1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
|
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.seq.homol;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.StrandedFeature;
import org.biojava.bio.seq.impl.SimpleSequence;
import org.biojava.bio.symbol.RangeLocation;
import org.biojava.utils.ChangeListener;
public class SimpleSimilarityPairFeatureTest extends TestCase
{
protected Sequence qSeq;
protected Sequence sSeq;
protected SimilarityPairFeature qf;
protected SimilarityPairFeature sf;
public SimpleSimilarityPairFeatureTest(String name)
{
super(name);
}
protected void setUp() throws Exception
{
qSeq = new SimpleSequence(DNATools.createDNA("aacgtaggttccatgc"),
"fragment1",
"fragment1",
Annotation.EMPTY_ANNOTATION);
sSeq = new SimpleSequence(DNATools.createDNA("ttaacgtttttttttt"),
"fragment2",
"fragment2",
Annotation.EMPTY_ANNOTATION);
// Query sequence feature
SimilarityPairFeature.Template qt =
new SimilarityPairFeature.Template();
qt.type = "similarity";
qt.source = "test";
qt.location = new RangeLocation(1, 5);
qt.strand = StrandedFeature.POSITIVE;
qt.score = 1.0D;
qt.annotation = Annotation.EMPTY_ANNOTATION;
// Subject sequence feature
SimilarityPairFeature.Template st =
new SimilarityPairFeature.Template();
st.type = "similarity";
st.source = "test";
st.location = new RangeLocation(3, 7);
st.strand = StrandedFeature.POSITIVE;
st.score = 1.0D;
st.annotation = Annotation.EMPTY_ANNOTATION;
qt.alignment = SimilarityPairFeature.EMPTY_PAIRWISE;
st.alignment = SimilarityPairFeature.EMPTY_PAIRWISE;
qf = (SimilarityPairFeature) qSeq.createFeature(qt);
sf = (SimilarityPairFeature) sSeq.createFeature(st);
sf.setSibling(qf);
qf.setSibling(sf);
qf.addChangeListener(ChangeListener.ALWAYS_VETO);
sf.addChangeListener(ChangeListener.ALWAYS_VETO);
}
public void testGetType()
{
assertEquals("similarity", qf.getType());
assertEquals("similarity", sf.getType());
}
public void testGetSource()
{
assertEquals("test", qf.getSource());
assertEquals("test", sf.getSource());
}
public void testGetLocation()
{
assertEquals(1, qf.getLocation().getMin());
assertEquals(5, qf.getLocation().getMax());
assertEquals(3, sf.getLocation().getMin());
assertEquals(7, sf.getLocation().getMax());
}
public void testGetStrand()
{
assertEquals(StrandedFeature.POSITIVE, qf.getStrand());
assertEquals(StrandedFeature.POSITIVE, sf.getStrand());
}
public void testGetScore()
{
assertEquals(1.0D, qf.getScore(), 0.0D);
assertEquals(1.0D, sf.getScore(), 0.0D);
}
public void testGetAnnotation()
{
assertEquals(Annotation.EMPTY_ANNOTATION, qf.getAnnotation());
assertEquals(Annotation.EMPTY_ANNOTATION, sf.getAnnotation());
}
public void testGetAlignment()
{
assertEquals(SimilarityPairFeature.EMPTY_PAIRWISE, qf.getAlignment());
assertEquals(SimilarityPairFeature.EMPTY_PAIRWISE, sf.getAlignment());
}
public void testGetSibling()
{
assertEquals(qf, sf.getSibling());
assertEquals(sf, qf.getSibling());
}
}
|
