X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=d229a3917a423d34c1152d6366efb9b842792c6c;hb=705d1c84c9a03bb0378593e4d8d8a90c8a11f831;hp=7f7ec31b38fbbecb748a8e4c3de821eb65935998;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 7f7ec31..d229a39 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -34,12 +34,15 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLociI; import jalview.datamodel.Mapping; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.SequenceFeatures; +import jalview.gui.JvOptionPane; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; import jalview.io.FileFormat; @@ -56,11 +59,20 @@ 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 { - public static Sequence ts = new Sequence("short", + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + private static Sequence ts = new Sequence("short", "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm"); @Test(groups = { "Functional" }) @@ -1033,14 +1045,18 @@ public class AlignmentUtilsTests 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 + * 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.getDatasetSequence().addDBRef(dna1xref); + dna1.addDBRef(dna1xref); + assertEquals(2, dna1.getDBRefs().length); // to self and to pep1 DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2", new Mapping(mapfordna2)); - dna2.getDatasetSequence().addDBRef(dna2xref); + dna2.addDBRef(dna2xref); + assertEquals(2, dna2.getDBRefs().length); // to self and to pep2 /* * execute method under test: @@ -1095,6 +1111,38 @@ public class AlignmentUtilsTests assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap()); /* + * verify cDNA has added a dbref with mapping to CDS + */ + assertEquals(3, dna1.getDBRefs().length); + DBRefEntry dbRefEntry = dna1.getDBRefs()[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().length); + dbRefEntry = dna2.getDBRefs()[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().length); + dbRefEntry = cds1Dss.getDBRefs()[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().length); + dbRefEntry = cds2Dss.getDBRefs()[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 * the mappings are on the shared alignment dataset * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep) @@ -1169,12 +1217,12 @@ public class AlignmentUtilsTests /* * check cds2 acquired a variant feature in position 5 */ - SequenceFeature[] sfs = cds2Dss.getSequenceFeatures(); + List sfs = cds2Dss.getSequenceFeatures(); assertNotNull(sfs); - assertEquals(1, sfs.length); - assertEquals("variant", sfs[0].type); - assertEquals(5, sfs[0].begin); - assertEquals(5, sfs[0].end); + assertEquals(1, sfs.size()); + assertEquals("variant", sfs.get(0).type); + assertEquals(5, sfs.get(0).begin); + assertEquals(5, sfs.get(0).end); } /** @@ -1479,39 +1527,39 @@ public class AlignmentUtilsTests * 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()); @@ -1541,10 +1589,10 @@ public class AlignmentUtilsTests // desc4 and desc8 are the 'omit these' varargs AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8"); - SequenceFeature[] sfs = cds.getSequenceFeatures(); - assertEquals(1, sfs.length); + List sfs = cds.getSequenceFeatures(); + assertEquals(1, sfs.size()); - SequenceFeature sf = sfs[0]; + SequenceFeature sf = sfs.get(0); assertEquals("type5", sf.getType()); assertEquals(1, sf.getBegin()); assertEquals(6, sf.getEnd()); @@ -1574,10 +1622,10 @@ public class AlignmentUtilsTests // "type5" is the 'select this type' argument AlignmentUtils.transferFeatures(dna, cds, map, "type5"); - SequenceFeature[] sfs = cds.getSequenceFeatures(); - assertEquals(1, sfs.length); + List sfs = cds.getSequenceFeatures(); + assertEquals(1, sfs.size()); - SequenceFeature sf = sfs[0]; + SequenceFeature sf = sfs.get(0); assertEquals("type5", sf.getType()); assertEquals(1, sf.getBegin()); assertEquals(6, sf.getEnd()); @@ -2068,24 +2116,29 @@ public class AlignmentUtilsTests * var6 P -> H COSMIC * var6 P -> R COSMIC */ - SequenceFeature[] sfs = peptide.getSequenceFeatures(); - assertEquals(5, sfs.length); + List sfs = peptide.getSequenceFeatures(); + SequenceFeatures.sortFeatures(sfs, true); + assertEquals(5, sfs.size()); - SequenceFeature sf = sfs[0]; + /* + * features are sorted by start position ascending, but in no + * particular order where start positions match; asserts here + * simply match the data returned (the order is not important) + */ + SequenceFeature sf = sfs.get(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("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()); - // link to variation is urlencoded assertEquals( - "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG", + "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", sf.links.get(0)); assertEquals(ensembl, sf.getFeatureGroup()); - sf = sfs[1]; + sf = sfs.get(1); assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); assertEquals("p.Lys1Gln", sf.getDescription()); @@ -2098,43 +2151,44 @@ public class AlignmentUtilsTests sf.links.get(0)); assertEquals(dbSnp, sf.getFeatureGroup()); - sf = sfs[2]; + sf = sfs.get(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("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.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", + "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG", sf.links.get(0)); assertEquals(ensembl, sf.getFeatureGroup()); - // var5 generates two distinct protein variant features - sf = sfs[3]; + sf = sfs.get(3); assertEquals(3, sf.getBegin()); assertEquals(3, sf.getEnd()); - assertEquals("p.Pro3His", sf.getDescription()); + 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.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", + "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", sf.links.get(0)); assertEquals(cosmic, sf.getFeatureGroup()); - sf = sfs[4]; + // var5 generates two distinct protein variant features + sf = sfs.get(4); assertEquals(3, sf.getBegin()); assertEquals(3, sf.getEnd()); - assertEquals("p.Pro3Arg", sf.getDescription()); + 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.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", + "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", sf.links.get(0)); assertEquals(cosmic, sf.getFeatureGroup()); } @@ -2516,4 +2570,67 @@ public class AlignmentUtilsTests assertEquals(s_as3, 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.getMap(); + 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(1, toMap.getToRanges().size()); + assertEquals(4, toMap.getToRanges().get(0).length); + assertEquals(158, toMap.getToRanges().get(0)[0]); + assertEquals(164, toMap.getToRanges().get(0)[1]); + assertEquals(210, toMap.getToRanges().get(0)[2]); + assertEquals(214, toMap.getToRanges().get(0)[3]); + // 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.getMap(); + assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]", + toMap.toString()); + } }