JAL-2023 adjustments to mappings added for split frame to avoid

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index d48c14a..7e77fc1 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.
@@ -332,8 +327,8 @@ public class CrossRef
           }
           if (l > 0)
           {
-            System.out
-                    .println("Attempting to retrieve cross referenced sequences.");
+            // System.out
+            // .println("Attempting to retrieve cross referenced sequences.");
             DBRefEntry[] t = new DBRefEntry[l];
             l = 0;
             for (int r = 0; r < xrfs.length; r++)
@@ -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++)
@@ -385,6 +379,15 @@ public class CrossRef
                                 .findIdMatch(map.getTo());
                         if (matched != null)
                         {
+                          /*
+                           * already got an xref to this sequence; update this
+                           * map to point to the same sequence, and add
+                           * any new dbrefs to it
+                           */
+                          for (DBRefEntry ref : map.getTo().getDBRefs())
+                          {
+                            matched.addDBRef(ref); // add or update mapping
+                          }
                           map.setTo(matched);
                         }
                         else
@@ -417,7 +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();
@@ -444,10 +448,6 @@ public class CrossRef
                           }
                           else
                           {
-                            if (!addedPeers.contains(map.getTo()))
-                            {
-                              addedPeers.add(map.getTo());
-                            }
                             cf.addMap(retrieved[rs].getDatasetSequence(),
                                     map.getTo(), map.getMap());
                           }