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  1. Project Clover database Wed Nov 12 2025 13:01:44 GMT
  2. Package jalview.datamodel

File AlignmentTest.java

 

Code metrics

84
605
44
1
1,633
1,081
94
0.16
13.75
44
2.14

Classes

Class Line # Actions
AlignmentTest 56 605 94
0.890859589.1%
 

Contributing tests

This file is covered by 32 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.datamodel;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertFalse;
25    import static org.testng.AssertJUnit.assertNotNull;
26    import static org.testng.AssertJUnit.assertNull;
27    import static org.testng.AssertJUnit.assertSame;
28    import static org.testng.AssertJUnit.assertTrue;
29   
30    import java.io.IOException;
31    import java.util.Arrays;
32    import java.util.Iterator;
33    import java.util.List;
34   
35    import org.testng.Assert;
36    import org.testng.annotations.BeforeClass;
37    import org.testng.annotations.BeforeMethod;
38    import org.testng.annotations.Test;
39   
40    import jalview.analysis.AlignmentGenerator;
41    import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
42    import jalview.gui.JvOptionPane;
43    import jalview.io.DataSourceType;
44    import jalview.io.FileFormat;
45    import jalview.io.FileFormatI;
46    import jalview.io.FormatAdapter;
47    import jalview.util.Comparison;
48    import jalview.util.MapList;
49   
50    /**
51    * Unit tests for Alignment datamodel.
52    *
53    * @author gmcarstairs
54    *
55    */
 
56    public class AlignmentTest
57    {
58   
 
59  1 toggle @BeforeClass(alwaysRun = true)
60    public void setUpJvOptionPane()
61    {
62  1 JvOptionPane.setInteractiveMode(false);
63  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
64    }
65   
66    // @formatter:off
67    private static final String TEST_DATA =
68    "# STOCKHOLM 1.0\n" +
69    "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
70    "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
71    "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
72    "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
73    "#=GR D.melanogaster.1 SS ................((((\n" +
74    "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
75    "#=GR D.melanogaster.2 SS ................((((\n" +
76    "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
77    "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
78    "//";
79   
80    private static final String AA_SEQS_1 =
81    ">Seq1Name/5-8\n" +
82    "K-QY--L\n" +
83    ">Seq2Name/12-15\n" +
84    "-R-FP-W-\n";
85   
86    private static final String CDNA_SEQS_1 =
87    ">Seq1Name/100-111\n" +
88    "AC-GG--CUC-CAA-CT\n" +
89    ">Seq2Name/200-211\n" +
90    "-CG-TTA--ACG---AAGT\n";
91   
92    private static final String CDNA_SEQS_2 =
93    ">Seq1Name/50-61\n" +
94    "GCTCGUCGTACT\n" +
95    ">Seq2Name/60-71\n" +
96    "GGGTCAGGCAGT\n";
97    // @formatter:on
98   
99    private AlignmentI al;
100   
101    /**
102    * Helper method to load an alignment and ensure dataset sequences are set up.
103    *
104    * @param data
105    * @param format
106    * TODO
107    * @return
108    * @throws IOException
109    */
 
110  45 toggle protected AlignmentI loadAlignment(final String data, FileFormatI format)
111    throws IOException
112    {
113  45 AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
114    format);
115  45 a.setDataset(null);
116  45 return a;
117    }
118   
119    /**
120    * assert wrapper: tests all references in the given alignment are consistent
121    *
122    * @param alignment
123    */
 
124  0 toggle public static void assertAlignmentDatasetRefs(AlignmentI alignment)
125    {
126  0 verifyAlignmentDatasetRefs(alignment, true, null);
127    }
128   
129    /**
130    * assert wrapper: tests all references in the given alignment are consistent
131    *
132    * @param alignment
133    * @param message
134    * - prefixed to any assert failed messages
135    */
 
136  1 toggle public static void assertAlignmentDatasetRefs(AlignmentI alignment,
137    String message)
138    {
139  1 verifyAlignmentDatasetRefs(alignment, true, message);
140    }
141   
142    /**
143    * verify sequence and dataset references are properly contained within
144    * dataset
145    *
146    * @param alignment
147    * - the alignmentI object to verify (either alignment or dataset)
148    * @param raiseAssert
149    * - when set, testng assertions are raised.
150    * @param message
151    * - null or a string message to prepend to the assert failed
152    * messages.
153    * @return true if alignment references were in order, otherwise false.
154    */
 
155  44 toggle public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment,
156    boolean raiseAssert, String message)
157    {
158  44 if (message == null)
159    {
160  24 message = "";
161    }
162  44 if (alignment == null)
163    {
164  0 if (raiseAssert)
165    {
166  0 Assert.fail(message + "Alignment for verification was null.");
167    }
168  0 return false;
169    }
170  44 if (alignment.getDataset() != null)
171    {
172  19 AlignmentI dataset = alignment.getDataset();
173    // check all alignment sequences have their dataset within the dataset
174  19 for (SequenceI seq : alignment.getSequences())
175    {
176  39 SequenceI seqds = seq.getDatasetSequence();
177  39 if (seqds.getDatasetSequence() != null)
178    {
179  0 if (raiseAssert)
180    {
181  0 Assert.fail(message
182    + " Alignment contained a sequence who's dataset sequence has a second dataset reference.");
183    }
184  0 return false;
185    }
186  39 if (dataset.findIndex(seqds) == -1)
187    {
188  0 if (raiseAssert)
189    {
190  0 Assert.fail(message
191    + " Alignment contained a sequence who's dataset sequence was not in the dataset.");
192    }
193  0 return false;
194    }
195    }
196  19 return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert,
197    message);
198    }
199    else
200    {
201  25 int dsp = -1;
202    // verify all dataset sequences
203  25 for (SequenceI seqds : alignment.getSequences())
204    {
205  80 dsp++;
206  80 if (seqds.getDatasetSequence() != null)
207    {
208  2 if (raiseAssert)
209    {
210  1 Assert.fail(message
211    + " Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
212    }
213  1 return false;
214    }
215  78 int foundp = alignment.findIndex(seqds);
216  78 if (foundp != dsp)
217    {
218  2 if (raiseAssert)
219    {
220  1 Assert.fail(message
221    + " Dataset sequence array contains a reference at "
222    + dsp + " to a sequence first seen at " + foundp + " ("
223    + seqds.toString() + ")");
224    }
225  1 return false;
226    }
227  76 if (seqds.getDBRefs() != null)
228    {
229  28 for (DBRefEntry dbr : seqds.getDBRefs())
230    {
231  28 if (dbr.getMap() != null)
232    {
233  28 SequenceI seqdbrmapto = dbr.getMap().getTo();
234  28 if (seqdbrmapto != null)
235    {
236  28 if (seqdbrmapto.getDatasetSequence() != null)
237    {
238  0 if (raiseAssert)
239    {
240  0 Assert.fail(message
241    + " DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
242    }
243  0 return false;
244   
245    }
246  28 if (alignment.findIndex(dbr.getMap().getTo()) == -1)
247    {
248  2 if (raiseAssert)
249    {
250  1 Assert.fail(message + " DBRefEntry " + dbr
251    + " for sequence " + seqds
252    + " in alignment has map to sequence not in dataset");
253    }
254  1 return false;
255    }
256    }
257    }
258    }
259    }
260    }
261    // finally, verify codonmappings involve only dataset sequences.
262  19 if (alignment.getCodonFrames() != null)
263    {
264  19 for (AlignedCodonFrame alc : alignment.getCodonFrames())
265    {
266  6 for (SequenceToSequenceMapping ssm : alc.getMappings())
267    {
268  6 if (ssm.getFromSeq().getDatasetSequence() != null)
269    {
270  0 if (raiseAssert)
271    {
272  0 Assert.fail(message
273    + " CodonFrame-SSM-FromSeq is not a dataset sequence");
274    }
275  0 return false;
276    }
277  6 if (alignment.findIndex(ssm.getFromSeq()) == -1)
278    {
279   
280  2 if (raiseAssert)
281    {
282  1 Assert.fail(message
283    + " CodonFrame-SSM-FromSeq is not contained in dataset");
284    }
285  1 return false;
286    }
287  4 if (ssm.getMapping().getTo().getDatasetSequence() != null)
288    {
289  0 if (raiseAssert)
290    {
291  0 Assert.fail(message
292    + " CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
293    }
294  0 return false;
295    }
296  4 if (alignment.findIndex(ssm.getMapping().getTo()) == -1)
297    {
298   
299  0 if (raiseAssert)
300    {
301  0 Assert.fail(message
302    + " CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
303    }
304  0 return false;
305    }
306    }
307    }
308    }
309    }
310  17 return true; // all relationships verified!
311    }
312   
313    /**
314    * call verifyAlignmentDatasetRefs with and without assertion raising enabled,
315    * to check expected pass/fail actually occurs in both conditions
316    *
317    * @param al
318    * @param expected
319    * @param msg
320    */
 
