X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=0e3d84bc767606531b35b4753bd1f848f3ad08da;hb=0b573ed90b14079f7326281f50c0c9cffdace586;hp=dd2547beaa8163251195caf000d7cfc9c3632284;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index dd2547b..0e3d84b 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;
@@ -63,6 +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)
    */
@@ -135,29 +136,16 @@ public class EnsemblGene extends EnsemblSeqProxy
   @Override
   public AlignmentI getSequenceRecords(String query) throws Exception
   {
-	  
-	  
-	  
- Platform.timeCheck("EG " + query, Platform.TIME_MARK);	  
-	  
     /*
      * convert to a non-duplicated list of gene identifiers
      */
     List<String> geneIds = getGeneIds(query);
-
-    
-    Platform.timeCheck("EG genIds " + geneIds.size(), Platform.TIME_MARK);	  
-
     AlignmentI al = null;
     for (String geneId : geneIds)
     {
       /*
        * fetch the gene sequence(s) with features and xrefs
        */
-    	
-        Platform.timeCheck("EG fetch " + geneId, Platform.TIME_MARK);	  
-    	
-    	
       AlignmentI geneAlignment = super.getSequenceRecords(geneId);
       if (geneAlignment == null)
       {
@@ -168,15 +156,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       {
         // ensure id has 'correct' case for the Ensembl identifier
         geneId = geneAlignment.getSequenceAt(0).getName();
-
-        
-        Platform.timeCheck("EG loci " + geneId, Platform.TIME_MARK);	  
-
-        
         findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
-
-        Platform.timeCheck("EG transcript " + geneId, Platform.TIME_MARK);	  
-
         getTranscripts(geneAlignment, geneId);
       }
       if (al == null)
@@ -188,9 +168,6 @@ public class EnsemblGene extends EnsemblSeqProxy
         al.append(geneAlignment);
       }
     }
-    
-    Platform.timeCheck("EG done", Platform.TIME_MARK);	  
-
     return al;
   }
 
@@ -209,7 +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
     {
@@ -231,7 +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];
@@ -482,7 +459,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       return;
     }
 
-    MapList geneMapping = loci.getMap();
+    MapList geneMapping = loci.getMapping();
 
     List<int[]> exons = mapping.getFromRanges();
     List<int[]> transcriptLoci = new ArrayList<>();
@@ -561,10 +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
   }
 
   /**