaStreamSequence0.getGCount());
49: assertEquals(0, fastaStreamSequence0.getACount());
50: assertEquals(16, fastaStreamSequence0.getOtherCount());
51: assertEquals(0, fastaStreamSequence0.getTCount());
52: assertEquals(16, fastaStreamSequence0.length());
53: assertTrue(strand0.isForwardStrand());
54: assertEquals(1, strand0.getDirection());
55: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
56: assertTrue(aGWindowAlgorithm0.scalingFlag());
57: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
58: assertEquals(1, aGWindowAlgorithm0.getValueCount());
59: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
60: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
61: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
62: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
63: assertNotNull(aGWindowAlgorithm0);
64: assertEquals((-5), Bases.MIN_PRIORITY);
65: assertEquals(0, Bases.MEDIUM_PRIORITY);
66: assertEquals(1, Bases.FORWARD);
67: assertEquals(5, Bases.MAX_PRIORITY);
68: assertEquals(2, Bases.REVERSE);
69: assertEquals(1, Strand.FORWARD);
70: assertEquals(2, Strand.REVERSE);
71:
72: Integer integer0 = aGWindowAlgorithm0.getDefaultMinWindowSize();
73: assertEquals(0, fastaStreamSequence0.getCCount());
74: assertEquals(4, fastaStreamSequence0.getFormatType());
75: assertEquals(0, fastaStreamSequence0.getGCount());
76: assertEquals(0, fastaStreamSequence0.getACount());
77: assertEquals(16, fastaStreamSequence0.getOtherCount());
78: assertEquals(0, fastaStreamSequence0.getTCount());
79: assertEquals(16, fastaStreamSequence0.length());
80: assertTrue(strand0.isForwardStrand());
81: assertEquals(1, strand0.getDirection());
82: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
83: assertTrue(aGWindowAlgorithm0.scalingFlag());
84: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
85: assertEquals(1, aGWindowAlgorithm0.getValueCount());
86: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
87: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
88: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
89: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
90: assertNotNull(integer0);
91: assertEquals(24, (int)integer0);
92: assertEquals((-5), Bases.MIN_PRIORITY);
93: assertEquals(0, Bases.MEDIUM_PRIORITY);
94: assertEquals(1, Bases.FORWARD);
95: assertEquals(5, Bases.MAX_PRIORITY);
96: assertEquals(2, Bases.REVERSE);
97: assertEquals(1, Strand.FORWARD);
98: assertEquals(2, Strand.REVERSE);
Test case 9
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("Joz- ^$d](\"INZS+");
2: assertEquals(4, fastaStreamSequence0.getFormatType());
3: assertEquals(0, fastaStreamSequence0.getACount());
4: assertEquals(0, fastaStreamSequence0.getCCount());
5: assertEquals(0, fastaStreamSequence0.getTCount());
6: assertEquals(16, fastaStreamSequence0.length());
7: assertEquals(16, fastaStreamSequence0.getOtherCount());
8: assertEquals(0, fastaStreamSequence0.getGCount());
9: assertNotNull(fastaStreamSequence0);
10:
11: Bases bases0 = new Bases(fastaStreamSequence0);
12: assertEquals(4, fastaStreamSequence0.getFormatType());
13: assertEquals(0, fastaStreamSequence0.getACount());
14: assertEquals(0, fastaStreamSequence0.getCCount());
15: assertEquals(0, fastaStreamSequence0.getTCount());
16: assertEquals(16, fastaStreamSequence0.length());
17: assertEquals(16, fastaStreamSequence0.getOtherCount());
18: assertEquals(0, fastaStreamSequence0.getGCount());
19: assertNotNull(bases0);
20: assertEquals(1, Bases.FORWARD);
21: assertEquals(2, Bases.REVERSE);
22: assertEquals((-5), Bases.MIN_PRIORITY);
23: assertEquals(0, Bases.MEDIUM_PRIORITY);
24: assertEquals(5, Bases.MAX_PRIORITY);
25:
26: Strand strand0 = bases0.getForwardStrand();
27: assertEquals(4, fastaStreamSequence0.getFormatType());
28: assertEquals(0, fastaStreamSequence0.getACount());
