Test case 1
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("centromere");
2: RawStreamSequence rawStreamSequence0 = new RawStreamSequence(emblStreamSequence0);
3: Bases bases0 = new Bases(rawStreamSequence0);
4: Strand strand0 = bases0.getForwardStrand();
5: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
6: cumulativeGCSkewAlgorithm0.getMinimumInternal();
Test case 2
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("E1J*nMUi");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
5: int int0 = cumulativeGCSkewAlgorithm0.getValueCount();
6: assertEquals(1, int0);
7: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
Test case 3
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("centromere");
2: RawStreamSequence rawStreamSequence0 = new RawStreamSequence(emblStreamSequence0);
3: Bases bases0 = new Bases(rawStreamSequence0);
4: Strand strand0 = bases0.getForwardStrand();
5: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
6: Float float0 = cumulativeGCSkewAlgorithm0.getMaximumInternal();
7: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
8: assertEquals(1.0F, (float)float0, 0.01F);
Test case 4
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("3\"ld32Y");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
5: float[] floatArray0 = new float[7];
6: cumulativeGCSkewAlgorithm0.getValues(0, (-5), floatArray0);
7: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
8: assertArrayEquals(new float[] {0.0F, 0.0F, 0.0F, 0.0F, 0.0F, 0.0F, 0.0F}, floatArray0, 0.01F);
Test case 5
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("K.?zfgN~e");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
5: float[] floatArray0 = new float[5];
6: cumulativeGCSkewAlgorithm0.getValues(372, 95401, floatArray0);
Test case 6
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("3\"ld32Y");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
5: float[] floatArray0 = new float[7];
6: cumulativeGCSkewAlgorithm0.getValues(0, 1637, floatArray0);
7: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
8: assertArrayEquals(new float[] {0.0F, 0.0F, 0.0F, 0.0F, 0.0F, 0.0F, 0.0F}, floatArray0, 0.01F);
Test case 7
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("3\"ld32Y");
2: assertEquals(0, fastaStreamSequence0.getCCount());
3: assertEquals(0, fastaStreamSequence0.getTCount());
4: assertEquals(0, fastaStreamSequence0.getACount());
5: assertEquals(7, fastaStreamSequence0.getOtherCount());
6: assertEquals(7, fastaStreamSequence0.length());
7: assertEquals(4, fastaStreamSequence0.getFormatType());
8: assertEquals(0, fastaStreamSequence0.getGCount());
9: assertNotNull(fastaStreamSequence0);
10:
11: Bases bases0 = new Bases(fastaStreamSequence0);
12: assertEquals(5, Bases.MAX_PRIORITY);
13: assertEquals(2, Bases.REVERSE);
14: assertEquals(0, Bases.MEDIUM_PRIORITY);
15: assertEquals((-5), Bases.MIN_PRIORITY);
16: assertEquals(1, Bases.FORWARD);
17: assertEquals(0, fastaStreamSequence0.getCCount());
18: assertEquals(0, fastaStreamSequence0.getTCount());
19: assertEquals(0, fastaStreamSequence0.getACount());
20: assertEquals(7, fastaStreamSequence0.getOtherCount());
21: assertEquals(7, fastaStreamSequence0.length());
22: assertEquals(4, fastaStreamSequence0.getFormatType());
23: assertEquals(0, fastaStreamSequence0.getGCount());
24: assertNotNull(bases0);
25:
26: Strand strand0 = bases0.getForwardStrand();
27: assertEquals(5, Bases.MAX_PRIORITY);
28: assertEquals(2, Bases.REVERSE);
29: assertEquals(0, Bases.MEDIUM_PRIORITY);
30: assertEquals((-5), Bases.MIN_PRIORITY);
31: assertEquals(1, Bases.FORWARD);
32: assertEquals(2, Strand.REVERSE);
33: assertEquals(1, Strand.FORWARD);
34: assertEquals(0, fastaStreamSequence0.getCCount());
35: assertEquals(0, fastaStreamSequence0.getTCount());
36: assertEquals(0, fastaStreamSequence0.getACount());
37: assertEquals(7, fastaStreamSequence0.getOtherCount());
38: assertEquals(7, fastaStreamSequence0.length());
39: assertEquals(4, fastaStreamSequence0.getFormatType());
40: assertEquals(0, fastaStreamSequence0.getGCount());
41: assertEquals(1, strand0.getDirection());
42: assertTrue(strand0.isForwardStrand());
43: assertNotNull(strand0);
44:
45: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals(2, Bases.REVERSE);
48: assertEquals(0, Bases.MEDIUM_PRIORITY);
49: assertEquals((-5), Bases.MIN_PRIORITY);
50: assertEquals(1, Bases.FORWARD);
51: assertEquals(2, Strand.REVERSE);
52: assertEquals(1, Strand.FORWARD);
53: assertEquals(0, fastaStreamSequence0.getCCount());
54: assertEquals(0, fastaStreamSequence0.getTCount());
55: assertEquals(0, fastaStreamSequence0.getACount());
56: assertEquals(7, fastaStreamSequence0.getOtherCount());
57: assertEquals(7, fastaStreamSequence0.length());
58: assertEquals(4, fastaStreamSequence0.getFormatType());
59: assertEquals(0, fastaStreamSequence0.getGCount());
60: assertEquals(1, strand0.getDirection());
61: assertTrue(strand0.isForwardStrand());
62: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
63: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
64: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
65: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
66: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
67: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
68: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
69: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
70: assertNotNull(cumulativeGCSkewAlgorithm0);
71:
72: Integer integer0 = cumulativeGCSkewAlgorithm0.getDefaultWindowSize();
73: assertEquals(60, (int)integer0);
74: assertEquals(5, Bases.MAX_PRIORITY);
75: assertEquals(2, Bases.REVERSE);
76: assertEquals(0, Bases.MEDIUM_PRIORITY);
77: assertEquals((-5), Bases.MIN_PRIORITY);
78: assertEquals(1, Bases.FORWARD);
79: assertEquals(2, Strand.REVERSE);
80: assertEquals(1, Strand.FORWARD);
81: assertEquals(0, fastaStreamSequence0.getCCount());
82: assertEquals(0, fastaStreamSequence0.getTCount());
83: assertEquals(0, fastaStreamSequence0.getACount());
84: assertEquals(7, fastaStreamSequence0.getOtherCount());
85: assertEquals(7, fastaStreamSequence0.length());
86: assertEquals(4, fastaStreamSequence0.getFormatType());
87: assertEquals(0, fastaStreamSequence0.getGCount());
88: assertEquals(1, strand0.getDirection());
89: assertTrue(strand0.isForwardStrand());
90: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
91: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
92: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
