JAL-3700 check for 'covering' mapping when matching CDS to peptides

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index fffa137..7fa8b29 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -107,6 +107,55 @@ 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
+     * another overlapping CDS in the parent dna sequence.
+     * 
+     * @param seq
+     * @return
+     */
+    public boolean covers(SequenceI seq)
+    {
+      List<int[]> mappedRanges = null;
+      MapList mapList = mapping.getMap();
+      if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
+      {
+        mappedRanges = mapList.getFromRanges();
+      }
+      else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
+      {
+        mappedRanges = mapList.getToRanges();
+      }
+      else
+      {
+        return false;
+      }
+
+      /*
+       * check that each mapped range lieS with the sequence range
+       * (necessary for circular CDS - example EMBL:J03321:AAA91567)
+       * and mapped length covers (at least) sequence length
+       */
+      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())
+        {
+          return false;
+        }
+        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;
+    }
   }
 
   private List<SequenceToSequenceMapping> mappings;
@@ -261,9 +310,12 @@ 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)
   {
@@ -783,4 +835,17 @@ public class AlignedCodonFrame
   {
     return mappings;
   }
+
+  public SequenceToSequenceMapping getCoveringMapping(SequenceI cds,
+          SequenceI peptide)
+  {
+    for (SequenceToSequenceMapping mapping : mappings)
+    {
+      if (mapping.covers(peptide) && mapping.covers(cds))
+      {
+        return mapping;
+      }
+    }
+    return null;
+  }
 }

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index b552c21..1aaec99 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -28,6 +28,7 @@ import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
@@ -364,52 +365,45 @@ public final class MappingUtils
 
       for (AlignedCodonFrame acf : codonFrames)
       {
-        SequenceI mappedSequence = targetIsNucleotide
-                ? acf.getDnaForAaSeq(selected)
-                : acf.getAaForDnaSeq(selected);
-        if (mappedSequence != null)
+        for (SequenceI seq : mapTo.getAlignment().getSequences())
         {
-          for (SequenceI seq : mapTo.getAlignment().getSequences())
+          SequenceI peptide = targetIsNucleotide ? selected : seq;
+          SequenceI cds = targetIsNucleotide ? seq : selected;
+          SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
+                  peptide);
+          if (s2s == null)
           {
-            int mappedStartResidue = 0;
-            int mappedEndResidue = 0;
-            if (seq.getDatasetSequence() == mappedSequence)
-            {
-              /*
-               * Found a sequence mapping. Locate the start/end mapped residues.
-               */
-              List<AlignedCodonFrame> mapping = Arrays
-                      .asList(new AlignedCodonFrame[]
-                      { acf });
-              SearchResultsI sr = buildSearchResults(selected,
-                      startResiduePos, mapping);
-              for (SearchResultMatchI m : sr.getResults())
-              {
-                mappedStartResidue = m.getStart();
-                mappedEndResidue = m.getEnd();
-              }
-              sr = buildSearchResults(selected, endResiduePos, mapping);
-              for (SearchResultMatchI m : sr.getResults())
-              {
-                mappedStartResidue = Math.min(mappedStartResidue,
-                        m.getStart());
-                mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
-              }
-
-              /*
-               * Find the mapped aligned columns, save the range. Note findIndex
-               * returns a base 1 position, SequenceGroup uses base 0
-               */
-              int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
-              minStartCol = minStartCol == -1 ? mappedStartCol
-                      : Math.min(minStartCol, mappedStartCol);
-              int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
-              maxEndCol = maxEndCol == -1 ? mappedEndCol
-                      : Math.max(maxEndCol, mappedEndCol);
-              mappedGroup.addSequence(seq, false);
-              break;
-            }
+            continue;
           }
+          int mappedStartResidue = 0;
+          int mappedEndResidue = 0;
+          List<AlignedCodonFrame> mapping = Arrays.asList(acf);
+          SearchResultsI sr = buildSearchResults(selected, startResiduePos,
+                  mapping);
+          for (SearchResultMatchI m : sr.getResults())
+          {
+            mappedStartResidue = m.getStart();
+            mappedEndResidue = m.getEnd();
+          }
+          sr = buildSearchResults(selected, endResiduePos, mapping);
+          for (SearchResultMatchI m : sr.getResults())
+          {
+            mappedStartResidue = Math.min(mappedStartResidue, m.getStart());
+            mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
+          }
+
+          /*
+           * Find the mapped aligned columns, save the range. Note findIndex
+           * returns a base 1 position, SequenceGroup uses base 0
+           */
+          int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
+          minStartCol = minStartCol == -1 ? mappedStartCol
+                  : Math.min(minStartCol, mappedStartCol);
+          int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
+          maxEndCol = maxEndCol == -1 ? mappedEndCol
+                  : Math.max(maxEndCol, mappedEndCol);
+          mappedGroup.addSequence(seq, false);
+          break;
         }
       }
     }
@@ -524,7 +518,7 @@ public final class MappingUtils
 
     if (colsel == null)
     {
-      return; // mappedColumns;
+      return; 
     }
 
     char fromGapChar = mapFrom.getAlignment().getGapCharacter();
@@ -546,10 +540,9 @@ public final class MappingUtils
     while (regions.hasNext())
     {
       mapHiddenColumns(regions.next(), codonFrames, newHidden,
-              fromSequences,
-              toSequences, fromGapChar);
+              fromSequences, toSequences, fromGapChar);
     }
-    return; // mappedColumns;
+    return; 
   }
 
   /**
@@ -667,7 +660,9 @@ public final class MappingUtils
          */
         for (SequenceI toSeq : toSequences)
         {
-          if (toSeq.getDatasetSequence() == mappedSeq)
+          if (toSeq.getDatasetSequence() == mappedSeq
+                  && mappedStartResidue >= toSeq.getStart()
+                  && mappedEndResidue <= toSeq.getEnd())
           {
             int mappedStartCol = toSeq.findIndex(mappedStartResidue);
             int mappedEndCol = toSeq.findIndex(mappedEndResidue);
@@ -965,7 +960,7 @@ public final class MappingUtils
 
     int min = Math.min(range[0], range[1]);
     int max = Math.max(range[0], range[1]);
-  
+
     return (min <= queryRange[0] && max >= queryRange[0]
             && min <= queryRange[1] && max >= queryRange[1]);
   }
@@ -980,8 +975,7 @@ public final class MappingUtils
    *          a list of (single) [start, end] ranges
    * @return
    */
-  public static void removeEndPositions(int positions,
-          List<int[]> ranges)
+  public static void removeEndPositions(int positions, List<int[]> ranges)
   {
     int toRemove = positions;
     Iterator<int[]> it = new ReverseListIterator<>(ranges);
@@ -993,8 +987,8 @@ public final class MappingUtils
         /*
          * not coded for [start1, end1, start2, end2, ...]
          */
-        System.err
-                .println("MappingUtils.removeEndPositions doesn't handle multiple  ranges");
+        System.err.println(
+                "MappingUtils.removeEndPositions doesn't handle multiple  ranges");
         return;
       }
 
@@ -1004,8 +998,8 @@ public final class MappingUtils
         /*
          * not coded for a reverse strand range (end < start)
          */
-        System.err
-                .println("MappingUtils.removeEndPositions doesn't handle reverse strand");
+        System.err.println(
+                "MappingUtils.removeEndPositions doesn't handle reverse strand");
         return;
       }
       if (length > toRemove)