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  1. Project Clover database Mon Nov 11 2024 15:14:12 GMT
  2. Package jalview.analysis

File TestAlignSeq.java

 

Code metrics

2
45
9
1
166
105
10
0.22
5
9
1.11

Classes

Class Line # Actions
TestAlignSeq 47 45 10
0.9642857396.4%
 

Contributing tests

This file is covered by 4 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
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    import java.nio.charset.Charset;
33    import java.util.Locale;
34   
35    import org.testng.annotations.BeforeClass;
36    import org.testng.annotations.BeforeMethod;
37    import org.testng.annotations.Test;
38   
39    import com.google.common.base.Charsets;
40   
41    /**
42    * Test the alignment -> Mapping routines
43    *
44    * @author jimp
45    *
46    */
 
47    public class TestAlignSeq
48    {
49   
 
50  1 toggle @BeforeClass(alwaysRun = true)
51    public void setUpJvOptionPane()
52    {
53  1 JvOptionPane.setInteractiveMode(false);
54  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55    }
56   
57    SequenceI s1, s2, s3;
58   
59    /**
60    * @throws java.lang.Exception
61    */
 
62  4 toggle @BeforeMethod(alwaysRun = true)
63    public void setUp() throws Exception
64    {
65  4 s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
66  4 s1.setStart(3);
67  4 s1.setEnd(18);
68  4 s2 = new Sequence("Seq2", "ASDFA");
69  4 s2.setStart(5);
70  4 s2.setEnd(9);
71  4 s3 = new Sequence("Seq3", "SDFAQQQSSS");
72   
73    }
74   
 
75  1 toggle @Test(groups = { "Functional" })
76    /**
77    * simple test that mapping from alignment corresponds identical positions.
78    */
79    public void testGetMappingForS1()
80    {
81  1 AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
82  1 System.out.println("s1: " + as.getAStr1());
83  1 System.out.println("s2: " + as.getAStr2());
84   
85    // aligned results match
86  1 assertEquals("ASDFA", as.getAStr1());
87  1 assertEquals(as.getAStr1(), as.getAStr2());
88   
89  1 Mapping s1tos2 = as.getMappingFromS1(false);
90  1 checkMapping(s1tos2, s1, s2);
91    }
92   
 
93  2 toggle public void checkMapping(Mapping s1tos2, SequenceI _s1, SequenceI _s2)
94    {
95  2 System.out.println(s1tos2.getMap().toString());
96  10 for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
97    {
98  8 int p = s1tos2.getPosition(i);
99  8 char s2c = _s2.getCharAt(i - _s2.getStart());
100  8 char s1c = _s1.getCharAt(p - _s1.getStart());
101  8 System.out.println("Position in s2: " + i + s2c
102    + " maps to position in s1: " + p + s1c);
103  8 assertEquals(s1c, s2c);
104    }
105    }
106   
 
107  1 toggle @Test(groups = { "Functional" })
108    /**
109    * simple test that mapping from alignment corresponds identical positions.
110    */
111    public void testGetMappingForS1_withLowerCase()
112    {
113    // make one of the sequences lower case
114  1 SequenceI ns2 = new Sequence(s2);
115  1 ns2.replace('D', 'd');
116  1 AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, AlignSeq.PEP);
117  1 System.out.println("s1: " + as.getAStr1());
118  1 System.out.println("s2: " + as.getAStr2());
119   
120    // aligned results match
121  1 assertEquals("ASDFA", as.getAStr1());
122  1 assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
123   
124  1 Mapping s1tos2 = as.getMappingFromS1(false);
125  1 assertEquals("ASdFA", as.getAStr2());
126    // verify mapping is consistent between original all-caps sequences
127  1 checkMapping(s1tos2, s1, s2);
128    }
129   
 
130  1 toggle @Test(groups = { "Functional" })
131    public void testExtractGaps()
132    {
133  1 assertNull(AlignSeq.extractGaps(null, null));
134  1 assertNull(AlignSeq.extractGaps(". -", null));
135  1 assertNull(AlignSeq.extractGaps(null, "AB-C"));
136   
137  1 assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
138    }
139   
 
140  1 toggle @Test(groups = { "Functional" })
141    public void testPrintAlignment()
142    {
143  1 AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
144  1 final StringBuilder baos = new StringBuilder();
145  1 PrintStream ps = new PrintStream(System.out)
146    {
 
147  1 toggle @Override
148    public void print(String x)
149    {
150  1 baos.append(x);
151    }
152   
 
153  0 toggle @Override
154    public void println()
155    {
156  0 baos.append("\n");
157    }
158    };
159   
160  1 as.printAlignment(ps);
161  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"
162    + "Seq1/4-13 SDFAQQQRRR\n" + " ||||||| \n"
163    + "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
164  1 assertEquals(expected, baos.toString());
165    }
166    }