X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=6d6cdb55194f818ce6c16d2e2b3079eb21c179af;hb=1c6ddae580d69eb0fa5b4291ba84fd6ba9b83621;hp=5dfd434e81bd29af02855a6f9e833f633959a1ee;hpb=36394666b7848eb7c2569188dad062c7d450d612;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 5dfd434..6d6cdb5 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -303,7 +303,8 @@ public class AlignedCodonFrame
 
   /**
    * Convenience method to return the first aligned sequence in the given
-   * alignment whose dataset has a mapping with the given dataset sequence.
+   * alignment whose dataset has a mapping with the given (aligned or dataset)
+   * sequence.
    * 
    * @param seq
    * 
@@ -317,11 +318,12 @@ public class AlignedCodonFrame
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.fromSeq == seq)
+      if (ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.mapping.to == sourceAligned.getDatasetSequence())
+          if (ssm.mapping.to == sourceAligned.getDatasetSequence()
+                  || ssm.mapping.to == sourceAligned)
           {
             return sourceAligned;
           }
@@ -334,7 +336,8 @@ public class AlignedCodonFrame
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.mapping.to == seq)
+      if (ssm.mapping.to == seq
+              || ssm.mapping.to == seq.getDatasetSequence())
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
@@ -443,13 +446,13 @@ public class AlignedCodonFrame
   }
 
   /**
-   * Returns any mappings found which are to (or from) the given sequence, and
-   * to distinct sequences.
+   * Returns any mappings found which are from the given sequence, and to
+   * distinct sequences.
    * 
    * @param seq
    * @return
    */
-  public List<Mapping> getMappingsForSequence(SequenceI seq)
+  public List<Mapping> getMappingsFromSequence(SequenceI seq)
   {
     List<Mapping> result = new ArrayList<Mapping>();
     List<SequenceI> related = new ArrayList<SequenceI>();
@@ -459,7 +462,7 @@ public class AlignedCodonFrame
     for (SequenceToSequenceMapping ssm : mappings)
     {
       final Mapping mapping = ssm.mapping;
-      if (ssm.fromSeq == seqDs || mapping.to == seqDs)
+      if (ssm.fromSeq == seqDs)
       {
         if (!related.contains(mapping.to))
         {
@@ -637,4 +640,38 @@ public class AlignedCodonFrame
   {
     return mappings.isEmpty();
   }
+
+  /**
+   * Method for debug / inspection purposes only, may change in future
+   */
+  @Override
+  public String toString()
+  {
+    return mappings == null ? "null" : mappings.toString();
+  }
+
+  /**
+   * Returns the first mapping found that is from 'fromSeq' to 'toSeq', or null
+   * if none found
+   * 
+   * @param fromSeq
+   *          aligned or dataset sequence
+   * @param toSeq
+   *          aligned or dataset sequence
+   * @return
+   */
+  public Mapping getMappingBetween(SequenceI fromSeq, SequenceI toSeq)
+  {
+    for (SequenceToSequenceMapping mapping : mappings)
+    {
+      SequenceI from = mapping.fromSeq;
+      SequenceI to = mapping.mapping.to;
+      if ((from == fromSeq || from == fromSeq.getDatasetSequence())
+              && (to == toSeq || to == toSeq.getDatasetSequence()))
+      {
+        return mapping.mapping;
+      }
+    }
+    return null;
+  }
 }