X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=75a7154595a919bf1f7454224813c8e50a519e22;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=cdcfa9642c5f3f57e3a4a0ff976b7904fc624955;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index cdcfa96..75a7154 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -23,7 +23,6 @@ package jalview.ext.ensembl; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsModelI; import jalview.datamodel.AlignmentI; -import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLociI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; @@ -34,6 +33,7 @@ import jalview.io.gff.SequenceOntologyI; import jalview.schemes.FeatureColour; import jalview.schemes.FeatureSettingsAdapter; import jalview.util.MapList; +import jalview.util.Platform; import java.awt.Color; import java.io.UnsupportedEncodingException; @@ -51,8 +51,6 @@ import com.stevesoft.pat.Regex; */ public class EnsemblGene extends EnsemblSeqProxy { - private static final String GENE_PREFIX = "gene:"; - /* * accepts anything as we will attempt lookup of gene or * transcript id or gene name @@ -64,6 +62,8 @@ public class EnsemblGene extends EnsemblSeqProxy EnsemblFeatureType.exon, EnsemblFeatureType.cds, EnsemblFeatureType.variation }; + private static final String CHROMOSOME = "chromosome"; + /** * Default constructor (to use rest.ensembl.org) */ @@ -100,6 +100,12 @@ public class EnsemblGene extends EnsemblSeqProxy return EnsemblSeqType.GENOMIC; } + @Override + protected String getObjectType() + { + return OBJECT_TYPE_GENE; + } + /** * Returns an alignment containing the gene(s) for the given gene or * transcript identifier, or external identifier (e.g. Uniprot id). If given a @@ -134,7 +140,6 @@ public class EnsemblGene extends EnsemblSeqProxy * convert to a non-duplicated list of gene identifiers */ List geneIds = getGeneIds(query); - AlignmentI al = null; for (String geneId : geneIds) { @@ -146,9 +151,11 @@ public class EnsemblGene extends EnsemblSeqProxy { continue; } - + if (geneAlignment.getHeight() == 1) { + // ensure id has 'correct' case for the Ensembl identifier + geneId = geneAlignment.getSequenceAt(0).getName(); findGeneLoci(geneAlignment.getSequenceAt(0), geneId); getTranscripts(geneAlignment, geneId); } @@ -179,7 +186,7 @@ public class EnsemblGene extends EnsemblSeqProxy if (geneLoci != null) { seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(), - geneLoci.getChromosomeId(), geneLoci.getMap()); + geneLoci.getChromosomeId(), geneLoci.getMapping()); } else { @@ -201,7 +208,7 @@ public class EnsemblGene extends EnsemblSeqProxy return false; } String[] tokens = description.split(":"); - if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME)) + if (tokens.length == 6 && tokens[0].startsWith(CHROMOSOME)) { String ref = tokens[1]; String chrom = tokens[2]; @@ -235,7 +242,7 @@ public class EnsemblGene extends EnsemblSeqProxy */ List getGeneIds(String accessions) { - List geneIds = new ArrayList(); + List geneIds = new ArrayList<>(); for (String acc : accessions.split(getAccessionSeparator())) { @@ -311,8 +318,8 @@ public class EnsemblGene extends EnsemblSeqProxy SequenceOntologyI.NMD_TRANSCRIPT_VARIANT, SequenceOntologyI.TRANSCRIPT, SequenceOntologyI.EXON, SequenceOntologyI.CDS }; - List sfs = gene.getFeatures().getFeaturesByOntology( - soTerms); + List sfs = gene.getFeatures() + .getFeaturesByOntology(soTerms); for (SequenceFeature sf : sfs) { gene.deleteFeature(sf); @@ -358,7 +365,7 @@ public class EnsemblGene extends EnsemblSeqProxy * look for exon features of the transcript, failing that for CDS * (for example ENSG00000124610 has 1 CDS but no exon features) */ - String parentId = "transcript:" + accId; + String parentId = accId; List splices = findFeatures(gene, SequenceOntologyI.EXON, parentId); if (splices.isEmpty()) @@ -370,7 +377,7 @@ public class EnsemblGene extends EnsemblSeqProxy int transcriptLength = 0; final char[] geneChars = gene.getSequence(); int offset = gene.getStart(); // to convert to 0-based positions - List mappedFrom = new ArrayList(); + List mappedFrom = new ArrayList<>(); for (SequenceFeature sf : splices) { @@ -389,7 +396,7 @@ public class EnsemblGene extends EnsemblSeqProxy * Ensembl has gene name as transcript Name * EnsemblGenomes doesn't, but has a url-encoded description field */ - String description = (String) transcriptFeature.getValue(NAME); + String description = transcriptFeature.getDescription(); if (description == null) { description = (String) transcriptFeature.getValue(DESCRIPTION); @@ -412,7 +419,7 @@ public class EnsemblGene extends EnsemblSeqProxy * transfer features to the new