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 2f33e43..b376c80 100644 (file)
--- 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
       {
@@ -138,29 +167,50 @@ 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 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
-     * 
+     * Note: recommend first using the .covers(,true,true) to ensure mapping covers both sequences
      * @param seq
      * @param pos
      * @param sr
@@ -402,7 +452,9 @@ public class AlignedCodonFrame
     }
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      ssm.markMappedRegion(ds, index, results);
+      if (ssm.covers(seq,true,true)) {
+        ssm.markMappedRegion(ds, index, results);
+      }
     }
   }