29: assertEquals(0, fastaStreamSequence0.getCCount());
30: assertEquals(0, fastaStreamSequence0.getTCount());
31: assertEquals(16, fastaStreamSequence0.length());
32: assertEquals(16, fastaStreamSequence0.getOtherCount());
33: assertEquals(0, fastaStreamSequence0.getGCount());
34: assertEquals(1, strand0.getDirection());
35: assertTrue(strand0.isForwardStrand());
36: assertNotNull(strand0);
37: assertEquals(1, Bases.FORWARD);
38: assertEquals(2, Bases.REVERSE);
39: assertEquals((-5), Bases.MIN_PRIORITY);
40: assertEquals(0, Bases.MEDIUM_PRIORITY);
41: assertEquals(5, Bases.MAX_PRIORITY);
42: assertEquals(2, Strand.REVERSE);
43: assertEquals(1, Strand.FORWARD);
44:
45: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
46: assertEquals(4, fastaStreamSequence0.getFormatType());
47: assertEquals(0, fastaStreamSequence0.getACount());
48: assertEquals(0, fastaStreamSequence0.getCCount());
49: assertEquals(0, fastaStreamSequence0.getTCount());
50: assertEquals(16, fastaStreamSequence0.length());
51: assertEquals(16, fastaStreamSequence0.getOtherCount());
52: assertEquals(0, fastaStreamSequence0.getGCount());
53: assertEquals(1, strand0.getDirection());
54: assertTrue(strand0.isForwardStrand());
55: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
56: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
57: assertTrue(aGWindowAlgorithm0.scalingFlag());
58: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
59: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
60: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
61: assertEquals(1, aGWindowAlgorithm0.getValueCount());
62: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
63: assertNotNull(aGWindowAlgorithm0);
64: assertEquals(1, Bases.FORWARD);
65: assertEquals(2, Bases.REVERSE);
66: assertEquals((-5), Bases.MIN_PRIORITY);
67: assertEquals(0, Bases.MEDIUM_PRIORITY);
68: assertEquals(5, Bases.MAX_PRIORITY);
69: assertEquals(2, Strand.REVERSE);
70: assertEquals(1, Strand.FORWARD);
71:
72: Integer integer0 = aGWindowAlgorithm0.getDefaultStepSize(0);
73: assertEquals(4, fastaStreamSequence0.getFormatType());
74: assertEquals(0, fastaStreamSequence0.getACount());
75: assertEquals(0, fastaStreamSequence0.getCCount());
76: assertEquals(0, fastaStreamSequence0.getTCount());
77: assertEquals(16, fastaStreamSequence0.length());
78: assertEquals(16, fastaStreamSequence0.getOtherCount());
79: assertEquals(0, fastaStreamSequence0.getGCount());
80: assertEquals(1, strand0.getDirection());
81: assertTrue(strand0.isForwardStrand());
82: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
83: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
84: assertTrue(aGWindowAlgorithm0.scalingFlag());
85: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
86: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
87: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
88: assertEquals(1, aGWindowAlgorithm0.getValueCount());
89: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
90: assertNull(integer0);
91: assertEquals(1, Bases.FORWARD);
92: assertEquals(2, Bases.REVERSE);
93: assertEquals((-5), Bases.MIN_PRIORITY);
94: assertEquals(0, Bases.MEDIUM_PRIORITY);
95: assertEquals(5, Bases.MAX_PRIORITY);
96: assertEquals(2, Strand.REVERSE);
97: assertEquals(1, Strand.FORWARD);
Test case 10
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("Joz- ^$d]-(\"INZS+");
2: assertEquals(4, fastaStreamSequence0.getFormatType());
3: assertEquals(17, fastaStreamSequence0.length());
4: assertEquals(0, fastaStreamSequence0.getACount());
5: assertEquals(0, fastaStreamSequence0.getCCount());
6: assertEquals(0, fastaStreamSequence0.getTCount());
7: assertEquals(0, fastaStreamSequence0.getGCount());
8: assertEquals(17, fastaStreamSequence0.getOtherCount());
9: assertNotNull(fastaStreamSequence0);