93: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
94: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
95: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
96: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
97: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
98: assertNotNull(integer0);
Test case 8
1: BioJavaSequence bioJavaSequence0 = new BioJavaSequence((SymbolList) null);
2: assertNotNull(bioJavaSequence0);
3:
4: Bases bases0 = new Bases(bioJavaSequence0);
5: assertEquals((-5), Bases.MIN_PRIORITY);
6: assertEquals(1, Bases.FORWARD);
7: assertEquals(0, Bases.MEDIUM_PRIORITY);
8: assertEquals(5, Bases.MAX_PRIORITY);
9: assertEquals(2, Bases.REVERSE);
10: assertNotNull(bases0);
11:
12: Strand strand0 = bases0.getForwardStrand();
13: assertEquals((-5), Bases.MIN_PRIORITY);
14: assertEquals(1, Bases.FORWARD);
15: assertEquals(0, Bases.MEDIUM_PRIORITY);
16: assertEquals(5, Bases.MAX_PRIORITY);
17: assertEquals(2, Bases.REVERSE);
18: assertEquals(1, Strand.FORWARD);
19: assertEquals(2, Strand.REVERSE);
20: assertEquals(1, strand0.getDirection());
21: assertTrue(strand0.isForwardStrand());
22: assertNotNull(strand0);
23:
24: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
25: assertEquals((-5), Bases.MIN_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals(0, Bases.MEDIUM_PRIORITY);
28: assertEquals(5, Bases.MAX_PRIORITY);
29: assertEquals(2, Bases.REVERSE);
30: assertEquals(1, Strand.FORWARD);
31: assertEquals(2, Strand.REVERSE);
32: assertEquals(1, strand0.getDirection());
33: assertTrue(strand0.isForwardStrand());
34: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
35: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
36: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
37: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
38: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
39: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
40: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
41: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
42: assertNotNull(cumulativeGCSkewAlgorithm0);
43:
44: Integer integer0 = cumulativeGCSkewAlgorithm0.getDefaultMaxWindowSize();
45: assertEquals(5000, (int)integer0);
46: assertEquals((-5), Bases.MIN_PRIORITY);
47: assertEquals(1, Bases.FORWARD);
48: assertEquals(0, Bases.MEDIUM_PRIORITY);
49: assertEquals(5, Bases.MAX_PRIORITY);
50: assertEquals(2, Bases.REVERSE);
51: assertEquals(1, Strand.FORWARD);
52: assertEquals(2, Strand.REVERSE);
53: assertEquals(1, strand0.getDirection());
54: assertTrue(strand0.isForwardStrand());
55: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
56: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
57: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
58: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
59: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
60: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
61: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
62: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
63: assertNotNull(integer0);
Test case 9
1: BioJavaSequence bioJavaSequence0 = new BioJavaSequence((SymbolList) null);
2: assertNotNull(bioJavaSequence0);
3:
4: Bases bases0 = new Bases(bioJavaSequence0);
5: assertEquals(5, Bases.MAX_PRIORITY);
6: assertEquals(1, Bases.FORWARD);
7: assertEquals((-5), Bases.MIN_PRIORITY);
8: assertEquals(0, Bases.MEDIUM_PRIORITY);
9: assertEquals(2, Bases.REVERSE);
10: assertNotNull(bases0);
11:
12: Strand strand0 = bases0.getForwardStrand();
13: assertEquals(5, Bases.MAX_PRIORITY);
14: assertEquals(1, Bases.FORWARD);
15: assertEquals((-5), Bases.MIN_PRIORITY);
16: assertEquals(0, Bases.MEDIUM_PRIORITY);
17: assertEquals(2, Bases.REVERSE);
18: assertEquals(2, Strand.REVERSE);
19: assertEquals(1, Strand.FORWARD);
20: assertEquals(1, strand0.getDirection());
21: assertTrue(strand0.isForwardStrand());
22: assertNotNull(strand0);
23:
24: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
25: assertEquals(5, Bases.MAX_PRIORITY);
26: assertEquals(1, Bases.FORWARD);
27: assertEquals((-5), Bases.MIN_PRIORITY);
28: assertEquals(0, Bases.MEDIUM_PRIORITY);
29: assertEquals(2, Bases.REVERSE);
30: assertEquals(2, Strand.REVERSE);
31: assertEquals(1, Strand.FORWARD);
32: assertEquals(1, strand0.getDirection());
33: assertTrue(strand0.isForwardStrand());
34: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
35: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
36: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
37: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
38: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
39: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
40: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
41: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
42: assertNotNull(cumulativeGCSkewAlgorithm0);
43:
44: Integer integer0 = cumulativeGCSkewAlgorithm0.getDefaultMinWindowSize();
45: assertEquals(10, (int)integer0);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals(1, Bases.FORWARD);
48: assertEquals((-5), Bases.MIN_PRIORITY);
49: assertEquals(0, Bases.MEDIUM_PRIORITY);
50: assertEquals(2, Bases.REVERSE);
51: assertEquals(2, Strand.REVERSE);
52: assertEquals(1, Strand.FORWARD);
53: assertEquals(1, strand0.getDirection());
54: assertTrue(strand0.isForwardStrand());
55: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
56: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
57: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
58: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
59: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
60: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
61: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
62: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
63: assertNotNull(integer0);
Test case 10
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("3\"ld32Y");
2: assertEquals(0, fastaStreamSequence0.getTCount());
3: assertEquals(0, fastaStreamSequence0.getCCount());
4: assertEquals(0, fastaStreamSequence0.getACount());
5: assertEquals(7, fastaStreamSequence0.length());
6: assertEquals(0, fastaStreamSequence0.getGCount());
7: assertEquals(7, fastaStreamSequence0.getOtherCount());
8: assertEquals(4, fastaStreamSequence0.getFormatType());
9: assertNotNull(fastaStreamSequence0);
10:
11: Bases bases0 = new Bases(fastaStreamSequence0);
12: assertEquals(5, Bases.MAX_PRIORITY);
13: assertEquals((-5), Bases.MIN_PRIORITY);
14: assertEquals(1, Bases.FORWARD);
