Test case 1
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = bases0.getForwardStrand();
3: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
4: aTDeviationAlgorithm0.getAverage();
Test case 2
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("Scaled Chi Square");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
5: Float float0 = aTDeviationAlgorithm0.getMinimumInternal();
6: assertEquals((-1.0F), (float)float0, 0.01F);
7: assertTrue(aTDeviationAlgorithm0.scalingFlag());
Test case 3
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("Scaled Chi Square");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
5: int int0 = aTDeviationAlgorithm0.getValueCount();
6: assertEquals(1, int0);
7: assertTrue(aTDeviationAlgorithm0.scalingFlag());
Test case 4
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = bases0.getReverseStrand();
3: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
4: Float float0 = aTDeviationAlgorithm0.getMaximumInternal();
5: assertTrue(aTDeviationAlgorithm0.scalingFlag());
6: assertEquals(1.0F, (float)float0, 0.01F);
Test case 5
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("Y+dP9ZU-7#e[");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
5: float[] floatArray0 = new float[8];
6: aTDeviationAlgorithm0.getValues(592, 1197, floatArray0);
7: assertArrayEquals(new float[] {0.0F, 0.0F, 0.0F, 0.0F, 0.0F, 0.0F, 0.0F, 0.0F}, floatArray0, 0.01F);
8: assertTrue(aTDeviationAlgorithm0.scalingFlag());
Test case 6
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("Scaled Chi Square");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
5: float[] floatArray0 = new float[2];
6: aTDeviationAlgorithm0.getValues(1, 1333, floatArray0);
7: assertArrayEquals(new float[] {(-0.33333334F), 0.0F}, floatArray0, 0.01F);
8: assertTrue(aTDeviationAlgorithm0.scalingFlag());
Test case 7
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("Scaled Chi Square");
2: assertNotNull(emblStreamSequence0);
3: assertNull(emblStreamSequence0.getHeader());
4: assertEquals(17, emblStreamSequence0.length());
5: assertEquals(0, emblStreamSequence0.getTCount());
6: assertEquals(1, emblStreamSequence0.getFormatType());
7: assertEquals(14, emblStreamSequence0.getOtherCount());
8: assertEquals(2, emblStreamSequence0.getACount());
9: assertEquals(0, emblStreamSequence0.getGCount());
10: assertEquals(1, emblStreamSequence0.getCCount());
11:
12: Bases bases0 = new Bases(emblStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, Bases.REVERSE);
15: assertEquals(1, Bases.FORWARD);
16: assertEquals((-5), Bases.MIN_PRIORITY);
17: assertEquals(0, Bases.MEDIUM_PRIORITY);
18: assertEquals(5, Bases.MAX_PRIORITY);
19: assertNull(emblStreamSequence0.getHeader());
20: assertEquals(17, emblStreamSequence0.length());
21: assertEquals(0, emblStreamSequence0.getTCount());
22: assertEquals(1, emblStreamSequence0.getFormatType());
23: assertEquals(14, emblStreamSequence0.getOtherCount());
24: assertEquals(2, emblStreamSequence0.getACount());
25: assertEquals(0, emblStreamSequence0.getGCount());
26: assertEquals(1, emblStreamSequence0.getCCount());
27:
28: Strand strand0 = bases0.getReverseStrand();
29: assertNotNull(strand0);
30: assertEquals(2, Bases.REVERSE);
31: assertEquals(1, Bases.FORWARD);
32: assertEquals((-5), Bases.MIN_PRIORITY);
33: assertEquals(0, Bases.MEDIUM_PRIORITY);
34: assertEquals(5, Bases.MAX_PRIORITY);
35: assertEquals(1, Strand.FORWARD);
36: assertEquals(2, Strand.REVERSE);
37: assertNull(emblStreamSequence0.getHeader());
38: assertEquals(17, emblStreamSequence0.length());
39: assertEquals(0, emblStreamSequence0.getTCount());
40: assertEquals(1, emblStreamSequence0.getFormatType());
41: assertEquals(14, emblStreamSequence0.getOtherCount());
42: assertEquals(2, emblStreamSequence0.getACount());
43: assertEquals(0, emblStreamSequence0.getGCount());
44: assertEquals(1, emblStreamSequence0.getCCount());
45: assertFalse(strand0.isForwardStrand());
46: assertEquals(2, strand0.getDirection());
47:
48: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
49: assertNotNull(aTDeviationAlgorithm0);
50: assertEquals(2, Bases.REVERSE);
51: assertEquals(1, Bases.FORWARD);
52: assertEquals((-5), Bases.MIN_PRIORITY);
53: assertEquals(0, Bases.MEDIUM_PRIORITY);
54: assertEquals(5, Bases.MAX_PRIORITY);
55: assertEquals(1, Strand.FORWARD);
56: assertEquals(2, Strand.REVERSE);
57: assertNull(emblStreamSequence0.getHeader());
58: assertEquals(17, emblStreamSequence0.length());
59: assertEquals(0, emblStreamSequence0.getTCount());
60: assertEquals(1, emblStreamSequence0.getFormatType());
61: assertEquals(14, emblStreamSequence0.getOtherCount());
62: assertEquals(2, emblStreamSequence0.getACount());
63: assertEquals(0, emblStreamSequence0.getGCount());
64: assertEquals(1, emblStreamSequence0.getCCount());
65: assertFalse(strand0.isForwardStrand());
66: assertEquals(2, strand0.getDirection());
67: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
68: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
69: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
70: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
71: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
72: assertTrue(aTDeviationAlgorithm0.scalingFlag());
73: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
74: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
75:
76: Integer integer0 = aTDeviationAlgorithm0.getDefaultWindowSize();
77: assertNotNull(integer0);
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: assertEquals(1, Strand.FORWARD);