10:
11: Bases bases0 = new Bases(fastaStreamSequence0);
12: assertEquals(4, fastaStreamSequence0.getFormatType());
13: assertEquals(17, fastaStreamSequence0.length());
14: assertEquals(0, fastaStreamSequence0.getACount());
15: assertEquals(0, fastaStreamSequence0.getCCount());
16: assertEquals(0, fastaStreamSequence0.getTCount());
17: assertEquals(0, fastaStreamSequence0.getGCount());
18: assertEquals(17, fastaStreamSequence0.getOtherCount());
19: assertNotNull(bases0);
20: assertEquals((-5), Bases.MIN_PRIORITY);
21: assertEquals(0, Bases.MEDIUM_PRIORITY);
22: assertEquals(5, Bases.MAX_PRIORITY);
23: assertEquals(1, Bases.FORWARD);
24: assertEquals(2, Bases.REVERSE);
25:
26: Strand strand0 = bases0.getForwardStrand();
27: assertEquals(4, fastaStreamSequence0.getFormatType());
28: assertEquals(17, fastaStreamSequence0.length());
29: assertEquals(0, fastaStreamSequence0.getACount());
30: assertEquals(0, fastaStreamSequence0.getCCount());
31: assertEquals(0, fastaStreamSequence0.getTCount());
32: assertEquals(0, fastaStreamSequence0.getGCount());
33: assertEquals(17, fastaStreamSequence0.getOtherCount());
34: assertTrue(strand0.isForwardStrand());
35: assertEquals(1, strand0.getDirection());
36: assertNotNull(strand0);
37: assertEquals((-5), Bases.MIN_PRIORITY);
38: assertEquals(0, Bases.MEDIUM_PRIORITY);
39: assertEquals(5, Bases.MAX_PRIORITY);
40: assertEquals(1, Bases.FORWARD);
41: assertEquals(2, Bases.REVERSE);
42: assertEquals(2, Strand.REVERSE);
43: assertEquals(1, Strand.FORWARD);
44:
45: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
46: assertEquals(4, fastaStreamSequence0.getFormatType());
47: assertEquals(17, fastaStreamSequence0.length());
48: assertEquals(0, fastaStreamSequence0.getACount());
49: assertEquals(0, fastaStreamSequence0.getCCount());
50: assertEquals(0, fastaStreamSequence0.getTCount());
51: assertEquals(0, fastaStreamSequence0.getGCount());
52: assertEquals(17, fastaStreamSequence0.getOtherCount());
53: assertTrue(strand0.isForwardStrand());
54: assertEquals(1, strand0.getDirection());
55: assertEquals(1, aGWindowAlgorithm0.getValueCount());
56: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
57: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
58: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
59: assertTrue(aGWindowAlgorithm0.scalingFlag());
60: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
61: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
62: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
63: assertNotNull(aGWindowAlgorithm0);
64: assertEquals((-5), Bases.MIN_PRIORITY);
65: assertEquals(0, Bases.MEDIUM_PRIORITY);
66: assertEquals(5, Bases.MAX_PRIORITY);
67: assertEquals(1, Bases.FORWARD);
68: assertEquals(2, Bases.REVERSE);
69: assertEquals(2, Strand.REVERSE);
70: assertEquals(1, Strand.FORWARD);
71:
72: Integer integer0 = aGWindowAlgorithm0.getDefaultStepSize(78);
73: assertEquals(4, fastaStreamSequence0.getFormatType());
74: assertEquals(17, fastaStreamSequence0.length());
75: assertEquals(0, fastaStreamSequence0.getACount());
76: assertEquals(0, fastaStreamSequence0.getCCount());
77: assertEquals(0, fastaStreamSequence0.getTCount());
78: assertEquals(0, fastaStreamSequence0.getGCount());
79: assertEquals(17, fastaStreamSequence0.getOtherCount());
80: assertTrue(strand0.isForwardStrand());
81: assertEquals(1, strand0.getDirection());
82: assertEquals(1, aGWindowAlgorithm0.getValueCount());
83: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
84: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
85: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
86: assertTrue(aGWindowAlgorithm0.scalingFlag());
87: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
88: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
