Clover icon

Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.analysis

File DnaTest.java

 

Code metrics

8
199
19
1
573
406
23
0.12
10.47
19
1.21

Classes

Class Line # Actions
DnaTest 46 199 23
1.0100%
 

Contributing tests

This file is covered by 12 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.assertNotNull;
25    import static org.testng.AssertJUnit.assertTrue;
26   
27    import jalview.api.AlignViewportI;
28    import jalview.datamodel.AlignedCodon;
29    import jalview.datamodel.Alignment;
30    import jalview.datamodel.AlignmentI;
31    import jalview.datamodel.HiddenColumns;
32    import jalview.datamodel.Sequence;
33    import jalview.datamodel.SequenceI;
34    import jalview.gui.AlignViewport;
35    import jalview.gui.JvOptionPane;
36    import jalview.io.DataSourceType;
37    import jalview.io.FileFormat;
38    import jalview.io.FormatAdapter;
39   
40    import java.io.IOException;
41    import java.util.Iterator;
42   
43    import org.testng.annotations.BeforeClass;
44    import org.testng.annotations.Test;
45   
 
46    public class DnaTest
47    {
 
48  1 toggle @BeforeClass(alwaysRun = true)
49    public void setUpJvOptionPane()
50    {
51  1 JvOptionPane.setInteractiveMode(false);
52  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53    }
54   
55    // @formatter:off
56    // AA encoding codons as ordered on the Jalview help page Amino Acid Table
57    private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
58    + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
59    + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
60    + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
61    + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
62    + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
63    + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
64    + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
65    + "TAC" + "TAA" + "TAG" + "TGA";
66   
67    private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
68    + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
69    + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
70    + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
71    + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
72    + ">gi|27804621|gb|AY178912.1|/1-259\n"
73    + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
74    + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
75    + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
76    + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
77    + ">gi|27804623|gb|AY178913.1|/1-259\n"
78    + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
79    + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
80    + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
81    + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
82    + ">gi|27804627|gb|AY178915.1|/1-260\n"
83    + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
84    + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
85    + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
86    + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
87    + ">gi|27804631|gb|AY178917.1|/1-261\n"
88    + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
89    + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
90    + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
91    + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
92    + ">gi|27804635|gb|AY178919.1|/1-261\n"
93    + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
94    + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
95    + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
96    + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
97    + ">gi|27804641|gb|AY178922.1|/1-261\n"
98    + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
99    + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
100    + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
101    + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
102    + ">gi|27804647|gb|AY178925.1|/1-261\n"
103    + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
104    + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
105    + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
106    + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
107    + ">gi|27804649|gb|AY178926.1|/1-261\n"
108    + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
109    + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
110    + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
111    + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
112    + ">gi|27804653|gb|AY178928.1|/1-261\n"
113    + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
114    + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
115    + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
116    + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
117    + ">gi|27804659|gb|AY178931.1|/1-261\n"
118    + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
119    + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
120    + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
121    + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
122    // @formatter:on
123   
124    /**
125    * Corner case for this test is the presence of codons after codons that were
126    * not translated.
127    *
128    * @throws IOException
129    */
 
130  1 toggle @Test(groups = { "Functional" })
131    public void testTranslateCdna_withUntranslatableCodons()
132    throws IOException
133    {
134  1 AlignmentI alf = new FormatAdapter().readFile(
135    JAL_1312_example_align_fasta, DataSourceType.PASTE,
136    FileFormat.Fasta);
137  1 HiddenColumns cs = new HiddenColumns();
138  1 AlignViewportI av = new AlignViewport(alf, cs);
139  1 Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
140    false);
141  1 Dna dna = new Dna(av, contigs);
142  1 AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
143    .getStandardCodeTable());
144  1 assertNotNull("Couldn't do a full width translation of test data.",
145    translated);
146    }
147   
148    /**
149    * Test variant in which 15 column blocks at a time are translated (the rest
150    * hidden).
151    *
152    * @throws IOException
153    */
 