321  12 toggle private void assertVerifyAlignment(AlignmentI al, boolean expected,
322    String msg)
323    {
324  12 if (expected)
325    {
326  8 try
327    {
328   
329  8 Assert.assertTrue(verifyAlignmentDatasetRefs(al, true, null),
330    "Valid test alignment failed when raiseAsserts enabled:"
331    + msg);
332    } catch (AssertionError ae)
333    {
334  0 ae.printStackTrace();
335  0 Assert.fail(
336    "Valid test alignment raised assertion errors when raiseAsserts enabled: "
337    + msg,
338    ae);
339    }
340    // also check validation passes with asserts disabled
341  8 Assert.assertTrue(verifyAlignmentDatasetRefs(al, false, null),
342    "Valid test alignment tested false when raiseAsserts disabled:"
343    + msg);
344    }
345    else
346    {
347  4 boolean assertRaised = false;
348  4 try
349    {
350  4 verifyAlignmentDatasetRefs(al, true, null);
351    } catch (AssertionError ae)
352    {
353    // expected behaviour
354  4 assertRaised = true;
355    }
356  4 if (!assertRaised)
357    {
358  0 Assert.fail(
359    "Invalid test alignment passed when raiseAsserts enabled:"
360    + msg);
361    }
362    // also check validation passes with asserts disabled
363  4 Assert.assertFalse(verifyAlignmentDatasetRefs(al, false, null),
364    "Invalid test alignment tested true when raiseAsserts disabled:"
365    + msg);
366    }
367    }
368   
 
369  1 toggle @Test(groups = { "Functional" })
370    public void testVerifyAlignmentDatasetRefs()
371    {
372  1 SequenceI sq1 = new Sequence("sq1", "ASFDD"),
373    sq2 = new Sequence("sq2", "TTTTTT");
374   
375    // construct simple valid alignment dataset
376  1 Alignment al = new Alignment(new SequenceI[] { sq1, sq2 });
377    // expect this to pass
378  1 assertVerifyAlignment(al, true, "Simple valid alignment didn't verify");
379   
380    // check test for sequence->datasetSequence validity
381  1 sq1.setDatasetSequence(sq2);
382  1 assertVerifyAlignment(al, false,
383    "didn't detect dataset sequence with a dataset sequence reference.");
384   
385  1 sq1.setDatasetSequence(null);
386  1 assertVerifyAlignment(al, true,
387    "didn't reinstate validity after nulling dataset sequence dataset reference");
388   
389    // now create dataset and check again
390  1 al.createDatasetAlignment();
391  1 assertNotNull(al.getDataset());
392   
393  1 assertVerifyAlignment(al, true,
394    "verify failed after createDatasetAlignment");
395   
396    // create a dbref on sq1 with a sequence ref to sq2
397  1 DBRefEntry dbrs1tos2 = new DBRefEntry("UNIPROT", "1", "Q111111");
398  1 dbrs1tos2
399    .setMap(new Mapping(sq2.getDatasetSequence(), new int[]
400    { 1, 5 }, new int[] { 2, 6 }, 1, 1));
401  1 sq1.getDatasetSequence().addDBRef(dbrs1tos2);
402  1 assertVerifyAlignment(al, true,
403    "verify failed after addition of valid DBRefEntry/map");
404    // now create a dbref on a new sequence which maps to another sequence
405    // outside of the dataset
406  1 SequenceI sqout = new Sequence("sqout", "ututututucagcagcag"),
407    sqnew = new Sequence("sqnew", "EEERRR");
408  1 DBRefEntry sqnewsqout = new DBRefEntry("ENAFOO", "1", "R000001");
409  1 sqnewsqout
410    .setMap(new Mapping(sqout, new int[]
411    { 1, 6 }, new int[] { 1, 18 }, 1, 3));
412  1 al.getDataset().addSequence(sqnew);
413   
414  1 assertVerifyAlignment(al, true,
415    "verify failed after addition of new sequence to dataset");
416    // now start checking exception conditions
417  1 sqnew.addDBRef(sqnewsqout);
418  1 assertVerifyAlignment(al, false,
419    "verify passed when a dbref with map to sequence outside of dataset was added");
420    // make the verify pass by adding the outsider back in
421  1 al.getDataset().addSequence(sqout);
422  1 assertVerifyAlignment(al, true,
423    "verify should have passed after adding dbref->to sequence in to dataset");
424    // and now the same for a codon mapping...
425  1 SequenceI sqanotherout = new Sequence("sqanotherout",
426    "aggtutaggcagcagcag");
427   
428  1 AlignedCodonFrame alc = new AlignedCodonFrame();
429  1 alc.addMap(sqanotherout, sqnew,
430    new MapList(new int[]
431    { 1, 6 }, new int[] { 1, 18 }, 3, 1));
432   
433  1 al.addCodonFrame(alc);
434  1 Assert.assertEquals(al.getDataset().getCodonFrames().size(), 1);
435   
436  1 assertVerifyAlignment(al, false,
437    "verify passed when alCodonFrame mapping to sequence outside of dataset was added");
438    // make the verify pass by adding the outsider back in
439  1 al.getDataset().addSequence(sqanotherout);
440  1 assertVerifyAlignment(al, true,
441    "verify should have passed once all sequences involved in alCodonFrame were added to dataset");
442  1 al.getDataset().addSequence(sqanotherout);
443  1 assertVerifyAlignment(al, false,
444    "verify should have failed when a sequence was added twice to the dataset");
445  1 al.getDataset().deleteSequence(sqanotherout);
446  1 assertVerifyAlignment(al, true,
447    "verify should have passed after duplicate entry for sequence was removed");
448    }
449   
450    /**
451    * checks that the sequence data for an alignment's dataset is non-redundant.
452    * Fails if there are sequences with same id, sequence, start, and.
453    */
454   
 
455  6 toggle public static void assertDatasetIsNormalised(AlignmentI al)
456    {
457  6 assertDatasetIsNormalised(al, null);
458    }
459   
460    /**
461    * checks that the sequence data for an alignment's dataset is non-redundant.
462    * Fails if there are sequences with same id, sequence, start, and.
463    *
464    * @param al
465    * - alignment to verify
466    * @param message
467    * - null or message prepended to exception message.
468    */
 