89: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
90: assertNotNull(integer0);
91: assertEquals(7, (int)integer0);
92: assertEquals((-5), Bases.MIN_PRIORITY);
93: assertEquals(0, Bases.MEDIUM_PRIORITY);
94: assertEquals(5, Bases.MAX_PRIORITY);
95: assertEquals(1, Bases.FORWARD);
96: assertEquals(2, Bases.REVERSE);
97: assertEquals(2, Strand.REVERSE);
98: assertEquals(1, Strand.FORWARD);
Test case 11
1: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm((Strand) null);
Test case 12
1: Bases bases0 = new Bases((Sequence) null);
2: assertNotNull(bases0);
3: assertEquals(1, Bases.FORWARD);
4: assertEquals(0, Bases.MEDIUM_PRIORITY);
5: assertEquals(5, Bases.MAX_PRIORITY);
6: assertEquals((-5), Bases.MIN_PRIORITY);
7: assertEquals(2, Bases.REVERSE);
8:
9: Strand strand0 = bases0.getReverseStrand();
10: assertEquals(2, strand0.getDirection());
11: assertFalse(strand0.isForwardStrand());
12: assertNotNull(strand0);
13: assertEquals(1, Bases.FORWARD);
14: assertEquals(0, Bases.MEDIUM_PRIORITY);
15: assertEquals(5, Bases.MAX_PRIORITY);
16: assertEquals((-5), Bases.MIN_PRIORITY);
17: assertEquals(2, Bases.REVERSE);
18: assertEquals(2, Strand.REVERSE);
19: assertEquals(1, Strand.FORWARD);
20:
21: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
22: assertEquals(2, strand0.getDirection());
23: assertFalse(strand0.isForwardStrand());
24: assertEquals(1, aGWindowAlgorithm0.getValueCount());
25: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
26: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
27: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
28: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
29: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
30: assertTrue(aGWindowAlgorithm0.scalingFlag());
31: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
32: assertNotNull(aGWindowAlgorithm0);
33: assertEquals(1, Bases.FORWARD);
34: assertEquals(0, Bases.MEDIUM_PRIORITY);
35: assertEquals(5, Bases.MAX_PRIORITY);
36: assertEquals((-5), Bases.MIN_PRIORITY);
37: assertEquals(2, Bases.REVERSE);
38: assertEquals(2, Strand.REVERSE);
39: assertEquals(1, Strand.FORWARD);
40:
41: aGWindowAlgorithm0.getAverage();
Test case 13
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("j^Phtr2iwDtYs");
2: assertEquals(11, emblStreamSequence0.getOtherCount());
3: assertEquals(0, emblStreamSequence0.getCCount());
4: assertNull(emblStreamSequence0.getHeader());
5: assertEquals(2, emblStreamSequence0.getTCount());
6: assertEquals(13, emblStreamSequence0.length());
7: assertEquals(1, emblStreamSequence0.getFormatType());
8: assertEquals(0, emblStreamSequence0.getGCount());
9: assertEquals(0, emblStreamSequence0.getACount());
10: assertNotNull(emblStreamSequence0);
11:
12: Bases bases0 = new Bases(emblStreamSequence0);
13: assertEquals(11, emblStreamSequence0.getOtherCount());
14: assertEquals(0, emblStreamSequence0.getCCount());
15: assertNull(emblStreamSequence0.getHeader());
16: assertEquals(2, emblStreamSequence0.getTCount());
17: assertEquals(13, emblStreamSequence0.length());
18: assertEquals(1, emblStreamSequence0.getFormatType());
19: assertEquals(0, emblStreamSequence0.getGCount());
20: assertEquals(0, emblStreamSequence0.getACount());
21: assertNotNull(bases0);
22: assertEquals(2, Bases.REVERSE);
23: assertEquals(0, Bases.MEDIUM_PRIORITY);
24: assertEquals(5, Bases.MAX_PRIORITY);
25: assertEquals((-5), Bases.MIN_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27:
28: Strand strand0 = bases0.getForwardStrand();
29: assertEquals(11, emblStreamSequence0.getOtherCount());
30: assertEquals(0, emblStreamSequence0.getCCount());
31: assertNull(emblStreamSequence0.getHeader());
32: assertEquals(2, emblStreamSequence0.getTCount());
33: assertEquals(13, emblStreamSequence0.length());
34: assertEquals(1, emblStreamSequence0.getFormatType());
