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
|
/*
* 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;
import java.util.ArrayList;
import junit.framework.TestCase;
import org.biojava.bio.symbol.CircularLocation;
import org.biojava.bio.symbol.LocationTools;
import org.biojava.bio.symbol.Symbol;
import org.biojava.bio.symbol.SymbolList;
/**
* <code>CircularSequenceTest</code> tests are to ensure that the <code>CircularView</code>
* class can be instantiated and that the coordinate system works
*
* @author Mark Schreiber
*/
public class CircularSequenceTest extends TestCase
{
protected Sequence dna;
protected CircularView circ;
protected Symbol a = DNATools.a();
protected Symbol c = DNATools.c();
protected Symbol g = DNATools.g();
protected Symbol t = DNATools.t();
public CircularSequenceTest(String name)
{
super(name);
}
protected void setUp() throws Exception
{
dna = DNATools.createDNASequence("atcgctcaga","");
circ = new CircularView(dna);
}
public void testLocations(){
CircularLocation cloc = LocationTools.makeCircularLocation(1,5,dna.length());
assertEquals("atcgc", cloc.symbols(dna).seqString());
cloc = LocationTools.makeCircularLocation(1,10,dna.length());
assertEquals("atcgctcaga", cloc.symbols(dna).seqString());
cloc = LocationTools.makeCircularLocation(9,1,dna.length());
assertTrue(cloc.get5PrimeEnd() == 9);
assertEquals("gaa", cloc.symbols(dna).seqString());
// a more tricky case
ArrayList l = new ArrayList();
//this is the most 5'
l.add(LocationTools.makeCircularLocation(5,6, dna.length()));
//this is not the most 5'
l.add(LocationTools.makeCircularLocation(9,1,dna.length()));
l.add(LocationTools.makeCircularLocation(3,3, dna.length()));
cloc = (CircularLocation)LocationTools.union(l);
assertTrue(cloc.get5PrimeEnd() == 5);
assertEquals("ctgaac", cloc.symbols(dna).seqString());
}
public void testSubStr()
{
assertEquals("atc", circ.subStr(1,3));
assertEquals("aat", circ.subStr(0,2));
assertEquals("agaatc", circ.subStr(-2,3));
assertEquals("gaatc", circ.subStr(9,3));
assertEquals("gaatc", circ.subStr(9,13));
}
public void testSymbolAt()
{
assertEquals(a, circ.symbolAt(0));
assertEquals(c, circ.symbolAt(13));
assertEquals(g, circ.symbolAt(-1));
assertEquals(t, circ.symbolAt(-4));
}
public void testSubList() throws Exception
{
SymbolList s = DNATools.createDNA("agaatc");
//System.out.println(circ.subList(-2,3).seqString());
assertTrue(s.equals(circ.subList(-2,3)));
assertTrue(symsEq(circ.subList(-2,2), circ.subList(8,12)));
}
private boolean symsEq(SymbolList a, SymbolList b){
if(a.length() != b.length()) return false;
for(int i = 1; i <= a.length(); i++){
if(a.symbolAt(i) != b.symbolAt(i)) return false;
}
return true;
}
}
|