84: assertEquals(2, Strand.REVERSE);
85: assertNull(emblStreamSequence0.getHeader());
86: assertEquals(17, emblStreamSequence0.length());
87: assertEquals(0, emblStreamSequence0.getTCount());
88: assertEquals(1, emblStreamSequence0.getFormatType());
89: assertEquals(14, emblStreamSequence0.getOtherCount());
90: assertEquals(2, emblStreamSequence0.getACount());
91: assertEquals(0, emblStreamSequence0.getGCount());
92: assertEquals(1, emblStreamSequence0.getCCount());
93: assertFalse(strand0.isForwardStrand());
94: assertEquals(2, strand0.getDirection());
95: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
96: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
97: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
98: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
99: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
100: assertTrue(aTDeviationAlgorithm0.scalingFlag());
101: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
102: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
103: assertEquals(30, (int)integer0);
Test case 8
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("Scaled Chi Square");
2: assertNotNull(emblStreamSequence0);
3: assertNull(emblStreamSequence0.getHeader());
4: assertEquals(1, emblStreamSequence0.getFormatType());
5: assertEquals(0, emblStreamSequence0.getTCount());
6: assertEquals(14, emblStreamSequence0.getOtherCount());
7: assertEquals(17, emblStreamSequence0.length());
8: assertEquals(1, emblStreamSequence0.getCCount());
9: assertEquals(2, emblStreamSequence0.getACount());
10: assertEquals(0, emblStreamSequence0.getGCount());
11:
12: Bases bases0 = new Bases(emblStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(0, Bases.MEDIUM_PRIORITY);
15: assertEquals((-5), Bases.MIN_PRIORITY);
16: assertEquals(1, Bases.FORWARD);
17: assertEquals(5, Bases.MAX_PRIORITY);
18: assertEquals(2, Bases.REVERSE);
19: assertNull(emblStreamSequence0.getHeader());
20: assertEquals(1, emblStreamSequence0.getFormatType());
21: assertEquals(0, emblStreamSequence0.getTCount());
22: assertEquals(14, emblStreamSequence0.getOtherCount());
23: assertEquals(17, emblStreamSequence0.length());
24: assertEquals(1, emblStreamSequence0.getCCount());
25: assertEquals(2, emblStreamSequence0.getACount());
26: assertEquals(0, emblStreamSequence0.getGCount());
27:
28: Strand strand0 = bases0.getReverseStrand();
29: assertNotNull(strand0);
30: assertEquals(0, Bases.MEDIUM_PRIORITY);
31: assertEquals((-5), Bases.MIN_PRIORITY);
32: assertEquals(1, Bases.FORWARD);
33: assertEquals(5, Bases.MAX_PRIORITY);
34: assertEquals(2, Bases.REVERSE);
35: assertEquals(2, Strand.REVERSE);
36: assertEquals(1, Strand.FORWARD);
37: assertNull(emblStreamSequence0.getHeader());
38: assertEquals(1, emblStreamSequence0.getFormatType());
39: assertEquals(0, emblStreamSequence0.getTCount());
40: assertEquals(14, emblStreamSequence0.getOtherCount());
41: assertEquals(17, emblStreamSequence0.length());
42: assertEquals(1, emblStreamSequence0.getCCount());
43: assertEquals(2, emblStreamSequence0.getACount());
44: assertEquals(0, emblStreamSequence0.getGCount());
45: assertFalse(strand0.isForwardStrand());
46: assertEquals(2, strand0.getDirection());
47:
48: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
49: assertNotNull(aTDeviationAlgorithm0);
50: assertEquals(0, Bases.MEDIUM_PRIORITY);
51: assertEquals((-5), Bases.MIN_PRIORITY);
52: assertEquals(1, Bases.FORWARD);
53: assertEquals(5, Bases.MAX_PRIORITY);
54: assertEquals(2, Bases.REVERSE);
55: assertEquals(2, Strand.REVERSE);
56: assertEquals(1, Strand.FORWARD);
57: assertNull(emblStreamSequence0.getHeader());
58: assertEquals(1, emblStreamSequence0.getFormatType());
59: assertEquals(0, emblStreamSequence0.getTCount());
60: assertEquals(14, emblStreamSequence0.getOtherCount());
61: assertEquals(17, emblStreamSequence0.length());
62: assertEquals(1, emblStreamSequence0.getCCount());
63: assertEquals(2, emblStreamSequence0.getACount());
64: assertEquals(0, emblStreamSequence0.getGCount());
65: assertFalse(strand0.isForwardStrand());
66: assertEquals(2, strand0.getDirection());
67: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
68: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
69: assertTrue(aTDeviationAlgorithm0.scalingFlag());
70: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
71: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
72: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
73: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
74: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
75:
76: Integer integer0 = aTDeviationAlgorithm0.getDefaultMaxWindowSize();
77: assertNotNull(integer0);
78: assertEquals(0, Bases.MEDIUM_PRIORITY);
79: assertEquals((-5), Bases.MIN_PRIORITY);
80: assertEquals(1, Bases.FORWARD);
81: assertEquals(5, Bases.MAX_PRIORITY);
82: assertEquals(2, Bases.REVERSE);
83: assertEquals(2, Strand.REVERSE);
84: assertEquals(1, Strand.FORWARD);
85: assertNull(emblStreamSequence0.getHeader());
86: assertEquals(1, emblStreamSequence0.getFormatType());
87: assertEquals(0, emblStreamSequence0.getTCount());
88: assertEquals(14, emblStreamSequence0.getOtherCount());
89: assertEquals(17, emblStreamSequence0.length());
90: assertEquals(1, emblStreamSequence0.getCCount());
91: assertEquals(2, emblStreamSequence0.getACount());
92: assertEquals(0, emblStreamSequence0.getGCount());
93: assertFalse(strand0.isForwardStrand());
94: assertEquals(2, strand0.getDirection());
95: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
96: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
