Merge branch 'bug/JAL-3806_mappingCoversSequence_for2112' into develop

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

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index eda1a13..b376c80 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -20,13 +20,13 @@
  */
 package jalview.datamodel;
 
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-
 import java.util.AbstractList;
 import java.util.ArrayList;
 import java.util.List;
 
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+
 /**
  * Stores mapping between the columns of a protein alignment and a DNA alignment
  * and a list of individual codon to amino acid mappings between sequences.
@@ -107,7 +107,7 @@ public class AlignedCodonFrame
     {
       return mapping;
     }
-    
+
     /**
      * Returns true if the mapping covers the full length of the given sequence.
      * This allows us to distinguish the CDS that codes for a protein from
@@ -210,7 +210,7 @@ public class AlignedCodonFrame
     /**
      * Adds any regions mapped to or from position {@code pos} in sequence
      * {@code seq} to the given search results
-     * 
+     * Note: recommend first using the .covers(,true,true) to ensure mapping covers both sequences
      * @param seq
      * @param pos
      * @param sr
@@ -398,9 +398,12 @@ public class AlignedCodonFrame
   }
 
   /**
+   * Return the corresponding aligned or dataset dna sequence for given amino
+   * acid sequence, or null if not found. returns the sequence from the first
+   * mapping found that involves the protein sequence.
    * 
-   * @param sequenceRef
-   * @return null or corresponding aaSeq entry for dnaSeq entry
+   * @param aaSeqRef
+   * @return
    */
   public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
   {
@@ -430,7 +433,8 @@ public class AlignedCodonFrame
 
   /**
    * Add search results for regions in other sequences that translate or are
-   * translated from a particular position in seq
+   * translated from a particular position in seq (which may be an aligned or
+   * dataset sequence)
    * 
    * @param seq
    * @param index
@@ -441,71 +445,17 @@ public class AlignedCodonFrame
   public void markMappedRegion(SequenceI seq, int index,
           SearchResultsI results)
   {
-    int[] codon;
     SequenceI ds = seq.getDatasetSequence();
-    for (SequenceToSequenceMapping ssm : mappings)
+    if (ds == null)
     {
-      if (ssm.covers(seq,true,true))
-      {
-      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]);
-            }
-          }
-        }
-      }}
+      ds = seq;
     }
-  }
-
-  /**
-   * Returns the DNA codon positions (base 1) for the given position (base 1) in
-   * a mapped protein sequence, or null if no mapping is found.
-   * 
-   * Intended for use in aligning cDNA to match aligned protein. Only the first
-   * mapping found is returned, so not suitable for use if multiple protein
-   * sequences are mapped to the same cDNA (but aligning cDNA as protein is
-   * ill-defined for this case anyway).
-   * 
-   * @param seq
-   *          the DNA dataset sequence
-   * @param aaPos
-   *          residue position (base 1) in a protein sequence
-   * @return
-   */
-  public int[] getDnaPosition(SequenceI seq, int aaPos)
-  {
-    /*
-     * Adapted from markMappedRegion().
-     */
-    MapList ml = null;
-    int i = 0;
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.fromSeq == seq)
-      {
-        ml = getdnaToProt()[i];
-        break;
+      if (ssm.covers(seq,true,true)) {
+        ssm.markMappedRegion(ds, index, results);
       }
-      i++;
     }
-    return ml == null ? null : ml.locateInFrom(aaPos, aaPos);
   }
 
   /**
@@ -906,7 +856,7 @@ public class AlignedCodonFrame
    * Two AlignedCodonFrame objects are equal if they hold the same ordered list
    * of mappings
    * 
-   * @see SequenceToSequenceMapping#
+   * @see SequenceToSequenceMapping#equals
    */
   @Override
   public boolean equals(Object obj)
@@ -922,4 +872,55 @@ public class AlignedCodonFrame
   {
     return mappings;
   }
+
+  /**
+   * Returns the first mapping found which is between the two given sequences,
+   * and covers the full extent of both.
+   * 
+   * @param seq1
+   * @param seq2
+   * @return
+   */
+  public SequenceToSequenceMapping getCoveringMapping(SequenceI seq1,
+          SequenceI seq2)
+  {
+    for (SequenceToSequenceMapping mapping : mappings)
+    {
+      if (mapping.covers(seq2) && mapping.covers(seq1))
+      {
+        return mapping;
+      }
+    }
+    return null;
+  }
+
+  /**
+   * Returns the first mapping found which is between the given dataset 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;
+  }
 }