X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=bb705b682e16c8788db89ab44ee093ad51693b9f;hb=90ad4273c7105b7763247192e1c6739eed30ba4c;hp=473a534954a4ed1ddcb545d7ed21156fa7342f39;hpb=98ed247d8b6d868cb25550d816a1c165373ffb0f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 473a534..bb705b6 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -60,14 +60,15 @@ public class AlignedCodonFrame
     }
 
     /**
-     * Returns a hashCode derived from the hashcodes of the mappings
+     * Returns a hashCode derived from the hashcodes of the mappings and fromSeq
      * 
      * @see SequenceToSequenceMapping#hashCode()
      */
     @Override
     public int hashCode()
     {
-      return mapping.hashCode();
+      return (fromSeq == null ? 0 : fromSeq.hashCode() * 31)
+              + mapping.hashCode();
     }
 
     /**
@@ -88,7 +89,12 @@ public class AlignedCodonFrame
       {
         return that.mapping == null;
       }
-      return this.mapping.equals(that.mapping);
+      // TODO: can simplify by asserting fromSeq is a dataset sequence
+      return (this.fromSeq == that.fromSeq || (this.fromSeq != null
+              && that.fromSeq != null
+              && this.fromSeq.getDatasetSequence() != null && this.fromSeq
+              .getDatasetSequence() == that.fromSeq
+              .getDatasetSequence())) && this.mapping.equals(that.mapping);
     }
 
     public SequenceI getFromSeq()
@@ -466,7 +472,8 @@ public class AlignedCodonFrame
 
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.mapping.to == protein)
+      if (ssm.mapping.to == protein
+              && ssm.mapping.getMap().getFromRatio() == 3)
       {
         ml = ssm.mapping.map;
         dnaSeq = ssm.fromSeq;
@@ -696,7 +703,7 @@ public class AlignedCodonFrame
   }
 
   /**
-   * Returns the first mapping found that is from 'fromSeq' to 'toSeq', or null
+   * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or null
    * if none found
    * 
    * @param fromSeq
@@ -707,12 +714,17 @@ public class AlignedCodonFrame
    */
   public Mapping getMappingBetween(SequenceI fromSeq, SequenceI toSeq)
   {
+    SequenceI dssFrom = fromSeq.getDatasetSequence() == null ? fromSeq
+            : fromSeq.getDatasetSequence();
+    SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq : toSeq
+            .getDatasetSequence();
+
     for (SequenceToSequenceMapping mapping : mappings)
     {
       SequenceI from = mapping.fromSeq;
       SequenceI to = mapping.mapping.to;
-      if ((from == fromSeq || from == fromSeq.getDatasetSequence())
-              && (to == toSeq || to == toSeq.getDatasetSequence()))
+      if ((from == dssFrom && to == dssTo)
+              || (from == dssTo && to == dssFrom))
       {
         return mapping.mapping;
       }