From a48b78b602cf3df82ce2821dc3520f7248f3cdf9 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 30 Jan 2018 15:34:48 +0000 Subject: [PATCH] JAL-2897 generate peptide variants for synonymous codon variants --- src/jalview/analysis/AlignmentUtils.java | 118 ++++++++------- src/jalview/gui/CrossRefAction.java | 12 +- src/jalview/io/gff/SequenceOntologyI.java | 6 + test/jalview/analysis/AlignmentUtilsTests.java | 183 +++++++++++++++++------- test/jalview/io/vcf/VCFLoaderTest.java | 15 +- 5 files changed, 223 insertions(+), 111 deletions(-) diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index 9278361..3d22115 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -2428,10 +2428,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - String codon = base + base2 + base3; - if (addPeptideVariant(peptide, peptidePos, residue, var, codon)) + if (!base1.equals(base)) { - count++; + String codon = base + base2 + base3; + if (addPeptideVariant(peptide, peptidePos, residue, var, + codon)) + { + count++; + } } } } @@ -2450,10 +2454,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - String codon = base1 + base + base3; - if (addPeptideVariant(peptide, peptidePos, residue, var, codon)) + if (!base2.equals(base)) { - count++; + String codon = base1 + base + base3; + if (addPeptideVariant(peptide, peptidePos, residue, var, + codon)) + { + count++; + } } } } @@ -2472,10 +2480,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - String codon = base1 + base2 + base; - if (addPeptideVariant(peptide, peptidePos, residue, var, codon)) + if (!base3.equals(base)) { - count++; + String codon = base1 + base2 + base; + if (addPeptideVariant(peptide, peptidePos, residue, var, + codon)) + { + count++; + } } } } @@ -2507,57 +2519,67 @@ public class AlignmentUtils * e.g. multibase variants or HGMD_MUTATION etc * are currently ignored here */ - String trans = codon.contains("-") ? "-" + String trans = codon.contains("-") ? null : (codon.length() > CODON_LENGTH ? null : ResidueProperties.codonTranslate(codon)); - if (trans != null && !trans.equals(residue)) + if (trans == null) + { + return false; + } + String desc = codon; + String featureType = ""; + if (trans.equals(residue)) + { + featureType = SequenceOntologyI.SYNONYMOUS_VARIANT; + } + else { String residue3Char = StringUtils .toSentenceCase(ResidueProperties.aa2Triplet.get(residue)); String trans3Char = StringUtils .toSentenceCase(ResidueProperties.aa2Triplet.get(trans)); - String desc = "p." + residue3Char + peptidePos + trans3Char; - SequenceFeature sf = new SequenceFeature( - SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos, - peptidePos, var.getSource()); - StringBuilder attributes = new StringBuilder(32); - String id = (String) var.variant.getValue(ID); - if (id != null) - { - if (id.startsWith(SEQUENCE_VARIANT)) - { - id = id.substring(SEQUENCE_VARIANT.length()); - } - sf.setValue(ID, id); - attributes.append(ID).append("=").append(id); - // TODO handle other species variants JAL-2064 - StringBuilder link = new StringBuilder(32); - try - { - link.append(desc).append(" ").append(id).append( - "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=") - .append(URLEncoder.encode(id, "UTF-8")); - sf.addLink(link.toString()); - } catch (UnsupportedEncodingException e) - { - // as if - } - } - String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE); - if (clinSig != null) + desc = "p." + residue3Char + peptidePos + trans3Char; + featureType = SequenceOntologyI.NONSYNONYMOUS_VARIANT; + } + SequenceFeature sf = new SequenceFeature(featureType, desc, peptidePos, + peptidePos, var.getSource()); + + StringBuilder attributes = new StringBuilder(32); + String id = (String) var.variant.getValue(ID); + if (id != null) + { + if (id.startsWith(SEQUENCE_VARIANT)) { - sf.setValue(CLINICAL_SIGNIFICANCE, clinSig); - attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=") - .append(clinSig); + id = id.substring(SEQUENCE_VARIANT.length()); } - peptide.addSequenceFeature(sf); - if (attributes.length() > 0) + sf.setValue(ID, id); + attributes.append(ID).append("=").append(id); + // TODO handle other species variants JAL-2064 + StringBuilder link = new StringBuilder(32); + try + { + link.append(desc).append(" ").append(id).append( + "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=") + .append(URLEncoder.encode(id, "UTF-8")); + sf.addLink(link.toString()); + } catch (UnsupportedEncodingException e) { - sf.setAttributes(attributes.toString()); + // as if } - return true; } - return false; + String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE); + if (clinSig != null) + { + sf.setValue(CLINICAL_SIGNIFICANCE, clinSig); + attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=") + .append(clinSig); + } + peptide.addSequenceFeature(sf); + if (attributes.length() > 0) + { + sf.setAttributes(attributes.toString()); + } + return true; } /** diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java index 285e574..85f2498 100644 --- a/src/jalview/gui/CrossRefAction.java +++ b/src/jalview/gui/CrossRefAction.java @@ -176,10 +176,14 @@ public class CrossRefAction implements Runnable /* * copy feature rendering settings to split frame */ - newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings(myFeatureStyling); - copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings(myFeatureStyling); + FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer(); + fr1.transferSettings(myFeatureStyling); + fr1.findAllFeatures(true); + FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer(); + fr2.transferSettings(myFeatureStyling); + fr2.findAllFeatures(true); /* * apply 'database source' feature configuration diff --git a/src/jalview/io/gff/SequenceOntologyI.java b/src/jalview/io/gff/SequenceOntologyI.java index c0570e0..10ca7ec 100644 --- a/src/jalview/io/gff/SequenceOntologyI.java +++ b/src/jalview/io/gff/SequenceOntologyI.java @@ -42,6 +42,12 @@ public interface SequenceOntologyI // SO:0001060 public static final String SEQUENCE_VARIANT = "sequence_variant"; + // SO:0001819 + public static final String SYNONYMOUS_VARIANT = "synonymous_variant"; + + // SO:0001992 + public static final String NONSYNONYMOUS_VARIANT = "nonsynonymous_variant"; + // SO:0000147 public static final String EXON = "exon"; diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 1bff8bf..3e8390f 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -263,14 +263,14 @@ 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 @@ -507,7 +507,7 @@ public class AlignmentUtilsTests 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); @@ -605,14 +605,14 @@ 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 @@ -697,14 +697,14 @@ 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 @@ -774,14 +774,14 @@ 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 @@ -848,8 +848,8 @@ 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) @@ -1783,7 +1783,7 @@ 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); @@ -1932,6 +1932,7 @@ public class AlignmentUtilsTests 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"); @@ -2021,6 +2022,7 @@ public class AlignmentUtilsTests * variants: * GAA -> E source: Ensembl * CAA -> Q source: dbSNP + * TAA -> STOP source: dnSNP * AAG synonymous source: COSMIC * AAT -> N source: Ensembl * ...TTC synonymous source: dbSNP @@ -2036,39 +2038,50 @@ public class AlignmentUtilsTests String ensembl = "Ensembl"; String dbSnp = "dbSNP"; String cosmic = "COSMIC"; + SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1, 0f, ensembl); - sf1.setValue("alleles", "A,G"); // GAA -> E + sf1.setValue("alleles", "A,G"); // AAA -> GAA -> K/E sf1.setValue("ID", "var1.125A>G"); + SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1, 0f, dbSnp); - sf2.setValue("alleles", "A,C"); // CAA -> Q + sf2.setValue("alleles", "A,C"); // AAA -> CAA -> K/Q sf2.setValue("ID", "var2"); sf2.setValue("clinical_significance", "Dodgy"); - SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3, - 0f, cosmic); - sf3.setValue("alleles", "A,G"); // synonymous + + SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 1, 1, + 0f, dbSnp); + sf3.setValue("alleles", "A,T"); // AAA -> TAA -> stop codon sf3.setValue("ID", "var3"); - sf3.setValue("clinical_significance", "None"); + sf3.setValue("clinical_significance", "Bad"); + SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3, + 0f, cosmic); + sf4.setValue("alleles", "A,G"); // AAA -> AAG synonymous + sf4.setValue("ID", "var4"); + sf4.setValue("clinical_significance", "None"); + + SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 3, 3, 0f, ensembl); - 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, + sf5.setValue("alleles", "A,T"); // AAA -> AAT -> K/N + sf5.setValue("ID", "sequence_variant:var5"); // prefix gets stripped off + sf5.setValue("clinical_significance", "Benign"); + + SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 6, 6, 0f, dbSnp); - sf5.setValue("alleles", "T,C"); // synonymous - sf5.setValue("ID", "var5"); - sf5.setValue("clinical_significance", "Bad"); - SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8, - 0f, cosmic); - sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R + sf6.setValue("alleles", "T,C"); // TTT -> TTC synonymous sf6.setValue("ID", "var6"); - sf6.setValue("clinical_significance", "Good"); - List codon1Variants = new ArrayList(); - List codon2Variants = new ArrayList(); - List codon3Variants = new ArrayList(); + SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 8, 8, + 0f, cosmic); + sf7.setValue("alleles", "C,A,G"); // CCC -> CAC,CGC -> P/H/R + sf7.setValue("ID", "var7"); + sf7.