154  1 toggle @Test(groups = { "Functional" })
155    public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
156    throws IOException
157    {
158  1 AlignmentI alf = new FormatAdapter().readFile(
159    JAL_1312_example_align_fasta, DataSourceType.PASTE,
160    FileFormat.Fasta);
161  1 int vwidth = 15;
162  18 for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
163    {
164  17 HiddenColumns cs = new HiddenColumns();
165  17 if (ipos > 0)
166    {
167  16 cs.hideColumns(0, ipos - 1);
168    }
169  17 cs.hideColumns(ipos + vwidth, alf.getWidth());
170  17 Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
171    alf.getWidth(), false);
172  17 AlignViewportI av = new AlignViewport(alf, cs);
173  17 Dna dna = new Dna(av, vcontigs);
174  17 AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
175    .getStandardCodeTable());
176   
177  17 assertTrue("Translation failed (ipos=" + ipos
178    + ") No alignment data.", transAlf != null);
179  17 assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
180    transAlf.getHeight() > 0);
181  17 assertTrue("Translation failed (ipos=" + ipos + ") Translated "
182    + transAlf.getHeight() + " sequences from " + alf.getHeight()
183    + " sequences", alf.getHeight() == transAlf.getHeight());
184    }
185    }
186   
187    /**
188    * Test simple translation to Amino Acids (with STOP codons translated to *).
189    *
190    * @throws IOException
191    */
 
192  1 toggle @Test(groups = { "Functional" })
193    public void testTranslateCdna_simple() throws IOException
194    {
195  1 AlignmentI alf = new FormatAdapter().readFile(fasta,
196    DataSourceType.PASTE, FileFormat.Fasta);
197  1 HiddenColumns cs = new HiddenColumns();
198  1 AlignViewportI av = new AlignViewport(alf, cs);
199  1 Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
200    false);
201  1 Dna dna = new Dna(av, contigs);
202  1 AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
203    .getStandardCodeTable());
204  1 String aa = translated.getSequenceAt(0).getSequenceAsString();
205  1 assertEquals(
206    "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
207    aa);
208    }
209   
210    /**
211    * Test translation excluding hidden columns.
212    *
213    * @throws IOException
214    */
 
215  1 toggle @Test(groups = { "Functional" })
216    public void testTranslateCdna_hiddenColumns() throws IOException
217    {
218  1 AlignmentI alf = new FormatAdapter().readFile(fasta,
219    DataSourceType.PASTE, FileFormat.Fasta);
220  1 HiddenColumns cs = new HiddenColumns();
221  1 cs.hideColumns(6, 14); // hide codons 3/4/5
222  1 cs.hideColumns(24, 35); // hide codons 9-12
223  1 cs.hideColumns(177, 191); // hide codons 60-64
224  1 AlignViewportI av = new AlignViewport(alf, cs);
225  1 Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
226    false);
227  1 Dna dna = new Dna(av, contigs);
228  1 AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
229    .getStandardCodeTable());
230  1 String aa = translated.getSequenceAt(0).getSequenceAsString();
231  1 assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
232    }
233   
234    /**
235    * Use this test to help debug into any cases of interest.
236    */
 
237  1 toggle @Test(groups = { "Functional" })
238    public void testCompareCodonPos_oneOnly()
239    {
240  1 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
241    }
242   
243    /**
244    * Tests for method that compares 'alignment' of two codon position triplets.
245    */
 
