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  1. Project Clover database Wed Jun 18 2025 15:09:16 BST
  2. Package jalview.analysis

File AlignmentUtilsTests.java

 

Code metrics

14
1,284
55
1
2,959
1,915
62
0.05
23.35
55
1.13

Classes

Class Line # Actions
AlignmentUtilsTests 76 1,284 62
0.9327420693.3%
 

Contributing tests

This file is covered by 45 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.Assert.assertNotEquals;
24    import static org.testng.AssertJUnit.assertEquals;
25    import static org.testng.AssertJUnit.assertFalse;
26    import static org.testng.AssertJUnit.assertNotNull;
27    import static org.testng.AssertJUnit.assertNull;
28    import static org.testng.AssertJUnit.assertSame;
29    import static org.testng.AssertJUnit.assertTrue;
30   
31    import java.awt.Color;
32    import java.io.IOException;
33    import java.util.ArrayList;
34    import java.util.Arrays;
35    import java.util.HashMap;
36    import java.util.LinkedHashMap;
37    import java.util.List;
38    import java.util.Map;
39    import java.util.Set;
40    import java.util.SortedMap;
41    import java.util.TreeMap;
42   
43    import org.testng.Assert;
44    import org.testng.annotations.BeforeClass;
45    import org.testng.annotations.DataProvider;
46    import org.testng.annotations.Test;
47   
48    import jalview.datamodel.AlignedCodonFrame;
49    import jalview.datamodel.Alignment;
50    import jalview.datamodel.AlignmentAnnotation;
51    import jalview.datamodel.AlignmentI;
52    import jalview.datamodel.Annotation;
53    import jalview.datamodel.ContactListI;
54    import jalview.datamodel.ContactMatrixI;
55    import jalview.datamodel.DBRefEntry;
56    import jalview.datamodel.GeneLociI;
57    import jalview.datamodel.Mapping;
58    import jalview.datamodel.SearchResultMatchI;
59    import jalview.datamodel.SearchResultsI;
60    import jalview.datamodel.SeqDistanceContactMatrix;
61    import jalview.datamodel.Sequence;
62    import jalview.datamodel.SequenceFeature;
63    import jalview.datamodel.SequenceGroup;
64    import jalview.datamodel.SequenceI;
65    import jalview.gui.JvOptionPane;
66    import jalview.io.AppletFormatAdapter;
67    import jalview.io.DataSourceType;
68    import jalview.io.FileFormat;
69    import jalview.io.FileFormatI;
70    import jalview.io.FormatAdapter;
71    import jalview.io.gff.SequenceOntologyI;
72    import jalview.util.Comparison;
73    import jalview.util.MapList;
74    import jalview.util.MappingUtils;
75   
 
76    public class AlignmentUtilsTests
77    {
78    private static Sequence ts = new Sequence("short",
79    "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
80   
 
81  1 toggle @BeforeClass(alwaysRun = true)
82    public void setUpJvOptionPane()
83    {
84  1 JvOptionPane.setInteractiveMode(false);
85  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
86   
87  1 AlignmentAnnotation ann1 = new AlignmentAnnotation(
88    "Secondary Structure", "Secondary Structure",
89    new Annotation[] {});
90  1 AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
91    "jnetpred", new Annotation[] {});
92  1 AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
93    new Annotation[] {});
94  1 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
95    new Annotation[] {});
96   
97  1 AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] { ann1, ann3,
98    ann4 };
99   
100  1 AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] { ann2, ann3,
101    ann4 };
102   
103  1 AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] { ann3, ann4 };
104   
105  1 AlignmentAnnotation[] anns4 = new AlignmentAnnotation[0];
106   
107  1 AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] { ann1, ann2,
108    ann3, ann4 };
109    }
110   
 
111  1 toggle @Test(groups = { "Functional" })
112    public void testExpandContext()
113    {
114  1 AlignmentI al = new Alignment(new Sequence[] {});
115  6 for (int i = 4; i < 14; i += 2)
116    {
117  5 SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
118  5 al.addSequence(s1);
119    }
120  1 System.out.println(new AppletFormatAdapter()
121    .formatSequences(FileFormat.Clustal, al, true));
122  27 for (int flnk = -1; flnk < 25; flnk++)
123    {
124  26 AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
125  26 System.out.println("\nFlank size: " + flnk);
126  26 System.out.println(new AppletFormatAdapter()
127    .formatSequences(FileFormat.Clustal, exp, true));
128  26 if (flnk == -1)
129    {
130    /*
131    * Full expansion to complete sequences
132    */
133  1 for (SequenceI sq : exp.getSequences())
134    {
135  5 String ung = sq.getSequenceAsString().replaceAll("-+", "");
136  5 final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
137    + ung + "\n"
138    + sq.getDatasetSequence().getSequenceAsString();
139  5 assertTrue(errorMsg, ung.equalsIgnoreCase(
140    sq.getDatasetSequence().getSequenceAsString()));
141    }
142    }
143  25 else if (flnk == 24)
144    {
145    /*
146    * Last sequence is fully expanded, others have leading gaps to match
147    */
148  1 assertTrue(exp.getSequenceAt(4).getSequenceAsString()
149    .startsWith("abc"));
150  1 assertTrue(exp.getSequenceAt(3).getSequenceAsString()
151    .startsWith("--abc"));
152  1 assertTrue(exp.getSequenceAt(2).getSequenceAsString()
153    .startsWith("----abc"));
154  1 assertTrue(exp.getSequenceAt(1).getSequenceAsString()
155    .startsWith("------abc"));
156  1 assertTrue(exp.getSequenceAt(0).getSequenceAsString()
157    .startsWith("--------abc"));
158    }
159    }
160    }
161   
162    /**
163    * Test that annotations are correctly adjusted by expandContext
164    */
 
165  1 toggle @Test(groups = { "Functional" })
166    public void testExpandContext_annotation()
167    {
168  1 AlignmentI al = new Alignment(new Sequence[] {});
169  1 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
170    // subsequence DEF:
171  1 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
172  1 al.addSequence(seq1);
173   
174    /*
175    * Annotate DEF with 4/5/6 respectively
176    */
177  1 Annotation[] anns = new Annotation[] { new Annotation(4),
178    new Annotation(5), new Annotation(6) };
179  1 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
180    "secondary structure", anns);
181  1 seq1.addAlignmentAnnotation(ann);
182   
183    /*
184    * The annotations array should match aligned positions
185    */
186  1 assertEquals(3, ann.annotations.length);
187  1 assertEquals(4, ann.annotations[0].value, 0.001);
188  1 assertEquals(5, ann.annotations[1].value, 0.001);
189  1 assertEquals(6, ann.annotations[2].value, 0.001);
190   
191    /*
192    * Check annotation to sequence position mappings before expanding the
193    * sequence; these are set up in Sequence.addAlignmentAnnotation ->
194    * Annotation.setSequenceRef -> createSequenceMappings
195    */
196  1 assertNull(ann.getAnnotationForPosition(1));
197  1 assertNull(ann.getAnnotationForPosition(2));
198  1 assertNull(ann.getAnnotationForPosition(3));
199  1 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
200  1 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
201  1 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
202  1 assertNull(ann.getAnnotationForPosition(7));
203  1 assertNull(ann.getAnnotationForPosition(8));
204  1 assertNull(ann.getAnnotationForPosition(9));
205   
206    /*
207    * Expand the subsequence to the full sequence abcDEFghi
208    */
209  1 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
210  1 assertEquals("abcDEFghi",
211    expanded.getSequenceAt(0).getSequenceAsString());
212   
213    /*
214    * Confirm the alignment and sequence have the same SS annotation,
215    * referencing the expanded sequence
216    */
217  1 ann = expanded.getSequenceAt(0).getAnnotation()[0];
218  1 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
219  1 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
220   
221    /*
222    * The annotations array should have null values except for annotated
223    * positions
224    */
225  1 assertNull(ann.annotations[0]);
226  1 assertNull(ann.annotations[1]);
227  1 assertNull(ann.annotations[2]);
228  1 assertEquals(4, ann.annotations[3].value, 0.001);
229  1 assertEquals(5, ann.annotations[4].value, 0.001);
230  1 assertEquals(6, ann.annotations[5].value, 0.001);
231  1 assertNull(ann.annotations[6]);
232  1 assertNull(ann.annotations[7]);
233  1 assertNull(ann.annotations[8]);
234   
235    /*
236    * sequence position mappings should be unchanged
237    */
238  1 assertNull(ann.getAnnotationForPosition(1));
239  1 assertNull(ann.getAnnotationForPosition(2));
240  1 assertNull(ann.getAnnotationForPosition(3));
241  1 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
242  1 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
243  1 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
244  1 assertNull(ann.getAnnotationForPosition(7));
245  1 assertNull(ann.getAnnotationForPosition(8));
246  1 assertNull(ann.getAnnotationForPosition(9));
247    }
248   
249    /**
250    * Test method that returns a map of lists of sequences by sequence name.
251    *
252    * @throws IOException
253    */
 
254  1 toggle @Test(groups = { "Functional" })
255    public void testGetSequencesByName() throws IOException
256    {
257  1 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
258    + ">Seq1Name\nABCD\n";
259  1 AlignmentI al = loadAlignment(data, FileFormat.Fasta);
260  1 Map<String, List<SequenceI>> map = AlignmentUtils
261    .getSequencesByName(al);
262  1 assertEquals(2, map.keySet().size());
263  1 assertEquals(2, map.get("Seq1Name").size());
264  1 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
265  1 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
266  1 assertEquals(1, map.get("Seq2Name").size());
267  1 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
268    }
269   
270    /**
271    * Helper method to load an alignment and ensure dataset sequences are set up.
272    *
273    * @param data
274    * @param format
275    * TODO
276    * @return
277    * @throws IOException
278    */
 
279  1 toggle protected AlignmentI loadAlignment(final String data, FileFormatI format)
280    throws IOException
281    {
282  1 AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
283    format);
284  1 a.setDataset(null);
285  1 return a;
286    }
287   
288    /**
289    * Test mapping of protein to cDNA, for the case where we have no sequence
290    * cross-references, so mappings are made first-served 1-1 where sequences
291    * translate.
292    *
293    * @throws IOException
294    */
 
295  1 toggle @Test(groups = { "Functional" })
296    public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
297    {
298  1 List<SequenceI> protseqs = new ArrayList<>();
299  1 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
300  1 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
301  1 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
302  1 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
303  1 protein.setDataset(null);
304   
305  1 List<SequenceI> dnaseqs = new ArrayList<>();
306  1 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
307  1 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
308  1 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
309  1 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
310  1 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
311  1 cdna.setDataset(null);
312   
313  1 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
314   
315    // 3 mappings made, each from 1 to 1 sequence
316  1 assertEquals(3, protein.getCodonFrames().size());
317  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
318  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
319  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
320   
321    // V12345 mapped to A22222
322  1 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
323    .get(0);
324  1 assertEquals(1, acf.getdnaSeqs().length);
325  1 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
326    acf.getdnaSeqs()[0]);
327  1 Mapping[] protMappings = acf.getProtMappings();
328  1 assertEquals(1, protMappings.length);
329  1 MapList mapList = protMappings[0].getMap();
330  1 assertEquals(3, mapList.getFromRatio());
331  1 assertEquals(1, mapList.getToRatio());
332  1 assertTrue(
333    Arrays.equals(new int[]
334    { 1, 9 }, mapList.getFromRanges().get(0)));
335  1 assertEquals(1, mapList.getFromRanges().size());
336  1 assertTrue(
337    Arrays.equals(new int[]
338    { 1, 3 }, mapList.getToRanges().get(0)));
339  1 assertEquals(1, mapList.getToRanges().size());
340   
341    // V12346 mapped to A33333
342  1 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
343  1 assertEquals(1, acf.getdnaSeqs().length);
344  1 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
345    acf.getdnaSeqs()[0]);
346   
347    // V12347 mapped to A11111
348  1 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
349  1 assertEquals(1, acf.getdnaSeqs().length);
350  1 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
351    acf.getdnaSeqs()[0]);
352   
353    // no mapping involving the 'extra' A44444
354  1 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
355    }
356   
357    /**
358    * Test for the alignSequenceAs method that takes two sequences and a mapping.
359    */
 
360  1 toggle @Test(groups = { "Functional" })
361    public void testAlignSequenceAs_withMapping_noIntrons()
362    {
363  1 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
364   
365    /*
366    * No existing gaps in dna:
367    */
368  1 checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
369    "---GGG---AAA");
370   
371    /*
372    * Now introduce gaps in dna but ignore them when realigning.
373    */
374  1 checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
375    "---GGG---AAA");
376   
377    /*
378    * Now include gaps in dna when realigning. First retaining 'mapped' gaps
379    * only, i.e. those within the exon region.
380    */
381  1 checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
382    "---G-G--G---A--A-A");
383   
384    /*
385    * Include all gaps in dna when realigning (within and without the exon
386    * region). The leading gap, and the gaps between codons, are subsumed by
387    * the protein alignment gap.
388    */
389  1 checkAlignSequenceAs("-G-GG--AA-A---", "-A-L-", true, true, map,
390    "---G-GG---AA-A---");
391   
392    /*
393    * Include only unmapped gaps in dna when realigning (outside the exon
394    * region). The leading gap, and the gaps between codons, are subsumed by
395    * the protein alignment gap.
396    */
397  1 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
398    "---GGG---AAA---");
399    }
400   
401    /**
402    * Test for the alignSequenceAs method that takes two sequences and a mapping.
403    */
 