469  12 toggle public static void assertDatasetIsNormalised(AlignmentI al,
470    String message)
471    {
472  12 if (al.getDataset() != null)
473    {
474  6 assertDatasetIsNormalised(al.getDataset(), message);
475  5 return;
476    }
477    /*
478    * look for pairs of sequences with same ID, start, end, and sequence
479    */
480  6 List<SequenceI> seqSet = al.getSequences();
481  18 for (int p = 0; p < seqSet.size(); p++)
482    {
483  13 SequenceI pSeq = seqSet.get(p);
484  27 for (int q = p + 1; q < seqSet.size(); q++)
485    {
486  15 SequenceI qSeq = seqSet.get(q);
487  15 if (pSeq.getStart() != qSeq.getStart())
488    {
489  4 continue;
490    }
491  11 if (pSeq.getEnd() != qSeq.getEnd())
492    {
493  0 continue;
494    }
495  11 if (!pSeq.getName().equals(qSeq.getName()))
496    {
497  7 continue;
498    }
499  4 if (!Arrays.equals(pSeq.getSequence(), qSeq.getSequence()))
500    {
501  3 continue;
502    }
503  1 Assert.fail((message == null ? "" : message + " :")
504    + "Found similar sequences at position " + p + " and " + q
505    + "\n" + pSeq.toString());
506    }
507    }
508    }
509   
 
510  1 toggle @Test(groups = { "Functional", "Asserts" })
511    public void testAssertDatasetIsNormalised()
512    {
513  1 Sequence sq1 = new Sequence("s1/1-4", "asdf");
514  1 Sequence sq1shift = new Sequence("s1/2-5", "asdf");
515  1 Sequence sq1seqd = new Sequence("s1/1-4", "asdt");
516  1 Sequence sq2 = new Sequence("s2/1-4", "asdf");
517  1 Sequence sq1dup = new Sequence("s1/1-4", "asdf");
518   
519  1 Alignment al = new Alignment(new SequenceI[] { sq1 });
520  1 al.setDataset(null);
521   
522  1 try
523    {
524  1 assertDatasetIsNormalised(al);
525    } catch (AssertionError ae)
526    {
527  0 Assert.fail("Single sequence should be valid normalised dataset.");
528    }
529  1 al.addSequence(sq2);
530  1 try
531    {
532  1 assertDatasetIsNormalised(al);
533    } catch (AssertionError ae)
534    {
535  0 Assert.fail(
536    "Two different sequences should be valid normalised dataset.");
537    }
538    /*
539    * now change sq2's name in the alignment. should still be valid
540    */
541  1 al.findName(sq2.getName()).setName("sq1");
542  1 try
543    {
544  1 assertDatasetIsNormalised(al);
545    } catch (AssertionError ae)
546    {
547  0 Assert.fail(
548    "Two different sequences in dataset, but same name in alignment, should be valid normalised dataset.");
549    }
550   
551  1 al.addSequence(sq1seqd);
552  1 try
553    {
554  1 assertDatasetIsNormalised(al);
555    } catch (AssertionError ae)
556    {
557  0 Assert.fail(
558    "sq1 and sq1 with different sequence should be distinct.");
559    }
560   
561  1 al.addSequence(sq1shift);
562  1 try
563    {
564  1 assertDatasetIsNormalised(al);
565    } catch (AssertionError ae)
566    {
567  0 Assert.fail(
568    "sq1 and sq1 with different start/end should be distinct.");
569    }
570    /*
571    * finally, the failure case
572    */
573  1 al.addSequence(sq1dup);
574  1 boolean ssertRaised = false;
575  1 try
576    {
577  1 assertDatasetIsNormalised(al);
578   
579    } catch (AssertionError ae)
580    {
581  1 ssertRaised = true;
582    }
583  1 if (!ssertRaised)
584    {
585  0 Assert.fail("Expected identical sequence to raise exception.");
586    }
587    }
588   
589    /*
590    * Read in Stockholm format test data including secondary structure
591    * annotations.
592    */
 
593  32 toggle @BeforeMethod(alwaysRun = true)
594    public void setUp() throws IOException
595    {
596  32 al = loadAlignment(TEST_DATA, FileFormat.Stockholm);
597  32 int i = 0;
598  32 for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
599    {
600  96 ann.setCalcId("CalcIdFor" + al.getSequenceAt(i).getName());
601  96 i++;
602    }
603    }
604   
605    /**
606    * Test method that returns annotations that match on calcId.
607    */
 
608  1 toggle @Test(groups = { "Functional" })
609    public void testFindAnnotation_byCalcId()
610    {
611  1 Iterable<AlignmentAnnotation> anns = al
612    .findAnnotation("CalcIdForD.melanogaster.2");
613  1 Iterator<AlignmentAnnotation> iter = anns.iterator();
614  1 assertTrue(iter.hasNext());
615  1 AlignmentAnnotation ann = iter.next();
616  1 assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
617  1 assertFalse(iter.hasNext());
618   
619    // invalid id
620  1 anns = al.findAnnotation("CalcIdForD.melanogaster.?");
621  1 assertFalse(iter.hasNext());
622  1 anns = al.findAnnotation(null);
623  1 assertFalse(iter.hasNext());
624    }
625   
626    /**
627    * Test method that returns annotations that match on reference sequence,
628    * label, or calcId.
629    */
 
630  1 toggle @Test(groups = { "Functional" })
631    public void testFindAnnotations_bySeqLabelandorCalcId()
632    {
633    // TODO: finish testFindAnnotations_bySeqLabelandorCalcId test
634    /* Note - this is an incomplete test - need to check null or
635    * non-null [ matches, not matches ] behaviour for each of the three
636    * parameters..*/
637   
638    // search for a single, unique calcId with wildcards on other params
639  1 Iterable<AlignmentAnnotation> anns = al.findAnnotations(null,
640    "CalcIdForD.melanogaster.2", null);
641  1 Iterator<AlignmentAnnotation> iter = anns.iterator();
642  1 assertTrue(iter.hasNext());
643  1 AlignmentAnnotation ann = iter.next();
644  1 assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
645  1 assertFalse(iter.hasNext());
646   
647    // save reference to test sequence reference parameter
648  1 SequenceI rseq = ann.sequenceRef;
649   
650    // search for annotation associated with a single sequence
651  1 anns = al.findAnnotations(rseq, null, null);
652  1 iter = anns.iterator();
653  1 assertTrue(iter.hasNext());
654  1 ann = iter.next();
655  1 assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
656  1 assertFalse(iter.hasNext());
657   
658    // search for annotation with a non-existant calcId
659  1 anns = al.findAnnotations(null, "CalcIdForD.melanogaster.?", null);
660  1 iter = anns.iterator();
661  1 assertFalse(iter.hasNext());
662   
663    // search for annotation with a particular label - expect three
664  1 anns = al.findAnnotations(null, null, "Secondary Structure");
665  1 iter = anns.iterator();
666  1 assertTrue(iter.hasNext());
667  1 iter.next();
668  1 assertTrue(iter.hasNext());
669  1 iter.next();
670  1 assertTrue(iter.hasNext());
671  1 iter.next();
672    // third found.. so
673  1 assertFalse(iter.hasNext());
674   
675    // search for annotation on one sequence with a particular label - expect
676    // one
677  1 SequenceI sqfound;
678  1 anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null,
679    "Secondary Structure");
680  1 iter = anns.iterator();
681  1 assertTrue(iter.hasNext());
682    // expect reference to sequence 1 in the alignment
683  1 assertTrue(sqfound == iter.next().sequenceRef);
684  1 assertFalse(iter.hasNext());
685   
686    // null on all parameters == find all annotations
687  1 anns = al.findAnnotations(null, null, null);
688  1 iter = anns.iterator();
689  1 int n = al.getAlignmentAnnotation().length;
690  4 while (iter.hasNext())
691    {
692  3 n--;
693  3 iter.next();
694    }
695  1 assertTrue("Found " + n + " fewer annotations from search.", n == 0);
696    }
697   
 
698  1 toggle @Test(groups = { "Functional" })
699    public void testDeleteAllAnnotations_includingAutocalculated()
700    {
701  1 AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
702    "Consensus", 0.5);
703  1 aa.autoCalculated = true;
704  1 al.addAnnotation(aa);
705  1 AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
706  1 assertEquals("Wrong number of annotations before deleting", 4,
707    anns.length);
708  1 al.deleteAllAnnotations(true);
709  1 assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
710    }
711   
 
