X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=7990a5cfb6afb30796bdb60f1e1ca6945d1f0611;hb=d616b0e1ac213a82591cece50ea25c5bfbfa865f;hp=322fd54f23186b0562001da9d3bb7de9aeef0dca;hpb=d2ad79a5a6edf4c1dbbbc2f454579864dcf1e3b8;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 322fd54..7990a5c 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,6 +20,10 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -28,10 +32,6 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 /**
  * DOCUMENT ME!
  * 
@@ -164,6 +164,7 @@ public class AlignmentAnnotation
     }
     setScore(mxval);
   }
+
   /**
    * map of positions in the associated annotation
    */
@@ -244,6 +245,7 @@ public class AlignmentAnnotation
    * 
    * @see java.lang.Object#finalize()
    */
+  @Override
   protected void finalize() throws Throwable
   {
     sequenceRef = null;
@@ -692,10 +694,10 @@ public class AlignmentAnnotation
     this.scaleColLabel = annotation.scaleColLabel;
     this.showAllColLabels = annotation.showAllColLabels;
     this.calcId = annotation.calcId;
-    if (annotation.properties!=null)
+    if (annotation.properties != null)
     {
-      properties = new HashMap<String,String>();
-      for (Map.Entry<String, String> val:annotation.properties.entrySet())
+      properties = new HashMap<String, String>();
+      for (Map.Entry<String, String> val : annotation.properties.entrySet())
       {
         properties.put(val.getKey(), val.getValue());
       }
@@ -956,6 +958,12 @@ public class AlignmentAnnotation
 
   }
 
+  /**
+   * When positional annotation and a sequence reference is present, clears and
+   * resizes the annotations array to the current alignment width, and adds
+   * annotation according to aligned positions of the sequenceRef given by
+   * sequenceMapping.
+   */
   public void adjustForAlignment()
   {
     if (sequenceRef == null)
@@ -979,18 +987,20 @@ public class AlignmentAnnotation
     int position;
     Annotation[] temp = new Annotation[aSize];
     Integer index;
-
-    for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+    if (sequenceMapping != null)
     {
-      index = new Integer(a);
-      if (sequenceMapping.containsKey(index))
+      for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
       {
-        position = sequenceRef.findIndex(a) - 1;
+        index = new Integer(a);
+        Annotation annot = sequenceMapping.get(index);
+        if (annot != null)
+        {
+          position = sequenceRef.findIndex(a) - 1;
 
-        temp[position] = sequenceMapping.get(index);
+          temp[position] = annot;
+        }
       }
     }
-
     annotations = temp;
   }
 
@@ -1027,11 +1037,11 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Associate this annotion with the aligned residues of a particular sequence.
-   * sequenceMapping will be updated in the following way: null sequenceI -
-   * existing mapping will be discarded but annotations left in mapped
-   * positions. valid sequenceI not equal to current sequenceRef: mapping is
-   * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+   * Associate this annotation with the aligned residues of a particular
+   * sequence. sequenceMapping will be updated in the following way: null
+   * sequenceI - existing mapping will be discarded but annotations left in
+   * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
+   * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
    * parameter to specify correspondence between current and new sequenceRef
    * 
    * @param sequenceI
@@ -1042,7 +1052,8 @@ public class AlignmentAnnotation
     {
       if (sequenceRef != null)
       {
-        boolean rIsDs=sequenceRef.getDatasetSequence()==null,tIsDs=sequenceI.getDatasetSequence()==null;
+        boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI
+                .getDatasetSequence() == null;
         if (sequenceRef != sequenceI
                 && (rIsDs && !tIsDs && sequenceRef != sequenceI
                         .getDatasetSequence())
@@ -1238,8 +1249,10 @@ public class AlignmentAnnotation
   {
     if (sp2sq.getMappedWidth() != sp2sq.getWidth())
     {
-      // TODO: employ getWord/MappedWord to transfer annotation between cDNA and Protein reference frames
-      throw new Error("liftOver currently not implemented for transfer of annotation between different types of seqeunce");
+      // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
+      // Protein reference frames
+      throw new Error(
+              "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
     }
     boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
             .getTo() == sq.getDatasetSequence()) : false;
@@ -1292,7 +1305,8 @@ public class AlignmentAnnotation
    * @note caller should add the remapped annotation to newref if they have not
    *       already
    */
-  public void remap(SequenceI newref, int[][] mapping, int from, int to,
+  public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
+          int from, int to,
           int idxoffset)
   {
     if (mapping != null)
@@ -1300,7 +1314,7 @@ public class AlignmentAnnotation
       Map<Integer, Annotation> old = sequenceMapping;
       Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
       int index = -1;
-      for (int mp[] : mapping)
+      for (int mp[] : mapping.values())
       {
         if (index++ < 0)
         {
@@ -1354,9 +1368,9 @@ public class AlignmentAnnotation
 
   public void setProperty(String property, String value)
   {
-    if (properties==null)
+    if (properties == null)
     {
-      properties = new HashMap<String,String>();
+      properties = new HashMap<String, String>();
     }
     properties.put(property, value);
   }