2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.datamodel;
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;
30 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
31 import jalview.io.AppletFormatAdapter;
32 import jalview.io.FormatAdapter;
33 import jalview.util.MapList;
35 import java.io.IOException;
36 import java.util.ArrayList;
37 import java.util.Arrays;
38 import java.util.Iterator;
39 import java.util.List;
41 import org.testng.Assert;
42 import org.testng.annotations.BeforeMethod;
43 import org.testng.annotations.Test;
46 * Unit tests for Alignment datamodel.
51 public class AlignmentTest
54 private static final String TEST_DATA =
56 "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
57 "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
58 "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
59 "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
60 "#=GR D.melanogaster.1 SS ................((((\n" +
61 "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
62 "#=GR D.melanogaster.2 SS ................((((\n" +
63 "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
64 "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
67 private static final String AA_SEQS_1 =
73 private static final String CDNA_SEQS_1 =
74 ">Seq1Name/100-111\n" +
75 "AC-GG--CUC-CAA-CT\n" +
76 ">Seq2Name/200-211\n" +
77 "-CG-TTA--ACG---AAGT\n";
79 private static final String CDNA_SEQS_2 =
86 private AlignmentI al;
89 * Helper method to load an alignment and ensure dataset sequences are set up.
97 protected AlignmentI loadAlignment(final String data, String format)
100 AlignmentI a = new FormatAdapter().readFile(data,
101 AppletFormatAdapter.PASTE, format);
107 * verify sequence and dataset references are properly contained within
111 * - the alignmentI object to verify (either alignment or dataset)
113 * - when set, testng assertions are raised.
114 * @return true if alignment references were in order, otherwise false.
116 public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment,
119 if (alignment == null)
123 Assert.fail("Alignment for verification was null.");
127 if (alignment.getDataset() != null)
129 AlignmentI dataset = alignment.getDataset();
130 // check all alignment sequences have their dataset within the dataset
131 for (SequenceI seq : alignment.getSequences())
133 SequenceI seqds = seq.getDatasetSequence();
134 if (seqds.getDatasetSequence() != null)
138 Assert.fail("Alignment contained a sequence who's dataset sequence has a second dataset reference.");
142 if (dataset.findIndex(seqds) == -1)
146 Assert.fail("Alignment contained a sequence who's dataset sequence was not in the dataset.");
151 return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert);
155 // verify all dataset sequences
156 for (SequenceI seqds : alignment.getSequences())
158 if (seqds.getDatasetSequence() != null)
162 Assert.fail("Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
166 if (seqds.getDBRefs() != null)
168 for (DBRefEntry dbr : seqds.getDBRefs())
170 if (dbr.getMap() != null)
172 SequenceI seqdbrmapto = dbr.getMap().getTo();
173 if (seqdbrmapto != null)
175 if (seqdbrmapto.getDatasetSequence() != null)
179 Assert.fail("DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
184 if (alignment.findIndex(dbr.getMap().getTo()) == -1)
188 Assert.fail("DBRefEntry for sequence in alignment had map to sequence not in dataset");
197 // finally, verify codonmappings involve only dataset sequences.
198 if (alignment.getCodonFrames() != null)
200 for (AlignedCodonFrame alc : alignment.getCodonFrames())
202 for (SequenceToSequenceMapping ssm : alc.getMappings())
204 if (ssm.getFromSeq().getDatasetSequence() != null)
208 Assert.fail("CodonFrame-SSM-FromSeq is not a dataset sequence");
212 if (alignment.findIndex(ssm.getFromSeq()) == -1)
217 Assert.fail("CodonFrame-SSM-FromSeq is not contained in dataset");
221 if (ssm.getMapping().getTo().getDatasetSequence() != null)
225 Assert.fail("CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
229 if (alignment.findIndex(ssm.getMapping().getTo()) == -1)
234 Assert.fail("CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
242 return true; // all relationships verified!