35: assertEquals(0, emblStreamSequence0.getGCount());
36: assertEquals(0, emblStreamSequence0.getACount());
37: assertEquals(1, strand0.getDirection());
38: assertTrue(strand0.isForwardStrand());
39: assertNotNull(strand0);
40: assertEquals(2, Bases.REVERSE);
41: assertEquals(0, Bases.MEDIUM_PRIORITY);
42: assertEquals(5, Bases.MAX_PRIORITY);
43: assertEquals((-5), Bases.MIN_PRIORITY);
44: assertEquals(1, Bases.FORWARD);
45: assertEquals(1, Strand.FORWARD);
46: assertEquals(2, Strand.REVERSE);
47:
48: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
49: assertEquals(11, emblStreamSequence0.getOtherCount());
50: assertEquals(0, emblStreamSequence0.getCCount());
51: assertNull(emblStreamSequence0.getHeader());
52: assertEquals(2, emblStreamSequence0.getTCount());
53: assertEquals(13, emblStreamSequence0.length());
54: assertEquals(1, emblStreamSequence0.getFormatType());
55: assertEquals(0, emblStreamSequence0.getGCount());
56: assertEquals(0, emblStreamSequence0.getACount());
57: assertEquals(1, strand0.getDirection());
58: assertTrue(strand0.isForwardStrand());
59: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
60: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
61: assertTrue(aGWindowAlgorithm0.scalingFlag());
62: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
63: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
64: assertEquals(1, aGWindowAlgorithm0.getValueCount());
65: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
66: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
67: assertNotNull(aGWindowAlgorithm0);
68: assertEquals(2, Bases.REVERSE);
69: assertEquals(0, Bases.MEDIUM_PRIORITY);
70: assertEquals(5, Bases.MAX_PRIORITY);
71: assertEquals((-5), Bases.MIN_PRIORITY);
72: assertEquals(1, Bases.FORWARD);
73: assertEquals(1, Strand.FORWARD);
74: assertEquals(2, Strand.REVERSE);
75:
76: float[] floatArray0 = new float[6];
77: aGWindowAlgorithm0.getValues(0, (-5), floatArray0);
Test case 14
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("}])1@Fg", "m");
2: assertEquals(0, fastaStreamSequence0.getCCount());
3: assertEquals(0, fastaStreamSequence0.getTCount());
4: assertEquals(6, fastaStreamSequence0.getOtherCount());
5: assertEquals(4, fastaStreamSequence0.getFormatType());
6: assertEquals(1, fastaStreamSequence0.getGCount());
7: assertEquals(7, fastaStreamSequence0.length());
8: assertEquals(0, fastaStreamSequence0.getACount());
9: assertNotNull(fastaStreamSequence0);
10:
11: Bases bases0 = new Bases(fastaStreamSequence0);
12: assertEquals(0, fastaStreamSequence0.getCCount());
13: assertEquals(0, fastaStreamSequence0.getTCount());
14: assertEquals(6, fastaStreamSequence0.getOtherCount());
15: assertEquals(4, fastaStreamSequence0.getFormatType());
16: assertEquals(1, fastaStreamSequence0.getGCount());
17: assertEquals(7, fastaStreamSequence0.length());
18: assertEquals(0, fastaStreamSequence0.getACount());
19: assertNotNull(bases0);
20: assertEquals(2, Bases.REVERSE);
21: assertEquals(0, Bases.MEDIUM_PRIORITY);
22: assertEquals(5, Bases.MAX_PRIORITY);
23: assertEquals(1, Bases.FORWARD);
24: assertEquals((-5), Bases.MIN_PRIORITY);
25:
26: Strand strand0 = bases0.getReverseStrand();
27: assertEquals(0, fastaStreamSequence0.getCCount());
28: assertEquals(0, fastaStreamSequence0.getTCount());
29: assertEquals(6, fastaStreamSequence0.getOtherCount());
30: assertEquals(4, fastaStreamSequence0.getFormatType());
31: assertEquals(1, fastaStreamSequence0.getGCount());
32: assertEquals(7, fastaStreamSequence0.length());
33: assertEquals(0, fastaStreamSequence0.getACount());
34: assertFalse(strand0.isForwardStrand());
35: assertEquals(2, strand0.getDirection());
36: assertNotNull(strand0);
37: assertEquals(2, Bases.REVERSE);
38: assertEquals(0, Bases.MEDIUM_PRIORITY);
39: assertEquals(5, Bases.MAX_PRIORITY);