712  1 toggle @Test(groups = { "Functional" })
713    public void testDeleteAllAnnotations_excludingAutocalculated()
714    {
715  1 AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
716    "Consensus", 0.5);
717  1 aa.autoCalculated = true;
718  1 al.addAnnotation(aa);
719  1 AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
720  1 assertEquals("Wrong number of annotations before deleting", 4,
721    anns.length);
722  1 al.deleteAllAnnotations(false);
723  1 assertEquals("Not just one annotation left", 1,
724    al.getAlignmentAnnotation().length);
725    }
726   
 
727  1 toggle @Test(groups = { "Functional" })
728    public void testIsSecondaryStructurePresent()
729    {
730    // default - there are secondary structure annotations in test data
731  1 assertTrue(al.isSecondaryStructurePresent());
732  1 al.deleteAllAnnotations(true);
733  1 assertFalse(al.isSecondaryStructurePresent());
734   
735  1 AlignmentAnnotation aa = new AlignmentAnnotation("Secondary Structure",
736    "Secondary Structure", 0.5);
737  1 Annotation ae[] = new Annotation[] { new Annotation("H", "H", 'H', 0f),
738    new Annotation("H", "H", 'H', 0f),
739    new Annotation("H", "H", 'H', 0f),
740    new Annotation("H", "H", 'H', 0f) };
741  1 aa.annotations = ae;
742  1 aa.validateRangeAndDisplay();
743  1 al.addAnnotation(aa);
744    // Should return false when the alignment has secondary structure
745    // annotation but is not sequence associated
746  1 assertFalse(al.isSecondaryStructurePresent());
747  1 aa = new AlignmentAnnotation(aa);
748  1 al.getSequenceAt(0).addAlignmentAnnotation(aa);
749  1 al.addAnnotation(aa);
750    // Should return true when the alignment has secondary structure
751    // annotation which is sequence associated
752  1 assertTrue(al.isSecondaryStructurePresent());
753    }
754   
755    /**
756    * Tests for realigning as per a supplied alignment: Dna as Dna.
757    *
758    * Note: AlignedCodonFrame's state variables are named for protein-to-cDNA
759    * mapping, but can be exploited for a general 'sequence-to-sequence' mapping
760    * as here.
761    *
762    * @throws IOException
763    */
 
764  1 toggle @Test(groups = { "Functional" })
765    public void testAlignAs_dnaAsDna() throws IOException
766    {
767    // aligned cDNA:
768  1 AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
769    // unaligned cDNA:
770  1 AlignmentI al2 = loadAlignment(CDNA_SEQS_2, FileFormat.Fasta);
771   
772    /*
773    * Make mappings between sequences. The 'aligned cDNA' is playing the role
774    * of what would normally be protein here.
775    */
776  1 makeMappings(al1, al2);
777   
778  1 ((Alignment) al2).alignAs(al1, false, true);
779  1 assertEquals("GC-TC--GUC-GTACT",
780    al2.getSequenceAt(0).getSequenceAsString());
781  1 assertEquals("-GG-GTC--AGG--CAGT",
782    al2.getSequenceAt(1).getSequenceAsString());
783    }
784   
785    /**
786    * Aligning protein from cDNA.
787    *
788    * @throws IOException
789    */
 
790  1 toggle @Test(groups = { "Functional" })
791    public void testAlignAs_proteinAsCdna() throws IOException
792    {
793    // see also AlignmentUtilsTests
794  1 AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
795  1 AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
796  1 makeMappings(al1, al2);
797   
798    // Fudge - alignProteinAsCdna expects mappings to be on protein
799  1 al2.getCodonFrames().addAll(al1.getCodonFrames());
800   
801  1 ((Alignment) al2).alignAs(al1, false, true);
802  1 assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString());
803  1 assertEquals("-R-F-P-W", al2.getSequenceAt(1).getSequenceAsString());
804    }
805   
806    /**
807    * Test aligning cdna as per protein alignment.
808    *
809    * @throws IOException
810    */
 
811  1 toggle @Test(groups = { "Functional" }, enabled = true)
812    // TODO review / update this test after redesign of alignAs method
813    public void testAlignAs_cdnaAsProtein() throws IOException
814    {
815    /*
816    * Load alignments and add mappings for cDNA to protein
817    */
818  1 AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
819  1 AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
820  1 makeMappings(al1, al2);
821   
822    /*
823    * Realign DNA; currently keeping existing gaps in introns only
824    */
825  1 ((Alignment) al1).alignAs(al2, false, true);
826  1 assertEquals("ACG---GCUCCA------ACT---",
827    al1.getSequenceAt(0).getSequenceAsString());
828  1 assertEquals("---CGT---TAACGA---AGT---",
829    al1.getSequenceAt(1).getSequenceAsString());
830    }
831   
832    /**
833    * Test aligning cdna as per protein - single sequences
834    *
835    * @throws IOException
836    */
 
837  1 toggle @Test(groups = { "Functional" }, enabled = true)
838    // TODO review / update this test after redesign of alignAs method
839    public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException
840    {
841    /*
842    * simple case insert one gap
843    */
844  1 verifyAlignAs(">dna\nCAAaaa\n", ">protein\nQ-K\n", "CAA---aaa");
845   
846    /*
847    * simple case but with sequence offsets
848    */
849  1 verifyAlignAs(">dna/5-10\nCAAaaa\n", ">protein/20-21\nQ-K\n",
850    "CAA---aaa");
851   
852    /*
853    * insert gaps as per protein, drop gaps within codons
854    */
855  1 verifyAlignAs(">dna/10-18\nCA-Aa-aa--AGA\n", ">aa/6-8\n-Q-K--R\n",
856    "---CAA---aaa------AGA");
857    }
858   
859    /**
860    * Helper method that makes mappings and then aligns the first alignment as
861    * the second
862    *
863    * @param fromSeqs
864    * @param toSeqs
865    * @param expected
866    * @throws IOException
867    */
 
868  3 toggle public void verifyAlignAs(String fromSeqs, String toSeqs, String expected)
869    throws IOException
870    {
871    /*
872    * Load alignments and add mappings from nucleotide to protein (or from
873    * first to second if both the same type)
874    */
875  3 AlignmentI al1 = loadAlignment(fromSeqs, FileFormat.Fasta);
876  3 AlignmentI al2 = loadAlignment(toSeqs, FileFormat.Fasta);
877  3 makeMappings(al1, al2);
878   
879    /*
880    * Realign DNA; currently keeping existing gaps in introns only
881    */
882  3 ((Alignment) al1).alignAs(al2, false, true);
883  3 assertEquals(expected, al1.getSequenceAt(0).getSequenceAsString());
884    }
885   
886    /**
887    * Helper method to make mappings between sequences, and add the mappings to
888    * the 'mapped from' alignment
889    *
890    * @param alFrom
891    * @param alTo
892    */
 
893  6 toggle public void makeMappings(AlignmentI alFrom, AlignmentI alTo)
894    {
895  6 int ratio = (alFrom.isNucleotide() == alTo.isNucleotide() ? 1 : 3);
896   
897  6 AlignedCodonFrame acf = new AlignedCodonFrame();
898   
899  15 for (int i = 0; i < alFrom.getHeight(); i++)
900    {
901  9 SequenceI seqFrom = alFrom.getSequenceAt(i);
902  9 SequenceI seqTo = alTo.getSequenceAt(i);
903  9 MapList ml = new MapList(
904    new int[]
905    { seqFrom.getStart(), seqFrom.getEnd() },
906    new int[]
907    { seqTo.getStart(), seqTo.getEnd() }, ratio, 1);
908  9 acf.addMap(seqFrom, seqTo, ml);
909    }
910   
911    /*
912    * not sure whether mappings 'belong' or protein or nucleotide
913    * alignment, so adding to both ;~)
914    */
915  6 alFrom.addCodonFrame(acf);
916  6 alTo.addCodonFrame(acf);
917    }
918   
919    /**
920    * Test aligning dna as per protein alignment, for the case where there are
921    * introns (i.e. some dna sites have no mapping from a peptide).
922    *
923    * @throws IOException
924    */
 
