From e92b43b69e418df0a247a7148d6e4312f57b3787 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 18 Jul 2008 15:10:29 +0000
Subject: [PATCH] resolve 1:many mappings for sequence associated annotation
 to all alignment sequence(s) with same ID

---
 src/jalview/io/AnnotationFile.java |   41 +++++++++++++++++++++++++++---------
 1 file changed, 31 insertions(+), 10 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 016ee8f..13cfc38 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -323,6 +323,7 @@ public class AnnotationFile
   }
 
   SequenceI refSeq = null;
+  String refSeqId = null;
   public boolean readAnnotationFile(AlignmentI al,
                                     String file,
                                     String protocol)
@@ -420,7 +421,13 @@ public class AnnotationFile
 
         else if (token.equalsIgnoreCase("SEQUENCE_REF"))
         {
-          refSeq = al.findName(st.nextToken());
+          if (st.hasMoreTokens())
+          {
+            refSeq = al.findName(refSeqId=st.nextToken());
+          if (refSeq==null)
+          {
+            refSeqId=null;
+          }
           try
           {
             refSeqIndex = Integer.parseInt(st.nextToken());
@@ -435,7 +442,10 @@ public class AnnotationFile
           {
             refSeqIndex = 1;
           }
-
+          } else {
+            refSeq = null;
+            refSeqId = null;
+          }
           continue ;
         }
 
@@ -538,16 +548,27 @@ public class AnnotationFile
         if (refSeq != null)
         {
           annotation.belowAlignment=false;
-          annotation.createSequenceMapping(refSeq, refSeqIndex, false);
-          annotation.adjustForAlignment();
-          refSeq.addAlignmentAnnotation(annotation);
-        }
-
-        al.addAnnotation(annotation);
-
-        al.setAnnotationIndex(annotation,
+          do {
+            // copy before we do any mapping business.
+            // TODO: verify that undo/redo with 1:many sequence associated annotations can be undone correctly
+            AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
+            annotation.createSequenceMapping(refSeq, refSeqIndex, false);
+            annotation.adjustForAlignment();
+            refSeq.addAlignmentAnnotation(annotation);
+            al.addAnnotation(annotation);
+            al.setAnnotationIndex(annotation,
+                                al.getAlignmentAnnotation().length - existingAnnotations -
+                                1);
+            // and recover our virgin copy to use again if necessary.
+            annotation = ann;
+            
+          } while (refSeqId!=null && (refSeq=al.findName(refSeq, refSeqId, true))!=null);
+        } else {
+          al.addAnnotation(annotation);
+          al.setAnnotationIndex(annotation,
                               al.getAlignmentAnnotation().length - existingAnnotations -
                               1);
+        }
       }
 
     }
-- 
1.7.10.2