From e88632fe0e6a74b1a9519cf9e58e769ad406e066 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 26 Jan 2007 17:30:23 +0000
Subject: [PATCH] Adjusts annotations for sequence edits

---
 src/jalview/commands/EditCommand.java |  108 +++++++++++++++++++++------------
 1 file changed, 69 insertions(+), 39 deletions(-)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index ed356dc..0c833d0 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -179,10 +179,7 @@ public class EditCommand implements CommandI
                                      command.gapChar);
     }
 
-    if (command.fullAlignmentHeight)
-    {
-      adjustAnnotations(command, true);
-    }
+    adjustAnnotations(command, true);
   }
 
   void deleteGap(Edit command)
@@ -192,10 +189,7 @@ public class EditCommand implements CommandI
       command.seqs[s].deleteChars(command.position, command.position+command.number);
     }
 
-    if (command.fullAlignmentHeight)
-    {
-      adjustAnnotations(command, false);
-    }
+    adjustAnnotations(command, false);
   }
 
   void cut(Edit command)
@@ -219,11 +213,7 @@ public class EditCommand implements CommandI
       }
     }
 
-    if (command.fullAlignmentHeight)
-    {
-      adjustAnnotations(command, false);
-    }
-
+    adjustAnnotations(command, false);
   }
 
   void paste(Edit command)
@@ -263,10 +253,8 @@ public class EditCommand implements CommandI
       command.seqs[i].setSequence(tmp.toString());
     }
 
-    if (command.fullAlignmentHeight)
-    {
-      adjustAnnotations(command, true);
-    }
+
+    adjustAnnotations(command, true);
 
     command.string = null;
   }
@@ -274,9 +262,46 @@ public class EditCommand implements CommandI
 
   void adjustAnnotations(Edit command, boolean insert)
   {
-    AlignmentAnnotation [] annotations = command.al.getAlignmentAnnotation();
-    if(annotations!=null)
+
+    AlignmentAnnotation [] annotations = null;
+
+    if (command.fullAlignmentHeight)
+    {
+      annotations = command.al.getAlignmentAnnotation();
+    }
+    else
     {
+      int aSize = 0;
+      AlignmentAnnotation [] tmp;
+      for(int s=0; s<command.seqs.length; s++)
+      {
+        if(command.seqs[s].getAnnotation()==null)
+          continue;
+
+        if (aSize == 0)
+            annotations = command.seqs[s].getAnnotation();
+        else
+        {
+          tmp = new AlignmentAnnotation
+              [aSize + command.seqs[s].getAnnotation().length];
+
+          System.arraycopy(annotations,0,tmp,0,aSize);
+
+          System.arraycopy(command.seqs[s].getAnnotation(),
+              0,tmp,aSize,command.seqs[s].getAnnotation().length);
+
+          annotations = tmp;
+        }
+
+
+        aSize = annotations.length;
+      }
+    }
+
+    if(annotations==null)
+      return;
+
+
       if(!insert)
         command.deletedAnnotations = new Hashtable();
 
@@ -299,27 +324,33 @@ public class EditCommand implements CommandI
 
         if(insert)
         {
-          System.arraycopy(annotations[a].annotations,
-              0, temp, 0, command.position);
-
-          if(command.deletedAnnotations!=null
-             && command.deletedAnnotations.containsKey(annotations[a].annotationId))
+          if(command.position < annotations[a].annotations.length)
           {
-            Annotation [] restore = (Annotation [])
-                command.deletedAnnotations.get(annotations[a].annotationId);
+            System.arraycopy(annotations[a].annotations,
+                             0, temp, 0, command.position);
 
-            System.arraycopy(restore,
-                             0,
-                             temp,
-                             command.position,
-                             command.number);
+            if (command.deletedAnnotations != null
+                &&
+                command.deletedAnnotations.containsKey(annotations[a].annotationId))
+            {
+              Annotation[] restore = (Annotation[])
+                  command.deletedAnnotations.get(annotations[a].annotationId);
 
-          }
+              System.arraycopy(restore,
+                               0,
+                               temp,
+                               command.position,
+                               command.number);
 
-          System.arraycopy(annotations[a].annotations,
-              command.position, temp,
-              command.position+command.number,
-              aSize - command.position);
+            }
+
+            System.arraycopy(annotations[a].annotations,
+                             command.position, temp,
+                             command.position + command.number,
+                             aSize - command.position);
+          }
+          else
+            temp = annotations[a].annotations;
         }
         else
         {
@@ -346,7 +377,6 @@ public class EditCommand implements CommandI
 
         annotations[a].annotations = temp;
      }
-    }
   }
 
 
@@ -391,12 +421,12 @@ public class EditCommand implements CommandI
 
       alIndex = new int[seqs.length];
       for(int i=0; i<seqs.length; i++)
+      {
         alIndex[i] = al.findIndex(seqs[i]);
+      }
 
       fullAlignmentHeight = (al.getHeight()==seqs.length);
-
     }
-
   }
 
 }
-- 
1.7.10.2