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  1. Project Clover database Tue Nov 18 2025 10:51:49 GMT
  2. Package jalview.analysis

File DnaTest.java

 

Code metrics

8
199
19
1
579
412
23
0.12
10.47
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Classes

Class Line # Actions
DnaTest 46 199 23
1.0100%
 

Contributing tests

This file is covered by 12 tests. .

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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(
143    GeneticCodes.getInstance().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, alf.getWidth(),
171    false);
172  17 AlignViewportI av = new AlignViewport(alf, cs);
173  17 Dna dna = new Dna(av, vcontigs);
174  17 AlignmentI transAlf = dna.translateCdna(
175    GeneticCodes.getInstance().getStandardCodeTable());
176   
177  17 assertTrue(
178    "Translation failed (ipos=" + ipos + ") No alignment data.",
179    transAlf != null);
180  17 assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
181    transAlf.getHeight() > 0);
182  17 assertTrue(
183    "Translation failed (ipos=" + ipos + ") Translated "
184    + transAlf.getHeight() + " sequences from "
185    + alf.getHeight() + " sequences",
186    alf.getHeight() == transAlf.getHeight());
187    }
188    }
189   
190    /**
191    * Test simple translation to Amino Acids (with STOP codons translated to *).
192    *
193    * @throws IOException
194    */
 
195  1 toggle @Test(groups = { "Functional" })
196    public void testTranslateCdna_simple() throws IOException
197    {
198  1 AlignmentI alf = new FormatAdapter().readFile(fasta,
199    DataSourceType.PASTE, FileFormat.Fasta);
200  1 HiddenColumns cs = new HiddenColumns();
201  1 AlignViewportI av = new AlignViewport(alf, cs);
202  1 Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
203    false);
204  1 Dna dna = new Dna(av, contigs);
205  1 AlignmentI translated = dna.translateCdna(
206    GeneticCodes.getInstance().getStandardCodeTable());
207  1 String aa = translated.getSequenceAt(0).getSequenceAsString();
208  1 assertEquals(
209    "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
210    aa);
211    }
212   
213    /**
214    * Test translation excluding hidden columns.
215    *
216    * @throws IOException
217    */
 
218  1 toggle @Test(groups = { "Functional" })
219    public void testTranslateCdna_hiddenColumns() throws IOException
220    {
221  1 AlignmentI alf = new FormatAdapter().readFile(fasta,
222    DataSourceType.PASTE, FileFormat.Fasta);
223  1 HiddenColumns cs = new HiddenColumns();
224  1 cs.hideColumns(6, 14); // hide codons 3/4/5
225  1 cs.hideColumns(24, 35); // hide codons 9-12
226  1 cs.hideColumns(177, 191); // hide codons 60-64
227  1 AlignViewportI av = new AlignViewport(alf, cs);
228  1 Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
229    false);
230  1 Dna dna = new Dna(av, contigs);
231  1 AlignmentI translated = dna.translateCdna(
232    GeneticCodes.getInstance().getStandardCodeTable());
233  1 String aa = translated.getSequenceAt(0).getSequenceAsString();
234  1 assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW",
235    aa);
236    }
237   
238    /**
239    * Use this test to help debug into any cases of interest.
240    */
 
241  1 toggle @Test(groups = { "Functional" })
242    public void testCompareCodonPos_oneOnly()
243    {
244  1 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
245    }
246   
247    /**
248    * Tests for method that compares 'alignment' of two codon position triplets.
249    */
 
