From 55eef00ac2435b5cc0ee64b92ad87a915375a709 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 25 Sep 2017 10:07:32 +0100 Subject: [PATCH] JAL-2738 one constant in codebase for "alleles" attribute of GFF/SequenceFeature --- src/jalview/analysis/AlignmentUtils.java | 9 +++++---- src/jalview/ext/ensembl/EnsemblSeqProxy.java | 10 +++++----- src/jalview/io/gff/Gff3Helper.java | 4 +++- src/jalview/io/vcf/VCFLoader.java | 3 ++- 4 files changed, 15 insertions(+), 11 deletions(-) diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index 41fe77e..6acac01 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -36,6 +36,7 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.datamodel.features.SequenceFeatures; +import jalview.io.gff.Gff3Helper; import jalview.io.gff.SequenceOntologyI; import jalview.schemes.ResidueProperties; import jalview.util.Comparison; @@ -2374,7 +2375,7 @@ public class AlignmentUtils { if (var.variant != null) { - String alleles = (String) var.variant.getValue("alleles"); + String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES); if (alleles != null) { for (String base : alleles.split(",")) @@ -2396,7 +2397,7 @@ public class AlignmentUtils { if (var.variant != null) { - String alleles = (String) var.variant.getValue("alleles"); + String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES); if (alleles != null) { for (String base : alleles.split(",")) @@ -2418,7 +2419,7 @@ public class AlignmentUtils { if (var.variant != null) { - String alleles = (String) var.variant.getValue("alleles"); + String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES); if (alleles != null) { for (String base : alleles.split(",")) @@ -2555,7 +2556,7 @@ public class AlignmentUtils /* * extract dna variants to a string array */ - String alls = (String) sf.getValue("alleles"); + String alls = (String) sf.getValue(Gff3Helper.ALLELES); if (alls == null) { continue; // non-SNP VCF variant perhaps - can't process this diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 577111e..35ceea3 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -34,6 +34,7 @@ import jalview.datamodel.features.SequenceFeatures; import jalview.exceptions.JalviewException; import jalview.io.FastaFile; import jalview.io.FileParse; +import jalview.io.gff.Gff3Helper; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; import jalview.util.Comparison; @@ -59,8 +60,6 @@ import java.util.Map.Entry; */ public abstract class EnsemblSeqProxy extends EnsemblRestClient { - private static final String ALLELES = "alleles"; - protected static final String PARENT = "Parent"; protected static final String ID = "ID"; @@ -717,7 +716,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient */ static void reverseComplementAlleles(SequenceFeature sf) { - final String alleles = (String) sf.getValue(ALLELES); + final String alleles = (String) sf.getValue(Gff3Helper.ALLELES); if (alleles == null) { return; @@ -728,7 +727,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient reverseComplementAllele(complement, allele); } String comp = complement.toString(); - sf.setValue(ALLELES, comp); + sf.setValue(Gff3Helper.ALLELES, comp); sf.setDescription(comp); /* @@ -738,7 +737,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient String atts = sf.getAttributes(); if (atts != null) { - atts = atts.replace(ALLELES + "=" + alleles, ALLELES + "=" + comp); + atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles, + Gff3Helper.ALLELES + "=" + comp); sf.setAttributes(atts); } } diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java index c7e1d7a..a25a014 100644 --- a/src/jalview/io/gff/Gff3Helper.java +++ b/src/jalview/io/gff/Gff3Helper.java @@ -39,6 +39,8 @@ import java.util.Map; */ public class Gff3Helper extends GffHelperBase { + public static final String ALLELES = "alleles"; + protected static final String TARGET = "Target"; protected static final String ID = "ID"; @@ -399,7 +401,7 @@ public class Gff3Helper extends GffHelperBase /* * Ensembl returns dna variants as 'alleles' */ - desc = StringUtils.listToDelimitedString(attributes.get("alleles"), + desc = StringUtils.listToDelimitedString(attributes.get(ALLELES), ","); } diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java index e725a22..13966f4 100644 --- a/src/jalview/io/vcf/VCFLoader.java +++ b/src/jalview/io/vcf/VCFLoader.java @@ -17,6 +17,7 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.ext.ensembl.EnsemblMap; import jalview.ext.htsjdk.VCFReader; +import jalview.io.gff.Gff3Helper; import jalview.io.gff.SequenceOntologyI; import jalview.util.MapList; import jalview.util.MappingUtils; @@ -361,7 +362,7 @@ public class VCFLoader SequenceFeature sf = new SequenceFeature(type, alleles, featureStart, featureEnd, score, "VCF"); - sf.setValue("alleles", alleles); + sf.setValue(Gff3Helper.ALLELES, alleles); Map atts = variant.getAttributes(); for (Entry att : atts.entrySet()) -- 1.7.10.2