X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=f5154ec1da1d151cebd4e240ff86d20914c90c1e;hb=a81e74154d35e10958b58c3c9411aa9ee21880a6;hp=0927dda472b244a41fd8c2d5c293f5fb64503aa0;hpb=87a707afdbbe1675330f7e82faaf9443af89cefe;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 0927dda..f5154ec 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -118,44 +118,50 @@ public class AlignedCodonFrame
      */
     public boolean covers(SequenceI seq)
     {
-      return covers(seq,false,false);
+      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)
+     * @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)
+    public boolean covers(SequenceI seq, boolean localCover, boolean either)
     {
-      List<int[]> mappedRanges = null,otherRanges=null;
+      List<int[]> mappedRanges = null, otherRanges = null;
       MapList mapList = mapping.getMap();
-      int mstart=seq.getStart(),mend=seq.getEnd(),ostart,oend;
-              ;
+      int mstart = seq.getStart(), mend = seq.getEnd(), ostart, oend;
+      ;
       if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
       {
-        if (localCover && fromSeq !=seq)
+        if (localCover && fromSeq != seq)
         {
-          mstart=fromSeq.getStart();
-          mend=fromSeq.getEnd();
+          mstart = fromSeq.getStart();
+          mend = fromSeq.getEnd();
         }
         mappedRanges = mapList.getFromRanges();
-        otherRanges=mapList.getToRanges();
-        ostart=mapping.to.getStart();
-        oend=mapping.to.getEnd();
+        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)
+        if (localCover && mapping.to != seq)
         {
-          mstart=mapping.to.getStart();
-          mend=mapping.to.getEnd();
+          mstart = mapping.to.getStart();
+          mend = mapping.to.getEnd();
         }
         mappedRanges = mapList.getToRanges();
-        otherRanges=mapList.getFromRanges();
-        ostart=fromSeq.getStart();
-        oend=fromSeq.getEnd();
+        otherRanges = mapList.getFromRanges();
+        ostart = fromSeq.getStart();
+        oend = fromSeq.getEnd();
       }
       else
       {
@@ -167,12 +173,12 @@ public class AlignedCodonFrame
        * (necessary for circular CDS - example EMBL:J03321:AAA91567)
        * and mapped length covers (at least) sequence length
        */
-      int length = countRange(mappedRanges,mstart,mend);
+      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))
+        // add 3 to mapped length to allow for a mapped stop codon
+        if (length + 3 >= (mend - mstart + 1))
         {
           return true;
         }
@@ -191,9 +197,10 @@ public class AlignedCodonFrame
       }
       return false;
     }
-    private int countRange(List<int[]> mappedRanges,int mstart,int mend)
+
+    private int countRange(List<int[]> mappedRanges, int mstart, int mend)
     {
-      int length=0;
+      int length = 0;
       for (int[] range : mappedRanges)
       {
         int from = Math.min(range[0], range[1]);
@@ -209,7 +216,8 @@ public class AlignedCodonFrame
 
     /**
      * Adds any regions mapped to or from position {@code pos} in sequence
-     * {@code seq} to the given search results
+     * {@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
@@ -220,7 +228,11 @@ public class AlignedCodonFrame
       int[] codon = null;
       SequenceI mappedSeq = null;
       SequenceI ds = seq.getDatasetSequence();
-      
+      if (ds == null)
+      {
+        ds = seq;
+      }
+
       if (this.fromSeq == seq || this.fromSeq == ds)
       {
         codon = this.mapping.map.locateInTo(pos, pos);
@@ -429,7 +441,8 @@ 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
@@ -441,44 +454,17 @@ public class AlignedCodonFrame
           SearchResultsI results)
   {
     SequenceI ds = seq.getDatasetSequence();
-    for (SequenceToSequenceMapping ssm : mappings)
+    if (ds == null)
     {
-      ssm.markMappedRegion(ds, index, results);
+      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)
+      if (ssm.covers(seq, true, true))
       {
-        ml = getdnaToProt()[i];
-        break;
+        ssm.markMappedRegion(ds, index, results);
       }
-      i++;
     }
-    return ml == null ? null : ml.locateInFrom(aaPos, aaPos);
   }
 
   /**
@@ -493,39 +479,18 @@ 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)
     {
-      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)
+      if (ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.covers(sourceAligned,true,false))
+          if (ssm.mapping.to == sourceAligned.getDatasetSequence()
+                  || ssm.mapping.to == sourceAligned)
           {
-            if (map != null)
-            {
-              map.add(ssm);
-            }
             return sourceAligned;
           }
         }
@@ -537,19 +502,13 @@ public class AlignedCodonFrame
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      int mStart=ssm.getMapping().getMap().getToLowest(),mEnd=ssm.getMapping().map.getToHighest();
-      if ((ssm.mapping.to == seq
+      if (ssm.mapping.to == seq
               || ssm.mapping.to == seq.getDatasetSequence())
-              && seq.getStart()>=mStart && seq.getEnd()<=mEnd)
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.covers(sourceAligned,true,true))
+          if (ssm.fromSeq == sourceAligned.getDatasetSequence())
           {
-            if (map != null)
-            {
-              map.add(ssm);
-            }
             return sourceAligned;
           }
         }
@@ -945,9 +904,9 @@ public class AlignedCodonFrame
   }
 
   /**
-   * 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.
+   * 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