97: assertTrue(aTDeviationAlgorithm0.scalingFlag());
98: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
99: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
100: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
101: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
102: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
103: assertEquals(5000, (int)integer0);
Test case 9
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("Y+dP9ZU-7#e[");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getCCount());
4: assertNull(genbankStreamSequence0.getHeader());
5: assertEquals(12, genbankStreamSequence0.getOtherCount());
6: assertEquals(12, genbankStreamSequence0.length());
7: assertEquals(0, genbankStreamSequence0.getTCount());
8: assertEquals(2, genbankStreamSequence0.getFormatType());
9: assertEquals(0, genbankStreamSequence0.getGCount());
10: assertEquals(0, genbankStreamSequence0.getACount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(5, Bases.MAX_PRIORITY);
15: assertEquals(2, Bases.REVERSE);
16: assertEquals((-5), Bases.MIN_PRIORITY);
17: assertEquals(0, Bases.MEDIUM_PRIORITY);
18: assertEquals(1, Bases.FORWARD);
19: assertEquals(0, genbankStreamSequence0.getCCount());
20: assertNull(genbankStreamSequence0.getHeader());
21: assertEquals(12, genbankStreamSequence0.getOtherCount());
22: assertEquals(12, genbankStreamSequence0.length());
23: assertEquals(0, genbankStreamSequence0.getTCount());
24: assertEquals(2, genbankStreamSequence0.getFormatType());
25: assertEquals(0, genbankStreamSequence0.getGCount());
26: assertEquals(0, genbankStreamSequence0.getACount());
27:
28: Strand strand0 = bases0.getReverseStrand();
29: assertNotNull(strand0);
30: assertEquals(5, Bases.MAX_PRIORITY);
31: assertEquals(2, Bases.REVERSE);
32: assertEquals((-5), Bases.MIN_PRIORITY);
33: assertEquals(0, Bases.MEDIUM_PRIORITY);
34: assertEquals(1, Bases.FORWARD);
35: assertEquals(1, Strand.FORWARD);
36: assertEquals(2, Strand.REVERSE);
37: assertEquals(0, genbankStreamSequence0.getCCount());
38: assertNull(genbankStreamSequence0.getHeader());
39: assertEquals(12, genbankStreamSequence0.getOtherCount());
40: assertEquals(12, genbankStreamSequence0.length());
41: assertEquals(0, genbankStreamSequence0.getTCount());
42: assertEquals(2, genbankStreamSequence0.getFormatType());
43: assertEquals(0, genbankStreamSequence0.getGCount());
44: assertEquals(0, genbankStreamSequence0.getACount());
45: assertFalse(strand0.isForwardStrand());
46: assertEquals(2, strand0.getDirection());
47:
48: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
49: assertNotNull(aTDeviationAlgorithm0);
50: assertEquals(5, Bases.MAX_PRIORITY);
51: assertEquals(2, Bases.REVERSE);
52: assertEquals((-5), Bases.MIN_PRIORITY);
53: assertEquals(0, Bases.MEDIUM_PRIORITY);
54: assertEquals(1, Bases.FORWARD);
55: assertEquals(1, Strand.FORWARD);
56: assertEquals(2, Strand.REVERSE);
57: assertEquals(0, genbankStreamSequence0.getCCount());
58: assertNull(genbankStreamSequence0.getHeader());
59: assertEquals(12, genbankStreamSequence0.getOtherCount());
60: assertEquals(12, genbankStreamSequence0.length());
61: assertEquals(0, genbankStreamSequence0.getTCount());
62: assertEquals(2, genbankStreamSequence0.getFormatType());
63: assertEquals(0, genbankStreamSequence0.getGCount());
64: assertEquals(0, genbankStreamSequence0.getACount());
65: assertFalse(strand0.isForwardStrand());
66: assertEquals(2, strand0.getDirection());
67: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
68: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
69: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
70: assertTrue(aTDeviationAlgorithm0.scalingFlag());
71: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
72: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
73: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
74: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
75:
76: Integer integer0 = aTDeviationAlgorithm0.getDefaultMinWindowSize();
77: assertNotNull(integer0);
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: assertEquals(1, Strand.FORWARD);
84: assertEquals(2, Strand.REVERSE);
85: assertEquals(0, genbankStreamSequence0.getCCount());
86: assertNull(genbankStreamSequence0.getHeader());
87: assertEquals(12, genbankStreamSequence0.getOtherCount());
88: assertEquals(12, genbankStreamSequence0.length());
89: assertEquals(0, genbankStreamSequence0.getTCount());
90: assertEquals(2, genbankStreamSequence0.getFormatType());
91: assertEquals(0, genbankStreamSequence0.getGCount());
92: assertEquals(0, genbankStreamSequence0.getACount());
93: assertFalse(strand0.isForwardStrand());
94: assertEquals(2, strand0.getDirection());
95: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
96: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
97: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
98: assertTrue(aTDeviationAlgorithm0.scalingFlag());
99: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
100: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
101: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
102: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
103: assertEquals(10, (int)integer0);
Test case 10
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("Scaled Chi Square");
2: assertNotNull(emblStreamSequence0);
3: assertEquals(17, emblStreamSequence0.length());
4: assertEquals(14, emblStreamSequence0.getOtherCount());
5: assertEquals(1, emblStreamSequence0.getCCount());
6: assertEquals(1, emblStreamSequence0.getFormatType());