250  1 toggle @Test(groups = { "Functional" })
251    public void testCompareCodonPos()
252    {
253    /*
254    * Returns 0 for any null argument
255    */
256  1 assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
257  1 assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
258   
259    /*
260    * Work through 27 combinations. First 9 cases where first position matches.
261    */
262  1 assertMatches("AAA", "GGG"); // 2 and 3 match
263  1 assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
264  1 assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
265  1 assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
266  1 assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
267  1 assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
268  1 assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
269  1 assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
270  1 assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
271   
272    /*
273    * 9 cases where first position is shifted in first sequence.
274    */
275  1 assertFollows("-AAA", "G-GG"); // 2 and 3 match
276  1 assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
277    // 'enclosing' case: pick first to start precedes
278  1 assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
279  1 assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
280  1 assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
281    // 'enclosing' case: pick first to start precedes
282  1 assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
283  1 assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
284  1 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
285  1 assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
286   
287    /*
288    * 9 cases where first position is shifted in second sequence.
289    */
290  1 assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
291  1 assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
292  1 assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
293  1 assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
294    // 'enclosing' case with middle base deciding:
295  1 assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
296  1 assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
297  1 assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
298  1 assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
299  1 assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
300    }
301   
302    /**
303    * This test generates a random cDNA alignment and its translation, then
304    * reorders the cDNA and retranslates, and verifies that the translations are
305    * the same (apart from ordering).
306    */
 
307  1 toggle @Test(groups = { "Functional" })
308    public void testTranslateCdna_sequenceOrderIndependent()
309    {
310    /*
311    * Generate cDNA - 8 sequences of 12 bases each.
312    */
313  1 AlignmentI cdna = new AlignmentGenerator(true).generate(12, 8, 97, 5,
314    5);
315  1 HiddenColumns cs = new HiddenColumns();
316  1 AlignViewportI av = new AlignViewport(cdna, cs);
317  1 Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
318    false);
319  1 Dna dna = new Dna(av, contigs);
320  1 AlignmentI translated = dna.translateCdna(
321    GeneticCodes.getInstance().getStandardCodeTable());
322   
323    /*
324    * Jumble the cDNA sequences and translate.
325    */
326  1 SequenceI[] sorted = new SequenceI[cdna.getHeight()];
327  1 final int[] jumbler = new int[] { 6, 7, 3, 4, 2, 0, 1, 5 };
328  1 int seqNo = 0;
329  1 for (int i : jumbler)
330    {
331  8 sorted[seqNo++] = cdna.getSequenceAt(i);
332    }
333  1 AlignmentI cdnaReordered = new Alignment(sorted);
334  1 av = new AlignViewport(cdnaReordered, cs);
335  1 contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
336  1 dna = new Dna(av, contigs);
337  1 AlignmentI translated2 = dna.translateCdna(
338    GeneticCodes.getInstance().getStandardCodeTable());
339   
340    /*
341    * Check translated sequences are the same in both alignments.
342    */
343  1 System.out.println("Original");
344  1 System.out.println(translated.toString());
345  1 System.out.println("Sorted");
346  1 System.out.println(translated2.toString());
347   
348  1 int sortedSequenceIndex = 0;
349  1 for (int originalSequenceIndex : jumbler)
350    {
351  8 final String translation1 = translated
352    .getSequenceAt(originalSequenceIndex).getSequenceAsString();
353  8 final String translation2 = translated2
354    .getSequenceAt(sortedSequenceIndex).getSequenceAsString();
355  8 assertEquals(translation2, translation1);
356  8 sortedSequenceIndex++;
357    }
358    }
359   
360    /**
361    * Test that all the cases in testCompareCodonPos have a 'symmetric'
362    * comparison (without checking the actual comparison result).
363    */
 
