JAL-1705 reworked AlignmentUtils.makeCdsAlignment and associated code

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 0f7a754..3563eba 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -228,14 +228,10 @@ public class CrossRef
    * @param al
    *          alignment to search for cross-referenced sequences (and possibly
    *          add to)
-   * @param addedPeers
-   *          a list of sequences to add to if 'peers' to the original sequences
-   *          are found e.g. alternative protein products for a protein's gene
    * @return products (as dataset sequences)
    */
   public static Alignment findXrefSequences(SequenceI[] seqs,
-          final boolean dna, final String source, AlignmentI al,
-          List<SequenceI> addedPeers)
+          final boolean dna, final String source, AlignmentI al)
   {
     AlignmentI dataset = al.getDataset() == null ? al : al.getDataset();
     List<SequenceI> rseqs = new ArrayList<SequenceI>();
@@ -298,7 +294,6 @@ public class CrossRef
           {
             found |= searchDataset(dss, xref, dataset, rseqs, cf, false,
                     !dna);
-            // ,false,!dna);
             if (found)
             {
               xrfs[r] = null; // we've recovered seqs for this one.
@@ -363,7 +358,6 @@ public class CrossRef
 
               SequenceIdMatcher matcher = new SequenceIdMatcher(
                       dataset.getSequences());
-              matcher.addAll(addedPeers);
               List<SequenceFeature> copiedFeatures = new ArrayList<SequenceFeature>();
               CrossRef me = new CrossRef();
               for (int rs = 0; rs < retrieved.length; rs++)
@@ -392,7 +386,7 @@ public class CrossRef
                            */
                           for (DBRefEntry ref : map.getTo().getDBRefs())
                           {
-                            matched.addDBRef(ref);
+                            matched.addDBRef(ref); // add or update mapping
                           }
                           map.setTo(matched);
                         }
@@ -426,7 +420,8 @@ public class CrossRef
                             map.setTo(dss);
                             /*
                              * copy sequence features as well, avoiding
-                             * duplication (e.g. from 2 transcripts)
+                             * duplication (e.g. same variation from 2 
+                             * transcripts)
                              */
                             SequenceFeature[] sfs = ms
                                     .getSequenceFeatures();
@@ -453,10 +448,6 @@ public class CrossRef
                           }
                           else
                           {
-                            if (!addedPeers.contains(map.getTo()))
-                            {
-                              addedPeers.add(map.getTo());
-                            }
                             cf.addMap(retrieved[rs].getDatasetSequence(),
                                     map.getTo(), map.getMap());
                           }