X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=eb594be726254e46996edaa5e68af9b17af6adf4;hb=8f920d337154e092f5f9056ffde3cdf2735eca43;hp=559ae4cd8b05b9552fa26ca0f0da58bd00b53b85;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 559ae4c..eb594be 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -48,6 +48,11 @@ public class Mapping
     private final char[] alignedSeq;
 
     /*
+     * the sequence start residue
+     */
+    private int start;
+
+    /*
      * Next position (base 0) in the aligned sequence
      */
     private int alignedColumn = 0;
@@ -90,13 +95,14 @@ public class Mapping
     /**
      * Constructor
      * 
-     * @param cs
-     *          the aligned sequence characters
+     * @param seq
+     *          the aligned sequence
      * @param gapChar
      */
-    public AlignedCodonIterator(char[] cs, char gapChar)
+    public AlignedCodonIterator(SequenceI seq, char gapChar)
     {
-      this.alignedSeq = cs;
+      this.alignedSeq = seq.getSequence();
+      this.start = seq.getStart();
       this.gap = gapChar;
       fromRanges = map.getFromRanges().iterator();
       toRanges = map.getToRanges().iterator();
@@ -163,8 +169,10 @@ public class Mapping
     {
       // TODO should ideally handle toRatio other than 1 as well...
       // i.e. code like getNextCodon()
-      if (toPosition <= currentToRange[1]) {
-        char pep = Mapping.this.to.getSequence()[toPosition - 1];
+      if (toPosition <= currentToRange[1])
+      {
+        SequenceI seq = Mapping.this.to;
+        char pep = seq.getSequence()[toPosition - seq.getStart()];
         toPosition++;
         return String.valueOf(pep);
       }
@@ -241,8 +249,11 @@ public class Mapping
      */
     private int getAlignedColumn(int sequencePos)
     {
-      while (alignedBases < sequencePos
-              && alignedColumn < alignedSeq.length)
+      /*
+       * allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
+       */
+      int truePos = sequencePos - (start - 1);
+      while (alignedBases < truePos && alignedColumn < alignedSeq.length)
       {
         if (alignedSeq[alignedColumn++] != gap)
         {
@@ -466,8 +477,7 @@ public class Mapping
       int[] mp = map.shiftFrom(pos);
       if (mp != null)
       {
-        return new int[]
-        { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
+        return new int[] { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
       }
     }
     return null;
@@ -528,8 +538,7 @@ public class Mapping
       }
     }
     // give up and just return the feature.
-    return new SequenceFeature[]
-    { f };
+    return new SequenceFeature[] { f };
   }
 
   /**
@@ -565,8 +574,7 @@ public class Mapping
       }
       return map.locateInFrom(from, to);
     }
-    return new int[]
-    { from, to };
+    return new int[] { from, to };
   }
 
   /**
@@ -602,8 +610,7 @@ public class Mapping
       }
       return map.locateInTo(from, to);
     }
-    return new int[]
-    { from, to };
+    return new int[] { from, to };
   }
 
   /**
@@ -631,13 +638,11 @@ public class Mapping
         {
           for (int m = 0; m < mpr.length; m += 2)
           {
-            toRange.addElement(new int[]
-            { mpr[m], mpr[m + 1] });
+            toRange.addElement(new int[] { mpr[m], mpr[m + 1] });
             int[] xpos = locateRange(mpr[m], mpr[m + 1]);
             for (int x = 0; x < xpos.length; x += 2)
             {
-              fromRange.addElement(new int[]
-              { xpos[x], xpos[x + 1] });
+              fromRange.addElement(new int[] { xpos[x], xpos[x + 1] });
             }
           }
         }
@@ -663,24 +668,6 @@ public class Mapping
     return copy;
   }
 
-  public static void main(String[] args)
-  {
-    /**
-     * trite test of the intersectVisContigs method for a simple DNA -> Protein
-     * exon map and a range of visContigs
-     */
-    MapList fk = new MapList(new int[]
-    { 1, 6, 8, 13, 15, 23 }, new int[]
-    { 1, 7 }, 3, 1);
-    Mapping m = new Mapping(fk);
-    Mapping m_1 = m.intersectVisContigs(new int[]
-    { fk.getFromLowest(), fk.getFromHighest() });
-    Mapping m_2 = m.intersectVisContigs(new int[]
-    { 1, 7, 11, 20 });
-    System.out.println("" + m_1.map.getFromRanges());
-
-  }
-
   /**
    * get the sequence being mapped to - if any
    * 
@@ -706,6 +693,7 @@ public class Mapping
    * 
    * @see java.lang.Object#finalize()
    */
+  @Override
   protected void finalize() throws Throwable
   {
     map = null;
@@ -715,7 +703,7 @@ public class Mapping
 
   public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
   {
-    return new AlignedCodonIterator(seq.getSequence(), gapChar);
+    return new AlignedCodonIterator(seq, gapChar);
   }
 
 }