404  1 toggle @Test(groups = { "Functional" })
405    public void testAlignSequenceAs_withMapping_withIntrons()
406    {
407    /*
408    * Exons at codon 2 (AAA) and 4 (TTT)
409    */
410  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
411    new int[]
412    { 1, 2 }, 3, 1);
413   
414    /*
415    * Simple case: no gaps in dna
416    */
417  1 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
418    "GGG---AAACCCTTTGGG");
419   
420    /*
421    * Add gaps to dna - but ignore when realigning.
422    */
423  1 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-", false,
424    false, map, "GGG---AAACCCTTTGGG");
425   
426    /*
427    * Add gaps to dna - include within exons only when realigning.
428    */
429  1 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
430    false, map, "GGG---A--A---ACCCT-TTGGG");
431   
432    /*
433    * Include gaps outside exons only when realigning.
434    */
435  1 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
436    false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
437   
438    /*
439    * Include gaps following first intron if we are 'preserving mapped gaps'
440    */
441  1 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
442    true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
443   
444    /*
445    * Include all gaps in dna when realigning.
446    */
447  1 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
448    true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
449    }
450   
451    /**
452    * Test for the case where not all of the protein sequence is mapped to cDNA.
453    */
 
454  1 toggle @Test(groups = { "Functional" })
455    public void testAlignSequenceAs_withMapping_withUnmappedProtein()
456    {
457    /*
458    * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
459    */
460  1 final MapList map = new MapList(new int[] { 4, 6, 10, 12 },
461    new int[]
462    { 1, 1, 3, 3 }, 3, 1);
463   
464    /*
465    * -L- 'aligns' ccc------
466    */
467  1 checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map,
468    "gggAAAccc------TTTggg");
469    }
470   
471    /**
472    * Helper method that performs and verifies the method under test.
473    *
474    * @param alignee
475    * the sequence to be realigned
476    * @param alignModel
477    * the sequence whose alignment is to be copied
478    * @param preserveMappedGaps
479    * @param preserveUnmappedGaps
480    * @param map
481    * @param expected
482    */
 
483  14 toggle protected void checkAlignSequenceAs(final String alignee,
484    final String alignModel, final boolean preserveMappedGaps,
485    final boolean preserveUnmappedGaps, MapList map,
486    final String expected)
487    {
488  14 SequenceI alignMe = new Sequence("Seq1", alignee);
489  14 alignMe.createDatasetSequence();
490  14 SequenceI alignFrom = new Sequence("Seq2", alignModel);
491  14 alignFrom.createDatasetSequence();
492  14 AlignedCodonFrame acf = new AlignedCodonFrame();
493  14 acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(),
494    map);
495   
496  14 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
497    preserveMappedGaps, preserveUnmappedGaps);
498  14 assertEquals(expected, alignMe.getSequenceAsString());
499    }
500   
501    /**
502    * Test for the alignSequenceAs method where we preserve gaps in introns only.
503    */
 
504  1 toggle @Test(groups = { "Functional" })
505    public void testAlignSequenceAs_keepIntronGapsOnly()
506    {
507   
508    /*
509    * Intron GGGAAA followed by exon CCCTTT
510    */
511  1 MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3,
512    1);
513   
514  1 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
515    "GG-G-AA-ACCCTTT");
516    }
517   
518    /**
519    * Test the method that realigns protein to match mapped codon alignment.
520    */
 
521  1 toggle @Test(groups = { "Functional" })
522    public void testAlignProteinAsDna()
523    {
524    // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
525  1 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
526    // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
527  1 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
528    // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
529  1 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
530  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
531  1 dna.setDataset(null);
532   
533    // protein alignment will be realigned like dna
534  1 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
535  1 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
536  1 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
537  1 SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
538  1 AlignmentI protein = new Alignment(
539    new SequenceI[]
540    { prot1, prot2, prot3, prot4 });
541  1 protein.setDataset(null);
542   
543  1 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
544    1);
545  1 AlignedCodonFrame acf = new AlignedCodonFrame();
546  1 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
547  1 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
548  1 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
549  1 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
550  1 acfs.add(acf);
551  1 protein.setCodonFrames(acfs);
552   
553    /*
554    * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
555    * [8,9,10] [10,11,12] [11,12,13]
556    */
557  1 AlignmentUtils.alignProteinAsDna(protein, dna);
558  1 assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
559  1 assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
560  1 assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
561  1 assertEquals("R-QSV", prot4.getSequenceAsString());
562    }
563   
564    /**
565    * Test the method that tests whether a CDNA sequence translates to a protein
566    * sequence
567    */
 
568  1 toggle @Test(groups = { "Functional" })
569    public void testTranslatesAs()
570    {
571    // null arguments check
572  1 assertFalse(AlignmentUtils.translatesAs(null, 0, null));
573  1 assertFalse(AlignmentUtils.translatesAs(new char[] { 't' }, 0, null));
574  1 assertFalse(AlignmentUtils.translatesAs(null, 0, new char[] { 'a' }));
575   
576    // straight translation
577  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
578    "FPKG".toCharArray()));
579    // with extra start codon (not in protein)
580  1 assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
581    3, "FPKG".toCharArray()));
582    // with stop codon1 (not in protein)
583  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
584    0, "FPKG".toCharArray()));
585    // with stop codon1 (in protein as *)
586  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
587    0, "FPKG*".toCharArray()));
588    // with stop codon2 (not in protein)
589  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
590    0, "FPKG".toCharArray()));
591    // with stop codon3 (not in protein)
592  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
593    0, "FPKG".toCharArray()));
594    // with start and stop codon1
595  1 assertTrue(AlignmentUtils.translatesAs(
596    "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
597    // with start and stop codon1 (in protein as *)
598  1 assertTrue(AlignmentUtils.translatesAs(
599    "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
600    // with start and stop codon2
601  1 assertTrue(AlignmentUtils.translatesAs(
602    "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
603    // with start and stop codon3
604  1 assertTrue(AlignmentUtils.translatesAs(
605    "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
606   
607    // with embedded stop codons
608  1 assertTrue(AlignmentUtils.translatesAs(
609    "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
610    "F*PK*G".toCharArray()));
611   
612    // wrong protein
613  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
614    "FPMG".toCharArray()));
615   
616    // truncated dna
617  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
618    "FPKG".toCharArray()));
619   
620    // truncated protein
621  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
622    "FPK".toCharArray()));
623   
624    // overlong dna (doesn't end in stop codon)
625  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaagggttt".toCharArray(),
626    0, "FPKG".toCharArray()));
627   
628    // dna + stop codon + more
629  1 assertFalse(AlignmentUtils.translatesAs(
630    "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
631   
632    // overlong protein
633  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
634    "FPKGQ".toCharArray()));
635    }
636   
637    /**
638    * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
639    * stop codons in addition to the protein coding sequence.
640    *
641    * @throws IOException
642    */
 
643  1 toggle @Test(groups = { "Functional" })
644    public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
645    throws IOException
646    {
647  1 List<SequenceI> protseqs = new ArrayList<>();
648  1 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
649  1 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
650  1 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
651  1 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
652  1 protein.setDataset(null);
653   
654  1 List<SequenceI> dnaseqs = new ArrayList<>();
655    // start + SAR:
656  1 dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
657    // = EIQ + stop
658  1 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
659    // = start +EIQ + stop
660  1 dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
661  1 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
662  1 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
663  1 cdna.setDataset(null);
664   
665  1 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
666   
667    // 3 mappings made, each from 1 to 1 sequence
668  1 assertEquals(3, protein.getCodonFrames().size());
669  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
670  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
671  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
672   
673    // V12345 mapped from A22222
674  1 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
675    .get(0);
676  1 assertEquals(1, acf.getdnaSeqs().length);
677  1 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
678    acf.getdnaSeqs()[0]);
679  1 Mapping[] protMappings = acf.getProtMappings();
680  1 assertEquals(1, protMappings.length);
681  1 MapList mapList = protMappings[0].getMap();
682  1 assertEquals(3, mapList.getFromRatio());
683  1 assertEquals(1, mapList.getToRatio());
684  1 assertTrue(
685    Arrays.equals(new int[]
686    { 1, 9 }, mapList.getFromRanges().get(0)));
687  1 assertEquals(1, mapList.getFromRanges().size());
688  1 assertTrue(
689    Arrays.equals(new int[]
690    { 1, 3 }, mapList.getToRanges().get(0)));
691  1 assertEquals(1, mapList.getToRanges().size());
692   
693    // V12346 mapped from A33333 starting position 4
694  1 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
695  1 assertEquals(1, acf.getdnaSeqs().length);
696  1 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
697    acf.getdnaSeqs()[0]);
698  1 protMappings = acf.getProtMappings();
699  1 assertEquals(1, protMappings.length);
700  1 mapList = protMappings[0].getMap();
701  1 assertEquals(3, mapList.getFromRatio());
702  1 assertEquals(1, mapList.getToRatio());
703  1 assertTrue(
704    Arrays.equals(new int[]
705    { 4, 12 }, mapList.getFromRanges().get(0)));
706  1 assertEquals(1, mapList.getFromRanges().size());
707  1 assertTrue(
708    Arrays.equals(new int[]
709    { 1, 3 }, mapList.getToRanges().get(0)));
710  1 assertEquals(1, mapList.getToRanges().size());
711   
712    // V12347 mapped to A11111 starting position 4
713  1 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
714  1 assertEquals(1, acf.getdnaSeqs().length);
715  1 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
716    acf.getdnaSeqs()[0]);
717  1 protMappings = acf.getProtMappings();
718  1 assertEquals(1, protMappings.length);
719  1 mapList = protMappings[0].getMap();
720  1 assertEquals(3, mapList.getFromRatio());
721  1 assertEquals(1, mapList.getToRatio());
722  1 assertTrue(
723    Arrays.equals(new int[]
724    { 4, 12 }, mapList.getFromRanges().get(0)));
725  1 assertEquals(1, mapList.getFromRanges().size());
726  1 assertTrue(
727    Arrays.equals(new int[]
728    { 1, 3 }, mapList.getToRanges().get(0)));
729  1 assertEquals(1, mapList.getToRanges().size());
730   
731    // no mapping involving the 'extra' A44444
732  1 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
733    }
734   
735    /**
736    * Test mapping of protein to cDNA, for the case where we have some sequence
737    * cross-references. Verify that 1-to-many mappings are made where
738    * cross-references exist and sequences are mappable.
739    *
740    * @throws IOException
741    */
 
742  1 toggle @Test(groups = { "Functional" })
743    public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
744    {
745  1 List<SequenceI> protseqs = new ArrayList<>();
746  1 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
747  1 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
748  1 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
749  1 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
750  1 protein.setDataset(null);
751   
752  1 List<SequenceI> dnaseqs = new ArrayList<>();
753  1 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
754  1 dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
755  1 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
756  1 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
757  1 dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
758  1 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
759  1 cdna.setDataset(null);
760   
761    // Xref A22222 to V12345 (should get mapped)
762  1 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
763    // Xref V12345 to A44444 (should get mapped)
764  1 protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
765    // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
766  1 dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
767    // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
768    // it should get paired up with the unmapped A33333
769    // A11111 should be mapped to V12347
770    // A55555 is spare and has no xref so is not mapped
771   
772  1 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
773   
774    // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
775  1 assertEquals(3, protein.getCodonFrames().size());
776  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
777  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
778  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
779   
780    // one mapping for each of the first 4 cDNA sequences
781  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
782  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
783  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
784  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
785   
786    // V12345 mapped to A22222 and A44444
787  1 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
788    .get(0);
789  1 assertEquals(2, acf.getdnaSeqs().length);
790  1 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
791    acf.getdnaSeqs()[0]);
792  1 assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
793    acf.getdnaSeqs()[1]);
794   
795    // V12346 mapped to A33333
796  1 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
797  1 assertEquals(1, acf.getdnaSeqs().length);
798  1 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
799    acf.getdnaSeqs()[0]);
800   
801    // V12347 mapped to A11111
802  1 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
803  1 assertEquals(1, acf.getdnaSeqs().length);
804  1 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
805    acf.getdnaSeqs()[0]);
806   
807    // no mapping involving the 'extra' A55555
808  1 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
809    }
810   
811    /**
812    * Test mapping of protein to cDNA, for the case where we have some sequence
813    * cross-references. Verify that once we have made an xref mapping we don't
814    * also map un-xrefd sequeces.
815    *
816    * @throws IOException
817    */
 
818  1 toggle @Test(groups = { "Functional" })
819    public void testMapProteinAlignmentToCdna_prioritiseXrefs()
820    throws IOException
821    {
822  1 List<SequenceI> protseqs = new ArrayList<>();
823  1 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
824  1 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
825  1 AlignmentI protein = new Alignment(
826    protseqs.toArray(new SequenceI[protseqs.size()]));
827  1 protein.setDataset(null);
828   
829  1 List<SequenceI> dnaseqs = new ArrayList<>();
830  1 dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
831  1 dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
832  1 AlignmentI cdna = new Alignment(
833    dnaseqs.toArray(new SequenceI[dnaseqs.size()]));
834  1 cdna.setDataset(null);
835   
836    // Xref A22222 to V12345 (should get mapped)
837    // A11111 should then be mapped to the unmapped V12346
838  1 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
839   
840  1 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
841   
842    // 2 protein mappings made
843  1 assertEquals(2, protein.getCodonFrames().size());
844  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
845  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
846   
847    // one mapping for each of the cDNA sequences
848  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
849  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
850   
851    // V12345 mapped to A22222
852  1 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
853    .get(0);
854  1 assertEquals(1, acf.getdnaSeqs().length);
855  1 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
856    acf.getdnaSeqs()[0]);
857   
858    // V12346 mapped to A11111
859  1 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
860  1 assertEquals(1, acf.getdnaSeqs().length);
861  1 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
862    acf.getdnaSeqs()[0]);
863    }
864   
865    /**
866    * Test the method that shows or hides sequence annotations by type(s) and
867    * selection group.
868    */
 
