From 133454102814512287d6bb5b1f4e5c2601eea863 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 10 May 2006 12:56:30 +0000
Subject: [PATCH] Create sequence mapping for annotations

---
 src/jalview/datamodel/AlignmentAnnotation.java |   68 +++++++++++++++++++-----
 1 file changed, 54 insertions(+), 14 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index c3ccb0b..d75683c 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -29,11 +29,6 @@ public class AlignmentAnnotation
 {
     public SequenceI sequenceRef;
 
-    /** This annotation is the original loaded annotation
-     *  without any gaps. It is necessary to adjust the annotation
-     *  if sequences are updated */
-    public AlignmentAnnotation datasetAnnotation;
-
     /** DOCUMENT ME!! */
     public String label;
 
@@ -43,6 +38,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */
     public Annotation[] annotations;
 
+    public java.util.Hashtable sequenceMapping;
 
     /** DOCUMENT ME!! */
     public float graphMin;
@@ -243,21 +239,65 @@ public class AlignmentAnnotation
           return threshold;
       }
 
+      /**
+       * This
+       */
+      public void createSequenceMapping(SequenceI seqRef, int startRes)
+      {
+        if(seqRef == null)
+          return;
+
+        sequenceMapping = new java.util.Hashtable();
+
+        sequenceRef = seqRef;
+
+        if(startRes < sequenceRef.getStart())
+          startRes = sequenceRef.getStart();
+
+        int seqPos, seqIndex;
+
+        int fileOffset = 0;
+        if(startRes > sequenceRef.getStart())
+        {
+          fileOffset = startRes - sequenceRef.getStart();
+        }
+
+        for(int i = 0; i < annotations.length; i++)
+        {
+            seqPos = sequenceRef.findPosition(i - fileOffset)-1;
+            if(seqPos<annotations.length)
+            {
+              if (annotations[seqPos] != null)
+              {
+                seqIndex = sequenceRef.findIndex(i) + 1;
+
+                if(seqIndex>=startRes)
+                sequenceMapping.put(new Integer(seqIndex),
+                                    annotations[seqPos]);
+              }
+            }
+         }
+
+        adjustForAlignment();
+
+      }
+
       public void adjustForAlignment()
       {
           int a=0, aSize = sequenceRef.getLength();
 
-          int index = 0;
+          int position;
           Annotation[] temp = new Annotation[aSize];
-
-          for (a = 0; a < aSize; a++)
+          Integer index;
+          for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
           {
-            if (!jalview.util.Comparison.isGap(sequenceRef.getCharAt(a)))
-            {
-              index = sequenceRef.findPosition(a);
-              if(datasetAnnotation.annotations.length>index)
-                temp[a] = datasetAnnotation.annotations[index];
-            }
+              index = new Integer(a);
+              if(sequenceMapping.containsKey(index))
+              {
+                position = sequenceRef.findIndex(a)-1;
+
+                temp[position] = (Annotation)sequenceMapping.get(index);
+              }
           }
 
           annotations = temp;
-- 
1.7.10.2