246 * call verifyAlignmentDatasetRefs with and without assertion raising enabled,
247 * to check expected pass/fail actually occurs in both conditions
253 private void assertVerifyAlignment(AlignmentI al, boolean expected,
261 Assert.assertTrue(verifyAlignmentDatasetRefs(al, true),
262 "Valid test alignment failed when raiseAsserts enabled:"
264 } catch (AssertionError ae)
266 ae.printStackTrace();
268 "Valid test alignment raised assertion errors when raiseAsserts enabled: "
271 // also check validation passes with asserts disabled
272 Assert.assertTrue(verifyAlignmentDatasetRefs(al, false),
273 "Valid test alignment failed when raiseAsserts disabled:"
280 Assert.assertFalse(verifyAlignmentDatasetRefs(al, true));
281 Assert.fail("Invalid test alignment passed but no assertion raised when raiseAsserts enabled:"
283 } catch (AssertionError ae)
285 // expected behaviour
287 // also check validation passes with asserts disabled
288 Assert.assertFalse(verifyAlignmentDatasetRefs(al, false),
289 "Invalid test alignment passed when raiseAsserts disabled:"
293 @Test(groups = { "Functional" })
294 public void testVerifyAlignmentDatasetRefs()
296 SequenceI sq1 = new Sequence("sq1", "ASFDD"), sq2 = new Sequence("sq2",
299 // construct simple valid alignment dataset
300 Alignment al = new Alignment(new SequenceI[] {
302 // expect this to pass
303 assertVerifyAlignment(al, true, "Simple valid alignment didn't verify");
305 // check test for sequence->datasetSequence validity
306 sq1.setDatasetSequence(sq2);
307 assertVerifyAlignment(
310 "didn't detect dataset sequence with a dataset sequence reference.");
312 sq1.setDatasetSequence(null);
313 assertVerifyAlignment(
316 "didn't reinstate validity after nulling dataset sequence dataset reference");
318 // now create dataset and check again
319 al.createDatasetAlignment();
320 assertNotNull(al.getDataset());
322 assertVerifyAlignment(al, true,
323 "verify failed after createDatasetAlignment");
325 // create a dbref on sq1 with a sequence ref to sq2
326 DBRefEntry dbrs1tos2 = new DBRefEntry("UNIPROT", "1", "Q111111");
327 dbrs1tos2.setMap(new Mapping(sq2.getDatasetSequence(),
328 new int[] { 1, 5 }, new int[] { 2, 6 }, 1, 1));
329 sq1.getDatasetSequence().addDBRef(dbrs1tos2);
330 assertVerifyAlignment(al, true,
331 "verify failed after addition of valid DBRefEntry/map");
332 // now create a dbref on a new sequence which maps to another sequence
333 // outside of the dataset
334 SequenceI sqout = new Sequence("sqout", "ututututucagcagcag"), sqnew = new Sequence(
336 DBRefEntry sqnewsqout = new DBRefEntry("ENAFOO", "1", "R000001");
337 sqnewsqout.setMap(new Mapping(sqout, new int[] { 1, 6 }, new int[] { 1,
339 al.getDataset().addSequence(sqnew);
341 assertVerifyAlignment(al, true,
342 "verify failed after addition of new sequence to dataset");
343 // now start checking exception conditions
344 sqnew.addDBRef(sqnewsqout);
345 assertVerifyAlignment(
348 "verify passed when a dbref with map to sequence outside of dataset was added");
349 // make the verify pass by adding the outsider back in
350 al.getDataset().addSequence(sqout);
351 assertVerifyAlignment(al, true,
352 "verify should have passed after adding dbref->to sequence in to dataset");
353 // and now the same for a codon mapping...