40: assertEquals(1, Bases.FORWARD);
41: assertEquals((-5), Bases.MIN_PRIORITY);
42: assertEquals(1, Strand.FORWARD);
43: assertEquals(2, Strand.REVERSE);
44:
45: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
46: assertEquals(0, fastaStreamSequence0.getCCount());
47: assertEquals(0, fastaStreamSequence0.getTCount());
48: assertEquals(6, fastaStreamSequence0.getOtherCount());
49: assertEquals(4, fastaStreamSequence0.getFormatType());
50: assertEquals(1, fastaStreamSequence0.getGCount());
51: assertEquals(7, fastaStreamSequence0.length());
52: assertEquals(0, fastaStreamSequence0.getACount());
53: assertFalse(strand0.isForwardStrand());
54: assertEquals(2, strand0.getDirection());
55: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
56: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
57: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
58: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
59: assertTrue(aGWindowAlgorithm0.scalingFlag());
60: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
61: assertEquals(1, aGWindowAlgorithm0.getValueCount());
62: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
63: assertNotNull(aGWindowAlgorithm0);
64: assertEquals(2, Bases.REVERSE);
65: assertEquals(0, Bases.MEDIUM_PRIORITY);
66: assertEquals(5, Bases.MAX_PRIORITY);
67: assertEquals(1, Bases.FORWARD);
68: assertEquals((-5), Bases.MIN_PRIORITY);
69: assertEquals(1, Strand.FORWARD);
70: assertEquals(2, Strand.REVERSE);
71:
72: float[] floatArray0 = new float[8];
73: aGWindowAlgorithm0.getValues((-798), 50000, floatArray0);
Test case 15
1: RawStreamSequence rawStreamSequence0 = new RawStreamSequence("Cannot find the 'token' Tokenization for RNA!?");
2: assertEquals(0, rawStreamSequence0.getGCount());
3: assertEquals(4, rawStreamSequence0.getTCount());
4: assertEquals(3, rawStreamSequence0.getFormatType());
5: assertEquals(2, rawStreamSequence0.getACount());
6: assertEquals(0, rawStreamSequence0.getCCount());
7: assertEquals(46, rawStreamSequence0.length());
8: assertEquals(40, rawStreamSequence0.getOtherCount());
9: assertNotNull(rawStreamSequence0);
10:
11: Bases bases0 = new Bases(rawStreamSequence0);
12: assertEquals(0, rawStreamSequence0.getGCount());
13: assertEquals(4, rawStreamSequence0.getTCount());
14: assertEquals(3, rawStreamSequence0.getFormatType());
15: assertEquals(2, rawStreamSequence0.getACount());
16: assertEquals(0, rawStreamSequence0.getCCount());
17: assertEquals(46, rawStreamSequence0.length());
18: assertEquals(40, rawStreamSequence0.getOtherCount());
19: assertNotNull(bases0);
20: assertEquals((-5), Bases.MIN_PRIORITY);
21: assertEquals(1, Bases.FORWARD);
22: assertEquals(0, Bases.MEDIUM_PRIORITY);
23: assertEquals(5, Bases.MAX_PRIORITY);
24: assertEquals(2, Bases.REVERSE);
25:
26: Strand strand0 = bases0.getReverseStrand();
27: assertEquals(0, rawStreamSequence0.getGCount());
28: assertEquals(4, rawStreamSequence0.getTCount());
29: assertEquals(3, rawStreamSequence0.getFormatType());
30: assertEquals(2, rawStreamSequence0.getACount());
31: assertEquals(0, rawStreamSequence0.getCCount());
32: assertEquals(46, rawStreamSequence0.length());
33: assertEquals(40, rawStreamSequence0.getOtherCount());
34: assertFalse(strand0.isForwardStrand());
35: assertEquals(2, strand0.getDirection());
36: assertNotNull(strand0);
37: assertEquals((-5), Bases.MIN_PRIORITY);
38: assertEquals(1, Bases.FORWARD);
39: assertEquals(0, Bases.MEDIUM_PRIORITY);
40: assertEquals(5, Bases.MAX_PRIORITY);
41: assertEquals(2, Bases.REVERSE);
42: assertEquals(1, Strand.FORWARD);
43: assertEquals(2, Strand.REVERSE);
44:
45: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
46: assertEquals(0, rawStreamSequence0.getGCount());
47: assertEquals(4, rawStreamSequence0.getTCount());
48: assertEquals(3, rawStreamSequence0.getFormatType());
