X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=c526fa1390032571bc6c0f948d204636a97eb088;hb=HEAD;hp=9394385430c99ab0878c0d0638a2fa85d54477ff;hpb=f931c557266d95b3f4ab5b64bd108123c90e85ab;p=jalview.git diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 9394385..f017662 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -20,45 +20,66 @@ */ 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; 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.SearchResults; -import jalview.datamodel.SearchResults.Match; +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.gui.JvOptionPane; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +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.Test; - public class AlignmentUtilsTests { - public static Sequence ts = new Sequence("short", + private static Sequence ts = new Sequence("short", "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm"); + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = { "Functional" }) public void testExpandContext() { @@ -68,14 +89,14 @@ public class AlignmentUtilsTests SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7); al.addSequence(s1); } - System.out.println(new AppletFormatAdapter().formatSequences("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( - "Clustal", exp, true)); + System.out.println(new AppletFormatAdapter() + .formatSequences(FileFormat.Clustal, exp, true)); if (flnk == -1) { /* @@ -85,11 +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) @@ -159,8 +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, @@ -208,7 +228,7 @@ public class AlignmentUtilsTests { final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n" + ">Seq1Name\nABCD\n"; - AlignmentI al = loadAlignment(data, "FASTA"); + AlignmentI al = loadAlignment(data, FileFormat.Fasta); Map> map = AlignmentUtils .getSequencesByName(al); assertEquals(2, map.keySet().size()); @@ -228,11 +248,11 @@ public class AlignmentUtilsTests * @return * @throws IOException */ - protected AlignmentI loadAlignment(final String data, String format) + protected AlignmentI loadAlignment(final String data, FileFormatI format) throws IOException { - AlignmentI a = new FormatAdapter().readFile(data, - AppletFormatAdapter.PASTE, format); + AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE, + format); a.setDataset(null); return a; } @@ -247,14 +267,14 @@ public class AlignmentUtilsTests @Test(groups = { "Functional" }) public void testMapProteinAlignmentToCdna_noXrefs() throws IOException { - List protseqs = new ArrayList(); + List protseqs = new ArrayList<>(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12346", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12347", "SAR")); AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3])); protein.setDataset(null); - List dnaseqs = new ArrayList(); + List dnaseqs = new ArrayList<>(); dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ @@ -281,11 +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 @@ -358,7 +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 @@ -369,14 +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. @@ -387,14 +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-"); } /** @@ -406,8 +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------ @@ -438,7 +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); @@ -455,7 +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"); @@ -481,16 +507,18 @@ 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); acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map); - ArrayList acfs = new ArrayList(); + ArrayList acfs = new ArrayList<>(); acfs.add(acf); protein.setCodonFrames(acfs); @@ -554,28 +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())); } /** @@ -588,14 +616,14 @@ public class AlignmentUtilsTests public void testMapProteinAlignmentToCdna_withStartAndStopCodons() throws IOException { - List protseqs = new ArrayList(); + List protseqs = new ArrayList<>(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12346", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12347", "SAR")); AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3])); protein.setDataset(null); - List dnaseqs = new ArrayList(); + List dnaseqs = new ArrayList<>(); // start + SAR: dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC")); // = EIQ + stop @@ -625,11 +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 @@ -642,11 +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 @@ -659,11 +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 @@ -680,14 +714,14 @@ public class AlignmentUtilsTests @Test(groups = { "Functional" }) public void testMapProteinAlignmentToCdna_withXrefs() throws IOException { - List protseqs = new ArrayList(); + List protseqs = new ArrayList<>(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12346", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12347", "SAR")); AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3])); protein.setDataset(null); - List dnaseqs = new ArrayList(); + List dnaseqs = new ArrayList<>(); dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ @@ -757,18 +791,18 @@ public class AlignmentUtilsTests public void testMapProteinAlignmentToCdna_prioritiseXrefs() throws IOException { - List protseqs = new ArrayList(); + List protseqs = new ArrayList<>(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); protseqs.add(new Sequence("UNIPROT|V12346", "EIQ")); AlignmentI protein = new Alignment( protseqs.toArray(new SequenceI[protseqs.size()])); protein.setDataset(null); - List dnaseqs = new ArrayList(); + 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) @@ -819,11 +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 @@ -831,8 +868,8 @@ public class AlignmentUtilsTests al.addAnnotation(ann4); // Temp for seq1 al.addAnnotation(ann5); // Temp for seq2 al.addAnnotation(ann6); // Temp for no sequence - List types = new ArrayList(); - List scope = new ArrayList(); + List types = new ArrayList<>(); + List scope = new ArrayList<>(); /* * Set all sequence related Structure to hidden (ann1, ann2) @@ -973,10 +1010,17 @@ public class AlignmentUtilsTests @Test(groups = { "Functional" }) public void