7: assertEquals(0, emblStreamSequence0.getTCount());
8: assertEquals(2, emblStreamSequence0.getACount());
9: assertEquals(0, emblStreamSequence0.getGCount());
10: assertNull(emblStreamSequence0.getHeader());
11:
12: Bases bases0 = new Bases(emblStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(1, Bases.FORWARD);
15: assertEquals(2, Bases.REVERSE);
16: assertEquals(0, Bases.MEDIUM_PRIORITY);
17: assertEquals(5, Bases.MAX_PRIORITY);
18: assertEquals((-5), Bases.MIN_PRIORITY);
19: assertEquals(17, emblStreamSequence0.length());
20: assertEquals(14, emblStreamSequence0.getOtherCount());
21: assertEquals(1, emblStreamSequence0.getCCount());
22: assertEquals(1, emblStreamSequence0.getFormatType());
23: assertEquals(0, emblStreamSequence0.getTCount());
24: assertEquals(2, emblStreamSequence0.getACount());
25: assertEquals(0, emblStreamSequence0.getGCount());
26: assertNull(emblStreamSequence0.getHeader());
27:
28: Strand strand0 = bases0.getReverseStrand();
29: assertNotNull(strand0);
30: assertEquals(1, Bases.FORWARD);
31: assertEquals(2, Bases.REVERSE);
32: assertEquals(0, Bases.MEDIUM_PRIORITY);
33: assertEquals(5, Bases.MAX_PRIORITY);
34: assertEquals((-5), Bases.MIN_PRIORITY);
35: assertEquals(1, Strand.FORWARD);
36: assertEquals(2, Strand.REVERSE);
37: assertEquals(17, emblStreamSequence0.length());
38: assertEquals(14, emblStreamSequence0.getOtherCount());
39: assertEquals(1, emblStreamSequence0.getCCount());
40: assertEquals(1, emblStreamSequence0.getFormatType());
41: assertEquals(0, emblStreamSequence0.getTCount());
42: assertEquals(2, emblStreamSequence0.getACount());
43: assertEquals(0, emblStreamSequence0.getGCount());
44: assertNull(emblStreamSequence0.getHeader());
45: assertFalse(strand0.isForwardStrand());
46: assertEquals(2, strand0.getDirection());
47:
48: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
49: assertNotNull(aTDeviationAlgorithm0);
50: assertEquals(1, Bases.FORWARD);
51: assertEquals(2, Bases.REVERSE);
52: assertEquals(0, Bases.MEDIUM_PRIORITY);
53: assertEquals(5, Bases.MAX_PRIORITY);
54: assertEquals((-5), Bases.MIN_PRIORITY);
55: assertEquals(1, Strand.FORWARD);
56: assertEquals(2, Strand.REVERSE);
57: assertEquals(17, emblStreamSequence0.length());
58: assertEquals(14, emblStreamSequence0.getOtherCount());
59: assertEquals(1, emblStreamSequence0.getCCount());
60: assertEquals(1, emblStreamSequence0.getFormatType());
61: assertEquals(0, emblStreamSequence0.getTCount());
62: assertEquals(2, emblStreamSequence0.getACount());
63: assertEquals(0, emblStreamSequence0.getGCount());
64: assertNull(emblStreamSequence0.getHeader());
65: assertFalse(strand0.isForwardStrand());
66: assertEquals(2, strand0.getDirection());
67: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
68: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
69: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
70: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
71: assertTrue(aTDeviationAlgorithm0.scalingFlag());
72: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
73: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
74: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
75:
76: Integer integer0 = aTDeviationAlgorithm0.getDefaultStepSize((-5));
77: assertNull(integer0);
78: assertEquals(1, Bases.FORWARD);
79: assertEquals(2, Bases.REVERSE);
80: assertEquals(0, Bases.MEDIUM_PRIORITY);
81: assertEquals(5, Bases.MAX_PRIORITY);
82: assertEquals((-5), Bases.MIN_PRIORITY);
83: assertEquals(1, Strand.FORWARD);
84: assertEquals(2, Strand.REVERSE);
85: assertEquals(17, emblStreamSequence0.length());
86: assertEquals(14, emblStreamSequence0.getOtherCount());
87: assertEquals(1, emblStreamSequence0.getCCount());
88: assertEquals(1, emblStreamSequence0.getFormatType());
89: assertEquals(0, emblStreamSequence0.getTCount());
90: assertEquals(2, emblStreamSequence0.getACount());
91: assertEquals(0, emblStreamSequence0.getGCount());
92: assertNull(emblStreamSequence0.getHeader());
93: assertFalse(strand0.isForwardStrand());
94: assertEquals(2, strand0.getDirection());
95: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
96: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
97: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
98: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
99: assertTrue(aTDeviationAlgorithm0.scalingFlag());
100: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
101: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
102: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
Test case 11
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("Y+dP9ZU-7#e[");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getTCount());
4: assertEquals(0, genbankStreamSequence0.getACount());
5: assertNull(genbankStreamSequence0.getHeader());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertEquals(12, genbankStreamSequence0.getOtherCount());
8: assertEquals(12, genbankStreamSequence0.length());
9: assertEquals(2, genbankStreamSequence0.getFormatType());
10: assertEquals(0, genbankStreamSequence0.getGCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals((-5), Bases.MIN_PRIORITY);
15: assertEquals(0, Bases.MEDIUM_PRIORITY);
16: assertEquals(2, Bases.REVERSE);
17: assertEquals(1, Bases.FORWARD);
18: assertEquals(5, Bases.MAX_PRIORITY);
19: assertEquals(0, genbankStreamSequence0.getTCount());
20: assertEquals(0, genbankStreamSequence0.getACount());
21: assertNull(genbankStreamSequence0.getHeader());
22: assertEquals(0, genbankStreamSequence0.getCCount());
23: assertEquals(12, genbankStreamSequence0.getOtherCount());
