From 51eebe77f74dda2f4ff336dfe0fea0ed68b86e5b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 29 Aug 2006 15:24:22 +0000
Subject: [PATCH] createMapping alreadyMapped

---
 src/jalview/gui/Jalview2XML.java        |    2 +-
 src/jalview/io/AnnotationFile.java      |    2 +-
 src/jalview/io/JnetAnnotationMaker.java |   15 +++++++++------
 3 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8cf676d..e65f37d 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1089,7 +1089,7 @@ public class Jalview2XML
                 if(an[i].getSequenceRef()!=null)
                 {
                   jaa.createSequenceMapping(
-                      al.findName(an[i].getSequenceRef()), 1
+                      al.findName(an[i].getSequenceRef()), 1, true
                       );
                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
                 }
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index d004c1a..08b5862 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -287,7 +287,7 @@ public class AnnotationFile
 
        if(refSeq!=null)
        {
-         annotation.createSequenceMapping(refSeq, refSeqIndex);
+         annotation.createSequenceMapping(refSeq, refSeqIndex, false);
          refSeq.addAlignmentAnnotation(annotation);
        }
 
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 862b578..60fb601 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -18,11 +18,6 @@
 */package jalview.io;
 
 import jalview.datamodel.*;
-import java.net.URL;
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
-import java.io.FileReader;
-
 
 public class JnetAnnotationMaker
 {
@@ -57,6 +52,11 @@ public class JnetAnnotationMaker
     AlignmentAnnotation annot;
     Annotation[] annotations = null;
 
+    int existingAnnotations = 0;
+    if(al.getAlignmentAnnotation()!=null)
+       existingAnnotations = al.getAlignmentAnnotation().length;
+
+
     while (i < preds.length)
     {
       String id = preds[i].getName().toUpperCase();
@@ -111,11 +111,14 @@ public class JnetAnnotationMaker
 
         if (seqRef != null)
         {
-          annot.createSequenceMapping(seqRef, 0);
+          annot.createSequenceMapping(seqRef, 1, false);
           seqRef.addAlignmentAnnotation(annot);
         }
 
         al.addAnnotation(annot);
+        al.setAnnotationIndex(annot,
+                              al.getAlignmentAnnotation().
+                              length - existingAnnotations - 1);
 
         if (noMsa)
         {
-- 
1.7.10.2