354 SequenceI sqanotherout = new Sequence("sqanotherout",
355 "aggtutaggcagcagcag");
357 AlignedCodonFrame alc = new AlignedCodonFrame();
358 alc.addMap(sqanotherout, sqnew, new MapList(new int[] { 1, 6 },
359 new int[] { 1, 18 }, 3, 1));
361 al.addCodonFrame(alc);
362 Assert.assertEquals(al.getDataset().getCodonFrames().size(), 1);
364 assertVerifyAlignment(
367 "verify passed when alCodonFrame mapping to sequence outside of dataset was added");
368 // make the verify pass by adding the outsider back in
369 al.getDataset().addSequence(sqanotherout);
370 assertVerifyAlignment(
373 "verify should have passed once all sequences involved in alCodonFrame were added to dataset");
377 * Read in Stockholm format test data including secondary structure
380 @BeforeMethod(alwaysRun = true)
381 public void setUp() throws IOException
383 al = loadAlignment(TEST_DATA, "STH");
385 for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
387 ann.setCalcId("CalcIdFor" + al.getSequenceAt(i).getName());
393 * Test method that returns annotations that match on calcId.
395 @Test(groups = { "Functional" })
396 public void testFindAnnotation_byCalcId()
398 Iterable<AlignmentAnnotation> anns = al
399 .findAnnotation("CalcIdForD.melanogaster.2");
400 Iterator<AlignmentAnnotation> iter = anns.iterator();
401 assertTrue(iter.hasNext());
402 AlignmentAnnotation ann = iter.next();
403 assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
404 assertFalse(iter.hasNext());
407 @Test(groups = { "Functional" })
408 public void testDeleteAllAnnotations_includingAutocalculated()
410 AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
412 aa.autoCalculated = true;
413 al.addAnnotation(aa);
414 AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
415 assertEquals("Wrong number of annotations before deleting", 4,
417 al.deleteAllAnnotations(true);
418 assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
421 @Test(groups = { "Functional" })
422 public void testDeleteAllAnnotations_excludingAutocalculated()
424 AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
426 aa.autoCalculated = true;
427 al.addAnnotation(aa);
428 AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
429 assertEquals("Wrong number of annotations before deleting", 4,
431 al.deleteAllAnnotations(false);
432 assertEquals("Not just one annotation left", 1,
433 al.getAlignmentAnnotation().length);
437 * Tests for realigning as per a supplied alignment: Dna as Dna.
439 * Note: AlignedCodonFrame's state variables are named for protein-to-cDNA
440 * mapping, but can be exploited for a general 'sequence-to-sequence' mapping
443 * @throws IOException
445 @Test(groups = { "Functional" })
446 public void testAlignAs_dnaAsDna() throws IOException
449 AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
451 AlignmentI al2 = loadAlignment(CDNA_SEQS_2, "FASTA");
454 * Make mappings between sequences. The 'aligned cDNA' is playing the role
455 * of what would normally be protein here.
457 makeMappings(al1, al2);
459 ((Alignment) al2).alignAs(al1, false, true);
460 assertEquals("GC-TC--GUC-GTACT", al2.getSequenceAt(0)
461 .getSequenceAsString());
462 assertEquals("-GG-GTC--AGG--CAGT", al2.getSequenceAt(1)
463 .getSequenceAsString());
467 * Aligning protein from cDNA.
469 * @throws IOException
471 @Test(groups = { "Functional" })
472 public void testAlignAs_proteinAsCdna() throws IOException
474 // see also AlignmentUtilsTests
475 AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
476 AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
477 makeMappings(al1, al2);
479 // Fudge - alignProteinAsCdna expects mappings to be on protein
480 al2.getCodonFrames().addAll(al1.getCodonFrames());
482 ((Alignment) al2).alignAs(al1, false, true);
483 assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString());
484 assertEquals("-R-F-P-W", al2.getSequenceAt(1).getSequenceAsString());
488 * Test aligning cdna as per protein alignment.
