JAL-3076 refactor for more efficient scan of 'gene' features

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

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index f96f1d5..19065f2 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -581,8 +581,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
           String accId, int start)
   {
-    List<SequenceFeature> sfs = sourceSequence.getFeatures()
-            .getPositionalFeatures();
+    List<SequenceFeature> sfs = getIdentifyingFeatures(sourceSequence,
+            accId);
     if (sfs.isEmpty())
     {
       return null;
@@ -599,47 +599,31 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     for (SequenceFeature sf : sfs)
     {
+      int strand = sf.getStrand();
+      strand = strand == 0 ? 1 : strand; // treat unknown as forward
+
+      if (directionSet && strand != direction)
+      {
+        // abort - mix of forward and backward
+        System.err
+                .println("Error: forward and backward strand for " + accId);
+        return null;
+      }
+      direction = strand;
+      directionSet = true;
+
       /*
-       * accept the target feature type or a specialisation of it
-       * (e.g. coding_exon for exon)
+       * add to CDS ranges, semi-sorted forwards/backwards
        */
-      if (identifiesSequence(sf, accId))
+      if (strand < 0)
       {
-        int strand = sf.getStrand();
-        strand = strand == 0 ? 1 : strand; // treat unknown as forward
-
-        if (directionSet && strand != direction)
-        {
-          // abort - mix of forward and backward
-          System.err.println(
-                  "Error: forward and backward strand for " + accId);
-          return null;
-        }
-        direction = strand;
-        directionSet = true;
-
-        /*
-         * add to CDS ranges, semi-sorted forwards/backwards
-         */
-        if (strand < 0)
-        {
-          regions.add(0, new int[] { sf.getEnd(), sf.getBegin() });
-        }
-        else
-        {
-          regions.add(new int[] { sf.getBegin(), sf.getEnd() });
-        }
-        mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1);
-
-        if (!isSpliceable())
-        {
-          /*
-           * 'gene' sequence is contiguous so we can stop as soon as its
-           * identifying feature has been found
-           */
-          break;
-        }
+        regions.add(0, new int[] { sf.getEnd(), sf.getBegin() });
       }
+      else
+      {
+        regions.add(new int[] { sf.getBegin(), sf.getEnd() });
+      }
+      mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1);
     }
 
     if (regions.isEmpty())
@@ -664,28 +648,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   }
 
   /**
-   * Answers true if the sequence being retrieved may occupy discontiguous
-   * regions on the genomic sequence.
-   */
-  protected boolean isSpliceable()
-  {
-    return true;
-  }
-
-  /**
-   * Returns true if the sequence feature marks positions of the genomic
-   * sequence feature which are within the sequence being retrieved. For
-   * example, an 'exon' feature whose parent is the target transcript marks the
-   * cdna positions of the transcript.
-   * 
-   * @param sf
-   * @param accId
-   * @return
-   */
-  protected abstract boolean identifiesSequence(SequenceFeature sf,
-          String accId);
-
-  /**
    * Answers a list of sequence features that mark positions of the genomic
    * sequence feature which are within the sequence being retrieved. For
    * example, an 'exon' feature whose parent is the target transcript marks the