15: assertEquals(2, Bases.REVERSE);
16: assertEquals(0, Bases.MEDIUM_PRIORITY);
17: assertEquals(0, fastaStreamSequence0.getTCount());
18: assertEquals(0, fastaStreamSequence0.getCCount());
19: assertEquals(0, fastaStreamSequence0.getACount());
20: assertEquals(7, fastaStreamSequence0.length());
21: assertEquals(0, fastaStreamSequence0.getGCount());
22: assertEquals(7, fastaStreamSequence0.getOtherCount());
23: assertEquals(4, fastaStreamSequence0.getFormatType());
24: assertNotNull(bases0);
25:
26: Strand strand0 = bases0.getForwardStrand();
27: assertEquals(5, Bases.MAX_PRIORITY);
28: assertEquals((-5), Bases.MIN_PRIORITY);
29: assertEquals(1, Bases.FORWARD);
30: assertEquals(2, Bases.REVERSE);
31: assertEquals(0, Bases.MEDIUM_PRIORITY);
32: assertEquals(2, Strand.REVERSE);
33: assertEquals(1, Strand.FORWARD);
34: assertEquals(0, fastaStreamSequence0.getTCount());
35: assertEquals(0, fastaStreamSequence0.getCCount());
36: assertEquals(0, fastaStreamSequence0.getACount());
37: assertEquals(7, fastaStreamSequence0.length());
38: assertEquals(0, fastaStreamSequence0.getGCount());
39: assertEquals(7, fastaStreamSequence0.getOtherCount());
40: assertEquals(4, fastaStreamSequence0.getFormatType());
41: assertEquals(1, strand0.getDirection());
42: assertTrue(strand0.isForwardStrand());
43: assertNotNull(strand0);
44:
45: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
46: assertEquals(5, Bases.MAX_PRIORITY);
47: assertEquals((-5), Bases.MIN_PRIORITY);
48: assertEquals(1, Bases.FORWARD);
49: assertEquals(2, Bases.REVERSE);
50: assertEquals(0, Bases.MEDIUM_PRIORITY);
51: assertEquals(2, Strand.REVERSE);
52: assertEquals(1, Strand.FORWARD);
53: assertEquals(0, fastaStreamSequence0.getTCount());
54: assertEquals(0, fastaStreamSequence0.getCCount());
55: assertEquals(0, fastaStreamSequence0.getACount());
56: assertEquals(7, fastaStreamSequence0.length());
57: assertEquals(0, fastaStreamSequence0.getGCount());
58: assertEquals(7, fastaStreamSequence0.getOtherCount());
59: assertEquals(4, fastaStreamSequence0.getFormatType());
60: assertEquals(1, strand0.getDirection());
61: assertTrue(strand0.isForwardStrand());
62: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
63: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
64: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
65: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
66: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
67: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
68: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
69: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
70: assertNotNull(cumulativeGCSkewAlgorithm0);
71:
72: Integer integer0 = cumulativeGCSkewAlgorithm0.getDefaultStepSize(5);
73: assertEquals(5, Bases.MAX_PRIORITY);
74: assertEquals((-5), Bases.MIN_PRIORITY);
75: assertEquals(1, Bases.FORWARD);
76: assertEquals(2, Bases.REVERSE);
77: assertEquals(0, Bases.MEDIUM_PRIORITY);
78: assertEquals(2, Strand.REVERSE);
79: assertEquals(1, Strand.FORWARD);
80: assertEquals(0, fastaStreamSequence0.getTCount());
81: assertEquals(0, fastaStreamSequence0.getCCount());
82: assertEquals(0, fastaStreamSequence0.getACount());
83: assertEquals(7, fastaStreamSequence0.length());
84: assertEquals(0, fastaStreamSequence0.getGCount());
85: assertEquals(7, fastaStreamSequence0.getOtherCount());
86: assertEquals(4, fastaStreamSequence0.getFormatType());
87: assertEquals(1, strand0.getDirection());
88: assertTrue(strand0.isForwardStrand());
89: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
90: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
91: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
92: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
93: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
94: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
95: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
96: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
97: assertNull(integer0);
Test case 11
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("K.?zfgN~e");
2: assertEquals(8, genbankStreamSequence0.getOtherCount());
3: assertEquals(2, genbankStreamSequence0.getFormatType());
4: assertEquals(9, genbankStreamSequence0.length());
5: assertEquals(1, genbankStreamSequence0.getGCount());
6: assertEquals(0, genbankStreamSequence0.getACount());
7: assertNull(genbankStreamSequence0.getHeader());
8: assertEquals(0, genbankStreamSequence0.getCCount());
9: assertEquals(0, genbankStreamSequence0.getTCount());
10: assertNotNull(genbankStreamSequence0);
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertEquals(2, Bases.REVERSE);
14: assertEquals(0, Bases.MEDIUM_PRIORITY);
15: assertEquals(5, Bases.MAX_PRIORITY);
16: assertEquals(1, Bases.FORWARD);
17: assertEquals((-5), Bases.MIN_PRIORITY);
18: assertEquals(8, genbankStreamSequence0.getOtherCount());
19: assertEquals(2, genbankStreamSequence0.getFormatType());
20: assertEquals(9, genbankStreamSequence0.length());
21: assertEquals(1, genbankStreamSequence0.getGCount());
22: assertEquals(0, genbankStreamSequence0.getACount());
23: assertNull(genbankStreamSequence0.getHeader());
24: assertEquals(0, genbankStreamSequence0.getCCount());
25: assertEquals(0, genbankStreamSequence0.getTCount());
26: assertNotNull(bases0);
27:
28: Strand strand0 = bases0.getForwardStrand();
29: assertEquals(2, Bases.REVERSE);
30: assertEquals(0, Bases.MEDIUM_PRIORITY);
31: assertEquals(5, Bases.MAX_PRIORITY);
32: assertEquals(1, Bases.FORWARD);
33: assertEquals((-5), Bases.MIN_PRIORITY);
34: assertEquals(2, Strand.REVERSE);
35: assertEquals(1, Strand.FORWARD);
36: assertEquals(8, genbankStreamSequence0.getOtherCount());
37: assertEquals(2, genbankStreamSequence0.getFormatType());
38: assertEquals(9, genbankStreamSequence0.length());
39: assertEquals(1, genbankStreamSequence0.getGCount());
40: assertEquals(0, genbankStreamSequence0.getACount());
41: assertNull(genbankStreamSequence0.getHeader());
42: assertEquals(0, genbankStreamSequence0.getCCount());
43: assertEquals(0, genbankStreamSequence0.getTCount());
44: assertTrue(strand0.isForwardStrand());
45: assertEquals(1, strand0.getDirection());
46: assertNotNull(strand0);
47:
48: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
49: assertEquals(2, Bases.REVERSE);
50: assertEquals(0, Bases.MEDIUM_PRIORITY);
51: assertEquals(5, Bases.MAX_PRIORITY);
52: assertEquals(1, Bases.FORWARD);
53: assertEquals((-5), Bases.MIN_PRIORITY);
54: assertEquals(2, Strand.REVERSE);