49: assertEquals(2, rawStreamSequence0.getACount());
50: assertEquals(0, rawStreamSequence0.getCCount());
51: assertEquals(46, rawStreamSequence0.length());
52: assertEquals(40, rawStreamSequence0.getOtherCount());
53: assertFalse(strand0.isForwardStrand());
54: assertEquals(2, strand0.getDirection());
55: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
56: assertEquals(1, aGWindowAlgorithm0.getValueCount());
57: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
58: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
59: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
60: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
61: assertTrue(aGWindowAlgorithm0.scalingFlag());
62: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
63: assertNotNull(aGWindowAlgorithm0);
64: assertEquals((-5), Bases.MIN_PRIORITY);
65: assertEquals(1, Bases.FORWARD);
66: assertEquals(0, Bases.MEDIUM_PRIORITY);
67: assertEquals(5, Bases.MAX_PRIORITY);
68: assertEquals(2, Bases.REVERSE);
69: assertEquals(1, Strand.FORWARD);
70: assertEquals(2, Strand.REVERSE);
71:
72: Float float0 = aGWindowAlgorithm0.getAverage();
73: assertEquals(0, rawStreamSequence0.getGCount());
74: assertEquals(4, rawStreamSequence0.getTCount());
75: assertEquals(3, rawStreamSequence0.getFormatType());
76: assertEquals(2, rawStreamSequence0.getACount());
77: assertEquals(0, rawStreamSequence0.getCCount());
78: assertEquals(46, rawStreamSequence0.length());
79: assertEquals(40, rawStreamSequence0.getOtherCount());
80: assertFalse(strand0.isForwardStrand());
81: assertEquals(2, strand0.getDirection());
82: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
83: assertEquals(1, aGWindowAlgorithm0.getValueCount());
84: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
85: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
86: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
87: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
88: assertTrue(aGWindowAlgorithm0.scalingFlag());
89: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
90: assertNotNull(float0);
91: assertEquals(4.347826F, (float)float0, 0.01F);
92: assertEquals((-5), Bases.MIN_PRIORITY);
93: assertEquals(1, Bases.FORWARD);
94: assertEquals(0, Bases.MEDIUM_PRIORITY);
95: assertEquals(5, Bases.MAX_PRIORITY);
96: assertEquals(2, Bases.REVERSE);
97: assertEquals(1, Strand.FORWARD);
98: assertEquals(2, Strand.REVERSE);
Test case 16
1: Short short0 = new Short((short)2953);
2: assertNotNull(short0);
3: assertEquals((short)2953, (short)short0);
4:
5: Integer integer0 = new Integer(103);
6: assertNotNull(integer0);
7: assertEquals(103, (int)integer0);
8:
9: PartialSequence partialSequence0 = new PartialSequence((char[]) null, 0, 0, short0, integer0);
10: assertEquals(103, (int)partialSequence0.getPhase());
11: assertEquals(0, partialSequence0.length());
12: assertEquals(0, partialSequence0.getACount());
13: assertFalse(partialSequence0.isComplement());
14: assertEquals(0, partialSequence0.getGCount());
15: assertEquals(0, partialSequence0.getCCount());
16: assertEquals(0, partialSequence0.getTCount());
17: assertEquals((short)2953, (short)partialSequence0.getStrand());
18: assertNotNull(partialSequence0);
19:
20: Bases bases0 = new Bases(partialSequence0);
21: assertEquals(103, (int)partialSequence0.getPhase());
22: assertEquals(0, partialSequence0.length());
23: assertEquals(0, partialSequence0.getACount());
24: assertFalse(partialSequence0.isComplement());
25: assertEquals(0, partialSequence0.getGCount());
26: assertEquals(0, partialSequence0.getCCount());
27: assertEquals(0, partialSequence0.getTCount());
28: assertEquals((short)2953, (short)partialSequence0.getStrand());
29: assertNotNull(bases0);
30: assertEquals(2, Bases.REVERSE);
31: assertEquals(5, Bases.MAX_PRIORITY);