sequence; we use EnsemblCdna to do this, * to filter out unwanted features types (see method retainFeature) */ - List mapTo = new ArrayList(); + List mapTo = new ArrayList<>(); mapTo.add(new int[] { 1, transcriptLength }); MapList mapping = new MapList(mappedFrom, mapTo, 1, 1); EnsemblCdna cdna = new EnsemblCdna(getDomain()); @@ -452,7 +459,7 @@ public class EnsemblGene extends EnsemblSeqProxy return; } - MapList geneMapping = loci.getMap(); + MapList geneMapping = loci.getMapping(); List exons = mapping.getFromRanges(); List transcriptLoci = new ArrayList<>(); @@ -462,8 +469,9 @@ public class EnsemblGene extends EnsemblSeqProxy transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1])); } - List transcriptRange = Arrays.asList(new int[] { - transcript.getStart(), transcript.getEnd() }); + List transcriptRange = Arrays + .asList(new int[] + { transcript.getStart(), transcript.getEnd() }); MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1); transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(), @@ -478,7 +486,7 @@ public class EnsemblGene extends EnsemblSeqProxy */ protected String getTranscriptId(SequenceFeature feature) { - return (String) feature.getValue("transcript_id"); + return (String) feature.getValue(JSON_ID); } /** @@ -498,9 +506,9 @@ public class EnsemblGene extends EnsemblSeqProxy protected List getTranscriptFeatures(String accId, SequenceI geneSequence) { - List transcriptFeatures = new ArrayList(); + List transcriptFeatures = new ArrayList<>(); - String parentIdentifier = GENE_PREFIX + accId; + String parentIdentifier = accId; List sfs = geneSequence.getFeatures() .getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT); @@ -510,7 +518,7 @@ public class EnsemblGene extends EnsemblSeqProxy for (SequenceFeature sf : sfs) { String parent = (String) sf.getValue(PARENT); - if (parentIdentifier.equals(parent)) + if (parentIdentifier.equalsIgnoreCase(parent)) { transcriptFeatures.add(sf); } @@ -531,29 +539,34 @@ public class EnsemblGene extends EnsemblSeqProxy @Override public String getTestQuery() { - return "ENSG00000157764"; // BRAF, 5 transcripts, reverse strand + return Platform.isJS() ? "ENSG00000123569" : "ENSG00000157764"; + // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand + // ENSG00000157764 // BRAF, 5 transcripts, reverse strand // ENSG00000090266 // NDUFB2, 15 transcripts, forward strand // ENSG00000101812 // H2BFM histone, 3 transcripts, forward strand - // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand } /** - * Answers true for a feature of type 'gene' (or a sub-type of gene in the - * Sequence Ontology), whose ID is the accession we are retrieving + * Answers a list of sequence features (if any) whose type is 'gene' (or a + * subtype of gene in the Sequence Ontology), and whose ID is the accession we + * are retrieving */ @Override - protected boolean identifiesSequence(SequenceFeature sf, String accId) + protected List getIdentifyingFeatures(SequenceI seq, + String accId) { - if (SequenceOntologyFactory.getInstance().isA(sf.getType(), - SequenceOntologyI.GENE)) + List result = new ArrayList<>(); + List sfs = seq.getFeatures() + .getFeaturesByOntology(SequenceOntologyI.GENE); + for (SequenceFeature sf : sfs) { - String id = (String) sf.getValue(ID); - if ((GENE_PREFIX + accId).equals(id)) + String id = (String) sf.getValue(JSON_ID); + if (accId.equalsIgnoreCase(id)) { - return true; + result.add(sf); } } - return false; + return result; } /** @@ -575,7 +588,7 @@ public class EnsemblGene extends EnsemblSeqProxy if (isTranscript(type)) { String parent = (String) sf.getValue(PARENT); - if (!(GENE_PREFIX + accessionId).equals(parent)) + if (!accessionId.equalsIgnoreCase(parent)) { return false; } @@ -584,17 +597,6 @@ public class EnsemblGene extends EnsemblSeqProxy } /** - * Answers false. This allows an optimisation - a single 'gene' feature is all - * that is needed to identify the positions of the gene on the genomic - * sequence. - */ - @Override - protected boolean isSpliceable() - { - return false; - } - - /** * Override to do nothing as Ensembl doesn't return a protein sequence for a * gene identifier */ @@ -627,10 +629,10 @@ public class EnsemblGene extends EnsemblSeqProxy SequenceOntologyI so = SequenceOntologyFactory.getInstance(); @Override - public boolean isFeatureDisplayed(String type) + public boolean isFeatureHidden(String type) { - return (so.isA(type, SequenceOntologyI.EXON) - || so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT)); + return (!so.isA(type, SequenceOntologyI.EXON) + && !so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT)); } @Override