869  1 toggle @Test(groups = { "Functional" })
870    public void testShowOrHideSequenceAnnotations()
871    {
872  1 SequenceI seq1 = new Sequence("Seq1", "AAA");
873  1 SequenceI seq2 = new Sequence("Seq2", "BBB");
874  1 SequenceI seq3 = new Sequence("Seq3", "CCC");
875  1 Annotation[] anns = new Annotation[] { new Annotation(2f) };
876  1 AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
877    anns);
878  1 ann1.setSequenceRef(seq1);
879  1 AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
880    anns);
881  1 ann2.setSequenceRef(seq2);
882  1 AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
883    anns);
884  1 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4",
885    anns);
886  1 ann4.setSequenceRef(seq1);
887  1 AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5",
888    anns);
889  1 ann5.setSequenceRef(seq2);
890  1 AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6",
891    anns);
892  1 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
893  1 al.addAnnotation(ann1); // Structure for Seq1
894  1 al.addAnnotation(ann2); // Structure for Seq2
895  1 al.addAnnotation(ann3); // Structure for no sequence
896  1 al.addAnnotation(ann4); // Temp for seq1
897  1 al.addAnnotation(ann5); // Temp for seq2
898  1 al.addAnnotation(ann6); // Temp for no sequence
899  1 List<String> types = new ArrayList<>();
900  1 List<SequenceI> scope = new ArrayList<>();
901   
902    /*
903    * Set all sequence related Structure to hidden (ann1, ann2)
904    */
905  1 types.add("Structure");
906  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
907    false);
908  1 assertFalse(ann1.visible);
909  1 assertFalse(ann2.visible);
910  1 assertTrue(ann3.visible); // not sequence-related, not affected
911  1 assertTrue(ann4.visible); // not Structure, not affected
912  1 assertTrue(ann5.visible); // "
913  1 assertTrue(ann6.visible); // not sequence-related, not affected
914   
915    /*
916    * Set Temp in {seq1, seq3} to hidden
917    */
918  1 types.clear();
919  1 types.add("Temp");
920  1 scope.add(seq1);
921  1 scope.add(seq3);
922  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
923    false);
924  1 assertFalse(ann1.visible); // unchanged
925  1 assertFalse(ann2.visible); // unchanged
926  1 assertTrue(ann3.visible); // not sequence-related, not affected
927  1 assertFalse(ann4.visible); // Temp for seq1 hidden
928  1 assertTrue(ann5.visible); // not in scope, not affected
929  1 assertTrue(ann6.visible); // not sequence-related, not affected
930   
931    /*
932    * Set Temp in all sequences to hidden
933    */
934  1 types.clear();
935  1 types.add("Temp");
936  1 scope.add(seq1);
937  1 scope.add(seq3);
938  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
939    false);
940  1 assertFalse(ann1.visible); // unchanged
941  1 assertFalse(ann2.visible); // unchanged
942  1 assertTrue(ann3.visible); // not sequence-related, not affected
943  1 assertFalse(ann4.visible); // Temp for seq1 hidden
944  1 assertFalse(ann5.visible); // Temp for seq2 hidden
945  1 assertTrue(ann6.visible); // not sequence-related, not affected
946   
947    /*
948    * Set all types in {seq1, seq3} to visible
949    */
950  1 types.clear();
951  1 scope.clear();
952  1 scope.add(seq1);
953  1 scope.add(seq3);
954  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
955    true);
956  1 assertTrue(ann1.visible); // Structure for seq1 set visible
957  1 assertFalse(ann2.visible); // not in scope, unchanged
958  1 assertTrue(ann3.visible); // not sequence-related, not affected
959  1 assertTrue(ann4.visible); // Temp for seq1 set visible
960  1 assertFalse(ann5.visible); // not in scope, unchanged
961  1 assertTrue(ann6.visible); // not sequence-related, not affected
962   
963    /*
964    * Set all types in all scope to hidden
965    */
966  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
967    false);
968  1 assertFalse(ann1.visible);
969  1 assertFalse(ann2.visible);
970  1 assertTrue(ann3.visible); // not sequence-related, not affected
971  1 assertFalse(ann4.visible);
972  1 assertFalse(ann5.visible);
973  1 assertTrue(ann6.visible); // not sequence-related, not affected
974    }
975   
976    /**
977    * Tests for the method that checks if one sequence cross-references another
978    */
 
979  1 toggle @Test(groups = { "Functional" })
980    public void testHasCrossRef()
981    {
982  1 assertFalse(AlignmentUtils.hasCrossRef(null, null));
983  1 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
984  1 assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
985  1 assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
986  1 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
987  1 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
988   
989    // different ref
990  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
991  1 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
992   
993    // case-insensitive; version number is ignored
994  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
995  1 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
996   
997    // right case!
998  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
999  1 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
1000    // test is one-way only
1001  1 assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
1002    }
1003   
1004    /**
1005    * Tests for the method that checks if either sequence cross-references the
1006    * other
1007    */
 
1008  1 toggle @Test(groups = { "Functional" })
1009    public void testHaveCrossRef()
1010    {
1011  1 assertFalse(AlignmentUtils.hasCrossRef(null, null));
1012  1 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
1013  1 assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
1014  1 assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
1015  1 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
1016  1 assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
1017   
1018  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
1019  1 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
1020    // next is true for haveCrossRef, false for hasCrossRef
1021  1 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
1022   
1023    // now the other way round
1024  1 seq1.setDBRefs(null);
1025  1 seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
1026  1 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
1027  1 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
1028   
1029    // now both ways
1030  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
1031  1 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
1032  1 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
1033    }
1034   
1035    /**
1036    * Test the method that extracts the cds-only part of a dna alignment.
1037    */
 
1038  1 toggle @Test(groups = { "Functional" })
1039    public void testMakeCdsAlignment()
1040    {
1041    /*
1042    * scenario:
1043    * dna1 --> [4, 6] [10,12] --> pep1
1044    * dna2 --> [1, 3] [7, 9] [13,15] --> pep2
1045    */
1046  1 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1047  1 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
1048  1 SequenceI pep1 = new Sequence("pep1", "GF");
1049  1 SequenceI pep2 = new Sequence("pep2", "GFP");
1050  1 pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1"));
1051  1 pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2"));
1052  1 dna1.createDatasetSequence();
1053  1 dna2.createDatasetSequence();
1054  1 pep1.createDatasetSequence();
1055  1 pep2.createDatasetSequence();
1056  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
1057  1 dna.setDataset(null);
1058   
1059    /*
1060    * put a variant feature on dna2 base 8
1061    * - should transfer to cds2 base 5
1062    */
1063  1 dna2.addSequenceFeature(
1064    new SequenceFeature("variant", "hgmd", 8, 8, 0f, null));
1065   
1066    /*
1067    * need a sourceDbRef if we are to construct dbrefs to the CDS
1068    * sequence from the dna contig sequences
1069    */
1070  1 DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
1071  1 dna1.getDatasetSequence().addDBRef(dbref);
1072  1 org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
1073  1 dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
1074  1 dna2.getDatasetSequence().addDBRef(dbref);
1075  1 org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
1076   
1077    /*
1078    * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
1079    * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
1080    */
1081  1 MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 },
1082    new int[]
1083    { 1, 2 }, 3, 1);
1084  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1085  1 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
1086    mapfordna1);
1087  1 dna.addCodonFrame(acf);
1088  1 MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1089    new int[]
1090    { 1, 3 }, 3, 1);
1091  1 acf = new AlignedCodonFrame();
1092  1 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
1093    mapfordna2);
1094  1 dna.addCodonFrame(acf);
1095   
1096    /*
1097    * In this case, mappings originally came from matching Uniprot accessions
1098    * - so need an xref on dna involving those regions.
1099    * These are normally constructed from CDS annotation
1100    */
1101  1 DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
1102    new Mapping(mapfordna1));
1103  1 dna1.addDBRef(dna1xref);
1104  1 assertEquals(2, dna1.getDBRefs().size()); // to self and to pep1
1105  1 DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
1106    new Mapping(mapfordna2));
1107  1 dna2.addDBRef(dna2xref);
1108  1 assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2
1109   
1110    /*
1111    * execute method under test:
1112    */
1113  1 AlignmentI cds = AlignmentUtils
1114    .makeCdsAlignment(new SequenceI[]
1115    { dna1, dna2 }, dna.getDataset(), null);
1116   
1117    /*
1118    * verify cds sequences
1119    */
1120  1 assertEquals(2, cds.getSequences().size());
1121  1 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
1122  1 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
1123   
1124    /*
1125    * verify shared, extended alignment dataset
1126    */
1127  1 assertSame(dna.getDataset(), cds.getDataset());
1128  1 SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence();
1129  1 SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence();
1130  1 assertTrue(dna.getDataset().getSequences().contains(cds1Dss));
1131  1 assertTrue(dna.getDataset().getSequences().contains(cds2Dss));
1132   
1133    /*
1134    * verify CDS has a dbref with mapping to peptide
1135    */
1136  1 assertNotNull(cds1Dss.getDBRefs());
1137  1 assertEquals(2, cds1Dss.getDBRefs().size());
1138  1 dbref = cds1Dss.getDBRefs().get(0);
1139  1 assertEquals(dna1xref.getSource(), dbref.getSource());
1140    // version is via ensembl's primary ref
1141  1 assertEquals(dna1xref.getVersion(), dbref.getVersion());
1142  1 assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
1143  1 assertNotNull(dbref.getMap());
1144  1 assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
1145  1 MapList cdsMapping = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 },
1146    3, 1);
1147  1 assertEquals(cdsMapping, dbref.getMap().getMap());
1148   
1149    /*
1150    * verify peptide has added a dbref with reverse mapping to CDS
1151    */
1152  1 assertNotNull(pep1.getDBRefs());
1153    // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
1154  1 assertEquals(2, pep1.getDBRefs().size());
1155  1 dbref = pep1.getDBRefs().get(1);
1156  1 assertEquals("ENSEMBL", dbref.getSource());
1157  1 assertEquals("0", dbref.getVersion());
1158  1 assertEquals("CDS|dna1", dbref.getAccessionId());
1159  1 assertNotNull(dbref.getMap());
1160  1 assertSame(cds1Dss, dbref.getMap().getTo());
1161  1 assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
1162   
1163    /*
1164    * verify cDNA has added a dbref with mapping to CDS
1165    */
1166  1 assertEquals(3, dna1.getDBRefs().size());
1167  1 DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
1168  1 assertSame(cds1Dss, dbRefEntry.getMap().getTo());
1169  1 MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
1170    new int[]
1171    { 1, 6 }, 1, 1);
1172  1 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1173  1 assertEquals(3, dna2.getDBRefs().size());
1174  1 dbRefEntry = dna2.getDBRefs().get(2);
1175  1 assertSame(cds2Dss, dbRefEntry.getMap().getTo());
1176  1 dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1177    new int[]
1178    { 1, 9 }, 1, 1);
1179  1 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1180   
1181    /*
1182    * verify CDS has added a dbref with mapping to cDNA
1183    */
1184  1 assertEquals(2, cds1Dss.getDBRefs().size());
1185  1 dbRefEntry = cds1Dss.getDBRefs().get(1);
1186  1 assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
1187  1 MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 },
1188    new int[]
1189    { 4, 6, 10, 12 }, 1, 1);
1190  1 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1191  1 assertEquals(2, cds2Dss.getDBRefs().size());
1192  1 dbRefEntry = cds2Dss.getDBRefs().get(1);
1193  1 assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
1194  1 cdsToDnaMapping = new MapList(new int[] { 1, 9 },
1195    new int[]
1196    { 1, 3, 7, 9, 13, 15 }, 1, 1);
1197  1 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1198   
1199    /*
1200    * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
1201    * the mappings are on the shared alignment dataset
1202    * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
1203    */
1204  1 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
1205  1 assertEquals(6, cdsMappings.size());
1206   
1207    /*
1208    * verify that mapping sets for dna and cds alignments are different
1209    * [not current behaviour - all mappings are on the alignment dataset]
1210    */
1211    // select -> subselect type to test.
1212    // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
1213    // assertEquals(4, dna.getCodonFrames().size());
1214    // assertEquals(4, cds.getCodonFrames().size());
1215   
1216    /*
1217    * Two mappings involve pep1 (dna to pep1, cds to pep1)
1218    * Mapping from pep1 to GGGTTT in first new exon sequence
1219    */
1220  1 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1221    .findMappingsForSequence(pep1, cdsMappings);
1222  1 assertEquals(2, pep1Mappings.size());
1223  1 List<AlignedCodonFrame> mappings = MappingUtils
1224    .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1225  1 assertEquals(1, mappings.size());
1226   
1227    // map G to GGG
1228  1 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
1229  1 assertEquals(1, sr.getResults().size());
1230  1 SearchResultMatchI m = sr.getResults().get(0);
1231  1 assertSame(cds1Dss, m.getSequence());
1232  1 assertEquals(1, m.getStart());
1233  1 assertEquals(3, m.getEnd());
1234    // map F to TTT
1235  1 sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
1236  1 m = sr.getResults().get(0);
1237  1 assertSame(cds1Dss, m.getSequence());
1238  1 assertEquals(4, m.getStart());
1239  1 assertEquals(6, m.getEnd());
1240   
1241    /*
1242    * Two mappings involve pep2 (dna to pep2, cds to pep2)
1243    * Verify mapping from pep2 to GGGTTTCCC in second new exon sequence
1244    */
1245  1 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1246    .findMappingsForSequence(pep2, cdsMappings);
1247  1 assertEquals(2, pep2Mappings.size());
1248  1 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
1249    pep2Mappings);
1250  1 assertEquals(1, mappings.size());
1251    // map G to GGG
1252  1 sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
1253  1 assertEquals(1, sr.getResults().size());
1254  1 m = sr.getResults().get(0);
1255  1 assertSame(cds2Dss, m.getSequence());
1256  1 assertEquals(1, m.getStart());
1257  1 assertEquals(3, m.getEnd());
1258    // map F to TTT
1259  1 sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
1260  1 m = sr.getResults().get(0);
1261  1 assertSame(cds2Dss, m.getSequence());
1262  1 assertEquals(4, m.getStart());
1263  1 assertEquals(6, m.getEnd());
1264    // map P to CCC
1265  1 sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
1266  1 m = sr.getResults().get(0);
1267  1 assertSame(cds2Dss, m.getSequence());
1268  1 assertEquals(7, m.getStart());
1269  1 assertEquals(9, m.getEnd());
1270   
1271    /*
1272    * check cds2 acquired a variant feature in position 5
1273    */
1274  1 List<SequenceFeature> sfs = cds2Dss.getSequenceFeatures();
1275  1 assertNotNull(sfs);
1276  1 assertEquals(1, sfs.size());
1277  1 assertEquals("variant", sfs.get(0).type);
1278  1 assertEquals(5, sfs.get(0).begin);
1279  1 assertEquals(5, sfs.get(0).end);
1280    }
1281   
1282    /**
1283    * Test the method that makes a cds-only alignment from a DNA sequence and its
1284    * product mappings, for the case where there are multiple exon mappings to
1285    * different protein products.
1286    */
 
