Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

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

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index d7b7eb9..bd83fe9 100644 (file)
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -20,12 +20,12 @@
  */
 package jalview.datamodel;
 
+import jalview.util.MapList;
+
 import java.util.Iterator;
 import java.util.NoSuchElementException;
 import java.util.Vector;
 
-import jalview.util.MapList;
-
 public class Mapping
 {
   /**
@@ -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();
@@ -149,8 +155,9 @@ public class Mapping
       int[] alignedCodon = getAlignedCodon(codon);
 
       String peptide = getPeptide();
+      int peptideCol = toPosition - 1 - Mapping.this.to.getStart();
       return new AlignedCodon(alignedCodon[0], alignedCodon[1],
-              alignedCodon[2], peptide);
+              alignedCodon[2], peptide, peptideCol);
     }
 
     /**
@@ -158,13 +165,17 @@ public class Mapping
      * sequence.
      * 
      * @return
+     * @throws NoSuchElementException
+     *           if the 'toRange' is exhausted (nothing to map to)
      */
     private String getPeptide()
     {
       // 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 +252,11 @@ 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 +480,7 @@ 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 +541,7 @@ public class Mapping
       }
     }
     // give up and just return the feature.
-    return new SequenceFeature[]
-    { f };
+    return new SequenceFeature[] { f };
   }
 
   /**
@@ -565,8 +577,7 @@ public class Mapping
       }
       return map.locateInFrom(from, to);
     }
-    return new int[]
-    { from, to };
+    return new int[] { from, to };
   }
 
   /**
@@ -602,8 +613,7 @@ public class Mapping
       }
       return map.locateInTo(from, to);
     }
-    return new int[]
-    { from, to };
+    return new int[] { from, to };
   }
 
   /**
@@ -631,13 +641,11 @@ 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] });
             }
           }
         }
@@ -688,6 +696,7 @@ public class Mapping
    * 
    * @see java.lang.Object#finalize()
    */
+  @Override
   protected void finalize() throws Throwable
   {
     map = null;
@@ -695,9 +704,28 @@ public class Mapping
     super.finalize();
   }
 
+  /**
+   * Returns an iterator which can serve up the aligned codon column positions
+   * and their corresponding peptide products
+   * 
+   * @param seq
+   *          an aligned (i.e. possibly gapped) sequence
+   * @param gapChar
+   * @return
+   */
   public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
   {
-    return new AlignedCodonIterator(seq.getSequence(), gapChar);
+    return new AlignedCodonIterator(seq, gapChar);
+  }
+
+  /**
+   * Readable representation for debugging only, not guaranteed not to change
+   */
+  @Override
+  public String toString()
+  {
+    return String.format("%s %s", this.map.toString(), this.to == null ? ""
+            : this.to.getName());
   }
 
 }