364  1 toggle @Test(groups = { "Functional" })
365    public void testCompareCodonPos_isSymmetric()
366    {
367  1 assertSymmetric("AAA", "GGG");
368  1 assertSymmetric("AA-A", "GGG");
369  1 assertSymmetric("AAA", "GG-G");
370  1 assertSymmetric("A-AA", "GG-G");
371  1 assertSymmetric("A-A-A", "GG-G");
372  1 assertSymmetric("A-AA", "GG--G");
373  1 assertSymmetric("AA-A", "G-GG");
374  1 assertSymmetric("AA--A", "G-GG");
375  1 assertSymmetric("AAA", "G-GG");
376  1 assertSymmetric("-AAA", "G-GG");
377  1 assertSymmetric("-AA-A", "G-GG");
378  1 assertSymmetric("-AAA", "G-G-G");
379  1 assertSymmetric("-A-AA", "G-G-G");
380  1 assertSymmetric("-A-A-A", "G-G-G");
381  1 assertSymmetric("-A-AA", "G-G--G");
382  1 assertSymmetric("-AA-A", "G--GG");
383  1 assertSymmetric("-AA--A", "G--GG");
384  1 assertSymmetric("-AAA", "G--GG");
385  1 assertSymmetric("A-AA", "-GGG");
386  1 assertSymmetric("A-A-A", "-GGG");
387  1 assertSymmetric("A-AA", "-GG-G");
388  1 assertSymmetric("A--AA", "-GG-G");
389  1 assertSymmetric("A--AA", "-GGG");
390  1 assertSymmetric("A--AA", "-GG--G");
391  1 assertSymmetric("AA-A", "-GGG");
392  1 assertSymmetric("AA--A", "-GGG");
393  1 assertSymmetric("AAA", "-GGG");
394    }
395   
 
396  27 toggle private void assertSymmetric(String codon1, String codon2)
397    {
398  27 assertEquals(
399    "Comparison of '" + codon1 + "' and '" + codon2
400    + " not symmetric",
401    Integer.signum(compare(codon1, codon2)),
402    -Integer.signum(compare(codon2, codon1)));
403    }
404   
405    /**
406    * Assert that the first sequence should map to the same position as the
407    * second in a translated alignment. Also checks that this is true if the
408    * order of the codons is reversed.
409    *
410    * @param codon1
411    * @param codon2
412    */
 
413  1 toggle private void assertMatches(String codon1, String codon2)
414    {
415  1 assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
416    compare(codon1, codon2));
417  1 assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
418    compare(codon2, codon1));
419    }
420   
421    /**
422    * Assert that the first sequence should precede the second in a translated
423    * alignment
424    *
425    * @param codon1
426    * @param codon2
427    */
 
428  13 toggle private void assertPrecedes(String codon1, String codon2)
429    {
430  13 assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'", -1,
431    compare(codon1, codon2));
432    }
433   
434    /**
435    * Assert that the first sequence should follow the second in a translated
436    * alignment
437    *
438    * @param codon1
439    * @param codon2
440    */
 
441  14 toggle private void assertFollows(String codon1, String codon2)
442    {
443  14 assertEquals("Expected '" + codon1 + "' follows '" + codon2 + "'", 1,
444    compare(codon1, codon2));
445    }
446   
447    /**
448    * Convert two nucleotide strings to base positions and pass to
449    * Dna.compareCodonPos, return the result.
450    *
451    * @param s1
452    * @param s2
453    * @return
454    */
 
455  83 toggle private int compare(String s1, String s2)
456    {
457  83 final AlignedCodon cd1 = convertCodon(s1);
458  83 final AlignedCodon cd2 = convertCodon(s2);
459  83 System.out.println("K: " + s1 + " " + cd1.toString());
460  83 System.out.println("G: " + s2 + " " + cd2.toString());
461  83 System.out.println();
462  83 return Dna.compareCodonPos(cd1, cd2);
463    }
464   
465    /**
466    * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
467    * should have exactly 3 non-gap characters, and use '-' for gaps.
468    *
469    * @param s
470    * @return
471    */
 
472  169 toggle private AlignedCodon convertCodon(String s)
473    {
474  169 int[] codon = new int[3];
475  169 int i = 0;
476  915 for (int j = 0; j < s.length(); j++)
477    {
478  746 if (s.charAt(j) != '-')
479    {
480  507 codon[i++] = j;
481    }
482    }
483  169 return new AlignedCodon(codon[0], codon[1], codon[2]);
484    }
485   
486    /**
487    * Weirdly, maybe worth a test to prove the helper method of this test class.
488    */
 
489  1 toggle @Test(groups = { "Functional" })
490    public void testConvertCodon()
491    {
492  1 assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
493  1 assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
494  1 assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
495    }
496   
497    /**
498    * Test dna complementing
499    */
 