490 * @throws IOException
492 @Test(groups = { "Functional" }, enabled = true)
493 // TODO review / update this test after redesign of alignAs method
494 public void testAlignAs_cdnaAsProtein() throws IOException
497 * Load alignments and add mappings for cDNA to protein
499 AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
500 AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
501 makeMappings(al1, al2);
504 * Realign DNA; currently keeping existing gaps in introns only
506 ((Alignment) al1).alignAs(al2, false, true);
507 assertEquals("ACG---GCUCCA------ACT---", al1.getSequenceAt(0)
508 .getSequenceAsString());
509 assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
510 .getSequenceAsString());
514 * Test aligning cdna as per protein - single sequences
516 * @throws IOException
518 @Test(groups = { "Functional" }, enabled = true)
519 // TODO review / update this test after redesign of alignAs method
520 public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException
523 * simple case insert one gap
525 verifyAlignAs(">dna\nCAAaaa\n", ">protein\nQ-K\n", "CAA---aaa");
528 * simple case but with sequence offsets
530 verifyAlignAs(">dna/5-10\nCAAaaa\n", ">protein/20-21\nQ-K\n",
534 * insert gaps as per protein, drop gaps within codons
536 verifyAlignAs(">dna/10-18\nCA-Aa-aa--AGA\n", ">aa/6-8\n-Q-K--R\n",
537 "---CAA---aaa------AGA");
541 * Helper method that makes mappings and then aligns the first alignment as
547 * @throws IOException
549 public void verifyAlignAs(String fromSeqs, String toSeqs, String expected)
553 * Load alignments and add mappings from nucleotide to protein (or from
554 * first to second if both the same type)
556 AlignmentI al1 = loadAlignment(fromSeqs, "FASTA");
557 AlignmentI al2 = loadAlignment(toSeqs, "FASTA");
558 makeMappings(al1, al2);
561 * Realign DNA; currently keeping existing gaps in introns only
563 ((Alignment) al1).alignAs(al2, false, true);
564 assertEquals(expected, al1.getSequenceAt(0).getSequenceAsString());
568 * Helper method to make mappings between sequences, and add the mappings to
569 * the 'mapped from' alignment
574 public void makeMappings(AlignmentI alFrom, AlignmentI alTo)
576 int ratio = (alFrom.isNucleotide() == alTo.isNucleotide() ? 1 : 3);
578 AlignedCodonFrame acf = new AlignedCodonFrame();
580 for (int i = 0; i < alFrom.getHeight(); i++)
582 SequenceI seqFrom = alFrom.getSequenceAt(i);
583 SequenceI seqTo = alTo.getSequenceAt(i);
584 MapList ml = new MapList(new int[] { seqFrom.getStart(),
586 new int[] { seqTo.getStart(), seqTo.getEnd() }, ratio, 1);
587 acf.addMap(seqFrom, seqTo, ml);
591 * not sure whether mappings 'belong' or protein or nucleotide
592 * alignment, so adding to both ;~)
594 alFrom.addCodonFrame(acf);
595 alTo.addCodonFrame(acf);
599 * Test aligning dna as per protein alignment, for the case where there are
600 * introns (i.e. some dna sites have no mapping from a peptide).
602 * @throws IOException
604 @Test(groups = { "Functional" }, enabled = false)
605 // TODO review / update this test after redesign of alignAs method
606 public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
609 * Load alignments and add mappings for cDNA to protein
611 String dna1 = "A-Aa-gG-GCC-cT-TT";
612 String dna2 = "c--CCGgg-TT--T-AA-A";
613 AlignmentI al1 = loadAlignment(">Dna1/6-17\n" + dna1
614 + "\n>Dna2/20-31\n" + dna2 + "\n", "FASTA");
615 AlignmentI al2 = loadAlignment(
616 ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", "FASTA");
617 AlignedCodonFrame acf = new AlignedCodonFrame();
618 // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
619 // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
620 MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 }, new int[]
622 acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
623 MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 }, new int[] { 11,
625 acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
626 al2.addCodonFrame(acf);
629 * Align ignoring gaps in dna introns and exons
