From d7e33557512a6e6c3c604aeb6ff67c023ee5c251 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 4 May 2007 10:31:18 +0000
Subject: [PATCH] Annotations do not extend when full alignment is adjusted

---
 src/jalview/commands/EditCommand.java |   20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index aece057..61e2595 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -112,7 +112,7 @@ public class EditCommand
   /**
    * append a new editCommand
    * Note. this shouldn't be called if the edit is an operation affects more alignment objects than the one referenced
-   * in al (for example, cut or pasting whole sequences). Use the form with an additional AlignmentI[] views parameter. 
+   * in al (for example, cut or pasting whole sequences). Use the form with an additional AlignmentI[] views parameter.
    * @param command
    * @param seqs
    * @param position
@@ -232,6 +232,7 @@ public class EditCommand
 
   final void insertGap(Edit command)
   {
+
     for (int s = 0; s < command.seqs.length; s++)
     {
       command.seqs[s].insertCharAt(command.position,
@@ -403,7 +404,6 @@ public class EditCommand
 
   final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility, AlignmentI[] views)
   {
-
     AlignmentAnnotation[] annotations = null;
 
     if (modifyVisibility && !insert)
@@ -440,7 +440,7 @@ public class EditCommand
               }
               command.seqs[s].setAlignmentAnnotation(null);
               if (alen!=tmp.length)
-              { 
+              {
                 // save the non-null annotation references only
                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
                 for (int aa=0,aapos=0;aa<tmp.length;aa++)
@@ -557,17 +557,13 @@ public class EditCommand
     Annotation[] temp;
     for (int a = 0; a < annotations.length; a++)
     {
-      if (annotations[a].autoCalculated)
+      if (annotations[a].autoCalculated || annotations[a].annotations == null)
       {
         continue;
       }
 
       int tSize = 0;
-      if (annotations[a].annotations == null)
-      {
-        // nothing to edit here ?
-        continue;
-      }
+
       aSize = annotations[a].annotations.length;
       if (insert)
       {
@@ -584,13 +580,13 @@ public class EditCommand
       {
         if (command.position < aSize)
         {
-          if (command.position + command.number > aSize)
+          if (command.position + command.number >= aSize)
           {
             tSize = aSize;
           }
           else
           {
-            tSize = aSize - command.number + command.position;
+            tSize = aSize - command.number;
           }
         }
         else
@@ -603,9 +599,9 @@ public class EditCommand
           tSize = aSize;
         }
         temp = new Annotation[tSize];
-
       }
 
+
       if (insert)
       {
         if (command.position < annotations[a].annotations.length)
-- 
1.7.10.2