55: assertEquals(1, Strand.FORWARD);
56: assertEquals(8, genbankStreamSequence0.getOtherCount());
57: assertEquals(2, genbankStreamSequence0.getFormatType());
58: assertEquals(9, genbankStreamSequence0.length());
59: assertEquals(1, genbankStreamSequence0.getGCount());
60: assertEquals(0, genbankStreamSequence0.getACount());
61: assertNull(genbankStreamSequence0.getHeader());
62: assertEquals(0, genbankStreamSequence0.getCCount());
63: assertEquals(0, genbankStreamSequence0.getTCount());
64: assertTrue(strand0.isForwardStrand());
65: assertEquals(1, strand0.getDirection());
66: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
67: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
68: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
69: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
70: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
71: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
72: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
73: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
74: assertNotNull(cumulativeGCSkewAlgorithm0);
75:
76: Integer integer0 = cumulativeGCSkewAlgorithm0.getDefaultStepSize(4331);
77: assertEquals(433, (int)integer0);
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: assertEquals(8, genbankStreamSequence0.getOtherCount());
86: assertEquals(2, genbankStreamSequence0.getFormatType());
87: assertEquals(9, genbankStreamSequence0.length());
88: assertEquals(1, genbankStreamSequence0.getGCount());
89: assertEquals(0, genbankStreamSequence0.getACount());
90: assertNull(genbankStreamSequence0.getHeader());
91: assertEquals(0, genbankStreamSequence0.getCCount());
92: assertEquals(0, genbankStreamSequence0.getTCount());
93: assertTrue(strand0.isForwardStrand());
94: assertEquals(1, strand0.getDirection());
95: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
96: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
97: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
98: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
99: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
100: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
101: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
102: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
103: assertNotNull(integer0);
Test case 12
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("");
2: assertEquals(0, emblStreamSequence0.length());
3: assertNull(emblStreamSequence0.getHeader());
4: assertEquals(1, emblStreamSequence0.getFormatType());
5: assertEquals(0, emblStreamSequence0.getACount());
6: assertEquals(0, emblStreamSequence0.getTCount());
7: assertEquals(0, emblStreamSequence0.getGCount());
8: assertEquals(0, emblStreamSequence0.getCCount());
9: assertEquals(0, emblStreamSequence0.getOtherCount());
10: assertNotNull(emblStreamSequence0);
11:
12: RawStreamSequence rawStreamSequence0 = new RawStreamSequence(emblStreamSequence0);
13: assertEquals(0, emblStreamSequence0.length());
14: assertNull(emblStreamSequence0.getHeader());
15: assertEquals(1, emblStreamSequence0.getFormatType());
16: assertEquals(0, emblStreamSequence0.getACount());
17: assertEquals(0, emblStreamSequence0.getTCount());
18: assertEquals(0, emblStreamSequence0.getGCount());
19: assertEquals(0, emblStreamSequence0.getCCount());
20: assertEquals(0, emblStreamSequence0.getOtherCount());
21: assertEquals(0, rawStreamSequence0.length());
22: assertEquals(0, rawStreamSequence0.getCCount());
23: assertEquals(0, rawStreamSequence0.getACount());
24: assertEquals(0, rawStreamSequence0.getGCount());
25: assertEquals(3, rawStreamSequence0.getFormatType());
26: assertEquals(0, rawStreamSequence0.getOtherCount());
27: assertEquals(0, rawStreamSequence0.getTCount());
28: assertNotNull(rawStreamSequence0);
29:
30: Bases bases0 = new Bases(rawStreamSequence0);
31: assertEquals((-5), Bases.MIN_PRIORITY);
32: assertEquals(0, Bases.MEDIUM_PRIORITY);
33: assertEquals(2, Bases.REVERSE);
34: assertEquals(1, Bases.FORWARD);
35: assertEquals(5, Bases.MAX_PRIORITY);
36: assertEquals(0, emblStreamSequence0.length());
37: assertNull(emblStreamSequence0.getHeader());
38: assertEquals(1, emblStreamSequence0.getFormatType());
39: assertEquals(0, emblStreamSequence0.getACount());
40: assertEquals(0, emblStreamSequence0.getTCount());
41: assertEquals(0, emblStreamSequence0.getGCount());
42: assertEquals(0, emblStreamSequence0.getCCount());
43: assertEquals(0, emblStreamSequence0.getOtherCount());
44: assertEquals(0, rawStreamSequence0.length());
45: assertEquals(0, rawStreamSequence0.getCCount());
46: assertEquals(0, rawStreamSequence0.getACount());
47: assertEquals(0, rawStreamSequence0.getGCount());
48: assertEquals(3, rawStreamSequence0.getFormatType());
49: assertEquals(0, rawStreamSequence0.getOtherCount());
50: assertEquals(0, rawStreamSequence0.getTCount());
51: assertNotNull(bases0);
52:
53: Strand strand0 = bases0.getForwardStrand();
54: assertEquals((-5), Bases.MIN_PRIORITY);
55: assertEquals(0, Bases.MEDIUM_PRIORITY);
56: assertEquals(2, Bases.REVERSE);
57: assertEquals(1, Bases.FORWARD);
58: assertEquals(5, Bases.MAX_PRIORITY);
59: assertEquals(2, Strand.REVERSE);
60: assertEquals(1, Strand.FORWARD);
61: assertEquals(0, emblStreamSequence0.length());
62: assertNull(emblStreamSequence0.getHeader());
63: assertEquals(1, emblStreamSequence0.getFormatType());
64: assertEquals(0, emblStreamSequence0.getACount());
65: assertEquals(0, emblStreamSequence0.getTCount());
66: assertEquals(0, emblStreamSequence0.getGCount());
67: assertEquals(0, emblStreamSequence0.getCCount());
68: assertEquals(0, emblStreamSequence0.getOtherCount());
69: assertEquals(0, rawStreamSequence0.length());
70: assertEquals(0, rawStreamSequence0.getCCount());
71: assertEquals(0, rawStreamSequence0.getACount());
72: assertEquals(0, rawStreamSequence0.getGCount());
73: assertEquals(3, rawStreamSequence0.getFormatType());
74: assertEquals(0, rawStreamSequence0.getOtherCount());
75: assertEquals(0, rawStreamSequence0.getTCount());
76: assertEquals(1, strand0.getDirection());
77: assertTrue(strand0.isForwardStrand());
78: assertNotNull(strand0);
79:
80: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
81: assertEquals((-5), Bases.MIN_PRIORITY);
82: assertEquals(0, Bases.MEDIUM_PRIORITY);
83: assertEquals(2, Bases.REVERSE);
84: assertEquals(1, Bases.FORWARD);
85: assertEquals(5, Bases.MAX_PRIORITY);
86: assertEquals(2, Strand.REVERSE);
87: assertEquals(1, Strand.FORWARD);
88: assertEquals(0, emblStreamSequence0.length());