testMakeCdsAlignment() { + /* + * scenario: + * dna1 --> [4, 6] [10,12] --> pep1 + * dna2 --> [1, 3] [7, 9] [13,15] --> pep2 + */ SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC"); SequenceI pep1 = new Sequence("pep1", "GF"); SequenceI pep2 = new Sequence("pep2", "GFP"); + pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1")); + pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2")); dna1.createDatasetSequence(); dna2.createDatasetSequence(); pep1.createDatasetSequence(); @@ -984,23 +1028,67 @@ public class AlignmentUtilsTests AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 }); dna.setDataset(null); - MapList map = new MapList(new int[] { 4, 6, 10, 12 }, - new int[] { 1, 2 }, 3, 1); + /* + * put a variant feature on dna2 base 8 + * - should transfer to cds2 base 5 + */ + dna2.addSequenceFeature( + new SequenceFeature("variant", "hgmd", 8, 8, 0f, null)); + + /* + * need a sourceDbRef if we are to construct dbrefs to the CDS + * sequence from the dna contig sequences + */ + DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1"); + dna1.getDatasetSequence().addDBRef(dbref); + org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0)); + dbref = new DBRefEntry("ENSEMBL", "0", "dna2"); + dna2.getDatasetSequence().addDBRef(dbref); + org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0)); + + /* + * 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); AlignedCodonFrame acf = new AlignedCodonFrame(); - acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map); + acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), + mapfordna1); dna.addCodonFrame(acf); - map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 }, - 3, 1); + MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, + new int[] + { 1, 3 }, 3, 1); acf = new AlignedCodonFrame(); - acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map); + acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), + mapfordna2); dna.addCodonFrame(acf); /* + * In this case, mappings originally came from matching Uniprot accessions + * - so need an xref on dna involving those regions. + * These are normally constructed from CDS annotation + */ + DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1", + new Mapping(mapfordna1)); + dna1.addDBRef(dna1xref); + 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().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 + */ assertEquals(2, cds.getSequences().size()); assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString()); assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString()); @@ -1009,18 +1097,76 @@ public class AlignmentUtilsTests * verify shared, extended alignment dataset */ assertSame(dna.getDataset(), cds.getDataset()); - assertTrue(dna.getDataset().getSequences() - .contains(cds.getSequenceAt(0).getDatasetSequence())); - assertTrue(dna.getDataset().getSequences() - .contains(cds.getSequenceAt(1).getDatasetSequence())); - - /* - * verify cds has dbref with mapping to protein and vice versa - */ - DBRefEntry[] cdsDbrefs = cds.getSequenceAt(0).getDBRefs(); - // assertNotNull(cdsDbrefs); - // assertEquals(1, cdsDbrefs.length); - // assertNotNull(cdsDbrefs[0].getMap()); + SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence(); + SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence(); + assertTrue(dna.getDataset().getSequences().contains(cds1Dss)); + assertTrue(dna.getDataset().getSequences().contains(cds2Dss)); + + /* + * verify CDS has a dbref with mapping to peptide + */ + assertNotNull(cds1Dss.getDBRefs()); + 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); + assertEquals(cdsMapping, dbref.getMap().getMap()); + + /* + * verify peptide has added a dbref with reverse mapping to CDS + */ + assertNotNull(pep1.getDBRefs()); + // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ? + assertEquals(2, pep1.getDBRefs().size()); + dbref = pep1.getDBRefs().get(1); + assertEquals("ENSEMBL", dbref.getSource()); + assertEquals("0", dbref.getVersion()); + assertEquals("CDS|dna1", dbref.getAccessionId()); + assertNotNull(dbref.getMap()); + assertSame(cds1Dss, dbref.getMap().getTo()); + assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap()); + + /* + * verify cDNA has added a dbref with mapping to CDS + */ + 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); + assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap()); + 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); + assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap()); + + /* + * verify CDS has added a dbref with mapping to cDNA + */ + 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); + assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap()); + 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); + assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap()); /* * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide @@ -1051,16 +1197,16 @@ public class AlignmentUtilsTests assertEquals(1, mappings.size()); // map G to GGG - SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings); + SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings); assertEquals(1, sr.getResults().size()); - Match m = sr.getResults().get(0); - assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence()); + SearchResultMatchI m = sr.getResults().get(0); + assertSame(cds1Dss, m.getSequence()); assertEquals(1, m.getStart()); assertEquals(3, m.getEnd()); // map F to TTT sr = MappingUtils.buildSearchResults(pep1, 2, mappings); m = sr.getResults().get(0); - assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence()); + assertSame(cds1Dss, m.getSequence()); assertEquals(4, m.getStart()); assertEquals(6, m.getEnd()); @@ -1078,21 +1224,31 @@ public class AlignmentUtilsTests sr = MappingUtils.buildSearchResults(pep2, 1, mappings); assertEquals(1, sr.getResults().size()); m = sr.getResults().get(0); - assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence()); + assertSame(cds2Dss, m.getSequence()); assertEquals(1, m.getStart()); assertEquals(3, m.getEnd()); // map F to TTT sr = MappingUtils.buildSearchResults(pep2, 2, mappings); m = sr.getResults().get(0); - assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence()); + assertSame(cds2Dss, m.getSequence()); assertEquals(4, m.getStart()); assertEquals(6, m.getEnd()); // map P to CCC sr = MappingUtils.buildSearchResults(pep2, 3, mappings); m = sr.getResults().get(0); - assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence()); + assertSame(cds2Dss, m.getSequence()); assertEquals(7, m.getStart()); assertEquals(9, m.getEnd()); + + /* + * check cds2 acquired a variant feature in position 5 + */ + List sfs = cds2Dss.getSequenceFeatures(); + assertNotNull(sfs); + assertEquals(1, sfs.size()); + assertEquals("variant", sfs.get(0).type); + assertEquals(5, sfs.get(0).begin); + assertEquals(5, sfs.get(0).end); } /** @@ -1111,12 +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 @@ -1129,7 +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); @@ -1149,8 +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 @@ -1175,7 +1333,7 @@ public class AlignmentUtilsTests SequenceI cdsSeq = cds.get(0); assertEquals("GGGTTT", cdsSeq.getSequenceAsString()); // assertEquals("dna1|A12345", cdsSeq.getName()); - assertEquals("dna1|pep1", cdsSeq.getName()); + assertEquals("CDS|dna1", cdsSeq.getName()); // assertEquals(1, cdsSeq.getDBRefs().length); // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0]; // assertEquals("EMBLCDS", cdsRef.getSource()); @@ -1185,7 +1343,7 @@ public class AlignmentUtilsTests cdsSeq = cds.get(1); assertEquals("aaaccc", cdsSeq.getSequenceAsString()); // assertEquals("dna1|A12346", cdsSeq.getName()); - assertEquals("dna1|pep2", cdsSeq.getName()); + assertEquals("CDS|dna1", cdsSeq.getName()); // assertEquals(1, cdsSeq.getDBRefs().length); // cdsRef = cdsSeq.getDBRefs()[0]; // assertEquals("EMBLCDS", cdsRef.getSource()); @@ -1195,7 +1353,7 @@ public class AlignmentUtilsTests cdsSeq = cds.get(2); assertEquals("aaaTTT", cdsSeq.getSequenceAsString()); // assertEquals("dna1|A12347", cdsSeq.getName()); - assertEquals("dna1|pep3", cdsSeq.getName()); + assertEquals("CDS|dna1", cdsSeq.getName()); // assertEquals(1, cdsSeq.getDBRefs().length); // cdsRef = cdsSeq.getDBRefs()[0]; // assertEquals("EMBLCDS", cdsRef.getSource()); @@ -1222,8 +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 @@ -1232,10 +1390,9 @@ public class AlignmentUtilsTests .findMappingsForSequence(cds.get(0), dnaMappings); 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)); + assertSame(cds.get(0).getDatasetSequence(), mapping.getTo()); + assertEquals("G(1) in CDS should map to G(4) in DNA", 4, + mapping.getMap().getToPosition(1)); /* * dna1 to pep2 @@ -1243,8 +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 @@ -1253,8 +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 @@ -1262,8 +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 @@ -1272,8 +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" }) @@ -1301,8 +1458,7 @@ public class AlignmentUtilsTests * @throws IOException */ @Test(groups = { "Functional" }) - public void testMapCdnaToProtein_forSubsequence() - throws IOException + public void testMapCdnaToProtein_forSubsequence() throws IOException { SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12); prot.createDatasetSequence(); @@ -1323,7 +1479,7 @@ public class AlignmentUtilsTests @Test(groups = { "Functional" }) public void testAlignSequenceAs_mappedProteinProtein() { - + SequenceI alignMe = new Sequence("Match", "MGAASEV"); alignMe.createDatasetSequence(); SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR"); @@ -1331,10 +1487,11 @@ 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); assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString()); @@ -1349,7 +1506,7 @@ public class AlignmentUtilsTests { // map first 3 codons to KPF; G is a trailing unmapped residue MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1); - + checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map, "AAA---CCCTTT---"); } @@ -1364,74 +1521,75 @@ 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 * that partially overlap 5' or 3' (start or end) of target sequence */ AlignmentUtils.transferFeatures(dna, cds, map, null); - SequenceFeature[] sfs = cds.getSequenceFeatures(); - assertEquals(6, sfs.length); + List sfs = cds.getSequenceFeatures(); + assertEquals(6, sfs.size()); - SequenceFeature sf = sfs[0]; + SequenceFeature sf = sfs.get(0); assertEquals("type2", sf.getType()); assertEquals("desc2", sf.getDescription()); assertEquals(2f, sf.getScore()); assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); - sf = sfs[1]; + sf = sfs.get(1); assertEquals("type3", sf.getType()); assertEquals("desc3", sf.getDescription()); assertEquals(3f, sf.getScore()); assertEquals(1, sf.getBegin()); assertEquals(3, sf.getEnd()); - sf = sfs[2]; + sf = sfs.get(2); assertEquals("type4", sf.getType()); assertEquals(2, sf.getBegin()); assertEquals(5, sf.getEnd()); - sf = sfs[3]; + sf = sfs.get(3); assertEquals("type5", sf.getType()); assertEquals(1, sf.getBegin()); assertEquals(6, sf.getEnd()); - sf = sfs[4]; + sf = sfs.get(4); assertEquals("type8", sf.getType()); assertEquals(6, sf.getBegin()); assertEquals(6, sf.getEnd()); - sf = sfs[5]; + sf = sfs.get(5); assertEquals("type9", sf.getType()); assertEquals(6, sf.getBegin()); assertEquals(6, sf.getEnd()); @@ -1447,24 +1605,25 @@ 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"); - SequenceFeature[] sfs = cds.getSequenceFeatures(); - assertEquals(1, sfs.length); - - SequenceFeature sf = sfs[0]; + List sfs = cds.getSequenceFeatures(); + assertEquals(1, sfs.size()); + + SequenceFeature sf = sfs.get(0); assertEquals("type5", sf.getType()); assertEquals(1, sf.getBegin()); assertEquals(6, sf.getEnd()); @@ -1478,26 +1637,27 @@ public class AlignmentUtilsTests { SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt"); 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"); - SequenceFeature[] sfs = cds.getSequenceFeatures(); - assertEquals(1, sfs.length); - - SequenceFeature sf = sfs[0]; + List sfs = cds.getSequenceFeatures(); + assertEquals(1, sfs.size()); + + SequenceFeature sf = sfs.get(0); assertEquals("type5", sf.getType()); assertEquals(1, sf.getBegin()); assertEquals(6, sf.getEnd()); @@ -1525,26 +1685,28 @@ public class AlignmentUtilsTests AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 }); 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()); assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString()); - + /* * verify shared, extended alignment dataset */ @@ -1560,7 +1722,7 @@ public class AlignmentUtilsTests */ List mappings = cds.getCodonFrames(); assertEquals(6, mappings.size()); - + /* * 2 mappings involve pep1 */ @@ -1575,10 +1737,10 @@ public class AlignmentUtilsTests List pep1CdsMappings = MappingUtils .