Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 0f6a5f3..3cca453 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -118,15 +118,50 @@ 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
       {
@@ -138,28 +173,51 @@ 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);
+
+      if (length != -1)
+      {
+        // add 3 to mapped length to allow for a mapped stop codon
+        if (length + 3 >= (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;
     }
 
     /**
      * 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
@@ -174,7 +232,7 @@ public class AlignedCodonFrame
       {
         ds = seq;
       }
-      
+
       if (this.fromSeq == seq || this.fromSeq == ds)
       {
         codon = this.mapping.map.locateInTo(pos, pos);
@@ -383,7 +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
@@ -395,9 +454,16 @@ public class AlignedCodonFrame
           SearchResultsI results)
   {
     SequenceI ds = seq.getDatasetSequence();
+    if (ds == null)
+    {
+      ds = seq;
+    }
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      ssm.markMappedRegion(ds, index, results);
+      if (ssm.covers(seq, true, true))
+      {
+        ssm.markMappedRegion(ds, index, results);
+      }
     }
   }
 
@@ -641,7 +707,8 @@ public class AlignedCodonFrame
             ds.setSequenceFeatures(dna.getSequenceFeatures());
             // dnaSeqs[i] = ds;
             ssm.fromSeq = ds;
-            System.out.println("Realised mapped sequence " + ds.getName());
+            jalview.bin.Console
+                    .outPrintln("Realised mapped sequence " + ds.getName());
           }
         }
       }
@@ -838,9 +905,9 @@ 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