From 1e968e44cb033e74e9f81d7140b5393f8ad6e305 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 5 Feb 2007 14:40:03 +0000
Subject: [PATCH] Fixed bug in trim right annotation adjust

---
 src/jalview/commands/EditCommand.java |   58 +++++++++++++++++++++++++++++----
 1 file changed, 51 insertions(+), 7 deletions(-)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 7effdfb..1d4880a 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -366,6 +366,8 @@ public class EditCommand implements CommandI
           continue;
         }
 
+        int tSize = 0;
+
         aSize = annotations[a].annotations.length;
         if(insert)
           temp = new Annotation[aSize + command.number];
@@ -373,13 +375,19 @@ public class EditCommand implements CommandI
         {
           if(command.position<aSize)
           {
-            if (aSize - command.number + command.position > 0)
-              temp = new Annotation[aSize - command.number + command.position];
+            if(command.position+command.number>aSize)
+              tSize = aSize;
             else
-              temp = new Annotation[aSize];
+            tSize = aSize - command.number + command.position;
           }
           else
-            temp = new Annotation[aSize];
+            tSize = aSize;
+
+          if(tSize<0)
+            tSize = aSize;
+
+          temp = new Annotation[tSize];
+
         }
 
         if(insert)
@@ -410,11 +418,28 @@ public class EditCommand implements CommandI
                              aSize - command.position);
           }
           else
-            temp = annotations[a].annotations;
+          {
+            if (command.deletedAnnotations != null
+                           &&
+                           command.deletedAnnotations.containsKey(annotations[a].annotationId))
+            {
+              Annotation[] restore = (Annotation[])
+                  command.deletedAnnotations.get(annotations[a].annotationId);
+
+              temp = new Annotation[annotations[a].annotations.length+
+                  restore.length];
+              System.arraycopy(annotations[a].annotations,
+                               0,temp,0,
+                               annotations[a].annotations.length);
+              System.arraycopy(restore,0,temp,annotations[a].annotations.length,restore.length);
+            }
+            else
+              temp = annotations[a].annotations;
+          }
         }
         else
         {
-          if(command.position < aSize &&  aSize - command.number+command.position>0)
+          if(tSize!=aSize)
           {
             System.arraycopy(annotations[a].annotations,
                              0, temp, 0, command.position);
@@ -432,7 +457,26 @@ public class EditCommand implements CommandI
                              aSize - command.position - command.number);
           }
           else
-            temp = annotations[a].annotations;
+          {
+            int dSize = aSize - command.position;
+
+            if(dSize>0)
+            {
+              Annotation[] deleted = new Annotation[command.number];
+              System.arraycopy(annotations[a].annotations,
+                               command.position, deleted, 0, dSize);
+
+              command.deletedAnnotations.put(annotations[a].annotationId,
+                                             deleted);
+
+              tSize = Math.min(annotations[a].annotations.length, command.position);
+              temp = new Annotation[tSize];
+              System.arraycopy(annotations[a].annotations,
+                  0, temp, 0, tSize);
+            }
+            else
+              temp = annotations[a].annotations;
+          }
         }
 
         annotations[a].annotations = temp;
-- 
1.7.10.2