24: assertEquals(12, genbankStreamSequence0.length());
25: assertEquals(2, genbankStreamSequence0.getFormatType());
26: assertEquals(0, genbankStreamSequence0.getGCount());
27:
28: Strand strand0 = bases0.getReverseStrand();
29: assertNotNull(strand0);
30: assertEquals((-5), Bases.MIN_PRIORITY);
31: assertEquals(0, Bases.MEDIUM_PRIORITY);
32: assertEquals(2, Bases.REVERSE);
33: assertEquals(1, Bases.FORWARD);
34: assertEquals(5, Bases.MAX_PRIORITY);
35: assertEquals(1, Strand.FORWARD);
36: assertEquals(2, Strand.REVERSE);
37: assertEquals(0, genbankStreamSequence0.getTCount());
38: assertEquals(0, genbankStreamSequence0.getACount());
39: assertNull(genbankStreamSequence0.getHeader());
40: assertEquals(0, genbankStreamSequence0.getCCount());
41: assertEquals(12, genbankStreamSequence0.getOtherCount());
42: assertEquals(12, genbankStreamSequence0.length());
43: assertEquals(2, genbankStreamSequence0.getFormatType());
44: assertEquals(0, genbankStreamSequence0.getGCount());
45: assertFalse(strand0.isForwardStrand());
46: assertEquals(2, strand0.getDirection());
47:
48: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
49: assertNotNull(aTDeviationAlgorithm0);
50: assertEquals((-5), Bases.MIN_PRIORITY);
51: assertEquals(0, Bases.MEDIUM_PRIORITY);
52: assertEquals(2, Bases.REVERSE);
53: assertEquals(1, Bases.FORWARD);
54: assertEquals(5, Bases.MAX_PRIORITY);
55: assertEquals(1, Strand.FORWARD);
56: assertEquals(2, Strand.REVERSE);
57: assertEquals(0, genbankStreamSequence0.getTCount());
58: assertEquals(0, genbankStreamSequence0.getACount());
59: assertNull(genbankStreamSequence0.getHeader());
60: assertEquals(0, genbankStreamSequence0.getCCount());
61: assertEquals(12, genbankStreamSequence0.getOtherCount());
62: assertEquals(12, genbankStreamSequence0.length());
63: assertEquals(2, genbankStreamSequence0.getFormatType());
64: assertEquals(0, genbankStreamSequence0.getGCount());
65: assertFalse(strand0.isForwardStrand());
66: assertEquals(2, strand0.getDirection());
67: assertTrue(aTDeviationAlgorithm0.scalingFlag());
68: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
69: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
70: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
71: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
72: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
73: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
74: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
75:
76: Integer integer0 = aTDeviationAlgorithm0.getDefaultStepSize(1197);
77: assertNotNull(integer0);
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: assertEquals(1, Strand.FORWARD);
84: assertEquals(2, Strand.REVERSE);
85: assertEquals(0, genbankStreamSequence0.getTCount());
86: assertEquals(0, genbankStreamSequence0.getACount());
87: assertNull(genbankStreamSequence0.getHeader());
88: assertEquals(0, genbankStreamSequence0.getCCount());
89: assertEquals(12, genbankStreamSequence0.getOtherCount());
90: assertEquals(12, genbankStreamSequence0.length());
91: assertEquals(2, genbankStreamSequence0.getFormatType());
92: assertEquals(0, genbankStreamSequence0.getGCount());
93: assertFalse(strand0.isForwardStrand());
94: assertEquals(2, strand0.getDirection());
95: assertTrue(aTDeviationAlgorithm0.scalingFlag());
96: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
97: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
98: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
99: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
100: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
101: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
102: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
103: assertEquals(119, (int)integer0);
Test case 12
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("Y+dP9ZU-7#e[");
2: assertNotNull(genbankStreamSequence0);
3: assertNull(genbankStreamSequence0.getHeader());
4: assertEquals(0, genbankStreamSequence0.getCCount());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(0, genbankStreamSequence0.getACount());
7: assertEquals(0, genbankStreamSequence0.getGCount());
8: assertEquals(12, genbankStreamSequence0.length());
9: assertEquals(2, genbankStreamSequence0.getFormatType());
10: assertEquals(12, genbankStreamSequence0.getOtherCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(5, Bases.MAX_PRIORITY);
15: assertEquals(2, Bases.REVERSE);
16: assertEquals(0, Bases.MEDIUM_PRIORITY);
17: assertEquals(1, Bases.FORWARD);
18: assertEquals((-5), Bases.MIN_PRIORITY);
19: assertNull(genbankStreamSequence0.getHeader());
20: assertEquals(0, genbankStreamSequence0.getCCount());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, genbankStreamSequence0.getACount());
23: assertEquals(0, genbankStreamSequence0.getGCount());
24: assertEquals(12, genbankStreamSequence0.length());
25: assertEquals(2, genbankStreamSequence0.getFormatType());
26: assertEquals(12, genbankStreamSequence0.getOtherCount());
27:
28: Strand strand0 = bases0.getReverseStrand();
29: assertNotNull(strand0);
30: assertEquals(5, Bases.MAX_PRIORITY);
31: assertEquals(2, Bases.REVERSE);
32: assertEquals(0, Bases.MEDIUM_PRIORITY);
33: assertEquals(1, Bases.FORWARD);
34: assertEquals((-5), Bases.MIN_PRIORITY);
35: assertEquals(1, Strand.FORWARD);
36: assertEquals(2, Strand.REVERSE);
37: assertNull(genbankStreamSequence0.getHeader());
38: assertEquals(0, genbankStreamSequence0.getCCount());
39: assertEquals(0, genbankStreamSequence0.getTCount());
40: assertEquals(0, genbankStreamSequence0.getACount());
