X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=25f1c2797784480a8b532645891ea6ab5a147a68;hb=48f5f04700dcb49463b20303c2075292f9d4d1d3;hp=7fa8b293e5a4f4ba4f0df0782491ea7bf9714a3a;hpb=e132642765c503cb0c93dc47f304007d0527c2cc;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 7fa8b29..25f1c27 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -118,15 +118,44 @@ public class AlignedCodonFrame
      */
     public boolean covers(SequenceI seq)
     {
-      List<int[]> mappedRanges = null;
+      return covers(seq,false,false);
+    }
+    /**
+     * 
+     * @param seq
+     * @param localCover - when true - compare extent of seq's dataset sequence rather than the local extent
+     * @param either - when true coverage is required for either seq or the mapped sequence 
+     * @return true if mapping covers full length of given sequence (or the other if either==true)
+     */
+    public boolean covers(SequenceI seq, boolean localCover,boolean either)
+    {
+      List<int[]> mappedRanges = null,otherRanges=null;
       MapList mapList = mapping.getMap();
+      int mstart=seq.getStart(),mend=seq.getEnd(),ostart,oend;
+              ;
       if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
       {
+        if (localCover && fromSeq !=seq)
+        {
+          mstart=fromSeq.getStart();
+          mend=fromSeq.getEnd();
+        }
         mappedRanges = mapList.getFromRanges();
+        otherRanges=mapList.getToRanges();
+        ostart=mapping.to.getStart();
+        oend=mapping.to.getEnd();
       }
       else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
       {
+        if (localCover && mapping.to !=seq)
+        {
+          mstart=mapping.to.getStart();
+          mend=mapping.to.getEnd();
+        }
         mappedRanges = mapList.getToRanges();
+        otherRanges=mapList.getFromRanges();
+        ostart=fromSeq.getStart();
+        oend=fromSeq.getEnd();
       }
       else
       {
@@ -138,23 +167,44 @@ public class AlignedCodonFrame
        * (necessary for circular CDS - example EMBL:J03321:AAA91567)
        * and mapped length covers (at least) sequence length
        */
-      int length = 0;
+      int length = countRange(mappedRanges,mstart,mend);
+
+      if (length != -1)
+      {
+        // add 1 to mapped length to allow for a mapped stop codon
+        if (length + 1 >= (mend - mstart + 1))
+        {
+          return true;
+        }
+      }
+      if (either)
+      {
+        // also check coverage of the other range
+        length = countRange(otherRanges, ostart, oend);
+        if (length != -1)
+        {
+          if (length + 1 >= (oend - ostart + 1))
+          {
+            return true;
+          }
+        }
+      }
+      return false;
+    }
+    private int countRange(List<int[]> mappedRanges,int mstart,int mend)
+    {
+      int length=0;
       for (int[] range : mappedRanges)
       {
         int from = Math.min(range[0], range[1]);
         int to = Math.max(range[0], range[1]);
-        if (from < seq.getStart() || to > seq.getEnd())
+        if (from < mstart || to > mend)
         {
-          return false;
+          return -1;
         }
         length += (to - from + 1);
       }
-      // add 1 to mapped length to allow for a mapped stop codon
-      if (length + 1 < (seq.getEnd() - seq.getStart() + 1))
-      {
-        return false;
-      }
-      return true;
+      return length;
     }
   }
 
@@ -311,8 +361,8 @@ 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.
+   * acid sequence, or null if not found. returns the sequence from the first
+   * mapping found that involves the protein sequence.
    * 
    * @param aaSeqRef
    * @return
@@ -433,18 +483,39 @@ public class AlignedCodonFrame
    */
   public SequenceI findAlignedSequence(SequenceI seq, AlignmentI al)
   {
+    return findAlignedSequence(seq, al, null);
+  }
+  /**
+   * Convenience method to return the first aligned sequence in the given
+   * alignment whose dataset has a mapping with the given (aligned or dataset)
+   * sequence, and optionally the mapping that relates them 
+   * 
+   * @param seq
+   * @param al
+   * @param map - list to add the mapping to
+   * @return sequence from al that maps to seq
+   */
+  public SequenceI findAlignedSequence(SequenceI seq, AlignmentI al,List<SequenceToSequenceMapping> map)
+  {
     /*
      * Search mapped protein ('to') sequences first.
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
+      int mStart=ssm.getMapping().getMap().getFromLowest(),mEnd=ssm.getMapping().map.getFromHighest();
+      if ((ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
+              // here AlignmentUtilsTest. testAlignProteinAsDna_incompleteStartCodon fails because mStart/mEnd is contained by seq
+              // without this filter, we don't get the correct mapping, however
+           )//   && seq.getStart()>=mStart && seq.getEnd()<=mEnd)
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.mapping.to == sourceAligned.getDatasetSequence()
-                  || ssm.mapping.to == sourceAligned)
+          if (ssm.covers(sourceAligned,true,false))
           {
+            if (map != null)
+            {
+              map.add(ssm);
+            }
             return sourceAligned;
           }
         }
@@ -456,13 +527,19 @@ public class AlignedCodonFrame
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.mapping.to == seq
+      int mStart=ssm.getMapping().getMap().getToLowest(),mEnd=ssm.getMapping().map.getToHighest();
+      if ((ssm.mapping.to == seq
               || ssm.mapping.to == seq.getDatasetSequence())
+              && seq.getStart()>=mStart && seq.getEnd()<=mEnd)
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.fromSeq == sourceAligned.getDatasetSequence())
+          if (ssm.covers(sourceAligned,true,true))
           {
+            if (map != null)
+            {
+              map.add(ssm);
+            }
             return sourceAligned;
           }
         }
@@ -819,7 +896,7 @@ 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)
@@ -836,12 +913,20 @@ public class AlignedCodonFrame
     return mappings;
   }
 
-  public SequenceToSequenceMapping getCoveringMapping(SequenceI cds,
-          SequenceI peptide)
+  /**
+   * 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(peptide) && mapping.covers(cds))
+      if (mapping.covers(seq2) && mapping.covers(seq1))
       {
         return mapping;
       }