From a9108fa3538ddb2ef02aa231e233dc978654d6f6 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 23 Apr 2010 15:59:56 +0000
Subject: [PATCH] skips any annotation that appears to be identical to
 existing autogenerated annotation on the alignment.

---
 src/jalview/io/AnnotationFile.java |   26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 87b21d3..aac48eb 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -433,6 +433,7 @@ public class AnnotationFile
   public boolean readAnnotationFile(AlignmentI al, String file,
           String protocol)
   {
+    Hashtable autoAnnots=new Hashtable();
     try
     {
       BufferedReader in = null;
@@ -462,9 +463,24 @@ public class AnnotationFile
       int graphStyle, index;
       int refSeqIndex = 1;
       int existingAnnotations = 0;
+      // when true - will add new rows regardless of whether they are duplicate auto-annotation like consensus or conservation graphs
+      boolean overrideAutoAnnot=false; 
       if (al.getAlignmentAnnotation() != null)
       {
         existingAnnotations = al.getAlignmentAnnotation().length;
+        if (existingAnnotations>0)
+        {
+          AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
+          for (int aai=0;aai<aa.length;aai++)
+          {
+            if (aa[aai].autoCalculated)
+            {
+              // make a note of the name and description
+              autoAnnots.put(aa[aai].graph+"\t"+aa[aai].label+"\t"+aa[aai].description+"\t"+(aa[aai].sequenceRef!=null ? aa[aai].sequenceRef.getDisplayId(true) : "")
+                      ,new Integer(1));
+            }
+          }
+        }
       }
 
       int alWidth = al.getWidth();
@@ -645,14 +661,20 @@ public class AnnotationFile
           }
 
         }
-
+        
         annotation = new AlignmentAnnotation(label, description,
                 (index == 0) ? null : annotations, 0, 0, graphStyle);
 
         annotation.score = score;
-
+        if (!overrideAutoAnnot && autoAnnots.containsKey(annotation.graph+"\t"+annotation.label+"\t"+annotation.description+"\t"+(refSeq!=null ? refSeq.getDisplayId(true) : "")))
+        {
+          // skip - we've already got an automatic annotation of this type.
+          continue;
+        }
+        // otherwise add it!
         if (refSeq != null)
         {
+          
           annotation.belowAlignment = false;
           // make a copy of refSeq so we can find other matches in the alignment
           SequenceI referedSeq = refSeq;
-- 
1.7.10.2