1287  1 toggle @Test(groups = { "Functional" })
1288    public void testMakeCdsAlignment_multipleProteins()
1289    {
1290  1 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1291  1 SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
1292  1 SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
1293  1 SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
1294  1 dna1.createDatasetSequence();
1295  1 pep1.createDatasetSequence();
1296  1 pep2.createDatasetSequence();
1297  1 pep3.createDatasetSequence();
1298  1 pep1.getDatasetSequence()
1299    .addDBRef(new DBRefEntry("EMBLCDS", "2", "A12345"));
1300  1 pep2.getDatasetSequence()
1301    .addDBRef(new DBRefEntry("EMBLCDS", "3", "A12346"));
1302  1 pep3.getDatasetSequence()
1303    .addDBRef(new DBRefEntry("EMBLCDS", "4", "A12347"));
1304   
1305    /*
1306    * Create the CDS alignment
1307    */
1308  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
1309  1 dna.setDataset(null);
1310   
1311    /*
1312    * Make the mappings from dna to protein
1313    */
1314    // map ...GGG...TTT to GF
1315  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1316    new int[]
1317    { 1, 2 }, 3, 1);
1318  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1319  1 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1320  1 dna.addCodonFrame(acf);
1321   
1322    // map aaa...ccc to KP
1323  1 map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
1324  1 acf = new AlignedCodonFrame();
1325  1 acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
1326  1 dna.addCodonFrame(acf);
1327   
1328    // map aaa......TTT to KF
1329  1 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
1330  1 acf = new AlignedCodonFrame();
1331  1 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
1332  1 dna.addCodonFrame(acf);
1333   
1334    /*
1335    * execute method under test
1336    */
1337  1 AlignmentI cdsal = AlignmentUtils
1338    .makeCdsAlignment(new SequenceI[]
1339    { dna1 }, dna.getDataset(), null);
1340   
1341    /*
1342    * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
1343    */
1344  1 List<SequenceI> cds = cdsal.getSequences();
1345  1 assertEquals(3, cds.size());
1346   
1347    /*
1348    * verify shared, extended alignment dataset
1349    */
1350  1 assertSame(cdsal.getDataset(), dna.getDataset());
1351  1 assertTrue(dna.getDataset().getSequences()
1352    .contains(cds.get(0).getDatasetSequence()));
1353  1 assertTrue(dna.getDataset().getSequences()
1354    .contains(cds.get(1).getDatasetSequence()));
1355  1 assertTrue(dna.getDataset().getSequences()
1356    .contains(cds.get(2).getDatasetSequence()));
1357   
1358    /*
1359    * verify aligned cds sequences and their xrefs
1360    */
1361  1 SequenceI cdsSeq = cds.get(0);
1362  1 assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
1363    // assertEquals("dna1|A12345", cdsSeq.getName());
1364  1 assertEquals("CDS|dna1", cdsSeq.getName());
1365    // assertEquals(1, cdsSeq.getDBRefs().length);
1366    // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
1367    // assertEquals("EMBLCDS", cdsRef.getSource());
1368    // assertEquals("2", cdsRef.getVersion());
1369    // assertEquals("A12345", cdsRef.getAccessionId());
1370   
1371  1 cdsSeq = cds.get(1);
1372  1 assertEquals("aaaccc", cdsSeq.getSequenceAsString());
1373    // assertEquals("dna1|A12346", cdsSeq.getName());
1374  1 assertEquals("CDS|dna1", cdsSeq.getName());
1375    // assertEquals(1, cdsSeq.getDBRefs().length);
1376    // cdsRef = cdsSeq.getDBRefs()[0];
1377    // assertEquals("EMBLCDS", cdsRef.getSource());
1378    // assertEquals("3", cdsRef.getVersion());
1379    // assertEquals("A12346", cdsRef.getAccessionId());
1380   
1381  1 cdsSeq = cds.get(2);
1382  1 assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
1383    // assertEquals("dna1|A12347", cdsSeq.getName());
1384  1 assertEquals("CDS|dna1", cdsSeq.getName());
1385    // assertEquals(1, cdsSeq.getDBRefs().length);
1386    // cdsRef = cdsSeq.getDBRefs()[0];
1387    // assertEquals("EMBLCDS", cdsRef.getSource());
1388    // assertEquals("4", cdsRef.getVersion());
1389    // assertEquals("A12347", cdsRef.getAccessionId());
1390   
1391    /*
1392    * Verify there are mappings from each cds sequence to its protein product
1393    * and also to its dna source
1394    */
1395  1 List<AlignedCodonFrame> newMappings = cdsal.getCodonFrames();
1396   
1397    /*
1398    * 6 mappings involve dna1 (to pep1/2/3, cds1/2/3)
1399    */
1400  1 List<AlignedCodonFrame> dnaMappings = MappingUtils
1401    .findMappingsForSequence(dna1, newMappings);
1402  1 assertEquals(6, dnaMappings.size());
1403   
1404    /*
1405    * dna1 to pep1
1406    */
1407  1 List<AlignedCodonFrame> mappings = MappingUtils
1408    .findMappingsForSequence(pep1, dnaMappings);
1409  1 assertEquals(1, mappings.size());
1410  1 assertEquals(1, mappings.get(0).getMappings().size());
1411  1 assertSame(pep1.getDatasetSequence(),
1412    mappings.get(0).getMappings().get(0).getMapping().getTo());
1413   
1414    /*
1415    * dna1 to cds1
1416    */
1417  1 List<AlignedCodonFrame> dnaToCds1Mappings = MappingUtils
1418    .findMappingsForSequence(cds.get(0), dnaMappings);
1419  1 Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
1420    .getMapping();
1421  1 assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
1422  1 assertEquals("G(1) in CDS should map to G(4) in DNA", 4,
1423    mapping.getMap().getToPosition(1));
1424   
1425    /*
1426    * dna1 to pep2
1427    */
1428  1 mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
1429  1 assertEquals(1, mappings.size());
1430  1 assertEquals(1, mappings.get(0).getMappings().size());
1431  1 assertSame(pep2.getDatasetSequence(),
1432    mappings.get(0).getMappings().get(0).getMapping().getTo());
1433   
1434    /*
1435    * dna1 to cds2
1436    */
1437  1 List<AlignedCodonFrame> dnaToCds2Mappings = MappingUtils
1438    .findMappingsForSequence(cds.get(1), dnaMappings);
1439  1 mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
1440  1 assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
1441  1 assertEquals("c(4) in CDS should map to c(7) in DNA", 7,
1442    mapping.getMap().getToPosition(4));
1443   
1444    /*
1445    * dna1 to pep3
1446    */
1447  1 mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
1448  1 assertEquals(1, mappings.size());
1449  1 assertEquals(1, mappings.get(0).getMappings().size());
1450  1 assertSame(pep3.getDatasetSequence(),
1451    mappings.get(0).getMappings().get(0).getMapping().getTo());
1452   
1453    /*
1454    * dna1 to cds3
1455    */
1456  1 List<AlignedCodonFrame> dnaToCds3Mappings = MappingUtils
1457    .findMappingsForSequence(cds.get(2), dnaMappings);
1458  1 mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
1459  1 assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
1460  1 assertEquals("T(4) in CDS should map to T(10) in DNA", 10,
1461    mapping.getMap().getToPosition(4));
1462    }
1463   
 
1464  1 toggle @Test(groups = { "Functional" })
1465    public void testIsMappable()
1466    {
1467  1 SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
1468  1 SequenceI aa1 = new Sequence("aa1", "RSG");
1469  1 AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
1470  1 AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
1471   
1472  1 assertFalse(AlignmentUtils.isMappable(null, null));
1473  1 assertFalse(AlignmentUtils.isMappable(al1, null));
1474  1 assertFalse(AlignmentUtils.isMappable(null, al1));
1475  1 assertFalse(AlignmentUtils.isMappable(al1, al1));
1476  1 assertFalse(AlignmentUtils.isMappable(al2, al2));
1477   
1478  1 assertTrue(AlignmentUtils.isMappable(al1, al2));
1479  1 assertTrue(AlignmentUtils.isMappable(al2, al1));
1480    }
1481   
1482    /**
1483    * Test creating a mapping when the sequences involved do not start at residue
1484    * 1
1485    *
1486    * @throws IOException
1487    */
 
1488  1 toggle @Test(groups = { "Functional" })
1489    public void testMapCdnaToProtein_forSubsequence() throws IOException
1490    {
1491  1 SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
1492  1 prot.createDatasetSequence();
1493   
1494  1 SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
1495  1 dna.createDatasetSequence();
1496   
1497  1 MapList map = AlignmentUtils.mapCdnaToProtein(prot, dna);
1498  1 assertEquals(10, map.getToLowest());
1499  1 assertEquals(12, map.getToHighest());
1500  1 assertEquals(40, map.getFromLowest());
1501  1 assertEquals(48, map.getFromHighest());
1502    }
1503   
1504    /**
1505    * Test for the alignSequenceAs method where we have protein mapped to protein
1506    */
 
1507  1 toggle @Test(groups = { "Functional" })
1508    public void testAlignSequenceAs_mappedProteinProtein()
1509    {
1510   
1511  1 SequenceI alignMe = new Sequence("Match", "MGAASEV");
1512  1 alignMe.createDatasetSequence();
1513  1 SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
1514  1 alignFrom.createDatasetSequence();
1515   
1516  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1517    // this is like a domain or motif match of part of a peptide sequence
1518  1 MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1,
1519    1);
1520  1 acf.addMap(alignFrom.getDatasetSequence(), alignMe.getDatasetSequence(),
1521    map);
1522   
1523  1 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
1524    true);
1525  1 assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString());
1526    }
1527   
1528    /**
1529    * Test for the alignSequenceAs method where there are trailing unmapped
1530    * residues in the model sequence
1531    */
 
1532  1 toggle @Test(groups = { "Functional" })
1533    public void testAlignSequenceAs_withTrailingPeptide()
1534    {
1535    // map first 3 codons to KPF; G is a trailing unmapped residue
1536  1 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
1537   
1538  1 checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,
1539    "AAA---CCCTTT---");
1540    }
1541   
1542    /**
1543    * Tests for transferring features between mapped sequences
1544    */
 