631 ((Alignment) al1).alignAs(al2, false, false);
632 assertEquals("---AAagG------GCCcTTT", al1.getSequenceAt(0)
633 .getSequenceAsString());
634 // note 1 gap in protein corresponds to 'gg-' in DNA (3 positions)
635 assertEquals("cCCGgg-TTT------AAA", al1.getSequenceAt(1)
636 .getSequenceAsString());
639 * Reset and realign, preserving gaps in dna introns and exons
641 al1.getSequenceAt(0).setSequence(dna1);
642 al1.getSequenceAt(1).setSequence(dna2);
643 ((Alignment) al1).alignAs(al2, true, true);
644 // String dna1 = "A-Aa-gG-GCC-cT-TT";
645 // String dna2 = "c--CCGgg-TT--T-AA-A";
646 // assumption: we include 'the greater of' protein/dna gap lengths, not both
647 assertEquals("---A-Aa-gG------GCC-cT-TT", al1.getSequenceAt(0)
648 .getSequenceAsString());
649 assertEquals("c--CCGgg-TT--T------AA-A", al1.getSequenceAt(1)
650 .getSequenceAsString());
653 @Test(groups = "Functional")
654 public void testCopyConstructor() throws IOException
656 AlignmentI protein = loadAlignment(AA_SEQS_1, FormatAdapter.PASTE);
657 // create sequence and alignment datasets
658 protein.setDataset(null);
659 AlignedCodonFrame acf = new AlignedCodonFrame();
660 List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
662 protein.getDataset().setCodonFrames(acfList);
663 AlignmentI copy = new Alignment(protein);
666 * copy has different aligned sequences but the same dataset sequences
668 assertFalse(copy.getSequenceAt(0) == protein.getSequenceAt(0));
669 assertFalse(copy.getSequenceAt(1) == protein.getSequenceAt(1));
670 assertSame(copy.getSequenceAt(0).getDatasetSequence(), protein
671 .getSequenceAt(0).getDatasetSequence());
672 assertSame(copy.getSequenceAt(1).getDatasetSequence(), protein
673 .getSequenceAt(1).getDatasetSequence());
675 // TODO should the copy constructor copy the dataset?
676 // or make a new one referring to the same dataset sequences??
677 assertNull(copy.getDataset());
678 // TODO test metadata is copied when AlignmentI is a dataset
680 // assertArrayEquals(copy.getDataset().getSequencesArray(), protein
681 // .getDataset().getSequencesArray());
685 * Test behaviour of createDataset
687 * @throws IOException
689 @Test(groups = "Functional")
690 public void testCreateDatasetAlignment() throws IOException
692 AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1,
693 AppletFormatAdapter.PASTE, "FASTA");
695 * create a dataset sequence on first sequence
696 * leave the second without one
698 protein.getSequenceAt(0).createDatasetSequence();
699 assertNotNull(protein.getSequenceAt(0).getDatasetSequence());
700 assertNull(protein.getSequenceAt(1).getDatasetSequence());
703 * add a mapping to the alignment
705 AlignedCodonFrame acf = new AlignedCodonFrame();
706 protein.addCodonFrame(acf);
707 assertNull(protein.getDataset());
708 assertTrue(protein.getCodonFrames().contains(acf));
711 * create the alignment dataset
712 * note this creates sequence datasets where missing
713 * as a side-effect (in this case, on seq2
715 // TODO promote this method to AlignmentI
716 ((Alignment) protein).createDatasetAlignment();
718 AlignmentI ds = protein.getDataset();
720 // side-effect: dataset created on second sequence
721 assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
722 // dataset alignment has references to dataset sequences
723 assertEquals(ds.getSequenceAt(0), protein.getSequenceAt(0)
724 .getDatasetSequence());
725 assertEquals(ds.getSequenceAt(1), protein.getSequenceAt(1)
726 .getDatasetSequence());
728 // codon frames should have been moved to the dataset
729 // getCodonFrames() should delegate to the dataset:
730 assertTrue(protein.getCodonFrames().contains(acf));
731 // prove the codon frames are indeed on the dataset:
732 assertTrue(ds.getCodonFrames().contains(acf));
736 * tests the addition of *all* sequences referred to by a sequence being added
739 @Test(groups = "Functional")
740 public void testCreateDatasetAlignmentWithMappedToSeqs()
742 // Alignment with two sequences, gapped.