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings); assertEquals(1, pep1CdsMappings.size()); - SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, + SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, pep1CdsMappings); assertEquals(1, sr.getResults().size()); - Match m = sr.getResults().get(0); + SearchResultMatchI m = sr.getResults().get(0); assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence()); assertEquals(1, m.getStart()); @@ -1595,7 +1757,7 @@ public class AlignmentUtilsTests m = sr.getResults().get(0); assertEquals(10, m.getStart()); assertEquals(12, m.getEnd()); - + /* * Get mapping of pep2 to cds2 and verify it * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence @@ -1637,17 +1799,19 @@ public class AlignmentUtilsTests SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-"); AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 }); dna.setDataset(null); - + // prot1 has 'X' for incomplete start codon (not mapped) 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); @@ -1659,7 +1823,7 @@ public class AlignmentUtilsTests map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1); acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map); - ArrayList acfs = new ArrayList(); + ArrayList acfs = new ArrayList<>(); acfs.add(acf); protein.setCodonFrames(acfs); @@ -1684,7 +1848,7 @@ public class AlignmentUtilsTests SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt"); dnaSeq.createDatasetSequence(); SequenceI ds = dnaSeq.getDatasetSequence(); - + // CDS for dna 5-6 (incomplete codon), 7-9 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null); sf.setPhase("2"); // skip 2 bases to start of next codon @@ -1692,9 +1856,9 @@ public class AlignmentUtilsTests // CDS for dna 13-15 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null); ds.addSequenceFeature(sf); - + List ranges = AlignmentUtils.findCdsPositions(dnaSeq); - + /* * check the mapping starts with the first complete codon */ @@ -1716,7 +1880,7 @@ public class AlignmentUtilsTests SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt"); dnaSeq.createDatasetSequence(); SequenceI ds = dnaSeq.getDatasetSequence(); - + // CDS for dna 10-12 SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null); @@ -1729,7 +1893,7 @@ public class AlignmentUtilsTests // exon feature should be ignored here sf = new SequenceFeature("exon", "", 7, 9, 0f, null); ds.addSequenceFeature(sf); - + List ranges = AlignmentUtils.findCdsPositions(dnaSeq); /* * verify ranges { [4-6], [12-10] } @@ -1745,314 +1909,6 @@ public class AlignmentUtilsTests } /** - * Test the method that computes a map of codon variants for each protein - * position from "sequence_variant" features on dna - */ - @Test(groups = "Functional") - public void testBuildDnaVariantsMap() - { - SequenceI dna = new Sequence("dna", "atgAAATTTGGGCCCtag"); - MapList map = new MapList(new int[] { 1, 18 }, new int[] { 1, 5 }, 3, 1); - - /* - * first with no variants on dna - */ - LinkedHashMap[]> variantsMap = AlignmentUtils - .buildDnaVariantsMap(dna, map); - assertTrue(variantsMap.isEmpty()); - - /* - * single allele codon 1, on base 1 - */ - SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1, - 0f, null); - sf1.setValue("alleles", "T"); - sf1.setValue("ID", "sequence_variant:rs758803211"); - dna.addSequenceFeature(sf1); - - /* - * two alleles codon 2, on bases 2 and 3 (distinct variants) - */ - SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 5, 5, - 0f, null); - sf2.setValue("alleles", "T"); - sf2.setValue("ID", "sequence_variant:rs758803212"); - dna.addSequenceFeature(sf2); - SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 6, 6, - 0f, null); - sf3.setValue("alleles", "G"); - sf3.setValue("ID", "sequence_variant:rs758803213"); - dna.addSequenceFeature(sf3); - - /* - * two alleles codon 3, both on base 2 (one variant) - */ - SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 8, 8, - 0f, null); - sf4.setValue("alleles", "C, G"); - sf4.setValue("ID", "sequence_variant:rs758803214"); - dna.addSequenceFeature(sf4); - - // no alleles on codon 4 - - /* - * alleles on codon 5 on all 3 bases (distinct variants) - */ - SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 13, - 13, 0f, null); - sf5.setValue("alleles", "C, G"); // (C duplicates given base value) - sf5.setValue("ID", "sequence_variant:rs758803215"); - dna.addSequenceFeature(sf5); - SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 14, - 14, 0f, null); - sf6.setValue("alleles", "g, a"); // should force to upper-case - sf6.setValue("ID", "sequence_variant:rs758803216"); - dna.addSequenceFeature(sf6); - SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 15, - 15, 0f, null); - sf7.setValue("alleles", "A, T"); - sf7.setValue("ID", "sequence_variant:rs758803217"); - dna.addSequenceFeature(sf7); - - /* - * build map - expect variants on positions 1, 2, 3, 5 - */ - variantsMap = AlignmentUtils.buildDnaVariantsMap(dna, map); - assertEquals(4, variantsMap.size()); - - /* - * protein residue 1: variant on codon (ATG) base 1, not on 2 or 3 - */ - List[] pep1Variants = variantsMap.get(1); - assertEquals(3, pep1Variants.length); - assertEquals(1, pep1Variants[0].size()); - assertEquals("A", pep1Variants[0].get(0).base); // codon[1] base - assertSame(sf1, pep1Variants[0].get(0).variant); // codon[1] variant - assertEquals(1, pep1Variants[1].size()); - assertEquals("T", pep1Variants[1].get(0).base); // codon[2] base - assertNull(pep1Variants[1].get(0).variant); // no variant here - assertEquals(1, pep1Variants[2].size()); - assertEquals("G", pep1Variants[2].get(0).base); // codon[3] base - assertNull(pep1Variants[2].get(0).variant); // no