925  0 toggle @Test(groups = { "Functional" }, enabled = false)
926    // TODO review / update this test after redesign of alignAs method
927    public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
928    {
929    /*
930    * Load alignments and add mappings for cDNA to protein
931    */
932  0 String dna1 = "A-Aa-gG-GCC-cT-TT";
933  0 String dna2 = "c--CCGgg-TT--T-AA-A";
934  0 AlignmentI al1 = loadAlignment(
935    ">Dna1/6-17\n" + dna1 + "\n>Dna2/20-31\n" + dna2 + "\n",
936    FileFormat.Fasta);
937  0 AlignmentI al2 = loadAlignment(
938    ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", FileFormat.Fasta);
939  0 AlignedCodonFrame acf = new AlignedCodonFrame();
940    // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
941    // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
942  0 MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 },
943    new int[]
944    { 7, 9 }, 3, 1);
945  0 acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
946  0 MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 },
947    new int[]
948    { 11, 13 }, 3, 1);
949  0 acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
950  0 al2.addCodonFrame(acf);
951   
952    /*
953    * Align ignoring gaps in dna introns and exons
954    */
955  0 ((Alignment) al1).alignAs(al2, false, false);
956  0 assertEquals("---AAagG------GCCcTTT",
957    al1.getSequenceAt(0).getSequenceAsString());
958    // note 1 gap in protein corresponds to 'gg-' in DNA (3 positions)
959  0 assertEquals("cCCGgg-TTT------AAA",
960    al1.getSequenceAt(1).getSequenceAsString());
961   
962    /*
963    * Reset and realign, preserving gaps in dna introns and exons
964    */
965  0 al1.getSequenceAt(0).setSequence(dna1);
966  0 al1.getSequenceAt(1).setSequence(dna2);
967  0 ((Alignment) al1).alignAs(al2, true, true);
968    // String dna1 = "A-Aa-gG-GCC-cT-TT";
969    // String dna2 = "c--CCGgg-TT--T-AA-A";
970    // assumption: we include 'the greater of' protein/dna gap lengths, not both
971  0 assertEquals("---A-Aa-gG------GCC-cT-TT",
972    al1.getSequenceAt(0).getSequenceAsString());
973  0 assertEquals("c--CCGgg-TT--T------AA-A",
974    al1.getSequenceAt(1).getSequenceAsString());
975    }
976   
 
977  1 toggle @Test(groups = "Functional")
978    public void testCopyConstructor() throws IOException
979    {
980  1 AlignmentI protein = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
981    // create sequence and alignment datasets
982  1 protein.setDataset(null);
983  1 AlignedCodonFrame acf = new AlignedCodonFrame();
984  1 List<AlignedCodonFrame> acfList = Arrays
985    .asList(new AlignedCodonFrame[]
986    { acf });
987  1 protein.getDataset().setCodonFrames(acfList);
988  1 AlignmentI copy = new Alignment(protein);
989   
990    /*
991    * copy has different aligned sequences but the same dataset sequences
992    */
993  1 assertFalse(copy.getSequenceAt(0) == protein.getSequenceAt(0));
994  1 assertFalse(copy.getSequenceAt(1) == protein.getSequenceAt(1));
995  1 assertSame(copy.getSequenceAt(0).getDatasetSequence(),
996    protein.getSequenceAt(0).getDatasetSequence());
997  1 assertSame(copy.getSequenceAt(1).getDatasetSequence(),
998    protein.getSequenceAt(1).getDatasetSequence());
999   
1000    // TODO should the copy constructor copy the dataset?
1001    // or make a new one referring to the same dataset sequences??
1002  1 assertNull(copy.getDataset());
1003    // TODO test metadata is copied when AlignmentI is a dataset
1004   
1005    // assertArrayEquals(copy.getDataset().getSequencesArray(), protein
1006    // .getDataset().getSequencesArray());
1007    }
1008   
1009    /**
1010    * Test behaviour of createDataset
1011    *
1012    * @throws IOException
1013    */
 
1014  1 toggle @Test(groups = "Functional")
1015    public void testCreateDatasetAlignment() throws IOException
1016    {
1017  1 AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1,
1018    DataSourceType.PASTE, FileFormat.Fasta);
1019    /*
1020    * create a dataset sequence on first sequence
1021    * leave the second without one
1022    */
1023  1 protein.getSequenceAt(0).createDatasetSequence();
1024  1 assertNotNull(protein.getSequenceAt(0).getDatasetSequence());
1025  1 assertNull(protein.getSequenceAt(1).getDatasetSequence());
1026   
1027    /*
1028    * add a mapping to the alignment
1029    */
1030  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1031  1 protein.addCodonFrame(acf);
1032  1 assertNull(protein.getDataset());
1033  1 assertTrue(protein.getCodonFrames().contains(acf));
1034   
1035    /*
1036    * create the alignment dataset
1037    * note this creates sequence datasets where missing
1038    * as a side-effect (in this case, on seq2
1039    */
1040    // TODO promote this method to AlignmentI
1041  1 ((Alignment) protein).createDatasetAlignment();
1042   
1043  1 AlignmentI ds = protein.getDataset();
1044   
1045    // side-effect: dataset created on second sequence
1046  1 assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
1047    // dataset alignment has references to dataset sequences
1048  1 assertEquals(ds.getSequenceAt(0),
1049    protein.getSequenceAt(0).getDatasetSequence());
1050  1 assertEquals(ds.getSequenceAt(1),
1051    protein.getSequenceAt(1).getDatasetSequence());
1052   
1053    // codon frames should have been moved to the dataset
1054    // getCodonFrames() should delegate to the dataset:
1055  1 assertTrue(protein.getCodonFrames().contains(acf));
1056    // prove the codon frames are indeed on the dataset:
1057  1 assertTrue(ds.getCodonFrames().contains(acf));
1058    }
1059   
1060    /**
1061    * tests the addition of *all* sequences referred to by a sequence being added
1062    * to the dataset
1063    */
 
1064  1 toggle @Test(groups = "Functional")
1065    public void testCreateDatasetAlignmentWithMappedToSeqs()
1066    {
1067    // Alignment with two sequences, gapped.
1068  1 SequenceI sq1 = new Sequence("sq1", "A--SDF");
1069  1 SequenceI sq2 = new Sequence("sq2", "G--TRQ");
1070   
1071    // cross-references to two more sequences.
1072  1 DBRefEntry dbr = new DBRefEntry("SQ1", "", "sq3");
1073  1 SequenceI sq3 = new Sequence("sq3", "VWANG");
1074  1 dbr.setMap(
1075    new Mapping(sq3, new MapList(new int[]
1076    { 1, 4 }, new int[] { 2, 5 }, 1, 1)));
1077  1 sq1.addDBRef(dbr);
1078   
1079  1 SequenceI sq4 = new Sequence("sq4", "ERKWI");
1080  1 DBRefEntry dbr2 = new DBRefEntry("SQ2", "", "sq4");
1081  1 dbr2.setMap(
1082    new Mapping(sq4, new MapList(new int[]
1083    { 1, 4 }, new int[] { 2, 5 }, 1, 1)));
1084  1 sq2.addDBRef(dbr2);
1085    // and a 1:1 codonframe mapping between them.
1086  1 AlignedCodonFrame alc = new AlignedCodonFrame();
1087  1 alc.addMap(sq1, sq2,
1088    new MapList(new int[]
1089    { 1, 4 }, new int[] { 1, 4 }, 1, 1));
1090   
1091  1 AlignmentI protein = new Alignment(new SequenceI[] { sq1, sq2 });
1092   
1093    /*
1094    * create the alignment dataset
1095    * note this creates sequence datasets where missing
1096    * as a side-effect (in this case, on seq2
1097    */
1098   
1099    // TODO promote this method to AlignmentI
1100  1 ((Alignment) protein).createDatasetAlignment();
1101   
1102  1 AlignmentI ds = protein.getDataset();
1103   
1104    // should be 4 sequences in dataset - two materialised, and two propagated
1105    // from dbref
1106  1 assertEquals(4, ds.getHeight());
1107  1 assertTrue(ds.getSequences().contains(sq1.getDatasetSequence()));
1108  1 assertTrue(ds.getSequences().contains(sq2.getDatasetSequence()));
1109  1 assertTrue(ds.getSequences().contains(sq3));
1110  1 assertTrue(ds.getSequences().contains(sq4));
1111    // Should have one codon frame mapping between sq1 and sq2 via dataset
1112    // sequences
1113  1 assertEquals(ds.getCodonFrame(sq1.getDatasetSequence()),
1114    ds.getCodonFrame(sq2.getDatasetSequence()));
1115    }
1116   
 
