1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
|
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
20 |
|
|
21 |
|
package jalview.analysis; |
22 |
|
|
23 |
|
import static org.testng.AssertJUnit.assertEquals; |
24 |
|
import static org.testng.AssertJUnit.assertNull; |
25 |
|
|
26 |
|
import jalview.datamodel.Mapping; |
27 |
|
import jalview.datamodel.Sequence; |
28 |
|
import jalview.datamodel.SequenceI; |
29 |
|
import jalview.gui.JvOptionPane; |
30 |
|
|
31 |
|
import java.io.PrintStream; |
32 |
|
|
33 |
|
import org.testng.annotations.BeforeClass; |
34 |
|
import org.testng.annotations.BeforeMethod; |
35 |
|
import org.testng.annotations.Test; |
36 |
|
|
37 |
|
|
38 |
|
|
39 |
|
|
40 |
|
@author |
41 |
|
|
42 |
|
|
|
|
| 94.9% |
Uncovered Elements: 2 (39) |
Complexity: 8 |
Complexity Density: 0.27 |
|
43 |
|
public class TestAlignSeq |
44 |
|
{ |
45 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
46 |
1 |
@BeforeClass(alwaysRun = true)... |
47 |
|
public void setUpJvOptionPane() |
48 |
|
{ |
49 |
1 |
JvOptionPane.setInteractiveMode(false); |
50 |
1 |
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
51 |
|
} |
52 |
|
|
53 |
|
SequenceI s1, s2, s3; |
54 |
|
|
55 |
|
|
56 |
|
@throws |
57 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
|
58 |
3 |
@BeforeMethod(alwaysRun = true)... |
59 |
|
public void setUp() throws Exception |
60 |
|
{ |
61 |
3 |
s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS"); |
62 |
3 |
s1.setStart(3); |
63 |
3 |
s1.setEnd(18); |
64 |
3 |
s2 = new Sequence("Seq2", "ASDFA"); |
65 |
3 |
s2.setStart(5); |
66 |
3 |
s2.setEnd(9); |
67 |
3 |
s3 = new Sequence("Seq3", "SDFAQQQSSS"); |
68 |
|
|
69 |
|
} |
70 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 2 |
Complexity Density: 0.22 |
1PASS
|
|
71 |
1 |
@Test(groups = { "Functional" })... |
72 |
|
|
73 |
|
|
74 |
|
|
75 |
|
public void testGetMappingForS1() |
76 |
|
{ |
77 |
1 |
AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP); |
78 |
1 |
System.out.println("s1: " + as.getAStr1()); |
79 |
1 |
System.out.println("s2: " + as.getAStr2()); |
80 |
|
|
81 |
|
|
82 |
1 |
assertEquals("ASDFA", as.getAStr1()); |
83 |
1 |
assertEquals(as.getAStr1(), as.getAStr2()); |
84 |
|
|
85 |
1 |
Mapping s1tos2 = as.getMappingFromS1(false); |
86 |
1 |
System.out.println(s1tos2.getMap().toString()); |
87 |
5 |
for (int i = s2.getStart(); i < s2.getEnd(); i++) |
88 |
|
{ |
89 |
4 |
System.out.println("Position in s2: " + i |
90 |
|
+ " maps to position in s1: " + s1tos2.getPosition(i)); |
91 |
|
|
92 |
|
|
93 |
|
|
94 |
|
} |
95 |
|
} |
96 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
1PASS
|
|
97 |
1 |
@Test(groups = { "Functional" })... |
98 |
|
public void testExtractGaps() |
99 |
|
{ |
100 |
1 |
assertNull(AlignSeq.extractGaps(null, null)); |
101 |
1 |
assertNull(AlignSeq.extractGaps(". -", null)); |
102 |
1 |
assertNull(AlignSeq.extractGaps(null, "AB-C")); |
103 |
|
|
104 |
1 |
assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D.")); |
105 |
|
} |
106 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
1PASS
|
|
107 |
1 |
@Test(groups = { "Functional" })... |
108 |
|
public void testPrintAlignment() |
109 |
|
{ |
110 |
1 |
AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP); |
111 |
1 |
final StringBuilder baos = new StringBuilder(); |
112 |
1 |
PrintStream ps = new PrintStream(System.out) |
113 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
114 |
1 |
@Override... |
115 |
|
public void print(String x) |
116 |
|
{ |
117 |
1 |
baos.append(x); |
118 |
|
} |
119 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
120 |
0 |
@Override... |
121 |
|
public void println() |
122 |
|
{ |
123 |
0 |
baos.append("\n"); |
124 |
|
} |
125 |
|
}; |
126 |
|
|
127 |
1 |
as.printAlignment(ps); |
128 |
1 |
String expected = "Score = 320.0\nLength of alignment = 10\nSequence Seq1/4-13 (Sequence length = 14)\nSequence Seq3/1-10 (Sequence length = 10)\n\n" |
129 |
|
+ "Seq1/4-13 SDFAQQQRRR\n" |
130 |
|
+ " ||||||| \n" |
131 |
|
+ "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n"; |
132 |
1 |
assertEquals(expected, baos.toString()); |
133 |
|
} |
134 |
|
} |