X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=d44be1cef0a5599a7610a297c1c65a7e44656a31;hb=e83ce5d8ef826fc0b509a51f154abdf734501077;hp=9c7ce638fdf95fca1caca1a5347c0d27115dbb55;hpb=cbeb7ad59d51b468c54ca3db2a2a7693060a2509;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 9c7ce63..d44be1c 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<String> geneIds = getGeneIds(query);
-
     AlignmentI al = null;
     for (String geneId : geneIds)
     {
@@ -151,14 +151,12 @@ 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);
       }
       if (al == null)
@@ -228,7 +226,8 @@ public class EnsemblGene extends EnsemblSeqProxy
         return true;
       } catch (NumberFormatException e)
       {
-        System.err.println("Bad integers in description " + description);
+        jalview.bin.Console
+                .errPrintln("Bad integers in description " + description);
       }
     }
     return false;
@@ -320,8 +319,8 @@ public class EnsemblGene extends EnsemblSeqProxy
         SequenceOntologyI.NMD_TRANSCRIPT_VARIANT,
         SequenceOntologyI.TRANSCRIPT, SequenceOntologyI.EXON,
         SequenceOntologyI.CDS };
-    List<SequenceFeature> sfs = gene.getFeatures().getFeaturesByOntology(
-            soTerms);
+    List<SequenceFeature> sfs = gene.getFeatures()
+            .getFeaturesByOntology(soTerms);
     for (SequenceFeature sf : sfs)
     {
       gene.deleteFeature(sf);
@@ -471,8 +470,9 @@ public class EnsemblGene extends EnsemblSeqProxy
       transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
     }
 
-    List<int[]> transcriptRange = Arrays.asList(new int[] {
-        transcript.getStart(), transcript.getEnd() });
+    List<int[]> transcriptRange = Arrays
+            .asList(new int[]
+            { transcript.getStart(), transcript.getEnd() });
     MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
 
     transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(),
@@ -540,10 +540,11 @@ 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
   }
 
   /**
@@ -629,10 +630,10 @@ 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