X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=f017662081eda164e5a0605f6c28743c97d82ec5;hb=HEAD;hp=128bc5c8e994369b950840d62d35f0cb093546f0;hpb=9b85e1552fa57f02cf6cd312cfbd7efdfd079ea3;p=jalview.git diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 128bc5c..f017662 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -20,6 +20,7 @@ */ package jalview.analysis; +import static org.testng.Assert.assertNotEquals; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNotNull; @@ -27,21 +28,35 @@ import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; -import jalview.analysis.AlignmentUtils.DnaVariant; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.SortedMap; +import java.util.TreeMap; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.ContactListI; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLociI; import jalview.datamodel.Mapping; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SeqDistanceContactMatrix; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.datamodel.features.SequenceFeatures; import jalview.gui.JvOptionPane; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; @@ -49,20 +64,10 @@ import jalview.io.FileFormat; import jalview.io.FileFormatI; import jalview.io.FormatAdapter; import jalview.io.gff.SequenceOntologyI; +import jalview.util.Comparison; import jalview.util.MapList; import jalview.util.MappingUtils; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -import java.util.TreeMap; - -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - public class AlignmentUtilsTests { private static Sequence ts = new Sequence("short", @@ -84,15 +89,14 @@ public class AlignmentUtilsTests SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7); al.addSequence(s1); } - System.out.println(new AppletFormatAdapter().formatSequences( - FileFormat.Clustal, - al, true)); + System.out.println(new AppletFormatAdapter() + .formatSequences(FileFormat.Clustal, al, true)); for (int flnk = -1; flnk < 25; flnk++) { AlignmentI exp = AlignmentUtils.expandContext(al, flnk); System.out.println("\nFlank size: " + flnk); - System.out.println(new AppletFormatAdapter().formatSequences( - FileFormat.Clustal, exp, true)); + System.out.println(new AppletFormatAdapter() + .formatSequences(FileFormat.Clustal, exp, true)); if (flnk == -1) { /* @@ -102,11 +106,10 @@ public class AlignmentUtilsTests { String ung = sq.getSequenceAsString().replaceAll("-+", ""); final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n" - + ung - + "\n" + + ung + "\n" + sq.getDatasetSequence().getSequenceAsString(); - assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence() - .getSequenceAsString())); + assertTrue(errorMsg, ung.equalsIgnoreCase( + sq.getDatasetSequence().getSequenceAsString())); } } else if (flnk == 24) @@ -176,8 +179,8 @@ public class AlignmentUtilsTests * Expand the subsequence to the full sequence abcDEFghi */ AlignmentI expanded = AlignmentUtils.expandContext(al, -1); - assertEquals("abcDEFghi", expanded.getSequenceAt(0) - .getSequenceAsString()); + assertEquals("abcDEFghi", + expanded.getSequenceAt(0).getSequenceAsString()); /* * Confirm the alignment and sequence have the same SS annotation, @@ -248,8 +251,8 @@ public class AlignmentUtilsTests protected AlignmentI loadAlignment(final String data, FileFormatI format) throws IOException { - AlignmentI a = new FormatAdapter().readFile(data, - DataSourceType.PASTE, format); + AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE, + format); a.setDataset(null); return a; } @@ -298,11 +301,13 @@ public class AlignmentUtilsTests MapList mapList = protMappings[0].getMap(); assertEquals(3, mapList.getFromRatio()); assertEquals(1, mapList.getToRatio()); - assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges() - .get(0))); + assertTrue( + Arrays.equals(new int[] + { 1, 9 }, mapList.getFromRanges().get(0))); assertEquals(1, mapList.getFromRanges().size()); - assertTrue(Arrays.equals(new int[] { 1, 3 }, - mapList.getToRanges().get(0))); + assertTrue( + Arrays.equals(new int[] + { 1, 3 }, mapList.getToRanges().get(0))); assertEquals(1, mapList.getToRanges().size()); // V12346 mapped to A33333 @@ -375,7 +380,8 @@ public class AlignmentUtilsTests * Exons at codon 2 (AAA) and 4 (TTT) */ MapList map = new MapList(new int[] { 4, 6, 10, 12 }, - new int[] { 1, 2 }, 3, 1); + new int[] + { 1, 2 }, 3, 1); /* * Simple case: no gaps in dna @@ -386,14 +392,14 @@ public class AlignmentUtilsTests /* * Add gaps to dna - but ignore when realigning. */ - checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-", - false, false, map, "GGG---AAACCCTTTGGG"); + checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-", false, + false, map, "GGG---AAACCCTTTGGG"); /* * Add gaps to dna - include within exons only when realigning. */ - checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", - true, false, map, "GGG---A--A---ACCCT-TTGGG"); + checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true, + false, map, "GGG---A--A---ACCCT-TTGGG"); /* * Include gaps outside exons only when realigning. @@ -404,14 +410,14 @@ public class AlignmentUtilsTests /* * Include gaps following first intron if we are 'preserving mapped gaps' */ - checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", - true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-"); + checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true, + true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-"); /* * Include all gaps in dna when realigning. */ - checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", - true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-"); + checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true, + true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-"); } /** @@ -423,8 +429,9 @@ public class AlignmentUtilsTests /* * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P */ - final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] { - 1, 1, 3, 3 }, 3, 1); + final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, + new int[] + { 1, 1, 3, 3 }, 3, 1); /* * -L- 'aligns' ccc------ @@ -455,8 +462,8 @@ public class AlignmentUtilsTests SequenceI alignFrom = new Sequence("Seq2", alignModel); alignFrom.createDatasetSequence(); AlignedCodonFrame acf = new AlignedCodonFrame(); - acf.addMap(alignMe.getDatasetSequence(), - alignFrom.getDatasetSequence(), map); + acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(), + map); AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-', preserveMappedGaps, preserveUnmappedGaps); @@ -473,7 +480,8 @@ public class AlignmentUtilsTests /* * Intron GGGAAA followed by exon CCCTTT */ - MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1); + MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, + 1); checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map, "GG-G-AA-ACCCTTT"); @@ -499,11 +507,13 @@ public class AlignmentUtilsTests SequenceI prot2 = new Sequence("Seq2", "CHYQ"); SequenceI prot3 = new Sequence("Seq3", "CHYQ"); SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged - AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2, - prot3, prot4 }); + AlignmentI protein = new Alignment( + new SequenceI[] + { prot1, prot2, prot3, prot4 }); protein.setDataset(null); - MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1); + MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, + 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map); acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map); @@ -572,28 +582,28 @@ public class AlignmentUtilsTests "F*PK*G".toCharArray())); // wrong protein - assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), - 0, "FPMG".toCharArray())); + assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0, + "FPMG".toCharArray())); // truncated dna assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0, "FPKG".toCharArray())); // truncated protein - assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), - 0, "FPK".toCharArray())); + assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0, + "FPK".toCharArray())); // overlong dna (doesn't end in stop codon) - assertFalse(AlignmentUtils.translatesAs( - "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray())); + assertFalse(AlignmentUtils.translatesAs("tttcccaaagggttt".toCharArray(), + 0, "FPKG".toCharArray())); // dna + stop codon + more assertFalse(AlignmentUtils.translatesAs( "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray())); // overlong protein - assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), - 0, "FPKGQ".toCharArray())); + assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0, + "FPKGQ".toCharArray())); } /** @@ -643,11 +653,13 @@ public class AlignmentUtilsTests MapList mapList = protMappings[0].getMap(); assertEquals(3, mapList.getFromRatio()); assertEquals(1, mapList.getToRatio()); - assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges() - .get(0))); + assertTrue( + Arrays.equals(new int[] + { 1, 9 }, mapList.getFromRanges().get(0))); assertEquals(1, mapList.getFromRanges().size()); - assertTrue(Arrays.equals(new int[] { 1, 3 }, - mapList.getToRanges().get(0))); + assertTrue( + Arrays.equals(new int[] + { 1, 3 }, mapList.getToRanges().get(0))); assertEquals(1, mapList.getToRanges().size()); // V12346 mapped from A33333 starting position 4 @@ -660,11 +672,13 @@ public class AlignmentUtilsTests mapList = protMappings[0].getMap(); assertEquals(3, mapList.getFromRatio()); assertEquals(1, mapList.getToRatio()); - assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges() - .get(0))); + assertTrue( + Arrays.equals(new int[] + { 4, 12 }, mapList.getFromRanges().get(0))); assertEquals(1, mapList.getFromRanges().size()); - assertTrue(Arrays.equals(new int[] { 1, 3 }, - mapList.getToRanges().get(0))); + assertTrue( + Arrays.equals(new int[] + { 1, 3 }, mapList.getToRanges().get(0))); assertEquals(1, mapList.getToRanges().size()); // V12347 mapped to A11111 starting position 4 @@ -677,11 +691,13 @@ public class AlignmentUtilsTests mapList = protMappings[0].getMap(); assertEquals(3, mapList.getFromRatio()); assertEquals(1, mapList.getToRatio()); - assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges() - .get(0))); + assertTrue( + Arrays.equals(new int[] + { 4, 12 }, mapList.getFromRanges().get(0))); assertEquals(1, mapList.getFromRanges().size()); - assertTrue(Arrays.equals(new int[] { 1, 3 }, - mapList.getToRanges().get(0))); + assertTrue( + Arrays.equals(new int[] + { 1, 3 }, mapList.getToRanges().get(0))); assertEquals(1, mapList.getToRanges().size()); // no mapping involving the 'extra' A44444 @@ -785,8 +801,8 @@ public class AlignmentUtilsTests List dnaseqs = new ArrayList<>(); dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ - AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs - .size()])); + AlignmentI cdna = new Alignment( + dnaseqs.toArray(new SequenceI[dnaseqs.size()])); cdna.setDataset(null); // Xref A22222 to V12345 (should get mapped) @@ -837,11 +853,14 @@ public class AlignmentUtilsTests ann2.setSequenceRef(seq2); AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3", anns); - AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns); + AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", + anns); ann4.setSequenceRef(seq1); - AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns); + AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", + anns); ann5.setSequenceRef(seq2); - AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns); + AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", + anns); AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 }); al.addAnnotation(ann1); // Structure for Seq1 al.addAnnotation(ann2); // Structure for Seq2 @@ -1013,8 +1032,8 @@ public class AlignmentUtilsTests * put a variant feature on dna2 base 8 * - should transfer to cds2 base 5 */ - dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8, - 0f, null)); + dna2.addSequenceFeature( + new SequenceFeature("variant", "hgmd", 8, 8, 0f, null)); /* * need a sourceDbRef if we are to construct dbrefs to the CDS @@ -1031,14 +1050,16 @@ public class AlignmentUtilsTests * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences) */ - MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] { - 1, 2 }, 3, 1); + MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, + new int[] + { 1, 2 }, 3, 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), mapfordna1); dna.addCodonFrame(acf); MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, - new int[] { 1, 3 }, 3, 1); + new int[] + { 1, 3 }, 3, 1); acf = new AlignedCodonFrame(); acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), mapfordna2); @@ -1052,17 +1073,18 @@ public class AlignmentUtilsTests DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1", new Mapping(mapfordna1)); dna1.addDBRef(dna1xref); - assertEquals(2, dna1.getDBRefs().length); // to self and to pep1 + assertEquals(2, dna1.getDBRefs().size()); // to self and to pep1 DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2", new Mapping(mapfordna2)); dna2.addDBRef(dna2xref); - assertEquals(2, dna2.getDBRefs().length); // to self and to pep2 + assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2 /* * execute method under test: */ - AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] { - dna1, dna2 }, dna.getDataset(), null); + AlignmentI cds = AlignmentUtils + .makeCdsAlignment(new SequenceI[] + { dna1, dna2 }, dna.getDataset(), null); /* * verify cds sequences @@ -1084,16 +1106,16 @@ public class AlignmentUtilsTests * verify CDS has a dbref with mapping to peptide */ assertNotNull(cds1Dss.getDBRefs()); - assertEquals(2, cds1Dss.getDBRefs().length); - dbref = cds1Dss.getDBRefs()[0]; + assertEquals(2, cds1Dss.getDBRefs().size()); + dbref = cds1Dss.getDBRefs().get(0); assertEquals(dna1xref.getSource(), dbref.getSource()); // version is via ensembl's primary ref assertEquals(dna1xref.getVersion(), dbref.getVersion()); assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId()); assertNotNull(dbref.getMap()); assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo()); - MapList cdsMapping = new MapList(new int[] { 1, 6 }, - new int[] { 1, 2 }, 3, 1); + MapList cdsMapping = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, + 3, 1); assertEquals(cdsMapping, dbref.getMap().getMap()); /* @@ -1101,8 +1123,8 @@ public class AlignmentUtilsTests */ assertNotNull(pep1.getDBRefs()); // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ? - assertEquals(2, pep1.getDBRefs().length); - dbref = pep1.getDBRefs()[1]; + assertEquals(2, pep1.getDBRefs().size()); + dbref = pep1.getDBRefs().get(1); assertEquals("ENSEMBL", dbref.getSource()); assertEquals("0", dbref.getVersion()); assertEquals("CDS|dna1", dbref.getAccessionId()); @@ -1113,33 +1135,37 @@ public class AlignmentUtilsTests /* * verify cDNA has added a dbref with mapping to CDS */ - assertEquals(3, dna1.getDBRefs().length); - DBRefEntry dbRefEntry = dna1.getDBRefs()[2]; + assertEquals(3, dna1.getDBRefs().size()); + DBRefEntry dbRefEntry = dna1.getDBRefs().get(2); assertSame(cds1Dss, dbRefEntry.getMap().getTo()); MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 }, - new int[] { 1, 6 }, 1, 1); + new int[] + { 1, 6 }, 1, 1); assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap()); - assertEquals(3, dna2.getDBRefs().length); - dbRefEntry = dna2.getDBRefs()[2]; + assertEquals(3, dna2.getDBRefs().size()); + dbRefEntry = dna2.getDBRefs().get(2); assertSame(cds2Dss, dbRefEntry.getMap().getTo()); dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, - new int[] { 1, 9 }, 1, 1); + new int[] + { 1, 9 }, 1, 1); assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap()); /* * verify CDS has added a dbref with mapping to cDNA */ - assertEquals(2, cds1Dss.getDBRefs().length); - dbRefEntry = cds1Dss.getDBRefs()[1]; + assertEquals(2, cds1Dss.getDBRefs().size()); + dbRefEntry = cds1Dss.getDBRefs().get(1); assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo()); - MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] { - 4, 6, 10, 12 }, 1, 1); + MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, + new int[] + { 4, 6, 10, 12 }, 1, 1); assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap()); - assertEquals(2, cds2Dss.getDBRefs().length); - dbRefEntry = cds2Dss.getDBRefs()[1]; + assertEquals(2, cds2Dss.getDBRefs().size()); + dbRefEntry = cds2Dss.getDBRefs().get(1); assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo()); - cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7, - 9, 13, 15 }, 1, 1); + cdsToDnaMapping = new MapList(new int[] { 1, 9 }, + new int[] + { 1, 3, 7, 9, 13, 15 }, 1, 1); assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap()); /* @@ -1241,12 +1267,12 @@ public class AlignmentUtilsTests pep1.createDatasetSequence(); pep2.createDatasetSequence(); pep3.createDatasetSequence(); - pep1.getDatasetSequence().addDBRef( - new DBRefEntry("EMBLCDS", "2", "A12345")); - pep2.getDatasetSequence().addDBRef( - new DBRefEntry("EMBLCDS", "3", "A12346")); - pep3.getDatasetSequence().addDBRef( - new DBRefEntry("EMBLCDS", "4", "A12347")); + pep1.getDatasetSequence() + .addDBRef(new DBRefEntry("EMBLCDS", "2", "A12345")); + pep2.getDatasetSequence() + .addDBRef(new DBRefEntry("EMBLCDS", "3", "A12346")); + pep3.getDatasetSequence() + .addDBRef(new DBRefEntry("EMBLCDS", "4", "A12347")); /* * Create the CDS alignment @@ -1259,7 +1285,8 @@ public class AlignmentUtilsTests */ // map ...GGG...TTT to GF MapList map = new MapList(new int[] { 4, 6, 10, 12 }, - new int[] { 1, 2 }, 3, 1); + new int[] + { 1, 2 }, 3, 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map); dna.addCodonFrame(acf); @@ -1279,8 +1306,9 @@ public class AlignmentUtilsTests /* * execute method under test */ - AlignmentI cdsal = AlignmentUtils.makeCdsAlignment( - new SequenceI[] { dna1 }, dna.getDataset(), null); + AlignmentI cdsal = AlignmentUtils + .makeCdsAlignment(new SequenceI[] + { dna1 }, dna.getDataset(), null); /* * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively @@ -1352,8 +1380,8 @@ public class AlignmentUtilsTests .findMappingsForSequence(pep1, dnaMappings); assertEquals(1, mappings.size()); assertEquals(1, mappings.get(0).getMappings().size()); - assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings() - .get(0).getMapping().getTo()); + assertSame(pep1.getDatasetSequence(), + mappings.get(0).getMappings().get(0).getMapping().getTo()); /* * dna1 to cds1 @@ -1363,8 +1391,8 @@ public class AlignmentUtilsTests Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0) .getMapping(); assertSame(cds.get(0).getDatasetSequence(), mapping.getTo()); - assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping - .getMap().getToPosition(1)); + assertEquals("G(1) in CDS should map to G(4) in DNA", 4, + mapping.getMap().getToPosition(1)); /* * dna1 to pep2 @@ -1372,8 +1400,8 @@ public class AlignmentUtilsTests mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings); assertEquals(1, mappings.size()); assertEquals(1, mappings.get(0).getMappings().size()); - assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings() - .get(0).getMapping().getTo()); + assertSame(pep2.getDatasetSequence(), + mappings.get(0).getMappings().get(0).getMapping().getTo()); /* * dna1 