89: assertNull(emblStreamSequence0.getHeader());
90: assertEquals(1, emblStreamSequence0.getFormatType());
91: assertEquals(0, emblStreamSequence0.getACount());
92: assertEquals(0, emblStreamSequence0.getTCount());
93: assertEquals(0, emblStreamSequence0.getGCount());
94: assertEquals(0, emblStreamSequence0.getCCount());
95: assertEquals(0, emblStreamSequence0.getOtherCount());
96: assertEquals(0, rawStreamSequence0.length());
97: assertEquals(0, rawStreamSequence0.getCCount());
98: assertEquals(0, rawStreamSequence0.getACount());
99: assertEquals(0, rawStreamSequence0.getGCount());
100: assertEquals(3, rawStreamSequence0.getFormatType());
101: assertEquals(0, rawStreamSequence0.getOtherCount());
102: assertEquals(0, rawStreamSequence0.getTCount());
103: assertEquals(1, strand0.getDirection());
104: assertTrue(strand0.isForwardStrand());
105: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
106: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
107: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
108: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
109: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
110: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
111: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
112: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
113: assertNotNull(cumulativeGCSkewAlgorithm0);
114:
115: Float float0 = cumulativeGCSkewAlgorithm0.getAverage();
116: assertEquals(0.0F, (float)float0, 0.01F);
117: assertEquals((-5), Bases.MIN_PRIORITY);
118: assertEquals(0, Bases.MEDIUM_PRIORITY);
119: assertEquals(2, Bases.REVERSE);
120: assertEquals(1, Bases.FORWARD);
121: assertEquals(5, Bases.MAX_PRIORITY);
122: assertEquals(2, Strand.REVERSE);
123: assertEquals(1, Strand.FORWARD);
124: assertEquals(0, emblStreamSequence0.length());
125: assertNull(emblStreamSequence0.getHeader());
126: assertEquals(1, emblStreamSequence0.getFormatType());
127: assertEquals(0, emblStreamSequence0.getACount());
128: assertEquals(0, emblStreamSequence0.getTCount());
129: assertEquals(0, emblStreamSequence0.getGCount());
130: assertEquals(0, emblStreamSequence0.getCCount());
131: assertEquals(0, emblStreamSequence0.getOtherCount());
132: assertEquals(0, rawStreamSequence0.length());
133: assertEquals(0, rawStreamSequence0.getCCount());
134: assertEquals(0, rawStreamSequence0.getACount());
135: assertEquals(0, rawStreamSequence0.getGCount());
136: assertEquals(3, rawStreamSequence0.getFormatType());
137: assertEquals(0, rawStreamSequence0.getOtherCount());
138: assertEquals(0, rawStreamSequence0.getTCount());
139: assertEquals(1, strand0.getDirection());
140: assertTrue(strand0.isForwardStrand());
141: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
142: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
143: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
144: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
145: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
146: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
147: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
148: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
149: assertNotNull(float0);
Test case 13
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("centromere");
2: assertEquals(0, emblStreamSequence0.getACount());
3: assertEquals(1, emblStreamSequence0.getFormatType());
4: assertEquals(1, emblStreamSequence0.getTCount());
5: assertNull(emblStreamSequence0.getHeader());
6: assertEquals(8, emblStreamSequence0.getOtherCount());
7: assertEquals(1, emblStreamSequence0.getCCount());
8: assertEquals(10, emblStreamSequence0.length());
9: assertEquals(0, emblStreamSequence0.getGCount());
10: assertNotNull(emblStreamSequence0);
11:
12: RawStreamSequence rawStreamSequence0 = new RawStreamSequence(emblStreamSequence0);
13: assertEquals(0, emblStreamSequence0.getACount());
14: assertEquals(1, emblStreamSequence0.getFormatType());
15: assertEquals(1, emblStreamSequence0.getTCount());
16: assertNull(emblStreamSequence0.getHeader());
17: assertEquals(8, emblStreamSequence0.getOtherCount());
18: assertEquals(1, emblStreamSequence0.getCCount());
19: assertEquals(10, emblStreamSequence0.length());
20: assertEquals(0, emblStreamSequence0.getGCount());
21: assertEquals(10, rawStreamSequence0.length());
22: assertEquals(8, rawStreamSequence0.getOtherCount());
23: assertEquals(1, rawStreamSequence0.getTCount());
24: assertEquals(1, rawStreamSequence0.getCCount());
25: assertEquals(0, rawStreamSequence0.getGCount());
26: assertEquals(3, rawStreamSequence0.getFormatType());
27: assertEquals(0, rawStreamSequence0.getACount());
28: assertNotNull(rawStreamSequence0);
29:
30: Bases bases0 = new Bases(rawStreamSequence0);
31: assertEquals((-5), Bases.MIN_PRIORITY);
32: assertEquals(0, Bases.MEDIUM_PRIORITY);
33: assertEquals(2, Bases.REVERSE);
34: assertEquals(1, Bases.FORWARD);
35: assertEquals(5, Bases.MAX_PRIORITY);
36: assertEquals(0, emblStreamSequence0.getACount());
37: assertEquals(1, emblStreamSequence0.getFormatType());
38: assertEquals(1, emblStreamSequence0.getTCount());
39: assertNull(emblStreamSequence0.getHeader());
40: assertEquals(8, emblStreamSequence0.getOtherCount());
41: assertEquals(1, emblStreamSequence0.getCCount());
42: assertEquals(10, emblStreamSequence0.length());
43: assertEquals(0, emblStreamSequence0.getGCount());
44: assertEquals(10, rawStreamSequence0.length());
45: assertEquals(8, rawStreamSequence0.getOtherCount());
46: assertEquals(1, rawStreamSequence0.getTCount());
47: assertEquals(1, rawStreamSequence0.getCCount());
48: assertEquals(0, rawStreamSequence0.getGCount());
49: assertEquals(3, rawStreamSequence0.getFormatType());
50: assertEquals(0, rawStreamSequence0.getACount());
51: assertNotNull(bases0);
52:
53: Strand strand0 = bases0.getForwardStrand();
54: assertEquals((-5), Bases.MIN_PRIORITY);
55: assertEquals(0, Bases.MEDIUM_PRIORITY);
56: assertEquals(2, Bases.REVERSE);
57: assertEquals(1, Bases.FORWARD);
58: assertEquals(5, Bases.MAX_PRIORITY);
59: assertEquals(1, Strand.FORWARD);
60: assertEquals(2, Strand.REVERSE);
61: assertEquals(0, emblStreamSequence0.getACount());
62: assertEquals(1, emblStreamSequence0.getFormatType());
63: assertEquals(1, emblStreamSequence0.getTCount());
64: assertNull(emblStreamSequence0.getHeader());
65: assertEquals(8, emblStreamSequence0.getOtherCount());
66: assertEquals(1, emblStreamSequence0.getCCount());
67: assertEquals(10, emblStreamSequence0.length());
