From bacecb72ddbc576bd80339b7b02c4c08313f6a83 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 15 Dec 2010 09:51:00 +0000
Subject: [PATCH] refactored key calc for hash to separate function

---
 src/jalview/io/AnnotationFile.java |   31 +++++++++++++++----------------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 3459517..5c3b7f8 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -526,14 +526,8 @@ public class AnnotationFile
             {
               // 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) : ""),
+                      .put(autoAnnotsKey(aa[aai], aa[aai].sequenceRef, (aa[aai].groupRef==null ? null : aa[aai].groupRef.getName())
+                              ),
                               new Integer(1));
             }
           }
@@ -747,14 +741,7 @@ public class AnnotationFile
         annotation.score = score;
         if (!overrideAutoAnnot
                 && autoAnnots
-                        .containsKey(annotation.graph
-                                + "\t"
-                                + annotation.label
-                                + "\t"
-                                + annotation.description
-                                + "\t"
-                                + (refSeq != null ? refSeq
-                                        .getDisplayId(true) : "")))
+                        .containsKey(autoAnnotsKey(annotation, refSeq, groupRef)))
         {
           // skip - we've already got an automatic annotation of this type.
           continue;
@@ -847,6 +834,18 @@ public class AnnotationFile
     return true;
   }
 
+  private Object autoAnnotsKey(AlignmentAnnotation annotation, SequenceI refSeq, String groupRef)
+  {
+    return annotation.graph
+    + "\t"
+    + annotation.label
+    + "\t"
+    + annotation.description
+    + "\t"
+    + (refSeq != null ? refSeq
+            .getDisplayId(true) : "");
+  }
+
   Annotation parseAnnotation(String string, int graphStyle)
   {
     boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
-- 
1.7.10.2