1545  1 toggle @Test(groups = { "Functional" })
1546    public void testTransferFeatures()
1547    {
1548  1 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1549  1 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1550   
1551    // no overlap
1552  1 dna.addSequenceFeature(
1553    new SequenceFeature("type1", "desc1", 1, 2, 1f, null));
1554    // partial overlap - to [1, 1]
1555  1 dna.addSequenceFeature(
1556    new SequenceFeature("type2", "desc2", 3, 4, 2f, null));
1557    // exact overlap - to [1, 3]
1558  1 dna.addSequenceFeature(
1559    new SequenceFeature("type3", "desc3", 4, 6, 3f, null));
1560    // spanning overlap - to [2, 5]
1561  1 dna.addSequenceFeature(
1562    new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
1563    // exactly overlaps whole mapped range [1, 6]
1564  1 dna.addSequenceFeature(
1565    new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
1566    // no overlap (internal)
1567  1 dna.addSequenceFeature(
1568    new SequenceFeature("type6", "desc6", 7, 9, 6f, null));
1569    // no overlap (3' end)
1570  1 dna.addSequenceFeature(
1571    new SequenceFeature("type7", "desc7", 13, 15, 7f, null));
1572    // overlap (3' end) - to [6, 6]
1573  1 dna.addSequenceFeature(
1574    new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
1575    // extended overlap - to [6, +]
1576  1 dna.addSequenceFeature(
1577    new SequenceFeature("type9", "desc9", 12, 13, 9f, null));
1578   
1579  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1580    new int[]
1581    { 1, 6 }, 1, 1);
1582   
1583    /*
1584    * transferFeatures() will build 'partial overlap' for regions
1585    * that partially overlap 5' or 3' (start or end) of target sequence
1586    */
1587  1 AlignmentUtils.transferFeatures(dna, cds, map, null);
1588  1 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1589  1 assertEquals(6, sfs.size());
1590   
1591  1 SequenceFeature sf = sfs.get(0);
1592  1 assertEquals("type2", sf.getType());
1593  1 assertEquals("desc2", sf.getDescription());
1594  1 assertEquals(2f, sf.getScore());
1595  1 assertEquals(1, sf.getBegin());
1596  1 assertEquals(1, sf.getEnd());
1597   
1598  1 sf = sfs.get(1);
1599  1 assertEquals("type3", sf.getType());
1600  1 assertEquals("desc3", sf.getDescription());
1601  1 assertEquals(3f, sf.getScore());
1602  1 assertEquals(1, sf.getBegin());
1603  1 assertEquals(3, sf.getEnd());
1604   
1605  1 sf = sfs.get(2);
1606  1 assertEquals("type4", sf.getType());
1607  1 assertEquals(2, sf.getBegin());
1608  1 assertEquals(5, sf.getEnd());
1609   
1610  1 sf = sfs.get(3);
1611  1 assertEquals("type5", sf.getType());
1612  1 assertEquals(1, sf.getBegin());
1613  1 assertEquals(6, sf.getEnd());
1614   
1615  1 sf = sfs.get(4);
1616  1 assertEquals("type8", sf.getType());
1617  1 assertEquals(6, sf.getBegin());
1618  1 assertEquals(6, sf.getEnd());
1619   
1620  1 sf = sfs.get(5);
1621  1 assertEquals("type9", sf.getType());
1622  1 assertEquals(6, sf.getBegin());
1623  1 assertEquals(6, sf.getEnd());
1624    }
1625   
1626    /**
1627    * Tests for transferring features between mapped sequences
1628    */
 
1629  1 toggle @Test(groups = { "Functional" })
1630    public void testTransferFeatures_withOmit()
1631    {
1632  1 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1633  1 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1634   
1635  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1636    new int[]
1637    { 1, 6 }, 1, 1);
1638   
1639    // [5, 11] maps to [2, 5]
1640  1 dna.addSequenceFeature(
1641    new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
1642    // [4, 12] maps to [1, 6]
1643  1 dna.addSequenceFeature(
1644    new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
1645    // [12, 12] maps to [6, 6]
1646  1 dna.addSequenceFeature(
1647    new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
1648   
1649    // desc4 and desc8 are the 'omit these' varargs
1650  1 AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
1651  1 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1652  1 assertEquals(1, sfs.size());
1653   
1654  1 SequenceFeature sf = sfs.get(0);
1655  1 assertEquals("type5", sf.getType());
1656  1 assertEquals(1, sf.getBegin());
1657  1 assertEquals(6, sf.getEnd());
1658    }
1659   
1660    /**
1661    * Tests for transferring features between mapped sequences
1662    */
 
1663  1 toggle @Test(groups = { "Functional" })
1664    public void testTransferFeatures_withSelect()
1665    {
1666  1 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1667  1 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1668   
1669  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1670    new int[]
1671    { 1, 6 }, 1, 1);
1672   
1673    // [5, 11] maps to [2, 5]
1674  1 dna.addSequenceFeature(
1675    new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
1676    // [4, 12] maps to [1, 6]
1677  1 dna.addSequenceFeature(
1678    new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
1679    // [12, 12] maps to [6, 6]
1680  1 dna.addSequenceFeature(
1681    new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
1682   
1683    // "type5" is the 'select this type' argument
1684  1 AlignmentUtils.transferFeatures(dna, cds, map, "type5");
1685  1 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1686  1 assertEquals(1, sfs.size());
1687   
1688  1 SequenceFeature sf = sfs.get(0);
1689  1 assertEquals("type5", sf.getType());
1690  1 assertEquals(1, sf.getBegin());
1691  1 assertEquals(6, sf.getEnd());
1692    }
1693   
1694    /**
1695    * Test the method that extracts the cds-only part of a dna alignment, for the
1696    * case where the cds should be aligned to match its nucleotide sequence.
1697    */
 
1698  1 toggle @Test(groups = { "Functional" })
1699    public void testMakeCdsAlignment_alternativeTranscripts()
1700    {
1701  1 SequenceI dna1 = new Sequence("dna1", "aaaGGGCC-----CTTTaaaGGG");
1702    // alternative transcript of same dna skips CCC codon
1703  1 SequenceI dna2 = new Sequence("dna2", "aaaGGGCC-----cttTaaaGGG");
1704    // dna3 has no mapping (protein product) so should be ignored here
1705  1 SequenceI dna3 = new Sequence("dna3", "aaaGGGCCCCCGGGcttTaaaGGG");
1706  1 SequenceI pep1 = new Sequence("pep1", "GPFG");
1707  1 SequenceI pep2 = new Sequence("pep2", "GPG");
1708  1 dna1.createDatasetSequence();
1709  1 dna2.createDatasetSequence();
1710  1 dna3.createDatasetSequence();
1711  1 pep1.createDatasetSequence();
1712  1 pep2.createDatasetSequence();
1713   
1714  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1715  1 dna.setDataset(null);
1716   
1717  1 MapList map = new MapList(new int[] { 4, 12, 16, 18 },
1718    new int[]
1719    { 1, 4 }, 3, 1);
1720  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1721  1 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1722  1 dna.addCodonFrame(acf);
1723  1 map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
1724    new int[]
1725    { 1, 3 }, 3, 1);
1726  1 acf = new AlignedCodonFrame();
1727  1 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1728  1 dna.addCodonFrame(acf);
1729   
1730  1 AlignmentI cds = AlignmentUtils
1731    .makeCdsAlignment(new SequenceI[]
1732    { dna1, dna2, dna3 }, dna.getDataset(), null);
1733  1 List<SequenceI> cdsSeqs = cds.getSequences();
1734  1 assertEquals(2, cdsSeqs.size());
1735  1 assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
1736  1 assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
1737   
1738    /*
1739    * verify shared, extended alignment dataset
1740    */
1741  1 assertSame(dna.getDataset(), cds.getDataset());
1742  1 assertTrue(dna.getDataset().getSequences()
1743    .contains(cdsSeqs.get(0).getDatasetSequence()));
1744  1 assertTrue(dna.getDataset().getSequences()
1745    .contains(cdsSeqs.get(1).getDatasetSequence()));
1746   
1747    /*
1748    * Verify 6 mappings: dna1 to cds1, cds1 to pep1, dna1 to pep1
1749    * and the same for dna2/cds2/pep2
1750    */
1751  1 List<AlignedCodonFrame> mappings = cds.getCodonFrames();
1752  1 assertEquals(6, mappings.size());
1753   
1754    /*
1755    * 2 mappings involve pep1
1756    */
1757  1 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1758    .findMappingsForSequence(pep1, mappings);
1759  1 assertEquals(2, pep1Mappings.size());
1760   
1761    /*
1762    * Get mapping of pep1 to cds1 and verify it
1763    * maps GPFG to 1-3,4-6,7-9,10-12
1764    */
1765  1 List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
1766    .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1767  1 assertEquals(1, pep1CdsMappings.size());
1768  1 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1,
1769    pep1CdsMappings);
1770  1 assertEquals(1, sr.getResults().size());
1771  1 SearchResultMatchI m = sr.getResults().get(0);
1772  1 assertEquals(cds.getSequenceAt(0).getDatasetSequence(),
1773    m.getSequence());
1774  1 assertEquals(1, m.getStart());
1775  1 assertEquals(3, m.getEnd());
1776  1 sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
1777  1 m = sr.getResults().get(0);
1778  1 assertEquals(4, m.getStart());
1779  1 assertEquals(6, m.getEnd());
1780  1 sr = MappingUtils.buildSearchResults(pep1, 3, pep1CdsMappings);
1781  1 m = sr.getResults().get(0);
1782  1 assertEquals(7, m.getStart());
1783  1 assertEquals(9, m.getEnd());
1784  1 sr = MappingUtils.buildSearchResults(pep1, 4, pep1CdsMappings);
1785  1 m = sr.getResults().get(0);
1786  1 assertEquals(10, m.getStart());
1787  1 assertEquals(12, m.getEnd());
1788   
1789    /*
1790    * Get mapping of pep2 to cds2 and verify it
1791    * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence
1792    */
1793  1 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1794    .findMappingsForSequence(pep2, mappings);
1795  1 assertEquals(2, pep2Mappings.size());
1796  1 List<AlignedCodonFrame> pep2CdsMappings = MappingUtils
1797    .findMappingsForSequence(cds.getSequenceAt(1), pep2Mappings);
1798  1 assertEquals(1, pep2CdsMappings.size());
1799  1 sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
1800  1 assertEquals(1, sr.getResults().size());
1801  1 m = sr.getResults().get(0);
1802  1 assertEquals(cds.getSequenceAt(1).getDatasetSequence(),
1803    m.getSequence());
1804  1 assertEquals(1, m.getStart());
1805  1 assertEquals(3, m.getEnd());
1806  1 sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
1807  1 m = sr.getResults().get(0);
1808  1 assertEquals(4, m.getStart());
1809  1 assertEquals(6, m.getEnd());
1810  1 sr = MappingUtils.buildSearchResults(pep2, 3, pep2CdsMappings);
1811  1 m = sr.getResults().get(0);
1812  1 assertEquals(7, m.getStart());
1813  1 assertEquals(9, m.getEnd());
1814    }
1815   
1816    /**
1817    * Test the method that realigns protein to match mapped codon alignment.
1818    */
 
1819  1 toggle @Test(groups = { "Functional" })
1820    public void testAlignProteinAsDna_incompleteStartCodon()
1821    {
1822    // seq1: incomplete start codon (not mapped), then [3, 11]
1823  1 SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
1824    // seq2 codons are [4, 5], [8, 11]
1825  1 SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
1826    // seq3 incomplete start codon at 'tt'
1827  1 SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
1828  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1829  1 dna.setDataset(null);
1830   
1831    // prot1 has 'X' for incomplete start codon (not mapped)
1832  1 SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
1833  1 SequenceI prot2 = new Sequence("Seq2", "NG");
1834  1 SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
1835  1 AlignmentI protein = new Alignment(
1836    new SequenceI[]
1837    { prot1, prot2, prot3 });
1838  1 protein.setDataset(null);
1839   
1840    // map dna1 [3, 11] to prot1 [2, 4] KFG
1841  1 MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3,
1842    1);
1843  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1844  1 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
1845   
1846    // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
1847  1 map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
1848  1 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
1849   
1850    // map dna3 [9, 11] to prot3 [2, 2] G
1851  1 map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
1852  1 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
1853   
1854  1 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
1855  1 acfs.add(acf);
1856  1 protein.setCodonFrames(acfs);
1857   
1858    /*
1859    * verify X is included in the aligned proteins, and placed just
1860    * before the first mapped residue
1861    * CCT is between CCC and TTT
1862    */
1863  1 AlignmentUtils.alignProteinAsDna(protein, dna);
1864  1 assertEquals("XK-FG", prot1.getSequenceAsString());
1865  1 assertEquals("--N-G", prot2.getSequenceAsString());
1866  1 assertEquals("---XG", prot3.getSequenceAsString());
1867    }
1868   
1869    /**
1870    * Tests for the method that maps the subset of a dna sequence that has CDS
1871    * (or subtype) feature - case where the start codon is incomplete.
1872    */
 
1873  1 toggle @Test(groups = "Functional")
1874    public void testFindCdsPositions_fivePrimeIncomplete()
1875    {
1876  1 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1877  1 dnaSeq.createDatasetSequence();
1878  1 SequenceI ds = dnaSeq.getDatasetSequence();
1879   
1880    // CDS for dna 5-6 (incomplete codon), 7-9
1881  1 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1882  1 sf.setPhase("2"); // skip 2 bases to start of next codon
1883  1 ds.addSequenceFeature(sf);
1884    // CDS for dna 13-15
1885  1 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1886  1 ds.addSequenceFeature(sf);
1887   
1888  1 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1889   
1890    /*
1891    * check the mapping starts with the first complete codon
1892    */
1893  1 assertEquals(6, MappingUtils.getLength(ranges));
1894  1 assertEquals(2, ranges.size());
1895  1 assertEquals(7, ranges.get(0)[0]);
1896  1 assertEquals(9, ranges.get(0)[1]);
1897  1 assertEquals(13, ranges.get(1)[0]);
1898  1 assertEquals(15, ranges.get(1)[1]);
1899    }
1900   
1901    /**
1902    * Tests for the method that maps the subset of a dna sequence that has CDS
1903    * (or subtype) feature.
1904    */
 
1905  1 toggle @Test(groups = "Functional")
1906    public void testFindCdsPositions()
1907    {
1908  1 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1909  1 dnaSeq.createDatasetSequence();
1910  1 SequenceI ds = dnaSeq.getDatasetSequence();
1911   
1912    // CDS for dna 10-12
1913  1 SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
1914    0f, null);
1915  1 sf.setStrand("+");
1916  1 ds.addSequenceFeature(sf);
1917    // CDS for dna 4-6
1918  1 sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1919  1 sf.setStrand("+");
1920  1 ds.addSequenceFeature(sf);
1921    // exon feature should be ignored here
1922  1 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1923  1 ds.addSequenceFeature(sf);
1924   
1925  1 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1926    /*
1927    * verify ranges { [4-6], [12-10] }
1928    * note CDS ranges are ordered ascending even if the CDS
1929    * features are not
1930    */
1931  1 assertEquals(6, MappingUtils.getLength(ranges));
1932  1 assertEquals(2, ranges.size());
1933  1 assertEquals(4, ranges.get(0)[0]);
1934  1 assertEquals(6, ranges.get(0)[1]);
1935  1 assertEquals(10, ranges.get(1)[0]);
1936  1 assertEquals(12, ranges.get(1)[1]);
1937    }
1938   
1939    /**
1940    * Tests for the method that maps the subset of a dna sequence that has CDS
1941    * (or subtype) feature, with CDS strand = '-' (reverse)
1942    */
1943    // test turned off as currently findCdsPositions is not strand-dependent
1944    // left in case it comes around again...
 