1117  1 toggle @Test(groups = "Functional")
1118    public void testAddCodonFrame()
1119    {
1120  1 AlignmentI align = new Alignment(new SequenceI[] {});
1121  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1122  1 align.addCodonFrame(acf);
1123  1 assertEquals(1, align.getCodonFrames().size());
1124  1 assertTrue(align.getCodonFrames().contains(acf));
1125    // can't add the same object twice:
1126  1 align.addCodonFrame(acf);
1127  1 assertEquals(1, align.getCodonFrames().size());
1128   
1129    // create dataset alignment - mappings move to dataset
1130  1 ((Alignment) align).createDatasetAlignment();
1131  1 assertSame(align.getCodonFrames(), align.getDataset().getCodonFrames());
1132  1 assertEquals(1, align.getCodonFrames().size());
1133   
1134  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
1135  1 align.addCodonFrame(acf2);
1136  1 assertTrue(align.getDataset().getCodonFrames().contains(acf));
1137    }
1138   
 
1139  1 toggle @Test(groups = "Functional")
1140    public void testAddSequencePreserveDatasetIntegrity()
1141    {
1142  1 Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
1143  1 Alignment align = new Alignment(new SequenceI[] { seq });
1144  1 align.createDatasetAlignment();
1145  1 AlignmentI ds = align.getDataset();
1146  1 SequenceI copy = new Sequence(seq);
1147  1 copy.insertCharAt(3, 5, '-');
1148  1 align.addSequence(copy);
1149  1 Assert.assertEquals(align.getDataset().getHeight(), 1,
1150    "Dataset shouldn't have more than one sequence.");
1151   
1152  1 Sequence seq2 = new Sequence("newtestSeq",
1153    "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
1154  1 align.addSequence(seq2);
1155  1 Assert.assertEquals(align.getDataset().getHeight(), 2,
1156    "Dataset should now have two sequences.");
1157   
1158  1 assertAlignmentDatasetRefs(align,
1159    "addSequence broke dataset reference integrity");
1160    }
1161   
1162    /**
1163    * Tests that dbrefs with mappings to sequence get updated if the sequence
1164    * acquires a dataset sequence
1165    */
 
1166  1 toggle @Test(groups = "Functional")
1167    public void testCreateDataset_updateDbrefMappings()
1168    {
1169  1 SequenceI pep = new Sequence("pep", "ASD");
1170  1 SequenceI dna = new Sequence("dna", "aaaGCCTCGGATggg");
1171  1 SequenceI cds = new Sequence("cds", "GCCTCGGAT");
1172   
1173    // add dbref from dna to peptide
1174  1 DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep");
1175  1 dbr.setMap(
1176    new Mapping(pep, new MapList(new int[]
1177    { 4, 15 }, new int[] { 1, 4 }, 3, 1)));
1178  1 dna.addDBRef(dbr);
1179   
1180    // add dbref from dna to peptide
1181  1 DBRefEntry dbr2 = new DBRefEntry("UNIPROT", "", "pep");
1182  1 dbr2.setMap(
1183    new Mapping(pep, new MapList(new int[]
1184    { 1, 12 }, new int[] { 1, 4 }, 3, 1)));
1185  1 cds.addDBRef(dbr2);
1186   
1187    // add dbref from peptide to dna
1188  1 DBRefEntry dbr3 = new DBRefEntry("EMBL", "", "dna");
1189  1 dbr3.setMap(
1190    new Mapping(dna, new MapList(new int[]
1191    { 1, 4 }, new int[] { 4, 15 }, 1, 3)));
1192  1 pep.addDBRef(dbr3);
1193   
1194    // add dbref from peptide to cds
1195  1 DBRefEntry dbr4 = new DBRefEntry("EMBLCDS", "", "cds");
1196  1 dbr4.setMap(
1197    new Mapping(cds, new MapList(new int[]
1198    { 1, 4 }, new int[] { 1, 12 }, 1, 3)));
1199  1 pep.addDBRef(dbr4);
1200   
1201  1 AlignmentI protein = new Alignment(new SequenceI[] { pep });
1202   
1203    /*
1204    * create the alignment dataset
1205    */
1206  1 ((Alignment) protein).createDatasetAlignment();
1207   
1208  1 AlignmentI ds = protein.getDataset();
1209   
1210    // should be 3 sequences in dataset
1211  1 assertEquals(3, ds.getHeight());
1212  1 assertTrue(ds.getSequences().contains(pep.getDatasetSequence()));
1213  1 assertTrue(ds.getSequences().contains(dna));
1214  1 assertTrue(ds.getSequences().contains(cds));
1215   
1216    /*
1217    * verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset
1218    */
1219  1 List<DBRefEntry> dbRefs = pep.getDBRefs();
1220  1 assertEquals(2, dbRefs.size());
1221  1 assertSame(dna, dbRefs.get(0).map.to);
1222  1 assertSame(cds, dbRefs.get(1).map.to);
1223  1 assertEquals(1, dna.getDBRefs().size());
1224  1 assertSame(pep.getDatasetSequence(), dna.getDBRefs().get(0).map.to);
1225  1 assertEquals(1, cds.getDBRefs().size());
1226  1 assertSame(pep.getDatasetSequence(), cds.getDBRefs().get(0).map.to);
1227    }
1228   
 
1229  1 toggle @Test(groups = { "Functional" })
1230    public void testFindGroup()
1231    {
1232  1 SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
1233  1 SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
1234  1 AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
1235   
1236  1 assertNull(a.findGroup(null, 0));
1237  1 assertNull(a.findGroup(seq1, 1));
1238  1 assertNull(a.findGroup(seq1, -1));
1239   
1240    /*
1241    * add a group consisting of just "DEF"
1242    */
1243  1 SequenceGroup sg1 = new SequenceGroup();
1244  1 sg1.addSequence(seq1, false);
1245  1 sg1.setStartRes(3);
1246  1 sg1.setEndRes(5);
1247  1 a.addGroup(sg1);
1248   
1249  1 assertNull(a.findGroup(seq1, 2)); // position not in group
1250  1 assertNull(a.findGroup(seq1, 6)); // position not in group
1251  1 assertNull(a.findGroup(seq2, 5)); // sequence not in group
1252  1 assertSame(a.findGroup(seq1, 3), sg1); // yes
1253  1 assertSame(a.findGroup(seq1, 4), sg1);
1254  1 assertSame(a.findGroup(seq1, 5), sg1);
1255   
1256    /*
1257    * add a group consisting of
1258    * EF--
1259    * KLMN
1260    */
1261  1 SequenceGroup sg2 = new SequenceGroup();
1262  1 sg2.addSequence(seq1, false);
1263  1 sg2.addSequence(seq2, false);
1264  1 sg2.setStartRes(4);
1265  1 sg2.setEndRes(7);
1266  1 a.addGroup(sg2);
1267   
1268  1 assertNull(a.findGroup(seq1, 2)); // unchanged
1269  1 assertSame(a.findGroup(seq1, 3), sg1); // unchanged
1270    /*
1271    * if a residue is in more than one group, method returns
1272    * the first found (in order groups were added)
1273    */
1274  1 assertSame(a.findGroup(seq1, 4), sg1);
1275  1 assertSame(a.findGroup(seq1, 5), sg1);
1276   
1277    /*
1278    * seq2 only belongs to the second group
1279    */
1280  1 assertSame(a.findGroup(seq2, 4), sg2);
1281  1 assertSame(a.findGroup(seq2, 5), sg2);
1282  1 assertSame(a.findGroup(seq2, 6), sg2);
1283  1 assertSame(a.findGroup(seq2, 7), sg2);
1284  1 assertNull(a.findGroup(seq2, 3));
1285  1 assertNull(a.findGroup(seq2, 8));
1286    }
1287   
 