68: assertEquals(0, emblStreamSequence0.getGCount());
69: assertEquals(10, rawStreamSequence0.length());
70: assertEquals(8, rawStreamSequence0.getOtherCount());
71: assertEquals(1, rawStreamSequence0.getTCount());
72: assertEquals(1, rawStreamSequence0.getCCount());
73: assertEquals(0, rawStreamSequence0.getGCount());
74: assertEquals(3, rawStreamSequence0.getFormatType());
75: assertEquals(0, rawStreamSequence0.getACount());
76: assertEquals(1, strand0.getDirection());
77: assertTrue(strand0.isForwardStrand());
78: assertNotNull(strand0);
79:
80: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
81: assertEquals((-5), Bases.MIN_PRIORITY);
82: assertEquals(0, Bases.MEDIUM_PRIORITY);
83: assertEquals(2, Bases.REVERSE);
84: assertEquals(1, Bases.FORWARD);
85: assertEquals(5, Bases.MAX_PRIORITY);
86: assertEquals(1, Strand.FORWARD);
87: assertEquals(2, Strand.REVERSE);
88: assertEquals(0, emblStreamSequence0.getACount());
89: assertEquals(1, emblStreamSequence0.getFormatType());
90: assertEquals(1, emblStreamSequence0.getTCount());
91: assertNull(emblStreamSequence0.getHeader());
92: assertEquals(8, emblStreamSequence0.getOtherCount());
93: assertEquals(1, emblStreamSequence0.getCCount());
94: assertEquals(10, emblStreamSequence0.length());
95: assertEquals(0, emblStreamSequence0.getGCount());
96: assertEquals(10, rawStreamSequence0.length());
97: assertEquals(8, rawStreamSequence0.getOtherCount());
98: assertEquals(1, rawStreamSequence0.getTCount());
99: assertEquals(1, rawStreamSequence0.getCCount());
100: assertEquals(0, rawStreamSequence0.getGCount());
101: assertEquals(3, rawStreamSequence0.getFormatType());
102: assertEquals(0, rawStreamSequence0.getACount());
103: assertEquals(1, strand0.getDirection());
104: assertTrue(strand0.isForwardStrand());
105: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
106: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
107: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
108: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
109: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
110: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
111: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
112: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
113: assertNotNull(cumulativeGCSkewAlgorithm0);
114:
115: Float float0 = cumulativeGCSkewAlgorithm0.getAverage();
116: assertEquals((-1.0F), (float)float0, 0.01F);
117: assertEquals((-5), Bases.MIN_PRIORITY);
118: assertEquals(0, Bases.MEDIUM_PRIORITY);
119: assertEquals(2, Bases.REVERSE);
120: assertEquals(1, Bases.FORWARD);
121: assertEquals(5, Bases.MAX_PRIORITY);
122: assertEquals(1, Strand.FORWARD);
123: assertEquals(2, Strand.REVERSE);
124: assertEquals(0, emblStreamSequence0.getACount());
125: assertEquals(1, emblStreamSequence0.getFormatType());
126: assertEquals(1, emblStreamSequence0.getTCount());
127: assertNull(emblStreamSequence0.getHeader());
128: assertEquals(8, emblStreamSequence0.getOtherCount());
129: assertEquals(1, emblStreamSequence0.getCCount());
130: assertEquals(10, emblStreamSequence0.length());
131: assertEquals(0, emblStreamSequence0.getGCount());
132: assertEquals(10, rawStreamSequence0.length());
133: assertEquals(8, rawStreamSequence0.getOtherCount());
134: assertEquals(1, rawStreamSequence0.getTCount());
135: assertEquals(1, rawStreamSequence0.getCCount());
136: assertEquals(0, rawStreamSequence0.getGCount());
137: assertEquals(3, rawStreamSequence0.getFormatType());
138: assertEquals(0, rawStreamSequence0.getACount());
139: assertEquals(1, strand0.getDirection());
140: assertTrue(strand0.isForwardStrand());
141: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
142: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
143: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
144: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
145: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
146: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
147: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
148: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
149: assertNotNull(float0);
Test case 14
1: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm((Strand) null);
Test case 15
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("K.?zfgN~e");
2: assertEquals(9, genbankStreamSequence0.length());
3: assertEquals(1, genbankStreamSequence0.getGCount());
4: assertEquals(0, genbankStreamSequence0.getACount());
5: assertEquals(0, genbankStreamSequence0.getTCount());
6: assertEquals(8, genbankStreamSequence0.getOtherCount());
7: assertEquals(2, genbankStreamSequence0.getFormatType());
8: assertNull(genbankStreamSequence0.getHeader());
9: assertEquals(0, genbankStreamSequence0.getCCount());
10: assertNotNull(genbankStreamSequence0);
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertEquals(5, Bases.MAX_PRIORITY);
14: assertEquals(2, Bases.REVERSE);
15: assertEquals(0, Bases.MEDIUM_PRIORITY);
16: assertEquals(1, Bases.FORWARD);
17: assertEquals((-5), Bases.MIN_PRIORITY);
18: assertEquals(9, genbankStreamSequence0.length());
19: assertEquals(1, genbankStreamSequence0.getGCount());
20: assertEquals(0, genbankStreamSequence0.getACount());
21: assertEquals(0, genbankStreamSequence0.getTCount());
22: assertEquals(8, genbankStreamSequence0.getOtherCount());
23: assertEquals(2, genbankStreamSequence0.getFormatType());
24: assertNull(genbankStreamSequence0.getHeader());
25: assertEquals(0, genbankStreamSequence0.getCCount());
26: assertNotNull(bases0);
27:
28: Strand strand0 = bases0.getForwardStrand();
29: assertEquals(5, Bases.MAX_PRIORITY);
30: assertEquals(2, Bases.REVERSE);
31: assertEquals(0, Bases.MEDIUM_PRIORITY);
32: assertEquals(1, Bases.FORWARD);
33: assertEquals((-5), Bases.MIN_PRIORITY);
34: assertEquals(1, Strand.FORWARD);
35: assertEquals(2, Strand.REVERSE);
36: assertEquals(9, genbankStreamSequence0.length());
37: assertEquals(1, genbankStreamSequence0.getGCount());
38: assertEquals(0, genbankStreamSequence0.getACount());
39: assertEquals(0, genbankStreamSequence0.getTCount());
40: assertEquals(8, genbankStreamSequence0.getOtherCount());
41: assertEquals(2, genbankStreamSequence0.getFormatType());
42: assertNull(genbankStreamSequence0.getHeader());
43: assertEquals(0, genbankStreamSequence0.getCCount());
44: assertEquals(1, strand0.getDirection());
45: assertTrue(strand0.isForwardStrand());
46: assertNotNull(strand0);
47:
48: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
