Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[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 dd2547b..ae85b45 100644 (file)
--- 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;
@@ -56,13 +55,15 @@ public class EnsemblGene extends EnsemblSeqProxy
    * accepts anything as we will attempt lookup of gene or 
    * transcript id or gene name
    */
-  private static final Regex ACCESSION_REGEX = new Regex(".*");
+  private static final Regex ACCESSION_REGEX = Platform.newRegex(".*");
 
   private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
       EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
       EnsemblFeatureType.exon, EnsemblFeatureType.cds,
       EnsemblFeatureType.variation };
 
+  private static final String CHROMOSOME = "chromosome";
+
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -135,48 +136,27 @@ 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)
       {
         continue;
       }
-      
+
       if (geneAlignment.getHeight() == 1)
       {
         // 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];
@@ -341,8 +318,8 @@ 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);
@@ -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<>();
@@ -492,8 +469,9 @@ 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(),
@@ -561,10 +539,11 @@ 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
   }
 
   /**
@@ -600,7 +579,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   @Override
   protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     String type = sf.getType();
     if (so.isA(type, SequenceOntologyI.GENE))
     {
@@ -647,13 +626,13 @@ public class EnsemblGene extends EnsemblSeqProxy
   {
     return new FeatureSettingsAdapter()
     {
-      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
 
       @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