Jalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>

[jalview.git] / src / jalview / ext / ensembl / EnsemblGene.java

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 7648536..dd2547b 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -34,6 +34,7 @@ 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;
@@ -134,17 +135,29 @@ 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)
       {
@@ -156,8 +169,14 @@ 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)
@@ -169,6 +188,9 @@ public class EnsemblGene extends EnsemblSeqProxy
         al.append(geneAlignment);
       }
     }
+    
+    Platform.timeCheck("EG done", Platform.TIME_MARK);   
+
     return al;
   }