49: assertEquals(5, Bases.MAX_PRIORITY);
50: assertEquals(2, Bases.REVERSE);
51: assertEquals(0, Bases.MEDIUM_PRIORITY);
52: assertEquals(1, Bases.FORWARD);
53: assertEquals((-5), Bases.MIN_PRIORITY);
54: assertEquals(1, Strand.FORWARD);
55: assertEquals(2, Strand.REVERSE);
56: assertEquals(9, genbankStreamSequence0.length());
57: assertEquals(1, genbankStreamSequence0.getGCount());
58: assertEquals(0, genbankStreamSequence0.getACount());
59: assertEquals(0, genbankStreamSequence0.getTCount());
60: assertEquals(8, genbankStreamSequence0.getOtherCount());
61: assertEquals(2, genbankStreamSequence0.getFormatType());
62: assertNull(genbankStreamSequence0.getHeader());
63: assertEquals(0, genbankStreamSequence0.getCCount());
64: assertEquals(1, strand0.getDirection());
65: assertTrue(strand0.isForwardStrand());
66: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
67: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
68: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
69: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
70: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
71: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
72: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
73: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
74: assertNotNull(cumulativeGCSkewAlgorithm0);
75:
76: float[] floatArray0 = new float[5];
77: cumulativeGCSkewAlgorithm0.getValues(4112, 2, floatArray0);
Test case 16
1: char[] charArray0 = new char[3];
2: Short short0 = new Short((short)341);
3: assertEquals((short)341, (short)short0);
4: assertNotNull(short0);
5:
6: Integer integer0 = JLayeredPane.MODAL_LAYER;
7: assertEquals(200, (int)integer0);
8: assertNotNull(integer0);
9:
10: PartialSequence partialSequence0 = new PartialSequence(charArray0, (-604), (-2856), short0, integer0);
11: assertArrayEquals(new char[] {'\u0000', '\u0000', '\u0000'}, charArray0);
12: assertEquals(0, partialSequence0.getGCount());
13: assertEquals(0, partialSequence0.getTCount());
14: assertEquals(0, partialSequence0.getCCount());
15: assertEquals((-604), partialSequence0.length());
16: assertFalse(partialSequence0.isComplement());
17: assertEquals(0, partialSequence0.getACount());
18: assertEquals(200, (int)partialSequence0.getPhase());
19: assertEquals(3, partialSequence0.getOtherCount());
20: assertEquals((short)341, (short)partialSequence0.getStrand());
21: assertNotNull(partialSequence0);
22:
23: Bases bases0 = new Bases(partialSequence0);
24: assertArrayEquals(new char[] {'\u0000', '\u0000', '\u0000'}, charArray0);
25: assertEquals(0, Bases.MEDIUM_PRIORITY);
26: assertEquals((-5), Bases.MIN_PRIORITY);
27: assertEquals(5, Bases.MAX_PRIORITY);
28: assertEquals(2, Bases.REVERSE);
29: assertEquals(1, Bases.FORWARD);
30: assertEquals(0, partialSequence0.getGCount());
31: assertEquals(0, partialSequence0.getTCount());
32: assertEquals(0, partialSequence0.getCCount());
33: assertEquals((-604), partialSequence0.length());
34: assertFalse(partialSequence0.isComplement());
35: assertEquals(0, partialSequence0.getACount());
36: assertEquals(200, (int)partialSequence0.getPhase());
37: assertEquals(3, partialSequence0.getOtherCount());
38: assertEquals((short)341, (short)partialSequence0.getStrand());
39: assertNotNull(bases0);
40:
41: Strand strand0 = bases0.getForwardStrand();
42: assertArrayEquals(new char[] {'\u0000', '\u0000', '\u0000'}, charArray0);
43: assertEquals(0, Bases.MEDIUM_PRIORITY);
44: assertEquals((-5), Bases.MIN_PRIORITY);
45: assertEquals(5, Bases.MAX_PRIORITY);
46: assertEquals(2, Bases.REVERSE);
47: assertEquals(1, Bases.FORWARD);
48: assertEquals(1, Strand.FORWARD);
49: assertEquals(2, Strand.REVERSE);
50: assertEquals(0, partialSequence0.getGCount());
51: assertEquals(0, partialSequence0.getTCount());
52: assertEquals(0, partialSequence0.getCCount());
53: assertEquals((-604), partialSequence0.length());
54: assertFalse(partialSequence0.isComplement());
55: assertEquals(0, partialSequence0.getACount());
56: assertEquals(200, (int)partialSequence0.getPhase());
57: assertEquals(3, partialSequence0.getOtherCount());
58: assertEquals((short)341, (short)partialSequence0.getStrand());
59: assertEquals(1, strand0.getDirection());
60: assertTrue(strand0.isForwardStrand());
61: assertNotNull(strand0);
62:
63: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
64: assertArrayEquals(new char[] {'\u0000', '\u0000', '\u0000'}, charArray0);
65: assertEquals(0, Bases.MEDIUM_PRIORITY);
66: assertEquals((-5), Bases.MIN_PRIORITY);
67: assertEquals(5, Bases.MAX_PRIORITY);
68: assertEquals(2, Bases.REVERSE);
69: assertEquals(1, Bases.FORWARD);
70: assertEquals(1, Strand.FORWARD);
71: assertEquals(2, Strand.REVERSE);
72: assertEquals(0, partialSequence0.getGCount());
73: assertEquals(0, partialSequence0.getTCount());
74: assertEquals(0, partialSequence0.getCCount());
75: assertEquals((-604), partialSequence0.length());
76: assertFalse(partialSequence0.isComplement());
77: assertEquals(0, partialSequence0.getACount());
78: assertEquals(200, (int)partialSequence0.getPhase());
79: assertEquals(3, partialSequence0.getOtherCount());
80: assertEquals((short)341, (short)partialSequence0.getStrand());
81: assertEquals(1, strand0.getDirection());
82: assertTrue(strand0.isForwardStrand());
83: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
84: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
85: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
86: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
87: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
88: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
89: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
90: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
91: assertNotNull(cumulativeGCSkewAlgorithm0);
92:
93: float[] floatArray0 = new float[9];
94: cumulativeGCSkewAlgorithm0.getValues(0, 341, floatArray0);
Test case 17
1: BioJavaSequence bioJavaSequence0 = new BioJavaSequence((SymbolList) null);
2: assertNotNull(bioJavaSequence0);
3:
4: Bases bases0 = new Bases(bioJavaSequence0);
5: assertEquals(1, Bases.FORWARD);
6: assertEquals(2, Bases.REVERSE);
7: assertEquals(5, Bases.MAX_PRIORITY);
8: assertEquals((-5), Bases.MIN_PRIORITY);
9: assertEquals(0, Bases.MEDIUM_PRIORITY);
10: assertNotNull(bases0);
11:
12: Strand strand0 = bases0.getForwardStrand();
13: assertEquals(1, Bases.FORWARD);
14: assertEquals(2, Bases.REVERSE);
15: assertEquals(5, Bases.MAX_PRIORITY);
16: assertEquals((-5), Bases.MIN_PRIORITY);