1288  1 toggle @Test(groups = { "Functional" })
1289    public void testDeleteSequenceByIndex()
1290    {
1291    // create random alignment
1292  1 AlignmentGenerator gen = new AlignmentGenerator(false);
1293  1 AlignmentI a = gen.generate(20, 15, 123, 5, 5);
1294   
1295    // delete sequence 10, alignment reduced by 1
1296  1 int height = a.getAbsoluteHeight();
1297  1 a.deleteSequence(10);
1298  1 assertEquals(a.getAbsoluteHeight(), height - 1);
1299   
1300    // try to delete -ve index, nothing happens
1301  1 a.deleteSequence(-1);
1302  1 assertEquals(a.getAbsoluteHeight(), height - 1);
1303   
1304    // try to delete beyond end of alignment, nothing happens
1305  1 a.deleteSequence(14);
1306  1 assertEquals(a.getAbsoluteHeight(), height - 1);
1307    }
1308   
 
1309  1 toggle @Test(groups = { "Functional" })
1310    public void testDeleteSequenceBySeq()
1311    {
1312    // create random alignment
1313  1 AlignmentGenerator gen = new AlignmentGenerator(false);
1314  1 AlignmentI a = gen.generate(20, 15, 123, 5, 5);
1315   
1316    // delete sequence 10, alignment reduced by 1
1317  1 int height = a.getAbsoluteHeight();
1318  1 SequenceI seq = a.getSequenceAt(10);
1319  1 a.deleteSequence(seq);
1320  1 assertEquals(a.getAbsoluteHeight(), height - 1);
1321   
1322    // try to delete non-existent sequence, nothing happens
1323  1 seq = new Sequence("cds", "GCCTCGGAT");
1324  1 assertEquals(a.getAbsoluteHeight(), height - 1);
1325    }
1326   
 
1327  1 toggle @Test(groups = { "Functional" })
1328    public void testDeleteHiddenSequence()
1329    {
1330    // create random alignment
1331  1 AlignmentGenerator gen = new AlignmentGenerator(false);
1332  1 AlignmentI a = gen.generate(20, 15, 123, 5, 5);
1333   
1334    // delete a sequence which is hidden, check it is NOT removed from hidden
1335    // sequences
1336  1 int height = a.getAbsoluteHeight();
1337  1 SequenceI seq = a.getSequenceAt(2);
1338  1 a.getHiddenSequences().hideSequence(seq);
1339  1 assertEquals(a.getHiddenSequences().getSize(), 1);
1340  1 a.deleteSequence(2);
1341  1 assertEquals(a.getAbsoluteHeight(), height - 1);
1342  1 assertEquals(a.getHiddenSequences().getSize(), 1);
1343   
1344    // delete a sequence which is not hidden, check hiddenSequences are not
1345    // affected
1346  1 a.deleteSequence(10);
1347  1 assertEquals(a.getAbsoluteHeight(), height - 2);
1348  1 assertEquals(a.getHiddenSequences().getSize(), 1);
1349    }
1350   
 
1351  1 toggle @Test(
1352    groups = "Functional",
1353    expectedExceptions =
1354    { IllegalArgumentException.class })
1355    public void testSetDataset_selfReference()
1356    {
1357  1 SequenceI seq = new Sequence("a", "a");
1358  1 AlignmentI alignment = new Alignment(new SequenceI[] { seq });
1359  1 alignment.setDataset(alignment);
1360    }
1361   
 
1362  1 toggle @Test(groups = "Functional")
1363    public void testAppend()
1364    {
1365  1 SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
1366  1 AlignmentI alignment = new Alignment(new SequenceI[] { seq });
1367  1 alignment.setGapCharacter('-');
1368  1 SequenceI seq2 = new Sequence("seq1", "KP..L.FQII.");
1369  1 AlignmentI alignment2 = new Alignment(new SequenceI[] { seq2 });
1370  1 alignment2.setGapCharacter('.');
1371   
1372  1 alignment.append(alignment2);
1373   
1374  1 assertEquals('-', alignment.getGapCharacter());
1375  1 assertSame(seq, alignment.getSequenceAt(0));
1376  1 assertEquals("KP--L-FQII-",
1377    alignment.getSequenceAt(1).getSequenceAsString());
1378   
1379    // todo test coverage for annotations, mappings, groups,
1380    // hidden sequences, properties
1381    }
1382   
1383    /**
1384    * test that calcId == null on findOrCreate doesn't raise an NPE, and yields
1385    * an annotation with a null calcId
1386    *
1387    */
 
1388  1 toggle @Test(groups = "Functional")
1389    public void testFindOrCreateForNullCalcId()
1390    {
1391  1 SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
1392  1 AlignmentI alignment = new Alignment(new SequenceI[] { seq });
1393   
1394  1 AlignmentAnnotation ala = alignment.findOrCreateAnnotation(
1395    "Temperature Factor", null, false, seq, null);
1396  1 assertNotNull(ala);
1397  1 assertEquals(seq, ala.sequenceRef);
1398  1 assertEquals("", ala.calcId);
1399    }
1400   
 
1401  1 toggle @Test(groups = "Functional")
1402    public void testPropagateInsertions()
1403    {
1404    // create an alignment with no gaps - this will be the profile seq and other
1405    // JPRED seqs
1406  1 AlignmentGenerator gen = new AlignmentGenerator(false);
1407  1 AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
1408   
1409    // get the profileseq
1410  1 SequenceI profileseq = al.getSequenceAt(0);
1411  1 SequenceI gappedseq = new Sequence(profileseq);
1412  1 gappedseq.insertCharAt(5, al.getGapCharacter());
1413  1 gappedseq.insertCharAt(6, al.getGapCharacter());
1414  1 gappedseq.insertCharAt(7, al.getGapCharacter());
1415  1 gappedseq.insertCharAt(8, al.getGapCharacter());
1416   
1417    // force different kinds of padding
1418  1 al.getSequenceAt(3).deleteChars(2, 23);
1419  1 al.getSequenceAt(4).deleteChars(2, 27);
1420  1 al.getSequenceAt(5).deleteChars(10, 27);
1421   
1422    // create an alignment view with the gapped sequence
1423  1 SequenceI[] seqs = new SequenceI[1];
1424  1 seqs[0] = gappedseq;
1425  1 AlignmentI newal = new Alignment(seqs);
1426  1 HiddenColumns hidden = new HiddenColumns();
1427  1 hidden.hideColumns(15, 17);
1428   
1429  1 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
1430    false);
1431   
1432    // confirm that original contigs are as expected
1433  1 Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
1434  1 int[] region = visible.next();
1435  1 assertEquals("[0, 14]", Arrays.toString(region));
1436  1 region = visible.next();
1437  1 assertEquals("[18, 24]", Arrays.toString(region));
1438   
1439    // propagate insertions
1440  1 HiddenColumns result = al.propagateInsertions(profileseq, view);
1441   
1442    // confirm that the contigs have changed to account for the gaps
1443  1 visible = result.getVisContigsIterator(0, 25, false);
1444  1 region = visible.next();
1445  1 assertEquals("[0, 10]", Arrays.toString(region));
1446  1 region = visible.next();
1447  1 assertEquals("[14, 24]", Arrays.toString(region));
1448   
1449    // confirm the alignment has been changed so that the other sequences have
1450    // gaps inserted where the columns are hidden
1451  1 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
1452  1 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
1453  1 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
1454  1 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
1455  1 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
1456   
1457    }
1458   
 
