JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index eb594be..1c196be 100644 (file)
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import jalview.util.Comparison;
 import jalview.util.MapList;
 
 import java.util.Iterator;
@@ -155,8 +156,9 @@ 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);
     }
 
     /**
@@ -164,6 +166,8 @@ public class Mapping
      * sequence.
      * 
      * @return
+     * @throws NoSuchElementException
+     *           if the 'toRange' is exhausted (nothing to map to)
      */
     private String getPeptide()
     {
@@ -255,7 +259,8 @@ public class Mapping
       int truePos = sequencePos - (start - 1);
       while (alignedBases < truePos && alignedColumn < alignedSeq.length)
       {
-        if (alignedSeq[alignedColumn++] != gap)
+        char c = alignedSeq[alignedColumn++];
+        if (c != gap && !Comparison.isGap(c))
         {
           alignedBases++;
         }
@@ -271,18 +276,23 @@ public class Mapping
 
   }
 
-  /**
+  /*
    * Contains the start-end pairs mapping from the associated sequence to the
    * sequence in the database coordinate system. It also takes care of step
    * difference between coordinate systems.
    */
   MapList map = null;
 
-  /**
+  /*
    * The sequence that map maps the associated sequence to (if any).
    */
   SequenceI to = null;
 
+  /*
+   * optional sequence id for the 'from' ranges
+   */
+  private String mappedFromId;
+
   public Mapping(MapList map)
   {
     super();
@@ -330,6 +340,7 @@ public class Mapping
         map = new MapList(map2.map);
       }
       to = map2.to;
+      mappedFromId = map2.mappedFromId;
     }
   }
 
@@ -353,14 +364,13 @@ public class Mapping
   /**
    * Equals that compares both the to references and MapList mappings.
    * 
-   * @param other
+   * @param o
    * @return
+   * @see MapList#equals
    */
   @Override
   public boolean equals(Object o)
   {
-    // TODO should override Object.hashCode() to ensure that equal objects have
-    // equal hashcodes
     if (o == null || !(o instanceof Mapping))
     {
       return false;
@@ -387,6 +397,21 @@ public class Mapping
   }
 
   /**
+   * Returns a hashCode made from the sequence and maplist
+   */
+  @Override
+  public int hashCode()
+  {
+    int hashCode = (this.to == null ? 1 : this.to.hashCode());
+    if (this.map != null)
+    {
+      hashCode = hashCode * 31 + this.map.hashCode();
+    }
+
+    return hashCode;
+  }
+
+  /**
    * get the 'initial' position in the associated sequence for a position in the
    * mapped reference frame
    * 
@@ -701,9 +726,46 @@ 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, 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());
+  }
+
+  /**
+   * Returns the identifier for the 'from' range sequence, or null if not set
+   * 
+   * @return
+   */
+  public String getMappedFromId()
+  {
+    return mappedFromId;
+  }
+
+  /**
+   * Sets the identifier for the 'from' range sequence
+   */
+  public void setMappedFromId(String mappedFromId)
+  {
+    this.mappedFromId = mappedFromId;
+  }
+
 }