41: assertEquals(0, genbankStreamSequence0.getGCount());
42: assertEquals(12, genbankStreamSequence0.length());
43: assertEquals(2, genbankStreamSequence0.getFormatType());
44: assertEquals(12, genbankStreamSequence0.getOtherCount());
45: assertFalse(strand0.isForwardStrand());
46: assertEquals(2, strand0.getDirection());
47:
48: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
49: assertNotNull(aTDeviationAlgorithm0);
50: assertEquals(5, Bases.MAX_PRIORITY);
51: assertEquals(2, Bases.REVERSE);
52: assertEquals(0, Bases.MEDIUM_PRIORITY);
53: assertEquals(1, Bases.FORWARD);
54: assertEquals((-5), Bases.MIN_PRIORITY);
55: assertEquals(1, Strand.FORWARD);
56: assertEquals(2, Strand.REVERSE);
57: assertNull(genbankStreamSequence0.getHeader());
58: assertEquals(0, genbankStreamSequence0.getCCount());
59: assertEquals(0, genbankStreamSequence0.getTCount());
60: assertEquals(0, genbankStreamSequence0.getACount());
61: assertEquals(0, genbankStreamSequence0.getGCount());
62: assertEquals(12, genbankStreamSequence0.length());
63: assertEquals(2, genbankStreamSequence0.getFormatType());
64: assertEquals(12, genbankStreamSequence0.getOtherCount());
65: assertFalse(strand0.isForwardStrand());
66: assertEquals(2, strand0.getDirection());
67: assertTrue(aTDeviationAlgorithm0.scalingFlag());
68: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
69: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
70: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
71: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
72: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
73: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
74: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
75:
76: Float float0 = aTDeviationAlgorithm0.getAverage();
77: assertNotNull(float0);
78: assertEquals(5, Bases.MAX_PRIORITY);
79: assertEquals(2, Bases.REVERSE);
80: assertEquals(0, Bases.MEDIUM_PRIORITY);
81: assertEquals(1, Bases.FORWARD);
82: assertEquals((-5), Bases.MIN_PRIORITY);
83: assertEquals(1, Strand.FORWARD);
84: assertEquals(2, Strand.REVERSE);
85: assertNull(genbankStreamSequence0.getHeader());
86: assertEquals(0, genbankStreamSequence0.getCCount());
87: assertEquals(0, genbankStreamSequence0.getTCount());
88: assertEquals(0, genbankStreamSequence0.getACount());
89: assertEquals(0, genbankStreamSequence0.getGCount());
90: assertEquals(12, genbankStreamSequence0.length());
91: assertEquals(2, genbankStreamSequence0.getFormatType());
92: assertEquals(12, genbankStreamSequence0.getOtherCount());
93: assertFalse(strand0.isForwardStrand());
94: assertEquals(2, strand0.getDirection());
95: assertTrue(aTDeviationAlgorithm0.scalingFlag());
96: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
97: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
98: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
99: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
100: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
101: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
102: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
103: assertEquals(0.0F, (float)float0, 0.01F);
Test case 13
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("Y+dP9ZU-7#e[");
2: assertNotNull(genbankStreamSequence0);
3: assertEquals(0, genbankStreamSequence0.getACount());
4: assertNull(genbankStreamSequence0.getHeader());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(0, genbankStreamSequence0.getCCount());
7: assertEquals(2, genbankStreamSequence0.getFormatType());
8: assertEquals(0, genbankStreamSequence0.getGCount());
9: assertEquals(12, genbankStreamSequence0.length());
10: assertEquals(12, genbankStreamSequence0.getOtherCount());
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, Bases.REVERSE);
15: assertEquals(1, Bases.FORWARD);
16: assertEquals((-5), Bases.MIN_PRIORITY);
17: assertEquals(0, Bases.MEDIUM_PRIORITY);
18: assertEquals(5, Bases.MAX_PRIORITY);
19: assertEquals(0, genbankStreamSequence0.getACount());
20: assertNull(genbankStreamSequence0.getHeader());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(0, genbankStreamSequence0.getCCount());
23: assertEquals(2, genbankStreamSequence0.getFormatType());
24: assertEquals(0, genbankStreamSequence0.getGCount());
25: assertEquals(12, genbankStreamSequence0.length());
26: assertEquals(12, genbankStreamSequence0.getOtherCount());
27:
28: Strand strand0 = bases0.getReverseStrand();
29: assertNotNull(strand0);
30: assertEquals(2, Bases.REVERSE);
31: assertEquals(1, Bases.FORWARD);
32: assertEquals((-5), Bases.MIN_PRIORITY);
33: assertEquals(0, Bases.MEDIUM_PRIORITY);
34: assertEquals(5, Bases.MAX_PRIORITY);
35: assertEquals(2, Strand.REVERSE);
36: assertEquals(1, Strand.FORWARD);
37: assertEquals(0, genbankStreamSequence0.getACount());
38: assertNull(genbankStreamSequence0.getHeader());
39: assertEquals(0, genbankStreamSequence0.getTCount());
40: assertEquals(0, genbankStreamSequence0.getCCount());
41: assertEquals(2, genbankStreamSequence0.getFormatType());
42: assertEquals(0, genbankStreamSequence0.getGCount());
43: assertEquals(12, genbankStreamSequence0.length());
44: assertEquals(12, genbankStreamSequence0.getOtherCount());
45: assertEquals(2, strand0.getDirection());
46: assertFalse(strand0.isForwardStrand());
47:
48: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
49: assertNotNull(aTDeviationAlgorithm0);
50: assertEquals(2, Bases.REVERSE);
51: assertEquals(1, Bases.FORWARD);
52: assertEquals((-5), Bases.MIN_PRIORITY);
53: assertEquals(0, Bases.MEDIUM_PRIORITY);
54: assertEquals(5, Bases.MAX_PRIORITY);