500  1 toggle @Test(groups = "Functional")
501    public void testGetComplement()
502    {
503  1 assertEquals('t', Dna.getComplement('a'));
504  1 assertEquals('T', Dna.getComplement('A'));
505  1 assertEquals('a', Dna.getComplement('t'));
506  1 assertEquals('A', Dna.getComplement('T'));
507  1 assertEquals('c', Dna.getComplement('g'));
508  1 assertEquals('C', Dna.getComplement('G'));
509  1 assertEquals('g', Dna.getComplement('c'));
510  1 assertEquals('G', Dna.getComplement('C'));
511    // note uU --> aA but not vice versa
512  1 assertEquals('a', Dna.getComplement('u'));
513  1 assertEquals('A', Dna.getComplement('U'));
514    // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
515  1 assertEquals('r', Dna.getComplement('y'));
516  1 assertEquals('R', Dna.getComplement('Y'));
517  1 assertEquals('y', Dna.getComplement('r'));
518  1 assertEquals('Y', Dna.getComplement('R'));
519  1 assertEquals('k', Dna.getComplement('m'));
520  1 assertEquals('K', Dna.getComplement('M'));
521  1 assertEquals('m', Dna.getComplement('k'));
522  1 assertEquals('M', Dna.getComplement('K'));
523  1 assertEquals('b', Dna.getComplement('v'));
524  1 assertEquals('B', Dna.getComplement('V'));
525  1 assertEquals('v', Dna.getComplement('b'));
526  1 assertEquals('V', Dna.getComplement('B'));
527  1 assertEquals('d', Dna.getComplement('h'));
528  1 assertEquals('D', Dna.getComplement('H'));
529  1 assertEquals('h', Dna.getComplement('d'));
530  1 assertEquals('H', Dna.getComplement('D'));
531  1 assertEquals('Q', Dna.getComplement('Q'));
532    }
533   
 
534  1 toggle @Test(groups = "Functional")
535    public void testReverseSequence()
536    {
537  1 String seq = "-Ac-GtU--rYkMbVdHNX-";
538  1 String seqRev = new StringBuilder(seq).reverse().toString();
539   
540    // reverse:
541  1 SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
542  1 assertEquals(1, reversed.getStart());
543  1 assertEquals(15, reversed.getEnd());
544  1 assertEquals(20, reversed.getLength());
545  1 assertEquals(seqRev, reversed.getSequenceAsString());
546  1 assertEquals("Seq1|rev", reversed.getName());
547   
548    // reverse complement:
549  1 SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
550  1 assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
551  1 assertEquals("Seq1|revcomp", revcomp.getName());
552    }
553   
 
554  1 toggle @Test(groups = "Functional")
555    public void testReverseCdna()
556    {
557  1 String seq = "-Ac-GtU--rYkMbVdHNX-";
558  1 String seqRev = new StringBuilder(seq).reverse().toString();
559  1 String seqDs = seq.replaceAll("-", "");
560  1 String seqDsRev = new StringBuilder(seqDs).reverse().toString();
561   
562  1 SequenceI dna = new Sequence("Seq1", seq);
563  1 Alignment al = new Alignment(new SequenceI[] { dna });
564  1 al.createDatasetAlignment();
565  1 assertEquals(seqDs,
566    al.getSequenceAt(0).getDatasetSequence().getSequenceAsString());
567   
568  1 HiddenColumns cs = new HiddenColumns();
569  1 AlignViewportI av = new AlignViewport(al, cs);
570  1 Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
571    false);
572  1 Dna testee = new Dna(av, contigs);
573  1 AlignmentI reversed = testee.reverseCdna(false);
574  1 assertEquals(1, reversed.getHeight());
575  1 assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
576  1 assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
577    .getSequenceAsString());
578    }
579    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 18 2025 11:02:12 GMT using coverage data from Tue Nov 18 2025 11:01:58 GMT.
  • OpenClover is free and open-source software.