JAL-1705 refactor show products, set initial split frame divider

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index d45750e..2f6076a 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -219,30 +219,23 @@ public class CrossRef
 
   /**
    * 
-   * @param dna
-   * @param seqs
-   * @return
-   */
-  public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
-          String source)
-  {
-    return findXrefSequences(seqs, dna, source, null);
-  }
-
-  /**
-   * 
    * @param seqs
    *          sequences whose xrefs are being retrieved
    * @param dna
    *          true if sequences are nucleotide
    * @param source
-   * @param dataset
-   *          alignment to search for product sequences.
+   * @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, boolean dna,
-          String source, AlignmentI dataset)
+          String source, AlignmentI al, List<SequenceI> addedPeers)
   {
+    AlignmentI dataset = al.getDataset() == null ? al : al.getDataset();
     List<SequenceI> rseqs = new ArrayList<SequenceI>();
     AlignedCodonFrame cf = new AlignedCodonFrame();
     for (SequenceI seq : seqs)
@@ -389,10 +382,12 @@ public class CrossRef
                           int sf = map.getMap().getToLowest();
                           int st = map.getMap().getToHighest();
                           SequenceI mappedrg = ms.getSubSequence(sf, st);
-                          SequenceI loc = dss.getSubSequence(sf, st);
+                          // SequenceI loc = dss.getSubSequence(sf, st);
                           if (mappedrg.getLength() > 0
-                                  && mappedrg.getSequenceAsString().equals(
-                                          loc.getSequenceAsString()))
+                                  && ms.getSequenceAsString().equals(
+                                          dss.getSequenceAsString()))
+                          // && mappedrg.getSequenceAsString().equals(
+                          // loc.getSequenceAsString()))
                           {
                             String msg = "Mapping updated from "
                                     + ms.getName()
@@ -414,8 +409,8 @@ public class CrossRef
                               for (SequenceFeature feat : sfs)
                               {
                                 /* 
-                                 * we override the equality test here (but not
-                                 * elsewhere) to ignore Parent attribute
+                                 * we override SequenceFeature.equals here (but
+                                 * not elsewhere) to ignore Parent attribute
                                  * TODO not quite working yet!
                                  */
                                 if (!copiedFeatures
@@ -430,6 +425,12 @@ public class CrossRef
                             cf.addMap(retrieved[rs].getDatasetSequence(),
                                     dss, map.getMap());
                           }
+                          else
+                          {
+                            addedPeers.add(map.getTo());
+                            cf.addMap(retrieved[rs].getDatasetSequence(),
+                                    map.getTo(), map.getMap());
+                          }
                         } catch (Exception e)
                         {
                           System.err
@@ -452,9 +453,7 @@ public class CrossRef
     Alignment ral = null;
     if (rseqs.size() > 0)
     {
-      SequenceI[] rsqs = new SequenceI[rseqs.size()];
-      rseqs.toArray(rsqs);
-      ral = new Alignment(rsqs);
+      ral = new Alignment(rseqs.toArray(new SequenceI[rseqs.size()]));
       if (cf != null && !cf.isEmpty())
       {
         ral.addCodonFrame(cf);