X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=5a2c46e0b3e2be52032af8a67f02cfbefdde6cfc;hb=521ce3c96d5977a9bd941894eda7a13dd09deea9;hp=b93f178e522c2efea539a3295a17a406155bb7a5;hpb=e0a4b92352ee3e31a8dea075a51ec080ae3945f2;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b93f178..5a2c46e 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;
@@ -50,7 +46,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */
     public float graphMax;
 
-    public java.util.Vector graphLines;
+    public GraphLine threshold;
 
     // Graphical hints and tips
 
@@ -143,6 +139,8 @@ public class AlignmentAnnotation
         this.annotations = annotations;
         graph = graphType;
 
+        boolean drawValues = true;
+
         if (min == max)
         {
             min = 999999999;
@@ -153,6 +151,11 @@ public class AlignmentAnnotation
                     continue;
                 }
 
+                if(drawValues && annotations[i].displayCharacter.length() > 1 )
+                {
+                  drawValues = false;
+                }
+
                 if (annotations[i].value > max)
                 {
                     max = annotations[i].value;
@@ -170,19 +173,30 @@ public class AlignmentAnnotation
 
         for (int i = 0; i < annotations.length; i++)
         {
-            if ((annotations[i] != null) &&
-                    ((annotations[i].secondaryStructure == 'H') ||
+            if (!hasIcons
+                && annotations[i] != null
+                && ((annotations[i].secondaryStructure == 'H') ||
                     (annotations[i].secondaryStructure == 'E')))
             {
                 hasIcons = true;
             }
 
-            if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0))
+            if (!hasText
+                && annotations[i]!=null
+                && annotations[i].displayCharacter.length() > 0)
             {
                 hasText = true;
             }
         }
+
+        if(!drawValues && graphType!=NO_GRAPH)
+        {
+          for (int i = 0; i < annotations.length; i++)
+          {
+            if (annotations[i] != null)
+              annotations[i].displayCharacter = "";
+          }
+        }
     }
 
     /**
@@ -233,38 +247,79 @@ public class AlignmentAnnotation
         return buffer.toString();
       }
 
-      public void addGraphLine(GraphLine line)
+      public void setThreshold(GraphLine line)
       {
-        if(graphLines==null)
-          graphLines = new java.util.Vector();
+        threshold = line;
+      }
 
-        graphLines.addElement(line);
+      public GraphLine getThreshold()
+      {
+          return threshold;
       }
 
-      public GraphLine getGraphLine(int index)
+      /**
+       * This
+       */
+      public void createSequenceMapping(SequenceI seqRef, int startRes)
       {
-        if(graphLines!=null && index<graphLines.size())
-          return (GraphLine)graphLines.elementAt(index);
+        if(seqRef == null)
+          return;
+
+        sequenceMapping = new java.util.Hashtable();
+
+        sequenceRef = seqRef;
+
+        if(startRes < sequenceRef.getStart())
+          startRes = sequenceRef.getStart();
+
+        int seqPos;
+
+        int fileOffset = 0;
+        if(startRes > sequenceRef.getStart())
+        {
+          fileOffset = startRes - sequenceRef.getStart();
+        }
+
+        for(int i = 0; i < annotations.length; i++)
+        {
+            seqPos = sequenceRef.findPosition(i + fileOffset);
+            if(seqPos<annotations.length)
+            {
+              if (annotations[i] != null)
+              {
+                  sequenceMapping.put(new Integer(seqPos),
+                                      annotations[i]);
+              }
+            }
+         }
+
+        adjustForAlignment();
 
-        else
-          return null;
       }
 
       public void adjustForAlignment()
       {
           int a=0, aSize = sequenceRef.getLength();
 
-          int index = 0;
+          if(aSize == 0)
+          {
+            //Its been deleted
+            return;
+          }
+
+          int position;
           Annotation[] temp = new Annotation[aSize];
+          Integer index;
 
-          for (a = 0; a < aSize; a++)
+          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;