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; @@ -2079,10 +2092,11 @@ public class AlignmentUtilsTests */ codon1Variants.add(new DnaVariant("A", sf1)); codon1Variants.add(new DnaVariant("A", sf2)); + codon1Variants.add(new DnaVariant("A", sf3)); codon2Variants.add(new DnaVariant("A")); - codon2Variants.add(new DnaVariant("A")); - codon3Variants.add(new DnaVariant("A", sf3)); + // codon2Variants.add(new DnaVariant("A")); codon3Variants.add(new DnaVariant("A", sf4)); + codon3Variants.add(new DnaVariant("A", sf5)); AlignmentUtils.computePeptideVariants(peptide, 1, codonVariants); /* @@ -2093,7 +2107,7 @@ public class AlignmentUtilsTests codon3Variants.clear(); codon1Variants.add(new DnaVariant("T")); codon2Variants.add(new DnaVariant("T")); - codon3Variants.add(new DnaVariant("T", sf5)); + codon3Variants.add(new DnaVariant("T", sf6)); AlignmentUtils.computePeptideVariants(peptide, 2, codonVariants); /* @@ -2103,7 +2117,7 @@ public class AlignmentUtilsTests codon2Variants.clear(); codon3Variants.clear(); codon1Variants.add(new DnaVariant("C")); - codon2Variants.add(new DnaVariant("C", sf6)); + codon2Variants.add(new DnaVariant("C", sf7)); codon3Variants.add(new DnaVariant("C")); AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants); @@ -2111,35 +2125,58 @@ public class AlignmentUtilsTests * verify added sequence features for * var1 K -> E Ensembl * var2 K -> Q dbSNP - * var4 K -> N Ensembl - * var6 P -> H COSMIC - * var6 P -> R COSMIC + * var3 K -> stop + * var4 synonymous + * var5 K -> N Ensembl + * var6 synonymous + * var7 P -> H COSMIC + * var8 P -> R COSMIC */ List sfs = peptide.getSequenceFeatures(); SequenceFeatures.sortFeatures(sfs, true); - assertEquals(5, sfs.size()); + assertEquals(8, sfs.size()); /* * 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) */ + // AAA -> AAT -> K/N SequenceFeature sf = sfs.get(0); assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Lys1Asn", sf.getDescription()); - assertEquals("var4", sf.getValue("ID")); + assertEquals("var5", sf.getValue("ID")); assertEquals("Benign", sf.getValue("clinical_significance")); - assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes()); + assertEquals("ID=var5;clinical_significance=Benign", + sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( - "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", + "p.Lys1Asn var5|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var5", sf.links.get(0)); assertEquals(ensembl, sf.getFeatureGroup()); + // AAA -> TAA -> stop codon sf = sfs.get(1); assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); + assertEquals("p.Lys1null", sf.getDescription()); // stop codon badly handled + assertEquals("var3", sf.getValue("ID")); + assertEquals("Bad", sf.getValue("clinical_significance")); + assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes()); + assertEquals(1, sf.links.size()); + assertEquals( + "p.Lys1null var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3", + sf.links.get(0)); + assertEquals(dbSnp, sf.getFeatureGroup()); + + // AAA -> CAA -> K/Q + sf = sfs.get(2); + assertEquals(1, sf.getBegin()); + assertEquals(1, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Lys1Gln", sf.getDescription()); assertEquals("var2", sf.getValue("ID")); assertEquals("Dodgy", sf.getValue("clinical_significance")); @@ -2150,9 +2187,11 @@ public class AlignmentUtilsTests sf.links.get(0)); assertEquals(dbSnp, sf.getFeatureGroup()); - sf = sfs.get(2); + // AAA -> GAA -> K/E + sf = sfs.get(3); assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Lys1Glu", sf.getDescription()); assertEquals("var1.125A>G", sf.getValue("ID")); assertNull(sf.getValue("clinical_significance")); @@ -2164,30 +2203,64 @@ public class AlignmentUtilsTests sf.links.get(0)); assertEquals(ensembl, sf.getFeatureGroup()); - sf = sfs.get(3); + // AAA -> AAG synonymous + sf = sfs.get(4); + assertEquals(1, sf.getBegin()); + assertEquals(1, sf.getEnd()); + assertEquals("synonymous_variant", sf.getType()); + assertEquals("AAG", sf.getDescription()); + assertEquals("var4", sf.getValue("ID")); + assertEquals("None", sf.getValue("clinical_significance")); + assertEquals("ID=var4;clinical_significance=None", sf.getAttributes()); + assertEquals(1, sf.links.size()); + assertEquals( + "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", + sf.links.get(0)); + assertEquals(cosmic, sf.getFeatureGroup()); + + // TTT -> TTC synonymous + sf = sfs.get(5); + assertEquals(2, sf.getBegin()); + assertEquals(2, sf.getEnd()); + assertEquals("synonymous_variant", sf.getType()); + assertEquals("TTC", sf.getDescription()); + assertEquals("var6", sf.getValue("ID")); + assertNull(sf.getValue("clinical_significance")); + assertEquals("ID=var6", sf.getAttributes()); + assertEquals(1, sf.links.size()); + assertEquals( + "TTC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", + sf.links.get(0)); + assertEquals(dbSnp, sf.getFeatureGroup()); + + // var7 generates two distinct protein variant features (two alleles) + // CCC -> CGC -> P/R + sf = sfs.get(6); assertEquals(3, sf.getBegin()); assertEquals(3, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Pro3Arg", sf.getDescription()); - assertEquals("var6", sf.getValue("ID")); + assertEquals("var7", sf.getValue("ID")); assertEquals("Good", sf.getValue("clinical_significance")); - assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes()); + assertEquals("ID=var7;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.Pro3Arg var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7", sf.links.get(0)); assertEquals(cosmic, sf.getFeatureGroup()); - // var5 generates two distinct protein variant features - sf = sfs.get(4); + // CCC -> CAC -> P/H + sf = sfs.get(7); assertEquals(3, sf.getBegin()); assertEquals(3, sf.getEnd()); + assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Pro3His", sf.getDescription()); - assertEquals("var6", sf.getValue("ID")); + assertEquals("var7", sf.getValue("ID")); assertEquals("Good", sf.getValue("clinical_significance")); - assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes()); + assertEquals("ID=var7;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.Pro3His var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7", sf.links.get(0)); assertEquals(cosmic, sf.getFeatureGroup()); } @@ -2308,7 +2381,7 @@ public class AlignmentUtilsTests 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>(); + Map> map = new TreeMap<>(); AlignmentUtils.addMappedPositions(seq1, from, mapping, map); /* @@ -2340,7 +2413,7 @@ public class AlignmentUtilsTests 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>(); + Map> map = new TreeMap<>(); AlignmentUtils.addMappedPositions(seq1, from, mapping, map); /* diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java index a02cc5a..7099282 100644 --- a/test/jalview/io/vcf/VCFLoaderTest.java +++ b/test/jalview/io/vcf/VCFLoaderTest.java @@ -170,7 +170,7 @@ public class VCFLoaderTest assertEquals(sf.getFeatureGroup(), "VCF"); assertEquals(sf.getBegin(), 1); assertEquals(sf.getEnd(), 1); - assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); + assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT); assertEquals(sf.getDescription(), "p.Ser1Thr"); } @@ -425,7 +425,7 @@ public class VCFLoaderTest assertEquals(sf.getFeatureGroup(), "VCF"); assertEquals(sf.getBegin(), 6); assertEquals(sf.getEnd(), 6); - assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); + assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT); assertEquals(sf.getDescription(), "p.Ala6Gly"); } @@ -570,12 +570,19 @@ public class VCFLoaderTest } } List proteinFeatures = peptide.getSequenceFeatures(); - assertEquals(proteinFeatures.size(), 1); + SequenceFeatures.sortFeatures(proteinFeatures, true); + assertEquals(proteinFeatures.size(), 2); sf = proteinFeatures.get(0); assertEquals(sf.getFeatureGroup(), "VCF"); + assertEquals(sf.getBegin(), 1); + assertEquals(sf.getEnd(), 1); + assertEquals(sf.getType(), SequenceOntologyI.SYNONYMOUS_VARIANT); + assertEquals(sf.getDescription(), "AGT"); + sf = proteinFeatures.get(1); + assertEquals(sf.getFeatureGroup(), "VCF"); assertEquals(sf.getBegin(), 4); assertEquals(sf.getEnd(), 4); - assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); + assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT); assertEquals(sf.getDescription(), "p.Glu4Gly"); /* -- 1.7.10.2