variant here - - /* - * protein residue 2: variants on codon (AAA) bases 2 and 3 - */ - List[] pep2Variants = variantsMap.get(2); - assertEquals(3, pep2Variants.length); - assertEquals(1, pep2Variants[0].size()); - // codon[1] base recorded while processing variant on codon[2] - assertEquals("A", pep2Variants[0].get(0).base); - assertNull(pep2Variants[0].get(0).variant); // no variant here - // codon[2] base and variant: - assertEquals(1, pep2Variants[1].size()); - assertEquals("A", pep2Variants[1].get(0).base); - assertSame(sf2, pep2Variants[1].get(0).variant); - // codon[3] base was recorded when processing codon[2] variant - // and then the variant for codon[3] added to it - assertEquals(1, pep2Variants[2].size()); - assertEquals("A", pep2Variants[2].get(0).base); - assertSame(sf3, pep2Variants[2].get(0).variant); - - /* - * protein residue 3: variants on codon (TTT) base 2 only - */ - List[] pep3Variants = variantsMap.get(3); - assertEquals(3, pep3Variants.length); - assertEquals(1, pep3Variants[0].size()); - assertEquals("T", pep3Variants[0].get(0).base); // codon[1] base - assertNull(pep3Variants[0].get(0).variant); // no variant here - assertEquals(1, pep3Variants[1].size()); - assertEquals("T", pep3Variants[1].get(0).base); // codon[2] base - assertSame(sf4, pep3Variants[1].get(0).variant); // codon[2] variant - assertEquals(1, pep3Variants[2].size()); - assertEquals("T", pep3Variants[2].get(0).base); // codon[3] base - assertNull(pep3Variants[2].get(0).variant); // no variant here - - /* - * three variants on protein position 5 - */ - List[] pep5Variants = variantsMap.get(5); - assertEquals(3, pep5Variants.length); - assertEquals(1, pep5Variants[0].size()); - assertEquals("C", pep5Variants[0].get(0).base); // codon[1] base - assertSame(sf5, pep5Variants[0].get(0).variant); // codon[1] variant - assertEquals(1, pep5Variants[1].size()); - assertEquals("C", pep5Variants[1].get(0).base); // codon[2] base - assertSame(sf6, pep5Variants[1].get(0).variant); // codon[2] variant - assertEquals(1, pep5Variants[2].size()); - assertEquals("C", pep5Variants[2].get(0).base); // codon[3] base - assertSame(sf7, pep5Variants[2].get(0).variant); // codon[3] variant - } - - /** - * Tests for the method that computes all peptide variants given codon - * variants - */ - @Test(groups = "Functional") - public void testComputePeptideVariants() - { - /* - * scenario: AAATTTCCC codes for KFP, with variants - * GAA -> E - * CAA -> Q - * AAG synonymous - * AAT -> N - * TTC synonymous - * CAC,CGC -> H,R (as one variant) - */ - SequenceI peptide = new Sequence("pep/10-12", "KFP"); - - /* - * two distinct variants for codon 1 position 1 - * second one has clinical significance - */ - SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1, - 0f, null); - sf1.setValue("alleles", "A,G"); // GAA -> E - sf1.setValue("ID", "var1.125A>G"); - SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1, - 0f, null); - sf2.setValue("alleles", "A,C"); // CAA -> Q - sf2.setValue("ID", "var2"); - sf2.setValue("clinical_significance", "Dodgy"); - SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3, - 0f, null); - sf3.setValue("alleles", "A,G"); // synonymous - sf3.setValue("ID", "var3"); - sf3.setValue("clinical_significance", "None"); - SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3, - 0f, null); - sf4.setValue("alleles", "A,T"); // AAT -> N - sf4.setValue("ID", "sequence_variant:var4"); // prefix gets stripped off - sf4.setValue("clinical_significance", "Benign"); - SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 6, 6, - 0f, null); - sf5.setValue("alleles", "T,C"); // synonymous - sf5.setValue("ID", "var5"); - sf5.setValue("clinical_significance", "Bad"); - SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8, - 0f, null); - sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R - sf6.setValue("ID", "var6"); - sf6.setValue("clinical_significance", "Good"); - - List codon1Variants = new ArrayList(); - List codon2Variants = new ArrayList(); - List codon3Variants = new ArrayList(); - List codonVariants[] = new ArrayList[3]; - codonVariants[0] = codon1Variants; - codonVariants[1] = codon2Variants; - codonVariants[2] = codon3Variants; - - /* - * compute variants for protein position 1 - */ - codon1Variants.add(new DnaVariant("A", sf1)); - codon1Variants.add(new DnaVariant("A", sf2)); - codon2Variants.add(new DnaVariant("A")); - codon2Variants.add(new DnaVariant("A")); - codon3Variants.add(new DnaVariant("A", sf3)); - codon3Variants.add(new DnaVariant("A", sf4)); - AlignmentUtils.computePeptideVariants(peptide, 1, codonVariants); - - /* - * compute variants for protein position 2 - */ - codon1Variants.clear(); - codon2Variants.clear(); - codon3Variants.clear(); - codon1Variants.add(new DnaVariant("T")); - codon2Variants.add(new DnaVariant("T")); - codon3Variants.add(new DnaVariant("T", sf5)); - AlignmentUtils.computePeptideVariants(peptide, 2, codonVariants); - - /* - * compute variants for protein position 3 - */ - codon1Variants.clear(); - codon2Variants.clear(); - codon3Variants.clear(); - codon1Variants.add(new DnaVariant("C")); - codon2Variants.add(new DnaVariant("C", sf6)); - codon3Variants.add(new DnaVariant("C")); - AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants); - - /* - * verify added sequence features for - * var1 K -> E - * var2 K -> Q - * var4 K -> N - * var6 P -> H - * var6 P -> R - */ - SequenceFeature[] sfs = peptide.getSequenceFeatures(); - assertEquals(5, sfs.length); - SequenceFeature sf = sfs[0]; - assertEquals(1, sf.getBegin()); - assertEquals(1, sf.getEnd()); - assertEquals("p.Lys1Glu", sf.getDescription()); - assertEquals("var1.125A>G", sf.getValue("ID")); - assertNull(sf.getValue("clinical_significance")); - assertEquals("ID=var1.125A>G", sf.getAttributes()); - assertEquals(1, sf.links.size()); - // link to variation is urlencoded - assertEquals( - "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG", - sf.links.get(0)); - assertEquals("Jalview", sf.getFeatureGroup()); - sf = sfs[1]; - assertEquals(1, sf.getBegin()); - assertEquals(1, sf.getEnd()); - assertEquals("p.Lys1Gln", sf.getDescription()); - assertEquals("var2", sf.getValue("ID")); - assertEquals("Dodgy", sf.getValue("clinical_significance")); - assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes()); - assertEquals(1, sf.links.size()); - assertEquals( - "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2", - sf.links.get(0)); - assertEquals("Jalview", sf.getFeatureGroup()); - sf = sfs[2]; - assertEquals(1, sf.getBegin()); - assertEquals(1, sf.getEnd()); - assertEquals("p.Lys1Asn", sf.getDescription()); - assertEquals("var4", sf.getValue("ID")); - assertEquals("Benign", sf.getValue("clinical_significance")); - assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes()); - assertEquals(1, sf.links.size()); - assertEquals( - "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", - sf.links.get(0)); - assertEquals("Jalview", sf.getFeatureGroup()); - sf = sfs[3]; - assertEquals(3, sf.getBegin()); - assertEquals(3, sf.getEnd()); - assertEquals("p.Pro3His", sf.getDescription()); - assertEquals("var6", sf.getValue("ID")); - assertEquals("Good", sf.getValue("clinical_significance")); - assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes()); - assertEquals(1, sf.links.size()); - assertEquals( - "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", - sf.links.get(0)); - // var5 generates two distinct protein variant features - assertEquals("Jalview", sf.getFeatureGroup()); - sf = sfs[4]; - assertEquals(3, sf.getBegin()); - assertEquals(3, sf.getEnd()); - assertEquals("p.Pro3Arg", sf.getDescription()); - assertEquals("var6", sf.getValue("ID")); - assertEquals("Good", sf.getValue("clinical_significance")); - assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes()); - assertEquals(1, sf.links.size()); - assertEquals( - "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", - sf.links.get(0)); - assertEquals("Jalview", sf.getFeatureGroup()); - } - - /** * Tests for the method that maps the subset of a dna sequence that has CDS * (or subtype) feature, with CDS strand = '-' (reverse) */ @@ -2064,7 +1920,7 @@ public class AlignmentUtilsTests SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt"); dnaSeq.createDatasetSequence(); SequenceI ds = dnaSeq.getDatasetSequence(); - + // CDS for dna 4-6 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null); sf.setStrand("-"); @@ -2076,7 +1932,7 @@ public class AlignmentUtilsTests sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null); sf.setStrand("-"); ds.addSequenceFeature(sf); - + List ranges = AlignmentUtils.findCdsPositions(dnaSeq); /* * verify ranges { [12-10], [6-4] } @@ -2102,7 +1958,7 @@ public class AlignmentUtilsTests SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt"); dnaSeq.createDatasetSequence(); SequenceI ds = dnaSeq.getDatasetSequence(); - + // CDS for dna 5-9 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null); sf.setStrand("-"); @@ -2112,9 +1968,9 @@ public class AlignmentUtilsTests sf.setStrand("-"); sf.setPhase("2"); // skip 2 bases to start of next codon ds.addSequenceFeature(sf); - + List ranges = AlignmentUtils.findCdsPositions(dnaSeq); - + /* * check the mapping starts with the first complete codon * expect ranges [13, 13], [9, 5] @@ -2156,7 +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" }) @@ -2166,10 +2023,10 @@ 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)); - Map> map = new TreeMap>(); + 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); /* @@ -2199,12 +2056,12 @@ 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)); - Map> map = new TreeMap>(); + 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); - + /* * verify map has seq1 residues in columns 3,4,6,7,11,12 */ @@ -2242,10 +2099,11 @@ public class AlignmentUtilsTests dna.setDataset(null); AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 }); emblPeptides.setDataset(null); - + 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); @@ -2256,17 +2114,19 @@ public class AlignmentUtilsTests acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map); acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map); dna.addCodonFrame(acf); - + /* * execute method under test to find CDS for EMBL peptides only */ - AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] { - dna1, dna2 }, dna.getDataset(), emblPeptides); - + AlignmentI cds = AlignmentUtils + .makeCdsAlignment(new SequenceI[] + { dna1, dna2 }, dna.getDataset(), + emblPeptides.getSequencesArray()); + assertEquals(2, cds.getSequences().size()); assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString()); assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString()); - + /* * verify shared, extended alignment dataset */ @@ -2275,7 +2135,7 @@ public class AlignmentUtilsTests .contains(cds.getSequenceAt(0).getDatasetSequence())); assertTrue(dna.getDataset().getSequences() .contains(cds.getSequenceAt(1).getDatasetSequence())); - + /* * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide * the mappings are on the shared alignment dataset @@ -2285,7 +2145,7 @@ public class AlignmentUtilsTests * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep) */ assertEquals(6, cdsMappings.size()); - + /* * verify that mapping sets for dna and cds alignments are different * [not current behaviour - all mappings are on the alignment dataset] @@ -2294,7 +2154,7 @@ public class AlignmentUtilsTests // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames()); // assertEquals(4, dna.getCodonFrames().size()); // assertEquals(4, cds.getCodonFrames().size()); - + /* * Two mappings involve pep3 (dna to pep3, cds to pep3) * Mapping from pep3 to GGGTTT in first new exon sequence @@ -2305,11 +2165,11 @@ public class AlignmentUtilsTests List mappings = MappingUtils .