X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=d59078bb5cf50ea90338e69ae21a52fc23464d46;hb=96a5726c430b26ed83fc8ee3be0c7ea871519fa1;hp=aca523eaf7a3b51ad4885729f819fa7f8b7a33bf;hpb=c604058f0c3be7bd38baa8ac01cff87989deecd5;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index aca523e..d59078b 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -156,6 +156,40 @@ public class AlignedCodonFrame
       }
       return true;
     }
+
+    /**
+     * Adds any regions mapped to or from position {@code pos} in sequence
+     * {@code seq} to the given search results
+     * 
+     * @param seq
+     * @param pos
+     * @param sr
+     */
+    public void markMappedRegion(SequenceI seq, int pos, SearchResultsI sr)
+    {
+      int[] codon = null;
+      SequenceI mappedSeq = null;
+      SequenceI ds = seq.getDatasetSequence();
+      
+      if (this.fromSeq == seq || this.fromSeq == ds)
+      {
+        codon = this.mapping.map.locateInTo(pos, pos);
+        mappedSeq = this.mapping.to;
+      }
+      else if (this.mapping.to == seq || this.mapping.to == ds)
+      {
+        codon = this.mapping.map.locateInFrom(pos, pos);
+        mappedSeq = this.fromSeq;
+      }
+
+      if (codon != null)
+      {
+        for (int i = 0; i < codon.length; i += 2)
+        {
+          sr.addResult(mappedSeq, codon[i], codon[i + 1]);
+        }
+      }
+    }
   }
 
   private List<SequenceToSequenceMapping> mappings;
@@ -356,34 +390,10 @@ public class AlignedCodonFrame
   public void markMappedRegion(SequenceI seq, int index,
           SearchResultsI results)
   {
-    int[] codon;
     SequenceI ds = seq.getDatasetSequence();
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.fromSeq == seq || ssm.fromSeq == ds)
-      {
-        codon = ssm.mapping.map.locateInTo(index, index);
-        if (codon != null)
-        {
-          for (int i = 0; i < codon.length; i += 2)
-          {
-            results.addResult(ssm.mapping.to, codon[i], codon[i + 1]);
-          }
-        }
-      }
-      else if (ssm.mapping.to == seq || ssm.mapping.to == ds)
-      {
-        {
-          codon = ssm.mapping.map.locateInFrom(index, index);
-          if (codon != null)
-          {
-            for (int i = 0; i < codon.length; i += 2)
-            {
-              results.addResult(ssm.fromSeq, codon[i], codon[i + 1]);
-            }
-          }
-        }
-      }
+      ssm.markMappedRegion(ds, index, results);
     }
   }
 
@@ -856,4 +866,34 @@ public class AlignedCodonFrame
     }
     return null;
   }
+
+  /**
+   * Returns the first mapping found which is between the given sequence and
+   * another, is a triplet mapping (3:1 or 1:3), and covers the full extent of
+   * both sequences involved.
+   * 
+   * @param seq
+   * @return
+   */
+  public SequenceToSequenceMapping getCoveringCodonMapping(SequenceI seq)
+  {
+    for (SequenceToSequenceMapping mapping : mappings)
+    {
+      if (mapping.getMapping().getMap().isTripletMap()
+              && mapping.covers(seq))
+      {
+        if (mapping.fromSeq == seq
+                && mapping.covers(mapping.getMapping().getTo()))
+        {
+          return mapping;
+        }
+        else if (mapping.getMapping().getTo() == seq
+                && mapping.covers(mapping.fromSeq))
+        {
+          return mapping;
+        }
+      }
+    }
+    return null;
+  }
 }