743 SequenceI sq1 = new Sequence("sq1", "A--SDF");
744 SequenceI sq2 = new Sequence("sq2", "G--TRQ");
746 // cross-references to two more sequences.
747 DBRefEntry dbr = new DBRefEntry("SQ1", "", "sq3");
748 SequenceI sq3 = new Sequence("sq3", "VWANG");
749 dbr.setMap(new Mapping(sq3, new MapList(new int[] { 1, 4 }, new int[] {
753 SequenceI sq4 = new Sequence("sq4", "ERKWI");
754 DBRefEntry dbr2 = new DBRefEntry("SQ2", "", "sq4");
755 dbr2.setMap(new Mapping(sq4, new MapList(new int[] { 1, 4 }, new int[] {
758 // and a 1:1 codonframe mapping between them.
759 AlignedCodonFrame alc = new AlignedCodonFrame();
760 alc.addMap(sq1, sq2, new MapList(new int[] { 1, 4 },
761 new int[] { 1, 4 }, 1, 1));
763 AlignmentI protein = new Alignment(new SequenceI[] { sq1, sq2 });
766 * create the alignment dataset
767 * note this creates sequence datasets where missing
768 * as a side-effect (in this case, on seq2
771 // TODO promote this method to AlignmentI
772 ((Alignment) protein).createDatasetAlignment();
774 AlignmentI ds = protein.getDataset();
776 // should be 4 sequences in dataset - two materialised, and two propagated
778 assertEquals(4, ds.getHeight());
779 assertTrue(ds.getSequences().contains(sq1.getDatasetSequence()));
780 assertTrue(ds.getSequences().contains(sq2.getDatasetSequence()));
781 assertTrue(ds.getSequences().contains(sq3));
782 assertTrue(ds.getSequences().contains(sq4));
783 // Should have one codon frame mapping between sq1 and sq2 via dataset
785 assertEquals(ds.getCodonFrame(sq1.getDatasetSequence()),
786 ds.getCodonFrame(sq2.getDatasetSequence()));
789 @Test(groups = "Functional")
790 public void testAddCodonFrame()
792 AlignmentI align = new Alignment(new SequenceI[] {});
793 AlignedCodonFrame acf = new AlignedCodonFrame();
794 align.addCodonFrame(acf);
795 assertEquals(1, align.getCodonFrames().size());
796 assertTrue(align.getCodonFrames().contains(acf));
797 // can't add the same object twice:
798 align.addCodonFrame(acf);
799 assertEquals(1, align.getCodonFrames().size());
801 // create dataset alignment - mappings move to dataset
802 ((Alignment) align).createDatasetAlignment();
803 assertSame(align.getCodonFrames(), align.getDataset().getCodonFrames());
804 assertEquals(1, align.getCodonFrames().size());
806 AlignedCodonFrame acf2 = new AlignedCodonFrame();
807 align.addCodonFrame(acf2);
808 assertTrue(align.getDataset().getCodonFrames().contains(acf));
811 @Test(groups = "Functional")
812 public void getVisibleStartAndEndIndexTest()
814 Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
815 AlignmentI align = new Alignment(new SequenceI[] { seq });
816 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
818 int[] startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
819 assertEquals(0, startEnd[0]);
820 assertEquals(25, startEnd[1]);
822 hiddenCols.add(new int[] { 0, 0 });
823 startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
824 assertEquals(1, startEnd[0]);
825 assertEquals(25, startEnd[1]);
827 hiddenCols.add(new int[] { 6, 9 });
828 hiddenCols.add(new int[] { 11, 12 });
829 startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
830 assertEquals(1, startEnd[0]);
831 assertEquals(25, startEnd[1]);
833 hiddenCols.add(new int[] { 24, 25 });
834 startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
835 System.out.println(startEnd[0] + " : " + startEnd[1]);
836 assertEquals(1, startEnd[0]);
837 assertEquals(23, startEnd[1]);