Merge branch 'develop' into features/JAL-2446NCList

[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 37c787b..365c1c2 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.schemes.FeatureColour;
@@ -109,7 +110,8 @@ public class EnsemblGene extends EnsemblSeqProxy
    * <li>resolves an external identifier by looking up xref-ed gene ids</li>
    * <li>fetches the gene sequence</li>
    * <li>fetches features on the sequence</li>
-   * <li>identifies "transcript" features whose Parent is the requested gene</li>
+   * <li>identifies "transcript" features whose Parent is the requested
+   * gene</li>
    * <li>fetches the transcript sequence for each transcript</li>
    * <li>makes a mapping from the gene to each transcript</li>
    * <li>copies features from gene to transcript sequences</li>
@@ -282,22 +284,20 @@ public class EnsemblGene extends EnsemblSeqProxy
    */
   protected void clearGeneFeatures(SequenceI gene)
   {
-    SequenceFeature[] sfs = gene.getSequenceFeatures();
-    if (sfs != null)
+    /*
+     * Note we include NMD_transcript_variant here because it behaves like 
+     * 'transcript' in Ensembl, although strictly speaking it is not 
+     * (it is a sub-type of sequence_variant)    
+     */
+    String[] soTerms = new String[] {
+        SequenceOntologyI.NMD_TRANSCRIPT_VARIANT,
+        SequenceOntologyI.TRANSCRIPT, SequenceOntologyI.EXON,
+        SequenceOntologyI.CDS };
+    List<SequenceFeature> sfs = gene.getFeatures().getFeaturesByOntology(
+            soTerms);
+    for (SequenceFeature sf : sfs)
     {
-      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
-      List<SequenceFeature> filtered = new ArrayList<SequenceFeature>();
-      for (SequenceFeature sf : sfs)
-      {
-        String type = sf.getType();
-        if (!isTranscript(type) && !so.isA(type, SequenceOntologyI.EXON)
-                && !so.isA(type, SequenceOntologyI.CDS))
-        {
-          filtered.add(sf);
-        }
-      }
-      gene.setSequenceFeatures(filtered
-              .toArray(new SequenceFeature[filtered.size()]));
+      gene.deleteFeature(sf);
     }
   }
 
@@ -314,8 +314,8 @@ public class EnsemblGene extends EnsemblSeqProxy
    *          the parent gene sequence, with features
    * @return
    */
-  SequenceI makeTranscript(SequenceFeature transcriptFeature,
-          AlignmentI al, SequenceI gene)
+  SequenceI makeTranscript(SequenceFeature transcriptFeature, AlignmentI al,
+          SequenceI gene)
   {
     String accId = getTranscriptId(transcriptFeature);
     if (accId == null)
@@ -347,6 +347,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     {
       splices = findFeatures(gene, SequenceOntologyI.CDS, parentId);
     }
+    SequenceFeatures.sortFeatures(splices, true);
 
     int transcriptLength = 0;
     final char[] geneChars = gene.getSequence();
@@ -363,7 +364,8 @@ public class EnsemblGene extends EnsemblSeqProxy
       mappedFrom.add(new int[] { sf.getBegin(), sf.getEnd() });
     }
 
-    Sequence transcript = new Sequence(accId, seqChars, 1, transcriptLength);
+    Sequence transcript = new Sequence(accId, seqChars, 1,
+            transcriptLength);
 
     /*
      * Ensembl has gene name as transcript Name
@@ -396,7 +398,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     mapTo.add(new int[] { 1, transcriptLength });
     MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
     EnsemblCdna cdna = new EnsemblCdna(getDomain());
-    cdna.transferFeatures(gene.getSequenceFeatures(),
+    cdna.transferFeatures(gene.getFeatures().getPositionalFeatures(),
             transcript.getDatasetSequence(), mapping, parentId);
 
     /*
@@ -437,19 +439,18 @@ public class EnsemblGene extends EnsemblSeqProxy
     List<SequenceFeature> transcriptFeatures = new ArrayList<SequenceFeature>();
 
     String parentIdentifier = GENE_PREFIX + accId;
-    SequenceFeature[] sfs = geneSequence.getSequenceFeatures();
+    // todo optimise here by transcript type!
+    List<SequenceFeature> sfs = geneSequence.getFeatures()
+            .getPositionalFeatures();
 
-    if (sfs != null)
+    for (SequenceFeature sf : sfs)
     {
-      for (SequenceFeature sf : sfs)
+      if (isTranscript(sf.getType()))
       {
-        if (isTranscript(sf.getType()))
+        String parent = (String) sf.getValue(PARENT);
+        if (parentIdentifier.equals(parent))
         {
-          String parent = (String) sf.getValue(PARENT);
-          if (parentIdentifier.equals(parent))
-          {
-            transcriptFeatures.add(sf);
-          }
+          transcriptFeatures.add(sf);
         }
       }
     }
@@ -567,8 +568,8 @@ public class EnsemblGene extends EnsemblSeqProxy
       @Override
       public boolean isFeatureDisplayed(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