JAL-1705 tests added, minor bugfix and refactoring

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

diff --git a/src/jalview/ext/ensembl/EnsemblCds.java b/src/jalview/ext/ensembl/EnsemblCds.java
index 7d0b6fd..22c0a06 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCds.java
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -1,8 +1,11 @@
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 import jalview.io.gff.SequenceOntology;
 
+import java.util.List;
+
 public class EnsemblCds extends EnsemblSeqProxy
 {
   /*
@@ -76,4 +79,18 @@ public class EnsemblCds extends EnsemblSeqProxy
     return false;
   }
 
+  /**
+   * Overrides this method to trivially return a range which is the whole of the
+   * nucleotide sequence. This is both faster than scanning for CDS features,
+   * and also means we don't need to keep CDS features on CDS sequence (where
+   * they are redundant information).
+   */
+  @Override
+  protected int getCdsRanges(SequenceI dnaSeq, List<int[]> ranges)
+  {
+    int len = dnaSeq.getLength();
+    ranges.add(new int[] { 1, len });
+    return len;
+  }
+
 }