55: assertEquals(2, Strand.REVERSE);
56: assertEquals(1, Strand.FORWARD);
57: assertEquals(0, genbankStreamSequence0.getACount());
58: assertNull(genbankStreamSequence0.getHeader());
59: assertEquals(0, genbankStreamSequence0.getTCount());
60: assertEquals(0, genbankStreamSequence0.getCCount());
61: assertEquals(2, genbankStreamSequence0.getFormatType());
62: assertEquals(0, genbankStreamSequence0.getGCount());
63: assertEquals(12, genbankStreamSequence0.length());
64: assertEquals(12, genbankStreamSequence0.getOtherCount());
65: assertEquals(2, strand0.getDirection());
66: assertFalse(strand0.isForwardStrand());
67: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
68: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
69: assertTrue(aTDeviationAlgorithm0.scalingFlag());
70: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
71: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
72: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
73: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
74: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
75:
76: genbankStreamSequence0.setFromChar(bases0.letter_index);
77: assertEquals(2, Bases.REVERSE);
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(5, genbankStreamSequence0.length());
83: assertEquals(1, genbankStreamSequence0.getTCount());
84: assertEquals(1, genbankStreamSequence0.getACount());
85: assertEquals(1, genbankStreamSequence0.getOtherCount());
86: assertNull(genbankStreamSequence0.getHeader());
87: assertEquals(1, genbankStreamSequence0.getGCount());
88: assertEquals(1, genbankStreamSequence0.getCCount());
89: assertEquals(2, genbankStreamSequence0.getFormatType());
90:
91: Float float0 = aTDeviationAlgorithm0.getAverage();
92: assertNotNull(float0);
93: assertEquals(2, Bases.REVERSE);
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, Strand.REVERSE);
99: assertEquals(1, Strand.FORWARD);
100: assertEquals(5, genbankStreamSequence0.length());
101: assertEquals(1, genbankStreamSequence0.getTCount());
102: assertEquals(1, genbankStreamSequence0.getACount());
103: assertEquals(1, genbankStreamSequence0.getOtherCount());
104: assertNull(genbankStreamSequence0.getHeader());
105: assertEquals(1, genbankStreamSequence0.getGCount());
106: assertEquals(1, genbankStreamSequence0.getCCount());
107: assertEquals(2, genbankStreamSequence0.getFormatType());
108: assertEquals(2, strand0.getDirection());
109: assertFalse(strand0.isForwardStrand());
110: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
111: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
112: assertTrue(aTDeviationAlgorithm0.scalingFlag());
113: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
114: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
115: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
116: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
117: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
118: assertEquals(0.0F, (float)float0, 0.01F);
Test case 14
1: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm((Strand) null);
Test case 15
1: Bases bases0 = new Bases((Sequence) null);
2: assertNotNull(bases0);
3: assertEquals((-5), Bases.MIN_PRIORITY);
4: assertEquals(0, Bases.MEDIUM_PRIORITY);
5: assertEquals(2, Bases.REVERSE);
6: assertEquals(1, Bases.FORWARD);
7: assertEquals(5, Bases.MAX_PRIORITY);
8:
9: Strand strand0 = bases0.getReverseStrand();
10: assertNotNull(strand0);
11: assertEquals((-5), Bases.MIN_PRIORITY);
12: assertEquals(0, Bases.MEDIUM_PRIORITY);
13: assertEquals(2, Bases.REVERSE);
14: assertEquals(1, Bases.FORWARD);
15: assertEquals(5, Bases.MAX_PRIORITY);
16: assertEquals(2, Strand.REVERSE);
17: assertEquals(1, Strand.FORWARD);
18: assertFalse(strand0.isForwardStrand());
19: assertEquals(2, strand0.getDirection());
20:
21: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
22: assertNotNull(aTDeviationAlgorithm0);
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: assertEquals(2, Strand.REVERSE);
29: assertEquals(1, Strand.FORWARD);
30: assertFalse(strand0.isForwardStrand());
31: assertEquals(2, strand0.getDirection());
32: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
33: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
34: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
35: assertTrue(aTDeviationAlgorithm0.scalingFlag());
36: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
37: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
38: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
39: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
40:
41: float[] floatArray0 = new float[8];
42: aTDeviationAlgorithm0.getValues(2, 1, floatArray0);
Test case 16
1: Bases bases0 = new Bases((Sequence) null);
2: assertNotNull(bases0);
3: assertEquals((-5), Bases.MIN_PRIORITY);
4: assertEquals(0, Bases.MEDIUM_PRIORITY);
5: assertEquals(5, Bases.MAX_PRIORITY);
6: assertEquals(1, Bases.FORWARD);
7: assertEquals(2, Bases.REVERSE);
8:
9: Strand strand0 = bases0.getForwardStrand();
10: assertNotNull(strand0);
11: assertEquals((-5), Bases.MIN_PRIORITY);
12: assertEquals(0, Bases.MEDIUM_PRIORITY);
13: assertEquals(5, Bases.MAX_PRIORITY);
14: assertEquals(1, Bases.FORWARD);
15: assertEquals(2, Bases.REVERSE);
16: assertEquals(1, Strand.FORWARD);
17: assertEquals(2, Strand.REVERSE);
18: assertEquals(1, strand0.getDirection());
19: assertTrue(strand0.isForwardStrand());
20:
21: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
22: assertNotNull(aTDeviationAlgorithm0);
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: assertEquals(1, Strand.FORWARD);
