JAL-2189 source formatting

[jalview.git] / src / jalview / datamodel / AlignedCodonFrame.java

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 18aaecf..c5204eb 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -93,8 +93,8 @@ public class AlignedCodonFrame
       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);
+              .getDatasetSequence() == that.fromSeq.getDatasetSequence()))
+              && this.mapping.equals(that.mapping);
     }
 
     public SequenceI getFromSeq()
@@ -128,6 +128,21 @@ public class AlignedCodonFrame
    */
   public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)
   {
+    addMap(dnaseq, aaseq, map, null);
+  }
+
+  /**
+   * Adds a mapping between the dataset sequences for the associated dna and
+   * protein sequence objects
+   * 
+   * @param dnaseq
+   * @param aaseq
+   * @param map
+   * @param mapFromId
+   */
+  public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map,
+          String mapFromId)
+  {
     // JBPNote DEBUG! THIS !
     // dnaseq.transferAnnotation(aaseq, mp);
     // aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
@@ -155,6 +170,7 @@ public class AlignedCodonFrame
      * otherwise, add a new sequence mapping
      */
     Mapping mp = new Mapping(toSeq, map);
+    mp.setMappedFromId(mapFromId);
     mappings.add(new SequenceToSequenceMapping(fromSeq, mp));
   }
 
@@ -472,7 +488,8 @@ 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;
@@ -702,8 +719,8 @@ public class AlignedCodonFrame
   }
 
   /**
-   * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or null
-   * if none found
+   * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or
+   * null if none found
    * 
    * @param fromSeq
    *          aligned or dataset sequence