1945  0 toggle @Test(groups = "Functional", enabled = false)
1946    public void testFindCdsPositions_reverseStrand()
1947    {
1948  0 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1949  0 dnaSeq.createDatasetSequence();
1950  0 SequenceI ds = dnaSeq.getDatasetSequence();
1951   
1952    // CDS for dna 4-6
1953  0 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1954  0 sf.setStrand("-");
1955  0 ds.addSequenceFeature(sf);
1956    // exon feature should be ignored here
1957  0 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1958  0 ds.addSequenceFeature(sf);
1959    // CDS for dna 10-12
1960  0 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
1961  0 sf.setStrand("-");
1962  0 ds.addSequenceFeature(sf);
1963   
1964  0 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1965    /*
1966    * verify ranges { [12-10], [6-4] }
1967    */
1968  0 assertEquals(6, MappingUtils.getLength(ranges));
1969  0 assertEquals(2, ranges.size());
1970  0 assertEquals(12, ranges.get(0)[0]);
1971  0 assertEquals(10, ranges.get(0)[1]);
1972  0 assertEquals(6, ranges.get(1)[0]);
1973  0 assertEquals(4, ranges.get(1)[1]);
1974    }
1975   
1976    /**
1977    * Tests for the method that maps the subset of a dna sequence that has CDS
1978    * (or subtype) feature - reverse strand case where the start codon is
1979    * incomplete.
1980    */
 
1981  0 toggle @Test(groups = "Functional", enabled = false)
1982    // test turned off as currently findCdsPositions is not strand-dependent
1983    // left in case it comes around again...
1984    public void testFindCdsPositions_reverseStrandThreePrimeIncomplete()
1985    {
1986  0 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1987  0 dnaSeq.createDatasetSequence();
1988  0 SequenceI ds = dnaSeq.getDatasetSequence();
1989   
1990    // CDS for dna 5-9
1991  0 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1992  0 sf.setStrand("-");
1993  0 ds.addSequenceFeature(sf);
1994    // CDS for dna 13-15
1995  0 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1996  0 sf.setStrand("-");
1997  0 sf.setPhase("2"); // skip 2 bases to start of next codon
1998  0 ds.addSequenceFeature(sf);
1999   
2000  0 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
2001   
2002    /*
2003    * check the mapping starts with the first complete codon
2004    * expect ranges [13, 13], [9, 5]
2005    */
2006  0 assertEquals(6, MappingUtils.getLength(ranges));
2007  0 assertEquals(2, ranges.size());
2008  0 assertEquals(13, ranges.get(0)[0]);
2009  0 assertEquals(13, ranges.get(0)[1]);
2010  0 assertEquals(9, ranges.get(1)[0]);
2011  0 assertEquals(5, ranges.get(1)[1]);
2012    }
2013   
 
2014  1 toggle @Test(groups = "Functional")
2015    public void testAlignAs_alternateTranscriptsUngapped()
2016    {
2017  1 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2018  1 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2019  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2020  1 ((Alignment) dna).createDatasetAlignment();
2021  1 SequenceI cds1 = new Sequence("cds1", "GGGTTT");
2022  1 SequenceI cds2 = new Sequence("cds2", "CCCAAA");
2023  1 AlignmentI cds = new Alignment(new SequenceI[] { cds1, cds2 });
2024  1 ((Alignment) cds).createDatasetAlignment();
2025   
2026  1 AlignedCodonFrame acf = new AlignedCodonFrame();
2027  1 MapList map = new MapList(new int[] { 4, 9 }, new int[] { 1, 6 }, 1, 1);
2028  1 acf.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), map);
2029  1 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 6 }, 1, 1);
2030  1 acf.addMap(dna2.getDatasetSequence(), cds2.getDatasetSequence(), map);
2031   
2032    /*
2033    * verify CDS alignment is as:
2034    * cccGGGTTTaaa (cdna)
2035    * CCCgggtttAAA (cdna)
2036    *
2037    * ---GGGTTT--- (cds)
2038    * CCC------AAA (cds)
2039    */
2040  1 dna.addCodonFrame(acf);
2041  1 AlignmentUtils.alignAs(cds, dna);
2042  1 assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2043  1 assertEquals("CCC------AAA",
2044    cds.getSequenceAt(1).getSequenceAsString());
2045    }
2046   
 
2047  1 toggle @Test(groups = { "Functional" })
2048    public void testAddMappedPositions()
2049    {
2050  1 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2051  1 SequenceI seq1 = new Sequence("cds", "AAATTT");
2052  1 from.createDatasetSequence();
2053  1 seq1.createDatasetSequence();
2054  1 Mapping mapping = new Mapping(seq1,
2055    new MapList(new int[]
2056    { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2057  1 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
2058  1 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2059   
2060    /*
2061    * verify map has seq1 residues in columns 3,4,6,7,11,12
2062    */
2063  1 assertEquals(6, map.size());
2064  1 assertEquals('A', map.get(3).get(seq1).charValue());
2065  1 assertEquals('A', map.get(4).get(seq1).charValue());
2066  1 assertEquals('A', map.get(6).get(seq1).charValue());
2067  1 assertEquals('T', map.get(7).get(seq1).charValue());
2068  1 assertEquals('T', map.get(11).get(seq1).charValue());
2069  1 assertEquals('T', map.get(12).get(seq1).charValue());
2070   
2071    /*
2072    *
2073    */
2074    }
2075   
2076    /**
2077    * Test case where the mapping 'from' range includes a stop codon which is
2078    * absent in the 'to' range
2079    */
 
2080  1 toggle @Test(groups = { "Functional" })
2081    public void testAddMappedPositions_withStopCodon()
2082    {
2083  1 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2084  1 SequenceI seq1 = new Sequence("cds", "AAATTT");
2085  1 from.createDatasetSequence();
2086  1 seq1.createDatasetSequence();
2087  1 Mapping mapping = new Mapping(seq1,
2088    new MapList(new int[]
2089    { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2090  1 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
2091  1 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2092   
2093    /*
2094    * verify map has seq1 residues in columns 3,4,6,7,11,12
2095    */
2096  1 assertEquals(6, map.size());
2097  1 assertEquals('A', map.get(3).get(seq1).charValue());
2098  1 assertEquals('A', map.get(4).get(seq1).charValue());
2099  1 assertEquals('A', map.get(6).get(seq1).charValue());
2100  1 assertEquals('T', map.get(7).get(seq1).charValue());
2101  1 assertEquals('T', map.get(11).get(seq1).charValue());
2102  1 assertEquals('T', map.get(12).get(seq1).charValue());
2103    }
2104   
2105    /**
2106    * Test for the case where the products for which we want CDS are specified.
2107    * This is to represent the case where EMBL has CDS mappings to both Uniprot
2108    * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
2109    * the protein sequences specified.
2110    */
 
2111  1 toggle @Test(groups = { "Functional" })
2112    public void testMakeCdsAlignment_filterProducts()
2113    {
2114  1 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
2115  1 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
2116  1 SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
2117  1 SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
2118  1 SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
2119  1 SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
2120  1 dna1.createDatasetSequence();
2121  1 dna2.createDatasetSequence();
2122  1 pep1.createDatasetSequence();
2123  1 pep2.createDatasetSequence();
2124  1 pep3.createDatasetSequence();
2125  1 pep4.createDatasetSequence();
2126  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2127  1 dna.setDataset(null);
2128  1 AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
2129  1 emblPeptides.setDataset(null);
2130   
2131  1 AlignedCodonFrame acf = new AlignedCodonFrame();
2132  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
2133    new int[]
2134    { 1, 2 }, 3, 1);
2135  1 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
2136  1 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
2137  1 dna.addCodonFrame(acf);
2138   
2139  1 acf = new AlignedCodonFrame();
2140  1 map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
2141    3, 1);
2142  1 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
2143  1 acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
2144  1 dna.addCodonFrame(acf);
2145   
2146    /*
2147    * execute method under test to find CDS for EMBL peptides only
2148    */
2149  1 AlignmentI cds = AlignmentUtils
2150    .makeCdsAlignment(new SequenceI[]
2151    { dna1, dna2 }, dna.getDataset(),
2152    emblPeptides.getSequencesArray());
2153   
2154  1 assertEquals(2, cds.getSequences().size());
2155  1 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2156  1 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
2157   
2158    /*
2159    * verify shared, extended alignment dataset
2160    */
2161  1 assertSame(dna.getDataset(), cds.getDataset());
2162  1 assertTrue(dna.getDataset().getSequences()
2163    .contains(cds.getSequenceAt(0).getDatasetSequence()));
2164  1 assertTrue(dna.getDataset().getSequences()
2165    .contains(cds.getSequenceAt(1).getDatasetSequence()));
2166   
2167    /*
2168    * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
2169    * the mappings are on the shared alignment dataset
2170    */
2171  1 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
2172    /*
2173    * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
2174    */
2175  1 assertEquals(6, cdsMappings.size());
2176   
2177    /*
2178    * verify that mapping sets for dna and cds alignments are different
2179    * [not current behaviour - all mappings are on the alignment dataset]
2180    */
2181    // select -> subselect type to test.
2182    // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
2183    // assertEquals(4, dna.getCodonFrames().size());
2184    // assertEquals(4, cds.getCodonFrames().size());
2185   
2186    /*
2187    * Two mappings involve pep3 (dna to pep3, cds to pep3)
2188    * Mapping from pep3 to GGGTTT in first new exon sequence
2189    */
2190  1 List<AlignedCodonFrame> pep3Mappings = MappingUtils
2191    .findMappingsForSequence(pep3, cdsMappings);
2192  1 assertEquals(2, pep3Mappings.size());
2193  1 List<AlignedCodonFrame> mappings = MappingUtils
2194    .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
2195  1 assertEquals(1, mappings.size());
2196   
2197    // map G to GGG
2198  1 SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
2199  1 assertEquals(1, sr.getResults().size());
2200  1 SearchResultMatchI m = sr.getResults().get(0);
2201  1 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2202  1 assertEquals(1, m.getStart());
2203  1 assertEquals(3, m.getEnd());
2204    // map F to TTT
2205  1 sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
2206  1 m = sr.getResults().get(0);
2207  1 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2208  1 assertEquals(4, m.getStart());
2209  1 assertEquals(6, m.getEnd());
2210   
2211    /*
2212    * Two mappings involve pep4 (dna to pep4, cds to pep4)
2213    * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
2214    */
2215  1 List<AlignedCodonFrame> pep4Mappings = MappingUtils
2216    .findMappingsForSequence(pep4, cdsMappings);
2217  1 assertEquals(2, pep4Mappings.size());
2218  1 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
2219    pep4Mappings);
2220  1 assertEquals(1, mappings.size());
2221    // map G to GGG
2222  1 sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
2223  1 assertEquals(1, sr.getResults().size());
2224  1 m = sr.getResults().get(0);
2225  1 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2226  1 assertEquals(1, m.getStart());
2227  1 assertEquals(3, m.getEnd());
2228    // map F to TTT
2229  1 sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
2230  1 m = sr.getResults().get(0);
2231  1 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2232  1 assertEquals(4, m.getStart());
2233  1 assertEquals(6, m.getEnd());
2234    // map P to CCC
2235  1 sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
2236  1 m = sr.getResults().get(0);
2237  1 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2238  1 assertEquals(7, m.getStart());
2239  1 assertEquals(9, m.getEnd());
2240    }
2241   
2242    /**
2243    * Test the method that just copies aligned sequences, provided all sequences
2244    * to be aligned share the aligned sequence's dataset
2245    */
 
2246  1 toggle @Test(groups = "Functional")
2247    public void testAlignAsSameSequences()
2248    {
2249  1 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2250  1 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2251  1 AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
2252  1 ((Alignment) al1).createDatasetAlignment();
2253   
2254  1 SequenceI dna3 = new Sequence(dna1);
2255  1 SequenceI dna4 = new Sequence(dna2);
2256  1 assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
2257  1 assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
2258  1 String seq1 = "-cc-GG-GT-TT--aaa";
2259  1 dna3.setSequence(seq1);
2260  1 String seq2 = "C--C-Cgg--gtt-tAA-A-";
2261  1 dna4.setSequence(seq2);
2262  1 AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
2263  1 ((Alignment) al2).createDatasetAlignment();
2264   
2265    /*
2266    * alignment removes gapped columns (two internal, two trailing)
2267    */
2268  1 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2269  1 String aligned1 = "-cc-GG-GTTT-aaa";
2270  1 assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
2271  1 String aligned2 = "C--C-Cgg-gtttAAA";
2272  1 assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
2273   
2274    /*
2275    * add another sequence to 'aligned' - should still succeed, since
2276    * unaligned sequences still share a dataset with aligned sequences
2277    */
2278  1 SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
2279  1 dna5.createDatasetSequence();
2280  1 al2.addSequence(dna5);
2281  1 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2282  1 assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
2283  1 assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
2284   
2285    /*
2286    * add another sequence to 'unaligned' - should fail, since now not
2287    * all unaligned sequences share a dataset with aligned sequences
2288    */
2289  1 SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
2290  1 dna6.createDatasetSequence();
2291  1 al1.addSequence(dna6);
2292    // JAL-2110 JBP Comment: what's the use case for this behaviour ?
2293  1 assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
2294    }
2295   
 