to cds2 @@ -1382,8 +1410,8 @@ public class AlignmentUtilsTests .findMappingsForSequence(cds.get(1), dnaMappings); mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping(); assertSame(cds.get(1).getDatasetSequence(), mapping.getTo()); - assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping - .getMap().getToPosition(4)); + assertEquals("c(4) in CDS should map to c(7) in DNA", 7, + mapping.getMap().getToPosition(4)); /* * dna1 to pep3 @@ -1391,8 +1419,8 @@ public class AlignmentUtilsTests mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings); assertEquals(1, mappings.size()); assertEquals(1, mappings.get(0).getMappings().size()); - assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings() - .get(0).getMapping().getTo()); + assertSame(pep3.getDatasetSequence(), + mappings.get(0).getMappings().get(0).getMapping().getTo()); /* * dna1 to cds3 @@ -1401,8 +1429,8 @@ public class AlignmentUtilsTests .findMappingsForSequence(cds.get(2), dnaMappings); mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping(); assertSame(cds.get(2).getDatasetSequence(), mapping.getTo()); - assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping - .getMap().getToPosition(4)); + assertEquals("T(4) in CDS should map to T(10) in DNA", 10, + mapping.getMap().getToPosition(4)); } @Test(groups = { "Functional" }) @@ -1459,9 +1487,10 @@ public class AlignmentUtilsTests AlignedCodonFrame acf = new AlignedCodonFrame(); // this is like a domain or motif match of part of a peptide sequence - MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1); - acf.addMap(alignFrom.getDatasetSequence(), - alignMe.getDatasetSequence(), map); + MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, + 1); + acf.addMap(alignFrom.getDatasetSequence(), alignMe.getDatasetSequence(), + map); AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true, true); @@ -1492,35 +1521,36 @@ public class AlignmentUtilsTests SequenceI cds = new Sequence("cds/10-15", "TAGGCC"); // no overlap - dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type1", "desc1", 1, 2, 1f, null)); // partial overlap - to [1, 1] - dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type2", "desc2", 3, 4, 2f, null)); // exact overlap - to [1, 3] - dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type3", "desc3", 4, 6, 3f, null)); // spanning overlap - to [2, 5] - dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type4", "desc4", 5, 11, 4f, null)); // exactly overlaps whole mapped range [1, 6] - dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type5", "desc5", 4, 12, 5f, null)); // no overlap (internal) - dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type6", "desc6", 7, 9, 6f, null)); // no overlap (3' end) - dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15, - 7f, null)); + dna.addSequenceFeature( + new SequenceFeature("type7", "desc7", 13, 15, 7f, null)); // overlap (3' end) - to [6, 6] - dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12, - 8f, null)); + dna.addSequenceFeature( + new SequenceFeature("type8", "desc8", 12, 12, 8f, null)); // extended overlap - to [6, +] - dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13, - 9f, null)); + dna.addSequenceFeature( + new SequenceFeature("type9", "desc9", 12, 13, 9f, null)); MapList map = new MapList(new int[] { 4, 6, 10, 12 }, - new int[] { 1, 6 }, 1, 1); + new int[] + { 1, 6 }, 1, 1); /* * transferFeatures() will build 'partial overlap' for regions @@ -1575,17 +1605,18 @@ public class AlignmentUtilsTests SequenceI cds = new Sequence("cds/10-15", "TAGGCC"); MapList map = new MapList(new int[] { 4, 6, 10, 12 }, - new int[] { 1, 6 }, 1, 1); + new int[] + { 1, 6 }, 1, 1); // [5, 11] maps to [2, 5] - dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type4", "desc4", 5, 11, 4f, null)); // [4, 12] maps to [1, 6] - dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type5", "desc5", 4, 12, 5f, null)); // [12, 12] maps to [6, 6] - dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12, - 8f, null)); + dna.addSequenceFeature( + new SequenceFeature("type8", "desc8", 12, 12, 8f, null)); // desc4 and desc8 are the 'omit these' varargs AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8"); @@ -1608,17 +1639,18 @@ public class AlignmentUtilsTests SequenceI cds = new Sequence("cds/10-15", "TAGGCC"); MapList map = new MapList(new int[] { 4, 6, 10, 12 }, - new int[] { 1, 6 }, 1, 1); + new int[] + { 1, 6 }, 1, 1); // [5, 11] maps to [2, 5] - dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type4", "desc4", 5, 11, 4f, null)); // [4, 12] maps to [1, 6] - dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f, - null)); + dna.addSequenceFeature( + new SequenceFeature("type5", "desc5", 4, 12, 5f, null)); // [12, 12] maps to [6, 6] - dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12, - 8f, null)); + dna.addSequenceFeature( + new SequenceFeature("type8", "desc8", 12, 12, 8f, null)); // "type5" is the 'select this type' argument AlignmentUtils.transferFeatures(dna, cds, map, "type5"); @@ -1655,18 +1687,21 @@ public class AlignmentUtilsTests dna.setDataset(null); MapList map = new MapList(new int[] { 4, 12, 16, 18 }, - new int[] { 1, 4 }, 3, 1); + new int[] + { 1, 4 }, 3, 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map); dna.addCodonFrame(acf); map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 }, - new int[] { 1, 3 }, 3, 1); + new int[] + { 1, 3 }, 3, 1); acf = new AlignedCodonFrame(); acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map); dna.addCodonFrame(acf); - AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] { - dna1, dna2, dna3 }, dna.getDataset(), null); + AlignmentI cds = AlignmentUtils + .makeCdsAlignment(new SequenceI[] + { dna1, dna2, dna3 }, dna.getDataset(), null); List cdsSeqs = cds.getSequences(); assertEquals(2, cdsSeqs.size()); assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString()); @@ -1706,7 +1741,8 @@ public class AlignmentUtilsTests pep1CdsMappings); assertEquals(1, sr.getResults().size()); SearchResultMatchI m = sr.getResults().get(0); - assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence()); + assertEquals(cds.getSequenceAt(0).getDatasetSequence(), + m.getSequence()); assertEquals(1, m.getStart()); assertEquals(3, m.getEnd()); sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings); @@ -1735,7 +1771,8 @@ public class AlignmentUtilsTests sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings); assertEquals(1, sr.getResults().size()); m = sr.getResults().get(0); - assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence()); + assertEquals(cds.getSequenceAt(1).getDatasetSequence(), + m.getSequence()); assertEquals(1, m.getStart()); assertEquals(3, m.getEnd()); sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings); @@ -1767,12 +1804,14 @@ public class AlignmentUtilsTests SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start SequenceI prot2 = new Sequence("Seq2", "NG"); SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start - AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2, - prot3 }); + AlignmentI protein = new Alignment( + new SequenceI[] + { prot1, prot2, prot3 }); protein.setDataset(null); // map dna1 [3, 11] to prot1 [2, 4] KFG - MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1); + MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, + 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map); @@ -1973,7 +2012,8 @@ public class AlignmentUtilsTests dna.addCodonFrame(acf); AlignmentUtils.alignAs(cds, dna); assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString()); - assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString()); + assertEquals("CCC------AAA", + cds.getSequenceAt(1).getSequenceAsString()); } @Test(groups = { "Functional" }) @@ -1983,8 +2023,9 @@ public class AlignmentUtilsTests SequenceI seq1 = new Sequence("cds", "AAATTT"); from.createDatasetSequence(); seq1.createDatasetSequence(); - Mapping mapping = new Mapping(seq1, new MapList( - new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1)); + Mapping mapping = new Mapping(seq1, + new MapList(new int[] + { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1)); Map> map = new TreeMap<>(); AlignmentUtils.addMappedPositions(seq1, from, mapping, map); @@ -2015,8 +2056,9 @@ public class AlignmentUtilsTests SequenceI seq1 = new Sequence("cds", "AAATTT"); from.createDatasetSequence(); seq1.createDatasetSequence(); - Mapping mapping = new Mapping(seq1, new MapList( - new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1)); + Mapping mapping = new Mapping(seq1, + new MapList(new int[] + { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1)); Map> map = new TreeMap<>(); AlignmentUtils.addMappedPositions(seq1, from, mapping, map); @@ -2060,7 +2102,8 @@ public class AlignmentUtilsTests AlignedCodonFrame acf = new AlignedCodonFrame(); MapList map = new MapList(new int[] { 4, 6, 10, 12 }, - new int[] { 1, 2 }, 3, 1); + new int[] + { 1, 2 }, 3, 1); acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map); acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map); dna.addCodonFrame(acf); @@ -2075,8 +2118,10 @@ public class AlignmentUtilsTests /* * execute method under test to find CDS for EMBL peptides only */ - AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] { - dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray()); + AlignmentI cds = AlignmentUtils + .makeCdsAlignment(new SequenceI[] + { dna1, dna2 }, dna.getDataset(), + emblPeptides.getSequencesArray()); assertEquals(2, cds.getSequences().size()); assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString()); @@ -2194,11 +2239,9 @@ public class AlignmentUtilsTests */ assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2)); String aligned1 = "-cc-GG-GTTT-aaa"; - assertEquals(aligned1, - al1.getSequenceAt(0).getSequenceAsString()); + assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString()); String aligned2 = "C--C-Cgg-gtttAAA"; - assertEquals(aligned2, - al1.getSequenceAt(1).getSequenceAsString()); + assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString()); /* * add another sequence to 'aligned' - should still succeed, since @@ -2243,8 +2286,9 @@ public class AlignmentUtilsTests SequenceI uas1 = dna1.deriveSequence(); SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7); SequenceI uas3 = dna2.deriveSequence(); - AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2, - uas3 }); + AlignmentI tobealigned = new Alignment( + new SequenceI[] + { uas1, uas2, uas3 }); ((Alignment) tobealigned).createDatasetAlignment(); /* @@ -2417,7 +2461,7 @@ public class AlignmentUtilsTests * the given protein. That is, given a transcript-to-peptide mapping, find the * cds-to-peptide mapping that relates to both, and return the CDS sequence. */ - @Test + @Test(groups = "Functional") public void testFindCdsForProtein() { List mappings = new ArrayList<>(); @@ -2435,11 +2479,11 @@ public class AlignmentUtilsTests SequenceI pep1 = new Sequence("pep1", "MLS"); pep1.createDatasetSequence(); List seqMappings = new ArrayList<>(); - MapList mapList = new MapList( + MapList mapList = new MapList(new int[] { 5, 6, 9, 15 }, new int[] - { 5, 6, 9, 15 }, new int[] { 1, 3 }, 3, 1); + { 1, 3 }, 3, 1); Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList); - + // add dna to peptide mapping seqMappings.add(acf1); acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), @@ -2460,8 +2504,9 @@ public class AlignmentUtilsTests // need to tidy up use of lists of mappings in AlignedCodonFrame AlignedCodonFrame acf2 = new AlignedCodonFrame(); mappings.add(acf2); - MapList cdsToPeptideMapping = new MapList(new int[] - { 1, 9 }, new int[] { 1, 3 }, 3, 1); + MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 }, + new int[] + { 1, 3 }, 3, 1); acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(), cdsToPeptideMapping); assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings, @@ -2486,34 +2531,33 @@ public class AlignmentUtilsTests * cds-to-peptide mapping that relates to both, and return the CDS sequence. * This test is for the case where transcript and CDS are the same length. */ - @Test + @Test(groups = "Functional") public void testFindCdsForProtein_noUTR() { List mappings = new ArrayList<>(); AlignedCodonFrame acf1 = new AlignedCodonFrame(); mappings.add(acf1); - + SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA"); dna1.createDatasetSequence(); - + // NB we currently exclude STOP codon from CDS sequences // the test would need to change if this changes in future SequenceI cds1 = new Sequence("cds1", "ATGCTATCT"); cds1.createDatasetSequence(); - + SequenceI pep1 = new Sequence("pep1", "MLS"); pep1.createDatasetSequence(); List seqMappings = new ArrayList<>(); - MapList mapList = new MapList( - new int[] - { 1, 9 }, new int[] { 1, 3 }, 3, 1); + MapList mapList = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, + 1); Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList); - + // add dna to peptide mapping seqMappings.add(acf1); acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), mapList); - + /* * first case - transcript lacks CDS features - it appears to be * the CDS sequence and is returned @@ -2521,7 +2565,7 @@ public class AlignmentUtilsTests SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings, dnaToPeptide); assertSame(seq, dna1.getDatasetSequence()); - + /* * second case - transcript has CDS feature - this means it is * not returned as a match for CDS (CDS sequences don't have CDS features) @@ -2540,13 +2584,14 @@ public class AlignmentUtilsTests // need to tidy up use of lists of mappings in AlignedCodonFrame AlignedCodonFrame acf2 = new AlignedCodonFrame(); mappings.add(acf2); - MapList cdsToPeptideMapping = new MapList(new int[] - { 1, 9 }, new int[] { 1, 3 }, 3, 1); + MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 }, + new int[] + { 1, 3 }, 3, 1); acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(), cdsToPeptideMapping); assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings, dnaToPeptide)); - + /* * fourth case - add dna-to-CDS mapping - CDS is now found! */ @@ -2559,4 +2604,151 @@ public class AlignmentUtilsTests dnaToPeptide); assertSame(seq, cds1.getDatasetSequence()); } + + @Test(groups = "Functional") + public void testAddReferenceAnnotations() + { + SequenceI longseq = new Sequence("longA", "ASDASDASDASDAASDASDASDASDA"); + Annotation[] aa = new Annotation[longseq.getLength()]; + + for (int p = 0; p < aa.length; p++) + { + aa[p] = new Annotation("P", "pos " + (p + 1), (char) 0, + (float) p + 1); + } + AlignmentAnnotation refAnnot = new AlignmentAnnotation("LongSeqAnnot", + "Annotations", aa); + refAnnot.setCalcId("Test"); + longseq.addAlignmentAnnotation(refAnnot); + verifyExpectedSequenceAnnotation(refAnnot); + + Alignment ourAl = new Alignment( + new SequenceI[] + { longseq.getSubSequence(5, 10), + longseq.getSubSequence(7, 12) }); + ourAl.createDatasetAlignment(); + + // transfer annotation + SortedMap tipEntries = new TreeMap<>(); + Map> candidates = new LinkedHashMap<>(); + + AlignmentUtils.findAddableReferenceAnnotations(ourAl.getSequences(), + tipEntries, candidates, ourAl); + AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null); + + assertNotNull(ourAl.getAlignmentAnnotation()); + assertEquals(ourAl.getAlignmentAnnotation().length, 2); + + for (AlignmentAnnotation alan : ourAl.getAlignmentAnnotation()) + { + verifyExpectedSequenceAnnotation(alan); + } + // Everything above works for 2.11.3 and 2.11.2.x. + // now simulate copy/paste to new alignment + SequenceI[] newSeqAl = new SequenceI[2]; + // copy sequences but no annotation + newSeqAl[0] = new Sequence(ourAl.getSequenceAt(0), + ourAl.getSequenceAt(0).getAnnotation()); + newSeqAl[1] = new Sequence(ourAl.getSequenceAt(1), + ourAl.getSequenceAt(1).getAnnotation()); + + Alignment newAl = new Alignment(newSeqAl); + // delete annotation + for (SequenceI sq : newAl.getSequences()) + { + sq.setAlignmentAnnotation(new AlignmentAnnotation[0]); + } + // JAL-4182 scenario test + SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl)); + sg.setStartRes(0); + sg.setEndRes(newAl.getWidth()); + AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0], + newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg); + AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1], + newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg); + for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation()) + { + verifyExpectedSequenceAnnotation(alan); + } + } + + /** + * helper - tests annotation is mapped to position it was originally created + * for + * + * @param alan + */ + private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan) + { + for (int c = 0; c < alan.annotations.length; c++) + { + Annotation a = alan.annotations[c]; + if (a != null) + { + assertEquals("Misaligned annotation at " + c, + (float) alan.sequenceRef.findPosition(c), a.value); + } + else + { + assertTrue("Unexpected Null at position " + c, + c >= alan.sequenceRef.getLength() + || Comparison.isGap(alan.sequenceRef.getCharAt(c))); + } + } + } + + @Test(groups = "Functional") + public void testAddReferenceContactMap() + { + SequenceI sq = new Sequence("a", "SSSQ"); + ContactMatrixI cm = new SeqDistanceContactMatrix(4); + AlignmentAnnotation cm_aan = sq.addContactList(cm); + cm_aan.description = cm_aan.description + " cm1"; + SequenceI dssq = sq.createDatasetSequence(); + + // remove annotation on our non-dataset sequence + sq.removeAlignmentAnnotation(sq.getAnnotation()[0]); + // test transfer + Alignment al = new Alignment(new SequenceI[] { sq }); + SortedMap tipEntries = new TreeMap<>(); + Map> candidates = new LinkedHashMap<>(); + + AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(), + tipEntries, candidates, al); + AlignmentUtils.addReferenceAnnotations(candidates, al, null); + assertTrue("No contact map annotation transferred", + al.getAlignmentAnnotation() != null + && al.getAlignmentAnnotation().length == 1); + AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label) + .iterator().next(); + ContactMatrixI t_cm = al.getContactMatrixFor(alan); + assertNotNull("No contact map for the transferred annotation row.", + t_cm); + assertTrue(t_cm instanceof SeqDistanceContactMatrix); + assertTrue(((SeqDistanceContactMatrix) t_cm).hasReferenceSeq()); + + ContactListI cl = al.getContactListFor(alan, 1); + assertNotNull( + "No contact matrix recovered after reference annotation transfer", + cl); + // semantics of sequence associated contact list is slightly tricky - column + // 3 in alignment should have data + cl = al.getContactListFor(alan, 3); + assertNotNull( + "Contact matrix should have data for last position in sequence", + cl); + + ContactMatrixI cm2 = new SeqDistanceContactMatrix(4); + dssq.addContactList(cm2); + tipEntries = new TreeMap<>(); + candidates = new LinkedHashMap<>(); + + AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(), + tipEntries, candidates, al); + AlignmentUtils.addReferenceAnnotations(candidates, al, null); + assertTrue("Expected two contact map annotation transferred", + al.getAlignmentAnnotation() != null + && al.getAlignmentAnnotation().length == 2); + + } }