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings); assertEquals(1, mappings.size()); - + // map G to GGG - SearchResults sr = MappingUtils.buildSearchResults(pep3, 1, mappings); + SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings); assertEquals(1, sr.getResults().size()); - Match m = sr.getResults().get(0); + SearchResultMatchI m = sr.getResults().get(0); assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence()); assertEquals(1, m.getStart()); assertEquals(3, m.getEnd()); @@ -2319,7 +2179,7 @@ public class AlignmentUtilsTests assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence()); assertEquals(4, m.getStart()); assertEquals(6, m.getEnd()); - + /* * Two mappings involve pep4 (dna to pep4, cds to pep4) * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence @@ -2350,4 +2210,545 @@ public class AlignmentUtilsTests assertEquals(7, m.getStart()); assertEquals(9, m.getEnd()); } + + /** + * Test the method that just copies aligned sequences, provided all sequences + * to be aligned share the aligned sequence's dataset + */ + @Test(groups = "Functional") + public void testAlignAsSameSequences() + { + SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa"); + SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA"); + AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 }); + ((Alignment) al1).createDatasetAlignment(); + + SequenceI dna3 = new Sequence(dna1); + SequenceI dna4 = new Sequence(dna2); + assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence()); + assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence()); + String seq1 = "-cc-GG-GT-TT--aaa"; + dna3.setSequence(seq1); + String seq2 = "C--C-Cgg--gtt-tAA-A-"; + dna4.setSequence(seq2); + AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 }); + ((Alignment) al2).createDatasetAlignment(); + + /* + * alignment removes gapped columns (two internal, two trailing) + */ + assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2)); + String aligned1 = "-cc-GG-GTTT-aaa"; + assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString()); + String aligned2 = "C--C-Cgg-gtttAAA"; + assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString()); + + /* + * add another sequence to 'aligned' - should still succeed, since + * unaligned sequences still share a dataset with aligned sequences + */ + SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA"); + dna5.createDatasetSequence(); + al2.addSequence(dna5); + assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2)); + assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString()); + assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString()); + + /* + * add another sequence to 'unaligned' - should fail, since now not + * all unaligned sequences share a dataset with aligned sequences + */ + SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA"); + dna6.createDatasetSequence(); + al1.addSequence(dna6); + // JAL-2110 JBP Comment: what's the use case for this behaviour ? + assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2)); + } + + @Test(groups = "Functional") + public void testAlignAsSameSequencesMultipleSubSeq() + { + SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa"); + SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA"); + SequenceI as1 = dna1.deriveSequence(); // cccGGGTTTaaa/1-12 + SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7); // GGGT/4-7 + SequenceI as3 = dna2.deriveSequence(); // CCCgggtttAAA/1-12 + as1.insertCharAt(6, 5, '-'); + assertEquals("cccGGG-----TTTaaa", as1.getSequenceAsString()); + as2.insertCharAt(6, 5, '-'); + assertEquals("GGGT-----", as2.getSequenceAsString()); + as3.insertCharAt(3, 5, '-'); + assertEquals("CCC-----gggtttAAA", as3.getSequenceAsString()); + AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 }); + + // why do we need to cast this still ? + ((Alignment) aligned).createDatasetAlignment(); + SequenceI uas1 = dna1.deriveSequence(); + SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7); + SequenceI uas3 = dna2.deriveSequence(); + AlignmentI tobealigned = new Alignment( + new SequenceI[] + { uas1, uas2, uas3 }); + ((Alignment) tobealigned).createDatasetAlignment(); + + /* + * alignAs lines up dataset sequences and removes empty columns (two) + */ + assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned)); + assertEquals("cccGGG---TTTaaa", uas1.getSequenceAsString()); + assertEquals("GGGT", uas2.getSequenceAsString()); + assertEquals("CCC---gggtttAAA", uas3.getSequenceAsString()); + } + + @Test(groups = { "Functional" }) + public void testTransferGeneLoci() + { + SequenceI from = new Sequence("transcript", + "aaacccgggTTTAAACCCGGGtttaaacccgggttt"); + SequenceI to = new Sequence("CDS", "TTTAAACCCGGG"); + MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1, + 1); + + /* + * first with nothing to transfer + */ + AlignmentUtils.transferGeneLoci(from, map, to); + assertNull(to.getGeneLoci()); + + /* + * next with gene loci set on 'from' sequence + */ + int[] exons = new int[] { 100, 105, 155, 164, 210, 229 }; + MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1); + from.setGeneLoci("human", "GRCh38", "7", geneMap); + AlignmentUtils.transferGeneLoci(from, map, to); + + GeneLociI toLoci = to.getGeneLoci(); + assertNotNull(toLoci); + // DBRefEntry constructor upper-cases 'source' + assertEquals("HUMAN", toLoci.getSpeciesId()); + assertEquals("GRCh38", toLoci.getAssemblyId()); + assertEquals("7", toLoci.getChromosomeId()); + + /* + * transcript 'exons' are 1-6, 7-16, 17-36 + * CDS 1:12 is transcript 10-21 + * transcript 'CDS' is 10-16, 17-21 + * which is 'gene' 158-164, 210-214 + */ + MapList toMap = toLoci.getMapping(); + assertEquals(1, toMap.getFromRanges().size()); + assertEquals(2, toMap.getFromRanges().get(0).length); + assertEquals(1, toMap.getFromRanges().get(0)[0]); + assertEquals(12, toMap.getFromRanges().get(0)[1]); + assertEquals(2, toMap.getToRanges().size()); + assertEquals(2, toMap.getToRanges().get(0).length); + assertEquals(158, toMap.getToRanges().get(0)[0]); + assertEquals(164, toMap.getToRanges().get(0)[1]); + assertEquals(210, toMap.getToRanges().get(1)[0]); + assertEquals(214, toMap.getToRanges().get(1)[1]); + // or summarised as (but toString might change in future): + assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]", + toMap.toString()); + + /* + * an existing value is not overridden + */ + geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1); + from.setGeneLoci("inhuman", "GRCh37", "6", geneMap); + AlignmentUtils.transferGeneLoci(from, map, to); + assertEquals("GRCh38", toLoci.getAssemblyId()); + assertEquals("7", toLoci.getChromosomeId()); + toMap = toLoci.getMapping(); + assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]", + toMap.toString()); + } + + /** + * Tests for the method that maps nucleotide to protein based on CDS features + */ + @Test(groups = "Functional") + public void testMapCdsToProtein() + { + SequenceI peptide = new Sequence("pep", "KLQ"); + + /* + * Case 1: CDS 3 times length of peptide + * NB method only checks lengths match, not translation + */ + SequenceI dna = new Sequence("dna", "AACGacgtCTCCT"); + dna.createDatasetSequence(); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null)); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 13, null)); + MapList ml = AlignmentUtils.mapCdsToProtein(dna, peptide); + assertEquals(3, ml.getFromRatio()); + assertEquals(1, ml.getToRatio()); + assertEquals("[[1, 3]]", + Arrays.deepToString(ml.getToRanges().toArray())); + assertEquals("[[1, 4], [9, 13]]", + Arrays.deepToString(ml.getFromRanges().toArray())); + + /* + * Case 2: CDS 3 times length of peptide + stop codon + * (note code does not currently check trailing codon is a stop codon) + */ + dna = new Sequence("dna", "AACGacgtCTCCTCCC"); + dna.createDatasetSequence(); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null)); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null)); + ml = AlignmentUtils.mapCdsToProtein(dna, peptide); + assertEquals(3, ml.getFromRatio()); + assertEquals(1, ml.getToRatio()); + assertEquals("[[1, 3]]", + Arrays.deepToString(ml.getToRanges().toArray())); + assertEquals("[[1, 4], [9, 13]]", + Arrays.deepToString(ml.getFromRanges().toArray())); + + /* + * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made + */ + dna = new Sequence("dna", "AACGacgtCTCCTTGATCA"); + dna.createDatasetSequence(); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null)); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null)); + ml = AlignmentUtils.mapCdsToProtein(dna, peptide); + assertNull(ml); + + /* + * Case 4: CDS shorter than 3 * peptide - no mapping is made + */ + dna = new Sequence("dna", "AACGacgtCTCC"); + dna.createDatasetSequence(); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null)); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null)); + ml = AlignmentUtils.mapCdsToProtein(dna, peptide); + assertNull(ml); + + /* + * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated + */ + dna = new Sequence("dna", "AACGacgtCTCCTTG"); + dna.createDatasetSequence(); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null)); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null)); + ml = AlignmentUtils.mapCdsToProtein(dna, peptide); + assertEquals(3, ml.getFromRatio()); + assertEquals(1, ml.getToRatio()); + assertEquals("[[1, 3]]", + Arrays.deepToString(ml.getToRanges().toArray())); + assertEquals("[[1, 4], [9, 13]]", + Arrays.deepToString(ml.getFromRanges().toArray())); + + /* + * Case 6: incomplete start codon corresponding to X in peptide + */ + dna = new Sequence("dna", "ACGacgtCTCCTTGG"); + dna.createDatasetSequence(); + SequenceFeature sf = new SequenceFeature("CDS", "", 1, 3, null); + sf.setPhase("2"); // skip 2 positions (AC) to start of next codon (GCT) + dna.addSequenceFeature(sf); + dna.addSequenceFeature(new SequenceFeature("CDS", "", 8, 15, null)); + peptide = new Sequence("pep", "XLQ"); + ml = AlignmentUtils.mapCdsToProtein(dna, peptide); + assertEquals("[[2, 3]]", + Arrays.deepToString(ml.getToRanges().toArray())); + assertEquals("[[3, 3], [8, 12]]", + Arrays.deepToString(ml.getFromRanges().toArray())); + } + + /** + * Tests for the method that locates the CDS sequence that has a mapping to + * 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(groups = "Functional") + public void testFindCdsForProtein() + { + List mappings = new ArrayList<>(); + AlignedCodonFrame acf1 = new AlignedCodonFrame(); + mappings.add(acf1); + + SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg"); + 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[] { 5, 6, 9, 15 }, + 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 - no dna-to-CDS mapping exists - search fails + */ + SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1, + seqMappings, dnaToPeptide); + assertNull(seq); + + /* + * second case - CDS-to-peptide mapping exists but no dna-to-CDS + * - search fails + */ + // todo this test fails if the mapping is added to acf1, not acf2 + // 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); + acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(), + cdsToPeptideMapping); + assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings, + dnaToPeptide)); + + /* + * third case - add dna-to-CDS mapping - CDS is now found! + */ + MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 }, + new int[] + { 1, 9 }, 1, 1); + acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), + dnaToCdsMapping); + seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings, + dnaToPeptide); + assertSame(seq, cds1.getDatasetSequence()); + } + + /** + * Tests for the method that locates the CDS sequence that has a mapping to + * 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. + * This test is for the case where transcript and CDS are the same length. + */ + @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); + 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 + */ + 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) + */ + dna1.addSequenceFeature( + new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null)); + seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings, + dnaToPeptide); + assertNull(seq); + + /* + * third case - CDS-to-peptide mapping exists but no dna-to-CDS + * - search fails + */ + // todo this test fails if the mapping is added to acf1, not acf2 + // 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); + 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! + */ + MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 }, + new int[] + { 1, 9 }, 1, 1); + acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), + dnaToCdsMapping); + seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings, + 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); + + } }