246  1 toggle @Test(groups = { "Functional" })
247    public void testCompareCodonPos()
248    {
249    /*
250    * Returns 0 for any null argument
251    */
252  1 assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
253  1 assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
254   
255    /*
256    * Work through 27 combinations. First 9 cases where first position matches.
257    */
258  1 assertMatches("AAA", "GGG"); // 2 and 3 match
259  1 assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
260  1 assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
261  1 assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
262  1 assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
263  1 assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
264  1 assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
265  1 assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
266  1 assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
267   
268    /*
269    * 9 cases where first position is shifted in first sequence.
270    */
271  1 assertFollows("-AAA", "G-GG"); // 2 and 3 match
272  1 assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
273    // 'enclosing' case: pick first to start precedes
274  1 assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
275  1 assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
276  1 assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
277    // 'enclosing' case: pick first to start precedes
278  1 assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
279  1 assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
280  1 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
281  1 assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
282   
283    /*
284    * 9 cases where first position is shifted in second sequence.
285    */
286  1 assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
287  1 assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
288  1 assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
289  1 assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
290    // 'enclosing' case with middle base deciding:
291  1 assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
292  1 assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
293  1 assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
294  1 assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
295  1 assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
296    }
297   
298    /**
299    * This test generates a random cDNA alignment and its translation, then
300    * reorders the cDNA and retranslates, and verifies that the translations are
301    * the same (apart from ordering).
302    */
 
303  1 toggle @Test(groups = { "Functional" })
304    public void testTranslateCdna_sequenceOrderIndependent()
305    {
306    /*
307    * Generate cDNA - 8 sequences of 12 bases each.
308    */
309  1 AlignmentI cdna = new AlignmentGenerator(true)
310    .generate(12, 8, 97, 5, 5);
311  1 HiddenColumns cs = new HiddenColumns();
312  1 AlignViewportI av = new AlignViewport(cdna, cs);
313  1 Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
314    false);
315  1 Dna dna = new Dna(av, contigs);
316  1 AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
317    .getStandardCodeTable());
318   
319    /*
320    * Jumble the cDNA sequences and translate.
321    */
322  1 SequenceI[] sorted = new SequenceI[cdna.getHeight()];
323  1 final int[] jumbler = new int[] { 6, 7, 3, 4, 2, 0, 1, 5 };
324  1 int seqNo = 0;
325  1 for (int i : jumbler)
326    {
327  8 sorted[seqNo++] = cdna.getSequenceAt(i);
328    }
329  1 AlignmentI cdnaReordered = new Alignment(sorted);
330  1 av = new AlignViewport(cdnaReordered, cs);
331  1 contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
332  1 dna = new Dna(av, contigs);
333  1 AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
334    .getStandardCodeTable());
335   
336    /*
337    * Check translated sequences are the same in both alignments.
338    */
339  1 System.out.println("Original");
340  1 System.out.println(translated.toString());
341  1 System.out.println("Sorted");
342  1 System.out.println(translated2.toString());
343   
344  1 int sortedSequenceIndex = 0;
345  1 for (int originalSequenceIndex : jumbler)
346    {
347  8 final String translation1 = translated.getSequenceAt(
348    originalSequenceIndex).getSequenceAsString();
349  8 final String translation2 = translated2.getSequenceAt(
350    sortedSequenceIndex).getSequenceAsString();
351  8 assertEquals(translation2, translation1);
352  8 sortedSequenceIndex++;
353    }
354    }
355   
356    /**
357    * Test that all the cases in testCompareCodonPos have a 'symmetric'
358    * comparison (without checking the actual comparison result).
359    */
 