2296  1 toggle @Test(groups = "Functional")
2297    public void testAlignAsSameSequencesMultipleSubSeq()
2298    {
2299  1 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2300  1 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2301  1 SequenceI as1 = dna1.deriveSequence(); // cccGGGTTTaaa/1-12
2302  1 SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7); // GGGT/4-7
2303  1 SequenceI as3 = dna2.deriveSequence(); // CCCgggtttAAA/1-12
2304  1 as1.insertCharAt(6, 5, '-');
2305  1 assertEquals("cccGGG-----TTTaaa", as1.getSequenceAsString());
2306  1 as2.insertCharAt(6, 5, '-');
2307  1 assertEquals("GGGT-----", as2.getSequenceAsString());
2308  1 as3.insertCharAt(3, 5, '-');
2309  1 assertEquals("CCC-----gggtttAAA", as3.getSequenceAsString());
2310  1 AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
2311   
2312    // why do we need to cast this still ?
2313  1 ((Alignment) aligned).createDatasetAlignment();
2314  1 SequenceI uas1 = dna1.deriveSequence();
2315  1 SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
2316  1 SequenceI uas3 = dna2.deriveSequence();
2317  1 AlignmentI tobealigned = new Alignment(
2318    new SequenceI[]
2319    { uas1, uas2, uas3 });
2320  1 ((Alignment) tobealigned).createDatasetAlignment();
2321   
2322    /*
2323    * alignAs lines up dataset sequences and removes empty columns (two)
2324    */
2325  1 assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
2326  1 assertEquals("cccGGG---TTTaaa", uas1.getSequenceAsString());
2327  1 assertEquals("GGGT", uas2.getSequenceAsString());
2328  1 assertEquals("CCC---gggtttAAA", uas3.getSequenceAsString());
2329    }
2330   
 
2331  1 toggle @Test(groups = { "Functional" })
2332    public void testTransferGeneLoci()
2333    {
2334  1 SequenceI from = new Sequence("transcript",
2335    "aaacccgggTTTAAACCCGGGtttaaacccgggttt");
2336  1 SequenceI to = new Sequence("CDS", "TTTAAACCCGGG");
2337  1 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1,
2338    1);
2339   
2340    /*
2341    * first with nothing to transfer
2342    */
2343  1 AlignmentUtils.transferGeneLoci(from, map, to);
2344  1 assertNull(to.getGeneLoci());
2345   
2346    /*
2347    * next with gene loci set on 'from' sequence
2348    */
2349  1 int[] exons = new int[] { 100, 105, 155, 164, 210, 229 };
2350  1 MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1);
2351  1 from.setGeneLoci("human", "GRCh38", "7", geneMap);
2352  1 AlignmentUtils.transferGeneLoci(from, map, to);
2353   
2354  1 GeneLociI toLoci = to.getGeneLoci();
2355  1 assertNotNull(toLoci);
2356    // DBRefEntry constructor upper-cases 'source'
2357  1 assertEquals("HUMAN", toLoci.getSpeciesId());
2358  1 assertEquals("GRCh38", toLoci.getAssemblyId());
2359  1 assertEquals("7", toLoci.getChromosomeId());
2360   
2361    /*
2362    * transcript 'exons' are 1-6, 7-16, 17-36
2363    * CDS 1:12 is transcript 10-21
2364    * transcript 'CDS' is 10-16, 17-21
2365    * which is 'gene' 158-164, 210-214
2366    */
2367  1 MapList toMap = toLoci.getMapping();
2368  1 assertEquals(1, toMap.getFromRanges().size());
2369  1 assertEquals(2, toMap.getFromRanges().get(0).length);
2370  1 assertEquals(1, toMap.getFromRanges().get(0)[0]);
2371  1 assertEquals(12, toMap.getFromRanges().get(0)[1]);
2372  1 assertEquals(2, toMap.getToRanges().size());
2373  1 assertEquals(2, toMap.getToRanges().get(0).length);
2374  1 assertEquals(158, toMap.getToRanges().get(0)[0]);
2375  1 assertEquals(164, toMap.getToRanges().get(0)[1]);
2376  1 assertEquals(210, toMap.getToRanges().get(1)[0]);
2377  1 assertEquals(214, toMap.getToRanges().get(1)[1]);
2378    // or summarised as (but toString might change in future):
2379  1 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2380    toMap.toString());
2381   
2382    /*
2383    * an existing value is not overridden
2384    */
2385  1 geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1);
2386  1 from.setGeneLoci("inhuman", "GRCh37", "6", geneMap);
2387  1 AlignmentUtils.transferGeneLoci(from, map, to);
2388  1 assertEquals("GRCh38", toLoci.getAssemblyId());
2389  1 assertEquals("7", toLoci.getChromosomeId());
2390  1 toMap = toLoci.getMapping();
2391  1 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2392    toMap.toString());
2393    }
2394   
2395    /**
2396    * Tests for the method that maps nucleotide to protein based on CDS features
2397    */
 
2398  1 toggle @Test(groups = "Functional")
2399    public void testMapCdsToProtein()
2400    {
2401  1 SequenceI peptide = new Sequence("pep", "KLQ");
2402   
2403    /*
2404    * Case 1: CDS 3 times length of peptide
2405    * NB method only checks lengths match, not translation
2406    */
2407  1 SequenceI dna = new Sequence("dna", "AACGacgtCTCCT");
2408  1 dna.createDatasetSequence();
2409  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2410  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 13, null));
2411  1 MapList ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2412  1 assertEquals(3, ml.getFromRatio());
2413  1 assertEquals(1, ml.getToRatio());
2414  1 assertEquals("[[1, 3]]",
2415    Arrays.deepToString(ml.getToRanges().toArray()));
2416  1 assertEquals("[[1, 4], [9, 13]]",
2417    Arrays.deepToString(ml.getFromRanges().toArray()));
2418   
2419    /*
2420    * Case 2: CDS 3 times length of peptide + stop codon
2421    * (note code does not currently check trailing codon is a stop codon)
2422    */
2423  1 dna = new Sequence("dna", "AACGacgtCTCCTCCC");
2424  1 dna.createDatasetSequence();
2425  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2426  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
2427  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2428  1 assertEquals(3, ml.getFromRatio());
2429  1 assertEquals(1, ml.getToRatio());
2430  1 assertEquals("[[1, 3]]",
2431    Arrays.deepToString(ml.getToRanges().toArray()));
2432  1 assertEquals("[[1, 4], [9, 13]]",
2433    Arrays.deepToString(ml.getFromRanges().toArray()));
2434   
2435    /*
2436    * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made
2437    */
2438  1 dna = new Sequence("dna", "AACGacgtCTCCTTGATCA");
2439  1 dna.createDatasetSequence();
2440  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2441  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null));
2442  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2443  1 assertNull(ml);
2444   
2445    /*
2446    * Case 4: CDS shorter than 3 * peptide - no mapping is made
2447    */
2448  1 dna = new Sequence("dna", "AACGacgtCTCC");
2449  1 dna.createDatasetSequence();
2450  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2451  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null));
2452  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2453  1 assertNull(ml);
2454   
2455    /*
2456    * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated
2457    */
2458  1 dna = new Sequence("dna", "AACGacgtCTCCTTG");
2459  1 dna.createDatasetSequence();
2460  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2461  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
2462  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2463  1 assertEquals(3, ml.getFromRatio());
2464  1 assertEquals(1, ml.getToRatio());
2465  1 assertEquals("[[1, 3]]",
2466    Arrays.deepToString(ml.getToRanges().toArray()));
2467  1 assertEquals("[[1, 4], [9, 13]]",
2468    Arrays.deepToString(ml.getFromRanges().toArray()));
2469   
2470    /*
2471    * Case 6: incomplete start codon corresponding to X in peptide
2472    */
2473  1 dna = new Sequence("dna", "ACGacgtCTCCTTGG");
2474  1 dna.createDatasetSequence();
2475  1 SequenceFeature sf = new SequenceFeature("CDS", "", 1, 3, null);
2476  1 sf.setPhase("2"); // skip 2 positions (AC) to start of next codon (GCT)
2477  1 dna.addSequenceFeature(sf);
2478  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 8, 15, null));
2479  1 peptide = new Sequence("pep", "XLQ");
2480  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2481  1 assertEquals("[[2, 3]]",
2482    Arrays.deepToString(ml.getToRanges().toArray()));
2483  1 assertEquals("[[3, 3], [8, 12]]",
2484    Arrays.deepToString(ml.getFromRanges().toArray()));
2485    }
2486   
2487    /**
2488    * Tests for the method that locates the CDS sequence that has a mapping to
2489    * the given protein. That is, given a transcript-to-peptide mapping, find the
2490    * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2491    */
 
2492  1 toggle @Test(groups = "Functional")
2493    public void testFindCdsForProtein()
2494    {
2495  1 List<AlignedCodonFrame> mappings = new ArrayList<>();
2496  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2497  1 mappings.add(acf1);
2498   
2499  1 SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg");
2500  1 dna1.createDatasetSequence();
2501   
2502    // NB we currently exclude STOP codon from CDS sequences
2503    // the test would need to change if this changes in future
2504  1 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2505  1 cds1.createDatasetSequence();
2506   
2507  1 SequenceI pep1 = new Sequence("pep1", "MLS");
2508  1 pep1.createDatasetSequence();
2509  1 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2510  1 MapList mapList = new MapList(new int[] { 5, 6, 9, 15 },
2511    new int[]
2512    { 1, 3 }, 3, 1);
2513  1 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2514   
2515    // add dna to peptide mapping
2516  1 seqMappings.add(acf1);
2517  1 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2518    mapList);
2519   
2520    /*
2521    * first case - no dna-to-CDS mapping exists - search fails
2522    */
2523  1 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2524    seqMappings, dnaToPeptide);
2525  1 assertNull(seq);
2526   
2527    /*
2528    * second case - CDS-to-peptide mapping exists but no dna-to-CDS
2529    * - search fails
2530    */
2531    // todo this test fails if the mapping is added to acf1, not acf2
2532    // need to tidy up use of lists of mappings in AlignedCodonFrame
2533  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2534  1 mappings.add(acf2);
2535  1 MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
2536    new int[]
2537    { 1, 3 }, 3, 1);
2538  1 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2539    cdsToPeptideMapping);
2540  1 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2541    dnaToPeptide));
2542   
2543    /*
2544    * third case - add dna-to-CDS mapping - CDS is now found!
2545    */
2546  1 MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 },
2547    new int[]
2548    { 1, 9 }, 1, 1);
2549  1 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2550    dnaToCdsMapping);
2551  1 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2552    dnaToPeptide);
2553  1 assertSame(seq, cds1.getDatasetSequence());
2554    }
2555   
2556    /**
2557    * Tests for the method that locates the CDS sequence that has a mapping to
2558    * the given protein. That is, given a transcript-to-peptide mapping, find the
2559    * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2560    * This test is for the case where transcript and CDS are the same length.
2561    */
 
2562  1 toggle @Test(groups = "Functional")
2563    public void testFindCdsForProtein_noUTR()
2564    {
2565  1 List<AlignedCodonFrame> mappings = new ArrayList<>();
2566  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2567  1 mappings.add(acf1);
2568   
2569  1 SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
2570  1 dna1.createDatasetSequence();
2571   
2572    // NB we currently exclude STOP codon from CDS sequences
2573    // the test would need to change if this changes in future
2574  1 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2575  1 cds1.createDatasetSequence();
2576   
2577  1 SequenceI pep1 = new Sequence("pep1", "MLS");
2578  1 pep1.createDatasetSequence();
2579  1 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2580  1 MapList mapList = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3,
2581    1);
2582  1 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2583   
2584    // add dna to peptide mapping
2585  1 seqMappings.add(acf1);
2586  1 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2587    mapList);
2588   
2589    /*
2590    * first case - transcript lacks CDS features - it appears to be
2591    * the CDS sequence and is returned
2592    */
2593  1 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2594    seqMappings, dnaToPeptide);
2595  1 assertSame(seq, dna1.getDatasetSequence());
2596   
2597    /*
2598    * second case - transcript has CDS feature - this means it is
2599    * not returned as a match for CDS (CDS sequences don't have CDS features)
2600    */
2601  1 dna1.addSequenceFeature(
2602    new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null));
2603  1 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2604    dnaToPeptide);
2605  1 assertNull(seq);
2606   
2607    /*
2608    * third case - CDS-to-peptide mapping exists but no dna-to-CDS
2609    * - search fails
2610    */
2611    // todo this test fails if the mapping is added to acf1, not acf2
2612    // need to tidy up use of lists of mappings in AlignedCodonFrame
2613  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2614  1 mappings.add(acf2);
2615  1 MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
2616    new int[]
2617    { 1, 3 }, 3, 1);
2618  1 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2619    cdsToPeptideMapping);
2620  1 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2621    dnaToPeptide));
2622   
2623    /*
2624    * fourth case - add dna-to-CDS mapping - CDS is now found!
2625    */
2626  1 MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 },
2627    new int[]
2628    { 1, 9 }, 1, 1);
2629  1 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2630    dnaToCdsMapping);
2631  1 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2632    dnaToPeptide);
2633  1 assertSame(seq, cds1.getDatasetSequence());
2634    }
2635   
 
