X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;fp=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=0e3d84bc767606531b35b4753bd1f848f3ad08da;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=9c7ce638fdf95fca1caca1a5347c0d27115dbb55;hpb=9dabc02511e3a334a5749a504f57f69d6c9017bd;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index 9c7ce63..0e3d84b 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -33,6 +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; @@ -139,7 +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) { @@ -156,9 +156,7 @@ public class EnsemblGene extends EnsemblSeqProxy { // ensure id has 'correct' case for the Ensembl identifier geneId = geneAlignment.getSequenceAt(0).getName(); - findGeneLoci(geneAlignment.getSequenceAt(0), geneId); - getTranscripts(geneAlignment, geneId); } if (al == null) @@ -540,10 +538,11 @@ 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 } /**