360  1 toggle @Test(groups = { "Functional" })
361    public void testCompareCodonPos_isSymmetric()
362    {
363  1 assertSymmetric("AAA", "GGG");
364  1 assertSymmetric("AA-A", "GGG");
365  1 assertSymmetric("AAA", "GG-G");
366  1 assertSymmetric("A-AA", "GG-G");
367  1 assertSymmetric("A-A-A", "GG-G");
368  1 assertSymmetric("A-AA", "GG--G");
369  1 assertSymmetric("AA-A", "G-GG");
370  1 assertSymmetric("AA--A", "G-GG");
371  1 assertSymmetric("AAA", "G-GG");
372  1 assertSymmetric("-AAA", "G-GG");
373  1 assertSymmetric("-AA-A", "G-GG");
374  1 assertSymmetric("-AAA", "G-G-G");
375  1 assertSymmetric("-A-AA", "G-G-G");
376  1 assertSymmetric("-A-A-A", "G-G-G");
377  1 assertSymmetric("-A-AA", "G-G--G");
378  1 assertSymmetric("-AA-A", "G--GG");
379  1 assertSymmetric("-AA--A", "G--GG");
380  1 assertSymmetric("-AAA", "G--GG");
381  1 assertSymmetric("A-AA", "-GGG");
382  1 assertSymmetric("A-A-A", "-GGG");
383  1 assertSymmetric("A-AA", "-GG-G");
384  1 assertSymmetric("A--AA", "-GG-G");
385  1 assertSymmetric("A--AA", "-GGG");
386  1 assertSymmetric("A--AA", "-GG--G");
387  1 assertSymmetric("AA-A", "-GGG");
388  1 assertSymmetric("AA--A", "-GGG");
389  1 assertSymmetric("AAA", "-GGG");
390    }
391   
 
392  27 toggle private void assertSymmetric(String codon1, String codon2)
393    {
394  27 assertEquals("Comparison of '" + codon1 + "' and '" + codon2
395    + " not symmetric", Integer.signum(compare(codon1, codon2)),
396    -Integer.signum(compare(codon2, codon1)));
397    }
398   
399    /**
400    * Assert that the first sequence should map to the same position as the
401    * second in a translated alignment. Also checks that this is true if the
402    * order of the codons is reversed.
403    *
404    * @param codon1
405    * @param codon2
406    */
 
407  1 toggle private void assertMatches(String codon1, String codon2)
408    {
409  1 assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
410    compare(codon1, codon2));
411  1 assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
412    compare(codon2, codon1));
413    }
414   
415    /**
416    * Assert that the first sequence should precede the second in a translated
417    * alignment
418    *
419    * @param codon1
420    * @param codon2
421    */
 
422  13 toggle private void assertPrecedes(String codon1, String codon2)
423    {
424  13 assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'",
425    -1, compare(codon1, codon2));
426    }
427   
428    /**
429    * Assert that the first sequence should follow the second in a translated
430    * alignment
431    *
432    * @param codon1
433    * @param codon2
434    */
 
435  14 toggle private void assertFollows(String codon1, String codon2)
436    {
437  14 assertEquals("Expected '" + codon1 + "' follows '" + codon2 + "'", 1,
438    compare(codon1, codon2));
439    }
440   
441    /**
442    * Convert two nucleotide strings to base positions and pass to
443    * Dna.compareCodonPos, return the result.
444    *
445    * @param s1
446    * @param s2
447    * @return
448    */
 
449  83 toggle private int compare(String s1, String s2)
450    {
451  83 final AlignedCodon cd1 = convertCodon(s1);
452  83 final AlignedCodon cd2 = convertCodon(s2);
453  83 System.out.println("K: " + s1 + " " + cd1.toString());
454  83 System.out.println("G: " + s2 + " " + cd2.toString());
455  83 System.out.println();
456  83 return Dna.compareCodonPos(cd1, cd2);
457    }
458   
459    /**
460    * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
461    * should have exactly 3 non-gap characters, and use '-' for gaps.
462    *
463    * @param s
464    * @return
465    */
 
466  169 toggle private AlignedCodon convertCodon(String s)
467    {
468  169 int[] codon = new int[3];
469  169 int i = 0;
470  915 for (int j = 0; j < s.length(); j++)
471    {
472  746 if (s.charAt(j) != '-')
473    {
474  507 codon[i++] = j;
475    }
476    }
477  169 return new AlignedCodon(codon[0], codon[1], codon[2]);
478    }
479   
480    /**
481    * Weirdly, maybe worth a test to prove the helper method of this test class.
482    */
 