2636  1 toggle @Test(groups = "Functional")
2637    public void testAddReferenceAnnotations()
2638    {
2639  1 SequenceI longseq = new Sequence("longA", "ASDASDASDASDAASDASDASDASDA");
2640  1 Annotation[] aa = new Annotation[longseq.getLength()];
2641   
2642  27 for (int p = 0; p < aa.length; p++)
2643    {
2644  26 aa[p] = new Annotation("P", "pos " + (p + 1), (char) 0,
2645    (float) p + 1);
2646    }
2647  1 AlignmentAnnotation refAnnot = new AlignmentAnnotation("LongSeqAnnot",
2648    "Annotations", aa);
2649  1 refAnnot.setCalcId("Test");
2650  1 longseq.addAlignmentAnnotation(refAnnot);
2651  1 verifyExpectedSequenceAnnotation(refAnnot);
2652   
2653  1 Alignment ourAl = new Alignment(
2654    new SequenceI[]
2655    { longseq.getSubSequence(5, 10),
2656    longseq.getSubSequence(7, 12) });
2657  1 ourAl.createDatasetAlignment();
2658   
2659    // transfer annotation
2660  1 SortedMap<String, String> tipEntries = new TreeMap<>();
2661  1 Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
2662   
2663  1 AlignmentUtils.findAddableReferenceAnnotations(ourAl.getSequences(),
2664    tipEntries, candidates, ourAl);
2665  1 AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null);
2666   
2667  1 assertNotNull(ourAl.getAlignmentAnnotation());
2668  1 assertEquals(ourAl.getAlignmentAnnotation().length, 2);
2669   
2670  1 for (AlignmentAnnotation alan : ourAl.getAlignmentAnnotation())
2671    {
2672  2 verifyExpectedSequenceAnnotation(alan);
2673    }
2674    // Everything above works for 2.11.3 and 2.11.2.x.
2675    // now simulate copy/paste to new alignment
2676  1 SequenceI[] newSeqAl = new SequenceI[2];
2677    // copy sequences but no annotation
2678  1 newSeqAl[0] = new Sequence(ourAl.getSequenceAt(0),
2679    ourAl.getSequenceAt(0).getAnnotation());
2680  1 newSeqAl[1] = new Sequence(ourAl.getSequenceAt(1),
2681    ourAl.getSequenceAt(1).getAnnotation());
2682   
2683  1 Alignment newAl = new Alignment(newSeqAl);
2684    // delete annotation
2685  1 for (SequenceI sq : newAl.getSequences())
2686    {
2687  2 sq.setAlignmentAnnotation(new AlignmentAnnotation[0]);
2688    }
2689    // JAL-4182 scenario test
2690  1 SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl));
2691  1 sg.setStartRes(0);
2692  1 sg.setEndRes(newAl.getWidth());
2693  1 AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0],
2694    newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
2695  1 AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1],
2696    newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
2697  1 for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation())
2698    {
2699  2 verifyExpectedSequenceAnnotation(alan);
2700    }
2701    }
2702   
2703    /**
2704    * helper - tests annotation is mapped to position it was originally created
2705    * for
2706    *
2707    * @param alan
2708    */
 
2709  5 toggle private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan)
2710    {
2711  51 for (int c = 0; c < alan.annotations.length; c++)
2712    {
2713  46 Annotation a = alan.annotations[c];
2714  46 if (a != null)
2715    {
2716  46 assertEquals("Misaligned annotation at " + c,
2717    (float) alan.sequenceRef.findPosition(c), a.value);
2718    }
2719    else
2720    {
2721  0 assertTrue("Unexpected Null at position " + c,
2722    c >= alan.sequenceRef.getLength()
2723    || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
2724    }
2725    }
2726    }
2727   
 
2728  1 toggle @Test(groups = "Functional")
2729    public void testAddReferenceContactMap()
2730    {
2731  1 SequenceI sq = new Sequence("a", "SSSQ");
2732  1 ContactMatrixI cm = new SeqDistanceContactMatrix(4);
2733  1 AlignmentAnnotation cm_aan = sq.addContactList(cm);
2734  1 cm_aan.description = cm_aan.description + " cm1";
2735  1 SequenceI dssq = sq.createDatasetSequence();
2736   
2737    // remove annotation on our non-dataset sequence
2738  1 sq.removeAlignmentAnnotation(sq.getAnnotation()[0]);
2739    // test transfer
2740  1 Alignment al = new Alignment(new SequenceI[] { sq });
2741  1 SortedMap<String, String> tipEntries = new TreeMap<>();
2742  1 Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
2743   
2744  1 AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
2745    tipEntries, candidates, al);
2746  1 AlignmentUtils.addReferenceAnnotations(candidates, al, null);
2747  1 assertTrue("No contact map annotation transferred",
2748    al.getAlignmentAnnotation() != null
2749    && al.getAlignmentAnnotation().length == 1);
2750  1 AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
2751    .iterator().next();
2752  1 ContactMatrixI t_cm = al.getContactMatrixFor(alan);
2753  1 assertNotNull("No contact map for the transferred annotation row.",
2754    t_cm);
2755  1 assertTrue(t_cm instanceof SeqDistanceContactMatrix);
2756  1 assertTrue(((SeqDistanceContactMatrix) t_cm).hasReferenceSeq());
2757   
2758  1 ContactListI cl = al.getContactListFor(alan, 1);
2759  1 assertNotNull(
2760    "No contact matrix recovered after reference annotation transfer",
2761    cl);
2762    // semantics of sequence associated contact list is slightly tricky - column
2763    // 3 in alignment should have data
2764  1 cl = al.getContactListFor(alan, 3);
2765  1 assertNotNull(
2766    "Contact matrix should have data for last position in sequence",
2767    cl);
2768   
2769  1 ContactMatrixI cm2 = new SeqDistanceContactMatrix(4);
2770  1 dssq.addContactList(cm2);
2771  1 tipEntries = new TreeMap<>();
2772  1 candidates = new LinkedHashMap<>();
2773   
2774  1 AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
2775    tipEntries, candidates, al);
2776  1 AlignmentUtils.addReferenceAnnotations(candidates, al, null);
2777  1 assertTrue("Expected two contact map annotation transferred",
2778    al.getAlignmentAnnotation() != null
2779    && al.getAlignmentAnnotation().length == 2);
2780   
2781    }
2782   
 
2783  5 toggle @Test(
2784    groups = "Functional",
2785    dataProvider = "SecondaryStructureAnnotations")
2786    public void testSecondaryStructurePresentAndSources(
2787    AlignmentAnnotation[] annotations, boolean expectedSSPresent,
2788    ArrayList<String> expectedSSSources)
2789    {
2790  5 Assert.assertEquals(expectedSSPresent,
2791    AlignmentUtils.isSecondaryStructurePresent(annotations));
2792  5 Assert.assertEquals(expectedSSSources,
2793    AlignmentUtils.getSecondaryStructureSources(annotations));
2794    }
2795   
 
2796  1 toggle @DataProvider(name = "SecondaryStructureAnnotations")
2797    public static Object[][] provideSecondaryStructureAnnotations()
2798    {
2799  1 AlignmentAnnotation ann1 = new AlignmentAnnotation(
2800    "Secondary Structure", "Secondary Structure",
2801    new Annotation[] {});
2802  1 AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
2803    "jnetpred", new Annotation[] {});
2804  1 AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
2805    new Annotation[] {});
2806  1 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
2807    new Annotation[] {});
2808   
2809  1 List<String> ssSources1 = new ArrayList<>(
2810    Arrays.asList("3D Structures"));
2811  1 List<String> ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
2812  1 List<String> ssSources3 = new ArrayList<>(
2813    Arrays.asList("3D Structures", "JPred"));
2814  1 List<String> ssSources4 = new ArrayList<>();
2815   
2816  1 return new Object[][] {
2817    { new AlignmentAnnotation[]
2818    { ann1, ann3, ann4 }, true, ssSources1 },
2819    { new AlignmentAnnotation[]
2820    { ann2, ann3, ann4 }, true, ssSources2 },
2821    { new AlignmentAnnotation[]
2822    { ann3, ann4 }, false, ssSources4 },
2823    { new AlignmentAnnotation[] {}, false, ssSources4 },
2824    { new AlignmentAnnotation[]
2825    { ann1, ann2, ann3, ann4 }, true, ssSources3 } };
2826    }
2827   
 
2828  0 toggle @Test(dataProvider = "SecondaryStructureAnnotationColours")
2829    public void testSecondaryStructureAnnotationColour(char symbol,
2830    Color expectedColor)
2831    {
2832  0 Color actualColor = AlignmentUtils
2833    .getSecondaryStructureAnnotationColour(symbol);
2834  0 Assert.assertEquals(actualColor, expectedColor);
2835    }
2836   
 
2837  0 toggle @DataProvider(name = "SecondaryStructureAnnotationColours")
2838    public static Object[][] provideSecondaryStructureAnnotationColours()
2839    {
2840  0 return new Object[][] { { 'C', Color.gray }, { 'E', Color.green },
2841    { 'H', Color.red },
2842    { '-', Color.gray } };
2843    }
2844   
 
2845  0 toggle @Test(dataProvider = "SSAnnotationPresence")
2846    public void testIsSSAnnotationPresent(
2847    Map<SequenceI, List<AlignmentAnnotation>> annotations,
2848    boolean expectedPresence)
2849    {
2850  0 boolean actualPresence = AlignmentUtils
2851    .isSSAnnotationPresent(annotations);
2852  0 Assert.assertEquals(actualPresence, expectedPresence);
2853    }
2854   
 
2855  0 toggle @DataProvider(name = "SSAnnotationPresence")
2856    public static Object[][] provideSSAnnotationPresence()
2857    {
2858  0 Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
2859  0 SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
2860  0 List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
2861  0 annotationsList1.add(new AlignmentAnnotation("Secondary Structure",
2862    "Secondary Structure", new Annotation[] {}));
2863  0 annotations1.put(seq1, annotationsList1); // Annotation present secondary
2864    // structure for seq1
2865   
2866  0 Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
2867  0 SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
2868  0 List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
2869  0 annotationsList2.add(new AlignmentAnnotation("Other Annotation",
2870    "Other Annotation", new Annotation[] {}));
2871  0 annotations2.put(seq2, annotationsList2); // Annotation not related to any
2872    // of secondary structure for seq2
2873   
2874  0 Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
2875    // Empty annotation map
2876   
2877  0 Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
2878  0 SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
2879  0 List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
2880  0 annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred",
2881    new Annotation[] {}));
2882  0 annotations4.put(seq4, annotationsList4); // Annotation present from JPred
2883    // for seq4
2884   
2885  0 return new Object[][] { { annotations1, true }, // Annotations present
2886    // secondary structure
2887    // present
2888    { annotations2, false }, // No annotations related to any of the
2889    // secondary structure present
2890    { annotations3, false }, // Empty annotation map
2891    { annotations4, true }, // Annotations present from JPred secondary
2892    // structure present
2893    };
2894    }
2895   
 
2896  0 toggle @Test
2897    public void testGetSSSourceFromAnnotationDescription(
2898    AlignmentAnnotation[] annotations, String expectedSSSource)
2899    {
2900  0 List<String> actualSSSource = AlignmentUtils
2901    .extractSSSourceInAlignmentAnnotation(annotations);
2902  0 Assert.assertEquals(actualSSSource, expectedSSSource);
2903    }
2904   
 
2905  0 toggle @DataProvider(name = "SSSourceFromAnnotationDescription")
2906    public static Object[][] provideSSSourceFromAnnotationDescription()
2907    {
2908  0 Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
2909  0 SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
2910  0 List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
2911  0 annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output",
2912    new Annotation[] {}));
2913  0 annotations1.put(seq1, annotationsList1); // Annotation present from JPred
2914    // for seq1
2915   
2916  0 Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
2917  0 SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
2918  0 List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
2919  0 annotationsList2.add(new AlignmentAnnotation("Secondary Structure",
2920    "Secondary Structure for af-q43517-f1A", new Annotation[] {}));
2921  0 annotations2.put(seq2, annotationsList2); // Annotation present secondary
2922    // structure from Alphafold for
2923    // seq2
2924   
2925  0 Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
2926    // Empty annotation map
2927   
2928  0 Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
2929  0 SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
2930  0 List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
2931  0 annotationsList4.add(new AlignmentAnnotation("Secondary Structure",
2932    "Secondary Structure for 4zhpA", new Annotation[] {}));
2933  0 annotations4.put(seq4, annotationsList4); // Annotation present secondary
2934    // structure from pdb for seq4
2935   
2936  0 Map<SequenceI, List<AlignmentAnnotation>> annotations5 = new HashMap<>();
2937  0 SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
2938  0 List<AlignmentAnnotation> annotationsList5 = new ArrayList<>();
2939  0 annotationsList5.add(new AlignmentAnnotation("Secondary Structure",
2940    "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P",
2941    new Annotation[] {}));
2942  0 annotations5.put(seq5, annotationsList5); // Annotation present secondary
2943    // structure from Swiss model for
2944    // seq5
2945   
2946    // JPred Output - JPred
2947    // Secondary Structure for af-q43517-f1A - Alphafold
2948    // Secondary Structure for 4zhpA - Experimental
2949    // Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P -
2950    // Swiss Model
2951   
2952  0 return new Object[][] { { annotations1, "JPred" },
2953    { annotations2, "Alphafold" },
2954    { annotations3, null },
2955    { annotations4, "PDB" },
2956    { annotations5, "Swiss Model" } };
2957    }
2958   
2959    }
  • Report generated by OpenClover v 4.4.1 on Wed Jun 18 2025 15:16:08 BST using coverage data from Wed Jun 18 2025 15:15:57 BST.
  • OpenClover is free and open-source software.