32: assertEquals((-5), Bases.MIN_PRIORITY);
33: assertEquals(0, Bases.MEDIUM_PRIORITY);
34: assertEquals(1, Bases.FORWARD);
35:
36: Strand strand0 = bases0.getReverseStrand();
37: assertEquals(103, (int)partialSequence0.getPhase());
38: assertEquals(0, partialSequence0.length());
39: assertEquals(0, partialSequence0.getACount());
40: assertFalse(partialSequence0.isComplement());
41: assertEquals(0, partialSequence0.getGCount());
42: assertEquals(0, partialSequence0.getCCount());
43: assertEquals(0, partialSequence0.getTCount());
44: assertEquals((short)2953, (short)partialSequence0.getStrand());
45: assertFalse(strand0.isForwardStrand());
46: assertEquals(2, strand0.getDirection());
47: assertNotNull(strand0);
48: assertEquals(2, Bases.REVERSE);
49: assertEquals(5, Bases.MAX_PRIORITY);
50: assertEquals((-5), Bases.MIN_PRIORITY);
51: assertEquals(0, Bases.MEDIUM_PRIORITY);
52: assertEquals(1, Bases.FORWARD);
53: assertEquals(2, Strand.REVERSE);
54: assertEquals(1, Strand.FORWARD);
55:
56: AGWindowAlgorithm aGWindowAlgorithm0 = new AGWindowAlgorithm(strand0);
57: assertEquals(103, (int)partialSequence0.getPhase());
58: assertEquals(0, partialSequence0.length());
59: assertEquals(0, partialSequence0.getACount());
60: assertFalse(partialSequence0.isComplement());
61: assertEquals(0, partialSequence0.getGCount());
62: assertEquals(0, partialSequence0.getCCount());
63: assertEquals(0, partialSequence0.getTCount());
64: assertEquals((short)2953, (short)partialSequence0.getStrand());
65: assertFalse(strand0.isForwardStrand());
66: assertEquals(2, strand0.getDirection());
67: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
68: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
69: assertEquals(1, aGWindowAlgorithm0.getValueCount());
70: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
71: assertTrue(aGWindowAlgorithm0.scalingFlag());
72: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
73: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
74: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
75: assertNotNull(aGWindowAlgorithm0);
76: assertEquals(2, Bases.REVERSE);
77: assertEquals(5, Bases.MAX_PRIORITY);
78: assertEquals((-5), Bases.MIN_PRIORITY);
79: assertEquals(0, Bases.MEDIUM_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals(2, Strand.REVERSE);
82: assertEquals(1, Strand.FORWARD);
83:
84: Float float0 = aGWindowAlgorithm0.getAverage();
85: assertEquals(103, (int)partialSequence0.getPhase());
86: assertEquals(0, partialSequence0.length());
87: assertEquals(0, partialSequence0.getACount());
88: assertFalse(partialSequence0.isComplement());
89: assertEquals(0, partialSequence0.getGCount());
90: assertEquals(0, partialSequence0.getCCount());
91: assertEquals(0, partialSequence0.getTCount());
92: assertEquals((short)2953, (short)partialSequence0.getStrand());
93: assertFalse(strand0.isForwardStrand());
94: assertEquals(2, strand0.getDirection());
95: assertEquals(3.4028235E38F, aGWindowAlgorithm0.getUserMax(), 0.01F);
96: assertEquals("AG Content (%)", aGWindowAlgorithm0.getAlgorithmName());
97: assertEquals(1, aGWindowAlgorithm0.getValueCount());
98: assertFalse(aGWindowAlgorithm0.isRevCompDisplay());
99: assertTrue(aGWindowAlgorithm0.scalingFlag());
100: assertEquals(1.4E-45F, aGWindowAlgorithm0.getUserMin(), 0.01F);
101: assertFalse(aGWindowAlgorithm0.isUserMaxMin());
102: assertEquals("ag_content", aGWindowAlgorithm0.getAlgorithmShortName());
103: assertNotNull(float0);
104: assertEquals(Float.NaN, (float)float0, 0.01F);
105: assertEquals(2, Bases.REVERSE);
106: assertEquals(5, Bases.MAX_PRIORITY);
107: assertEquals((-5), Bases.MIN_PRIORITY);
108: assertEquals(0, Bases.MEDIUM_PRIORITY);
109: assertEquals(1, Bases.FORWARD);
110: assertEquals(2, Strand.REVERSE);
111: assertEquals(1, Strand.FORWARD);