483  1 toggle @Test(groups = { "Functional" })
484    public void testConvertCodon()
485    {
486  1 assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
487  1 assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
488  1 assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
489    }
490   
491    /**
492    * Test dna complementing
493    */
 
494  1 toggle @Test(groups = "Functional")
495    public void testGetComplement()
496    {
497  1 assertEquals('t', Dna.getComplement('a'));
498  1 assertEquals('T', Dna.getComplement('A'));
499  1 assertEquals('a', Dna.getComplement('t'));
500  1 assertEquals('A', Dna.getComplement('T'));
501  1 assertEquals('c', Dna.getComplement('g'));
502  1 assertEquals('C', Dna.getComplement('G'));
503  1 assertEquals('g', Dna.getComplement('c'));
504  1 assertEquals('G', Dna.getComplement('C'));
505    // note uU --> aA but not vice versa
506  1 assertEquals('a', Dna.getComplement('u'));
507  1 assertEquals('A', Dna.getComplement('U'));
508    // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
509  1 assertEquals('r', Dna.getComplement('y'));
510  1 assertEquals('R', Dna.getComplement('Y'));
511  1 assertEquals('y', Dna.getComplement('r'));
512  1 assertEquals('Y', Dna.getComplement('R'));
513  1 assertEquals('k', Dna.getComplement('m'));
514  1 assertEquals('K', Dna.getComplement('M'));
515  1 assertEquals('m', Dna.getComplement('k'));
516  1 assertEquals('M', Dna.getComplement('K'));
517  1 assertEquals('b', Dna.getComplement('v'));
518  1 assertEquals('B', Dna.getComplement('V'));
519  1 assertEquals('v', Dna.getComplement('b'));
520  1 assertEquals('V', Dna.getComplement('B'));
521  1 assertEquals('d', Dna.getComplement('h'));
522  1 assertEquals('D', Dna.getComplement('H'));
523  1 assertEquals('h', Dna.getComplement('d'));
524  1 assertEquals('H', Dna.getComplement('D'));
525  1 assertEquals('Q', Dna.getComplement('Q'));
526    }
527   
 
528  1 toggle @Test(groups = "Functional")
529    public void testReverseSequence()
530    {
531  1 String seq = "-Ac-GtU--rYkMbVdHNX-";
532  1 String seqRev = new StringBuilder(seq).reverse().toString();
533   
534    // reverse:
535  1 SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
536  1 assertEquals(1, reversed.getStart());
537  1 assertEquals(15, reversed.getEnd());
538  1 assertEquals(20, reversed.getLength());
539  1 assertEquals(seqRev, reversed.getSequenceAsString());
540  1 assertEquals("Seq1|rev", reversed.getName());
541   
542    // reverse complement:
543  1 SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
544  1 assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
545  1 assertEquals("Seq1|revcomp", revcomp.getName());
546    }
547   
 
548  1 toggle @Test(groups = "Functional")
549    public void testReverseCdna()
550    {
551  1 String seq = "-Ac-GtU--rYkMbVdHNX-";
552  1 String seqRev = new StringBuilder(seq).reverse().toString();
553  1 String seqDs = seq.replaceAll("-", "");
554  1 String seqDsRev = new StringBuilder(seqDs).reverse().toString();
555   
556  1 SequenceI dna = new Sequence("Seq1", seq);
557  1 Alignment al = new Alignment(new SequenceI[] { dna });
558  1 al.createDatasetAlignment();
559  1 assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
560    .getSequenceAsString());
561   
562  1 HiddenColumns cs = new HiddenColumns();
563  1 AlignViewportI av = new AlignViewport(al, cs);
564  1 Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
565    false);
566  1 Dna testee = new Dna(av, contigs);
567  1 AlignmentI reversed = testee.reverseCdna(false);
568  1 assertEquals(1, reversed.getHeight());
569  1 assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
570  1 assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
571    .getSequenceAsString());
572    }
573    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.