JAL-1705 refactoring etc for fetching Ensembl --> Uniprot

[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 ec5780f..2086eba 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCds.java
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -5,8 +5,19 @@ import jalview.datamodel.SequenceI;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 
+import java.util.ArrayList;
 import java.util.List;
 
+/**
+ * A client for direct fetching of CDS sequences from Ensembl (i.e. that part of
+ * the genomic sequence that is translated to protein)
+ * 
+ * TODO: not currently used as CDS sequences are computed from CDS features on
+ * transcripts - delete this class?
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblCds extends EnsemblSeqProxy
 {
   /*
@@ -18,13 +29,23 @@ public class EnsemblCds extends EnsemblSeqProxy
       EnsemblFeatureType.variation };
 
   /**
-   * Constructor
+   * Default constructor (to use rest.ensembl.org)
    */
   public EnsemblCds()
   {
     super();
   }
 
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblCds(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
@@ -86,12 +107,12 @@ public class EnsemblCds extends EnsemblSeqProxy
    * 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)
+  protected List<int[]> getCdsRanges(SequenceI dnaSeq)
   {
     int len = dnaSeq.getLength();
+    List<int[]> ranges = new ArrayList<int[]>();
     ranges.add(new int[] { 1, len });
-    return len;
+    return ranges;
   }
 
 }