17: assertEquals(0, Bases.MEDIUM_PRIORITY);
18: assertEquals(1, Strand.FORWARD);
19: assertEquals(2, Strand.REVERSE);
20: assertEquals(1, strand0.getDirection());
21: assertTrue(strand0.isForwardStrand());
22: assertNotNull(strand0);
23:
24: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
25: assertEquals(1, Bases.FORWARD);
26: assertEquals(2, Bases.REVERSE);
27: assertEquals(5, Bases.MAX_PRIORITY);
28: assertEquals((-5), Bases.MIN_PRIORITY);
29: assertEquals(0, Bases.MEDIUM_PRIORITY);
30: assertEquals(1, Strand.FORWARD);
31: assertEquals(2, Strand.REVERSE);
32: assertEquals(1, strand0.getDirection());
33: assertTrue(strand0.isForwardStrand());
34: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
35: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
36: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
37: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
38: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
39: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
40: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
41: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
42: assertNotNull(cumulativeGCSkewAlgorithm0);
43:
44: float[] floatArray0 = new float[5];
45: cumulativeGCSkewAlgorithm0.getValues(5, 169, floatArray0);
Test case 18
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("K.?zfgN~e");
2: assertEquals(8, genbankStreamSequence0.getOtherCount());
3: assertNull(genbankStreamSequence0.getHeader());
4: assertEquals(0, genbankStreamSequence0.getCCount());
5: assertEquals(9, genbankStreamSequence0.length());
6: assertEquals(1, genbankStreamSequence0.getGCount());
7: assertEquals(0, genbankStreamSequence0.getACount());
8: assertEquals(2, genbankStreamSequence0.getFormatType());
9: assertEquals(0, genbankStreamSequence0.getTCount());
10: assertNotNull(genbankStreamSequence0);
11:
12: Bases bases0 = new Bases(genbankStreamSequence0);
13: assertEquals(1, Bases.FORWARD);
14: assertEquals((-5), Bases.MIN_PRIORITY);
15: assertEquals(0, Bases.MEDIUM_PRIORITY);
16: assertEquals(2, Bases.REVERSE);
17: assertEquals(5, Bases.MAX_PRIORITY);
18: assertEquals(8, genbankStreamSequence0.getOtherCount());
19: assertNull(genbankStreamSequence0.getHeader());
20: assertEquals(0, genbankStreamSequence0.getCCount());
21: assertEquals(9, genbankStreamSequence0.length());
22: assertEquals(1, genbankStreamSequence0.getGCount());
23: assertEquals(0, genbankStreamSequence0.getACount());
24: assertEquals(2, genbankStreamSequence0.getFormatType());
25: assertEquals(0, genbankStreamSequence0.getTCount());
26: assertNotNull(bases0);
27:
28: Strand strand0 = bases0.getForwardStrand();
29: assertEquals(1, Bases.FORWARD);
30: assertEquals((-5), Bases.MIN_PRIORITY);
31: assertEquals(0, Bases.MEDIUM_PRIORITY);
32: assertEquals(2, Bases.REVERSE);
33: assertEquals(5, Bases.MAX_PRIORITY);
34: assertEquals(1, Strand.FORWARD);
35: assertEquals(2, Strand.REVERSE);
36: assertEquals(8, genbankStreamSequence0.getOtherCount());
37: assertNull(genbankStreamSequence0.getHeader());
38: assertEquals(0, genbankStreamSequence0.getCCount());
39: assertEquals(9, genbankStreamSequence0.length());
40: assertEquals(1, genbankStreamSequence0.getGCount());
41: assertEquals(0, genbankStreamSequence0.getACount());
42: assertEquals(2, genbankStreamSequence0.getFormatType());
43: assertEquals(0, genbankStreamSequence0.getTCount());
44: assertTrue(strand0.isForwardStrand());
45: assertEquals(1, strand0.getDirection());
46: assertNotNull(strand0);
47:
48: CumulativeGCSkewAlgorithm cumulativeGCSkewAlgorithm0 = new CumulativeGCSkewAlgorithm(strand0);
49: assertEquals(1, Bases.FORWARD);
50: assertEquals((-5), Bases.MIN_PRIORITY);
51: assertEquals(0, Bases.MEDIUM_PRIORITY);
52: assertEquals(2, Bases.REVERSE);
53: assertEquals(5, Bases.MAX_PRIORITY);
54: assertEquals(1, Strand.FORWARD);
55: assertEquals(2, Strand.REVERSE);
56: assertEquals(8, genbankStreamSequence0.getOtherCount());
57: assertNull(genbankStreamSequence0.getHeader());
58: assertEquals(0, genbankStreamSequence0.getCCount());
59: assertEquals(9, genbankStreamSequence0.length());
60: assertEquals(1, genbankStreamSequence0.getGCount());
61: assertEquals(0, genbankStreamSequence0.getACount());
62: assertEquals(2, genbankStreamSequence0.getFormatType());
63: assertEquals(0, genbankStreamSequence0.getTCount());
64: assertTrue(strand0.isForwardStrand());
65: assertEquals(1, strand0.getDirection());
66: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
67: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
68: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
69: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
70: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
71: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
72: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
73: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
74: assertNotNull(cumulativeGCSkewAlgorithm0);
75:
76: Float float0 = cumulativeGCSkewAlgorithm0.getAverage();
77: assertEquals(1.0F, (float)float0, 0.01F);
78: assertEquals(1, Bases.FORWARD);
79: assertEquals((-5), Bases.MIN_PRIORITY);
80: assertEquals(0, Bases.MEDIUM_PRIORITY);
81: assertEquals(2, Bases.REVERSE);
82: assertEquals(5, Bases.MAX_PRIORITY);
83: assertEquals(1, Strand.FORWARD);
84: assertEquals(2, Strand.REVERSE);
85: assertEquals(8, genbankStreamSequence0.getOtherCount());
86: assertNull(genbankStreamSequence0.getHeader());
87: assertEquals(0, genbankStreamSequence0.getCCount());
88: assertEquals(9, genbankStreamSequence0.length());
89: assertEquals(1, genbankStreamSequence0.getGCount());
90: assertEquals(0, genbankStreamSequence0.getACount());
91: assertEquals(2, genbankStreamSequence0.getFormatType());
92: assertEquals(0, genbankStreamSequence0.getTCount());
93: assertTrue(strand0.isForwardStrand());
94: assertEquals(1, strand0.getDirection());
95: assertFalse(cumulativeGCSkewAlgorithm0.isUserMaxMin());
96: assertEquals(1.4E-45F, cumulativeGCSkewAlgorithm0.getUserMin(), 0.01F);
97: assertTrue(cumulativeGCSkewAlgorithm0.scalingFlag());
98: assertEquals(1, cumulativeGCSkewAlgorithm0.getValueCount());
99: assertFalse(cumulativeGCSkewAlgorithm0.isRevCompDisplay());
100: assertEquals(3.4028235E38F, cumulativeGCSkewAlgorithm0.getUserMax(), 0.01F);
101: assertEquals("Cumulative GC Skew, (G-C)/(G+C)", cumulativeGCSkewAlgorithm0.getAlgorithmName());
102: assertEquals("gc_skew", cumulativeGCSkewAlgorithm0.getAlgorithmShortName());
103: assertNotNull(float0);