JAL-1551 formatting

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

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 1272538..bd83fe9 100644 (file)
--- 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();
@@ -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);
     }
 
     /**
@@ -158,6 +165,8 @@ public class Mapping
      * sequence.
      * 
      * @return
+     * @throws NoSuchElementException
+     *           if the 'toRange' is exhausted (nothing to map to)
      */
     private String getPeptide()
     {
@@ -165,7 +174,8 @@ public class Mapping
       // i.e. code like getNextCodon()
       if (toPosition <= currentToRange[1])
       {
-        char pep = Mapping.this.to.getSequence()[toPosition - 1];
+        SequenceI seq = Mapping.this.to;
+        char pep = seq.getSequence()[toPosition - seq.getStart()];
         toPosition++;
         return String.valueOf(pep);
       }
@@ -242,8 +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)
         {
@@ -683,6 +696,7 @@ public class Mapping
    * 
    * @see java.lang.Object#finalize()
    */
+  @Override
   protected void finalize() throws Throwable
   {
     map = null;
@@ -690,9 +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());
   }
 
 }