From 01f32ab5a70ee75304187d341e28a2bcc88e06fa Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 15 Dec 2010 14:49:47 +0000
Subject: [PATCH] more accurate determination of annotation modification

---
 src/jalview/io/AnnotationFile.java |   18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 5c3b7f8..ef46b86 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -502,6 +502,7 @@ public class AnnotationFile
   public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
           throws Exception
   {
+    boolean modified=false;
     String groupRef = null;
     Hashtable groupRefRows = new Hashtable();
 
@@ -577,22 +578,23 @@ public class AnnotationFile
         {
           // TODO: use graduated colour def'n here too
           colourAnnotations(al, st.nextToken(), st.nextToken());
-          continue;
+          modified=true;continue;
         }
 
         else if (token.equalsIgnoreCase("COMBINE"))
         {
           combineAnnotations(al, st);
-          continue;
+          modified=true;continue;
         }
         else if (token.equalsIgnoreCase("ROWPROPERTIES"))
         {
           addRowProperties(al, st);
-          continue;
+          modified=true;continue;
         }
         else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
+          modified=true;
           continue;
         }
 
@@ -657,18 +659,18 @@ public class AnnotationFile
         else if (token.equalsIgnoreCase("PROPERTIES"))
         {
           addProperties(al, st);
-          continue;
+          modified=true;          continue;
         }
 
         else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
         {
           setBelowAlignment(al, st);
-          continue;
+          modified=true;continue;
         }
         else if (token.equalsIgnoreCase("ALIGNMENT"))
         {
           addAlignmentDetails(al, st);
-          continue;
+          modified=true;continue;
         }
 
         // Parse out the annotation row
@@ -788,6 +790,8 @@ public class AnnotationFile
             ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
           }
         }
+        // and set modification flag
+        modified=true;
       }
       // Finally, resolve the groupRefs
       Enumeration en = groupRefRows.keys();
@@ -831,7 +835,7 @@ public class AnnotationFile
         ((Vector) groupRefRows.get(groupRef)).removeAllElements();
       }
     }
-    return true;
+    return modified;
   }
 
   private Object autoAnnotsKey(AlignmentAnnotation annotation, SequenceI refSeq, String groupRef)
-- 
1.7.10.2