29: assertEquals(2, Strand.REVERSE);
30: assertEquals(1, strand0.getDirection());
31: assertTrue(strand0.isForwardStrand());
32: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
33: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
34: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
35: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
36: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
37: assertTrue(aTDeviationAlgorithm0.scalingFlag());
38: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
39: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
40:
41: aTDeviationAlgorithm0.getValues(1, 2, (float[]) null);
Test case 17
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("Scaled Chi Square");
2: assertNotNull(emblStreamSequence0);
3: assertNull(emblStreamSequence0.getHeader());
4: assertEquals(17, emblStreamSequence0.length());
5: assertEquals(0, emblStreamSequence0.getTCount());
6: assertEquals(1, emblStreamSequence0.getFormatType());
7: assertEquals(2, emblStreamSequence0.getACount());
8: assertEquals(14, emblStreamSequence0.getOtherCount());
9: assertEquals(0, emblStreamSequence0.getGCount());
10: assertEquals(1, emblStreamSequence0.getCCount());
11:
12: Bases bases0 = new Bases(emblStreamSequence0);
13: assertNotNull(bases0);
14: assertEquals(2, Bases.REVERSE);
15: assertEquals(0, Bases.MEDIUM_PRIORITY);
16: assertEquals(5, Bases.MAX_PRIORITY);
17: assertEquals(1, Bases.FORWARD);
18: assertEquals((-5), Bases.MIN_PRIORITY);
19: assertNull(emblStreamSequence0.getHeader());
20: assertEquals(17, emblStreamSequence0.length());
21: assertEquals(0, emblStreamSequence0.getTCount());
22: assertEquals(1, emblStreamSequence0.getFormatType());
23: assertEquals(2, emblStreamSequence0.getACount());
24: assertEquals(14, emblStreamSequence0.getOtherCount());
25: assertEquals(0, emblStreamSequence0.getGCount());
26: assertEquals(1, emblStreamSequence0.getCCount());
27:
28: Strand strand0 = bases0.getReverseStrand();
29: assertNotNull(strand0);
30: assertEquals(2, Bases.REVERSE);
31: assertEquals(0, Bases.MEDIUM_PRIORITY);
32: assertEquals(5, Bases.MAX_PRIORITY);
33: assertEquals(1, Bases.FORWARD);
34: assertEquals((-5), Bases.MIN_PRIORITY);
35: assertEquals(2, Strand.REVERSE);
36: assertEquals(1, Strand.FORWARD);
37: assertNull(emblStreamSequence0.getHeader());
38: assertEquals(17, emblStreamSequence0.length());
39: assertEquals(0, emblStreamSequence0.getTCount());
40: assertEquals(1, emblStreamSequence0.getFormatType());
41: assertEquals(2, emblStreamSequence0.getACount());
42: assertEquals(14, emblStreamSequence0.getOtherCount());
43: assertEquals(0, emblStreamSequence0.getGCount());
44: assertEquals(1, emblStreamSequence0.getCCount());
45: assertFalse(strand0.isForwardStrand());
46: assertEquals(2, strand0.getDirection());
47:
48: ATDeviationAlgorithm aTDeviationAlgorithm0 = new ATDeviationAlgorithm(strand0);
49: assertNotNull(aTDeviationAlgorithm0);
50: assertEquals(2, Bases.REVERSE);
51: assertEquals(0, Bases.MEDIUM_PRIORITY);
52: assertEquals(5, Bases.MAX_PRIORITY);
53: assertEquals(1, Bases.FORWARD);
54: assertEquals((-5), Bases.MIN_PRIORITY);
55: assertEquals(2, Strand.REVERSE);
56: assertEquals(1, Strand.FORWARD);
57: assertNull(emblStreamSequence0.getHeader());
58: assertEquals(17, emblStreamSequence0.length());
59: assertEquals(0, emblStreamSequence0.getTCount());
60: assertEquals(1, emblStreamSequence0.getFormatType());
61: assertEquals(2, emblStreamSequence0.getACount());
62: assertEquals(14, emblStreamSequence0.getOtherCount());
63: assertEquals(0, emblStreamSequence0.getGCount());
64: assertEquals(1, emblStreamSequence0.getCCount());
65: assertFalse(strand0.isForwardStrand());
66: assertEquals(2, strand0.getDirection());
67: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
68: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
69: assertTrue(aTDeviationAlgorithm0.scalingFlag());
70: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
71: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
72: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
73: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
74: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
75:
76: Float float0 = aTDeviationAlgorithm0.getAverage();
77: assertNotNull(float0);
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: assertEquals(2, Strand.REVERSE);
84: assertEquals(1, Strand.FORWARD);
85: assertNull(emblStreamSequence0.getHeader());
86: assertEquals(17, emblStreamSequence0.length());
87: assertEquals(0, emblStreamSequence0.getTCount());
88: assertEquals(1, emblStreamSequence0.getFormatType());
89: assertEquals(2, emblStreamSequence0.getACount());
90: assertEquals(14, emblStreamSequence0.getOtherCount());
91: assertEquals(0, emblStreamSequence0.getGCount());
92: assertEquals(1, emblStreamSequence0.getCCount());
93: assertFalse(strand0.isForwardStrand());
94: assertEquals(2, strand0.getDirection());
95: assertFalse(aTDeviationAlgorithm0.isRevCompDisplay());
96: assertEquals(3.4028235E38F, aTDeviationAlgorithm0.getUserMax(), 0.01F);
97: assertTrue(aTDeviationAlgorithm0.scalingFlag());
98: assertFalse(aTDeviationAlgorithm0.isUserMaxMin());
99: assertEquals("AT Deviation (A-T)/(A+T)", aTDeviationAlgorithm0.getAlgorithmName());
100: assertEquals("at_deviation", aTDeviationAlgorithm0.getAlgorithmShortName());
101: assertEquals(1.4E-45F, aTDeviationAlgorithm0.getUserMin(), 0.01F);
102: assertEquals(1, aTDeviationAlgorithm0.getValueCount());
103: assertEquals((-1.0F), (float)float0, 0.01F);