X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=5a2c46e0b3e2be52032af8a67f02cfbefdde6cfc;hb=d6e1bbede5adc04f34c969213ac6a4c6d9e5d34a;hp=d75683c60e6833ee58dd22613b2a96b099593619;hpb=133454102814512287d6bb5b1f4e5c2601eea863;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index d75683c..5a2c46e 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -139,6 +139,8 @@ public class AlignmentAnnotation
         this.annotations = annotations;
         graph = graphType;
 
+        boolean drawValues = true;
+
         if (min == max)
         {
             min = 999999999;
@@ -149,6 +151,11 @@ public class AlignmentAnnotation
                     continue;
                 }
 
+                if(drawValues && annotations[i].displayCharacter.length() > 1 )
+                {
+                  drawValues = false;
+                }
+
                 if (annotations[i].value > max)
                 {
                     max = annotations[i].value;
@@ -166,19 +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 = "";
+          }
+        }
     }
 
     /**
@@ -254,7 +272,7 @@ public class AlignmentAnnotation
         if(startRes < sequenceRef.getStart())
           startRes = sequenceRef.getStart();
 
-        int seqPos, seqIndex;
+        int seqPos;
 
         int fileOffset = 0;
         if(startRes > sequenceRef.getStart())
@@ -264,16 +282,13 @@ public class AlignmentAnnotation
 
         for(int i = 0; i < annotations.length; i++)
         {
-            seqPos = sequenceRef.findPosition(i - fileOffset)-1;
+            seqPos = sequenceRef.findPosition(i + fileOffset);
             if(seqPos<annotations.length)
             {
-              if (annotations[seqPos] != null)
+              if (annotations[i] != null)
               {
-                seqIndex = sequenceRef.findIndex(i) + 1;
-
-                if(seqIndex>=startRes)
-                sequenceMapping.put(new Integer(seqIndex),
-                                    annotations[seqPos]);
+                  sequenceMapping.put(new Integer(seqPos),
+                                      annotations[i]);
               }
             }
          }
@@ -286,9 +301,16 @@ public class AlignmentAnnotation
       {
           int a=0, aSize = sequenceRef.getLength();
 
+          if(aSize == 0)
+          {
+            //Its been deleted
+            return;
+          }
+
           int position;
           Annotation[] temp = new Annotation[aSize];
           Integer index;
+
           for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
           {
               index = new Integer(a);