From: gmungoc Date: Mon, 5 Feb 2018 09:54:10 +0000 (+0000) Subject: Merge branch 'spikes/mungo' into trialMerge X-Git-Tag: Release_2_11_0~62 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=241bd0223b016b5ad5ec78520310a8de32842722;hp=9214cffc006412ed194565b82c8663df2ea641c6;p=jalview.git Merge branch 'spikes/mungo' into trialMerge Conflicts: src/jalview/analysis/AlignmentUtils.java test/jalview/analysis/AlignmentUtilsTests.java --- diff --git a/lib/groovy-all-2.4.6-indy.jar b/lib/groovy-all-2.4.6-indy.jar deleted file mode 100644 index 5f3d51c..0000000 Binary files a/lib/groovy-all-2.4.6-indy.jar and /dev/null differ diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index 5e11446..aa1a98b 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -2430,14 +2430,11 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - if (!base1.equalsIgnoreCase(base)) + if (!base1.equals(base)) { - String codon = base.toUpperCase() + base2.toLowerCase() - + base3.toLowerCase(); - String canonical = base1.toUpperCase() + base2.toLowerCase() - + base3.toLowerCase(); + String codon = base + base2 + base3; if (addPeptideVariant(peptide, peptidePos, residue, var, - codon, canonical)) + codon)) { count++; } @@ -2459,14 +2456,11 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - if (!base2.equalsIgnoreCase(base)) + if (!base2.equals(base)) { - String codon = base1.toLowerCase() + base.toUpperCase() - + base3.toLowerCase(); - String canonical = base1.toLowerCase() + base2.toUpperCase() - + base3.toLowerCase(); + String codon = base1 + base + base3; if (addPeptideVariant(peptide, peptidePos, residue, var, - codon, canonical)) + codon)) { count++; } @@ -2488,14 +2482,11 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - if (!base3.equalsIgnoreCase(base)) + if (!base3.equals(base)) { - String codon = base1.toLowerCase() + base2.toLowerCase() - + base.toUpperCase(); - String canonical = base1.toLowerCase() + base2.toLowerCase() - + base3.toUpperCase(); + String codon = base1 + base2 + base; if (addPeptideVariant(peptide, peptidePos, residue, var, - codon, canonical)) + codon)) { count++; } @@ -2518,13 +2509,10 @@ public class AlignmentUtils * @param residue * @param var * @param codon - * the variant codon e.g. aCg - * @param canonical - * the 'normal' codon e.g. aTg * @return true if a feature was added, else false */ static boolean addPeptideVariant(SequenceI peptide, int peptidePos, - String residue, DnaVariant var, String codon, String canonical) + String residue, DnaVariant var, String codon) { /* * get peptide translation of codon e.g. GAT -> D @@ -2539,7 +2527,7 @@ public class AlignmentUtils { return false; } - String desc = canonical + "/" + codon; + String desc = codon; String featureType = ""; if (trans.equals(residue)) { diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 37b93fd..2b45eee 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -2193,13 +2193,13 @@ public class AlignmentUtilsTests assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); assertEquals("stop_gained", sf.getType()); - assertEquals("Aaa/Taa", sf.getDescription()); + assertEquals("TAA", sf.getDescription()); 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( - "Aaa/Taa var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3", + "TAA var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3", sf.links.get(0)); assertEquals(dbSnp, sf.getFeatureGroup()); @@ -2208,13 +2208,28 @@ public class AlignmentUtilsTests assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); assertEquals("synonymous_variant", sf.getType()); - assertEquals("aaA/aaG", sf.getDescription()); + 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( - "aaA/aaG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", + "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", + sf.links.get(0)); + assertEquals(cosmic, sf.getFeatureGroup()); + + // 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()); @@ -2223,13 +2238,13 @@ public class AlignmentUtilsTests assertEquals(2, sf.getBegin()); assertEquals(2, sf.getEnd()); assertEquals("synonymous_variant", sf.getType()); - assertEquals("ttT/ttC", sf.getDescription()); + 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( - "ttT/ttC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", + "TTC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", sf.links.get(0)); assertEquals(dbSnp, sf.getFeatureGroup());