1459  1 toggle @Test(groups = "Functional")
1460    public void testPropagateInsertionsOverlap()
1461    {
1462    // test propagateInsertions where gaps and hiddenColumns overlap
1463   
1464    // create an alignment with no gaps - this will be the profile seq and other
1465    // JPRED seqs
1466  1 AlignmentGenerator gen = new AlignmentGenerator(false);
1467  1 AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
1468   
1469    // get the profileseq
1470  1 SequenceI profileseq = al.getSequenceAt(0);
1471  1 SequenceI gappedseq = new Sequence(profileseq);
1472  1 gappedseq.insertCharAt(5, al.getGapCharacter());
1473  1 gappedseq.insertCharAt(6, al.getGapCharacter());
1474  1 gappedseq.insertCharAt(7, al.getGapCharacter());
1475  1 gappedseq.insertCharAt(8, al.getGapCharacter());
1476   
1477    // create an alignment view with the gapped sequence
1478  1 SequenceI[] seqs = new SequenceI[1];
1479  1 seqs[0] = gappedseq;
1480  1 AlignmentI newal = new Alignment(seqs);
1481   
1482    // hide columns so that some overlap with the gaps
1483  1 HiddenColumns hidden = new HiddenColumns();
1484  1 hidden.hideColumns(7, 10);
1485   
1486  1 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
1487    false);
1488   
1489    // confirm that original contigs are as expected
1490  1 Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
1491  1 int[] region = visible.next();
1492  1 assertEquals("[0, 6]", Arrays.toString(region));
1493  1 region = visible.next();
1494  1 assertEquals("[11, 19]", Arrays.toString(region));
1495  1 assertFalse(visible.hasNext());
1496   
1497    // propagate insertions
1498  1 HiddenColumns result = al.propagateInsertions(profileseq, view);
1499   
1500    // confirm that the contigs have changed to account for the gaps
1501  1 visible = result.getVisContigsIterator(0, 20, false);
1502  1 region = visible.next();
1503  1 assertEquals("[0, 4]", Arrays.toString(region));
1504  1 region = visible.next();
1505  1 assertEquals("[7, 19]", Arrays.toString(region));
1506  1 assertFalse(visible.hasNext());
1507   
1508    // confirm the alignment has been changed so that the other sequences have
1509    // gaps inserted where the columns are hidden
1510  1 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
1511  1 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
1512  1 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
1513  1 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
1514    }
1515   
 
1516  1 toggle @Test(groups = { "Functional" })
1517    public void testPadGaps()
1518    {
1519  1 SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
1520  1 SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
1521  1 SequenceI seq3 = new Sequence("seq2", "-PQR");
1522  1 AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
1523  1 a.setGapCharacter('.'); // this replaces existing gaps
1524  1 assertEquals("ABCDEF..", seq1.getSequenceAsString());
1525  1 a.padGaps();
1526    // trailing gaps are pruned, short sequences padded with gap character
1527  1 assertEquals("ABCDEF.", seq1.getSequenceAsString());
1528  1 assertEquals(".JKLMNO", seq2.getSequenceAsString());
1529  1 assertEquals(".PQR...", seq3.getSequenceAsString());
1530    }
1531   
1532    /**
1533    * Test for setHiddenColumns, to check it returns true if the hidden columns
1534    * have changed, else false
1535    */
 
1536  1 toggle @Test(groups = { "Functional" })
1537    public void testSetHiddenColumns()
1538    {
1539  1 AlignmentI al = new Alignment(new SequenceI[] {});
1540  1 assertFalse(al.getHiddenColumns().hasHiddenColumns());
1541   
1542  1 HiddenColumns hc = new HiddenColumns();
1543  1 assertFalse(al.setHiddenColumns(hc)); // no change
1544  1 assertSame(hc, al.getHiddenColumns());
1545   
1546  1 hc.hideColumns(2, 4);
1547  1 assertTrue(al.getHiddenColumns().hasHiddenColumns());
1548   
1549    /*
1550    * set a different object but with the same columns hidden
1551    */
1552  1 HiddenColumns hc2 = new HiddenColumns();
1553  1 hc2.hideColumns(2, 4);
1554  1 assertFalse(al.setHiddenColumns(hc2)); // no change
1555  1 assertSame(hc2, al.getHiddenColumns());
1556   
1557  1 assertTrue(al.setHiddenColumns(null));
1558  1 assertNull(al.getHiddenColumns());
1559  1 assertTrue(al.setHiddenColumns(hc));
1560  1 assertSame(hc, al.getHiddenColumns());
1561   
1562  1 al.getHiddenColumns().hideColumns(10, 12);
1563  1 hc2.hideColumns(10, 12);
1564  1 assertFalse(al.setHiddenColumns(hc2)); // no change
1565   
1566    /*
1567    * hide columns 15-16 then 17-18 in hc
1568    * hide columns 15-18 in hc2
1569    * these are not now 'equal' objects even though they
1570    * represent the same set of columns
1571    */
1572  1 assertSame(hc2, al.getHiddenColumns());
1573  1 hc.hideColumns(15, 16);
1574  1 hc.hideColumns(17, 18);
1575  1 hc2.hideColumns(15, 18);
1576  1 assertFalse(hc.equals(hc2));
1577  1 assertTrue(al.setHiddenColumns(hc)); // 'changed'
1578    }
1579   
 
1580  1 toggle @Test(groups = { "Functional" })
1581    public void testGetWidth()
1582    {
1583  1 SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
1584  1 SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
1585  1 SequenceI seq3 = new Sequence("seq2", "-PQR");
1586  1 AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
1587   
1588  1 assertEquals(9, a.getWidth());
1589   
1590    // width includes hidden columns
1591  1 a.getHiddenColumns().hideColumns(2, 5);
1592  1 assertEquals(9, a.getWidth());
1593    }
1594   
 
1595  1 toggle @Test(groups = { "Functional" })
1596    public void testGetVisibleWidth()
1597    {
1598  1 SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
1599  1 SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
1600  1 SequenceI seq3 = new Sequence("seq2", "-PQR");
1601  1 AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
1602   
1603  1 assertEquals(9, a.getVisibleWidth());
1604   
1605    // width excludes hidden columns
1606  1 a.getHiddenColumns().hideColumns(2, 5);
1607  1 assertEquals(5, a.getVisibleWidth());
1608    }
1609   
 
1610  1 toggle @Test(groups = { "Functional" })
1611    public void testGetContactMap()
1612    {
1613    // TODO
1614    // 1. test adding/removing/manipulating contact maps with/without associated
1615    // sequence(s) or groups
1616    // 2. For sequence associated - ensure that inserting a gap in sequence
1617    // results in the contact map being relocated accordingly
1618    // 3. RENDERER QUESTION - should contact maps reflect gaps in the alignment
1619    // ?
1620   
1621    }
1622   
 
1623  1 toggle @Test(groups = { "Functional" })
1624    public void testEquals()
1625    {
1626  1 SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
1627  1 SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
1628  1 SequenceI seq3 = new Sequence("seq2", "-PQR");
1629  1 AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
1630  1 a.setDataset(null);
1631  1 assertEquals(a.getDataset(), a.getDataset());
1632    }
1633    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 12 2025 13:12:42 GMT using coverage data from Wed Nov 12 2025 13:12:28 GMT.
  • OpenClover is free and open-source software.