Annotation adjustment moved to EditCommand

[jalview.git] / src / jalview / commands / EditCommand.java

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index be11d44..ed356dc 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -20,6 +20,8 @@ package jalview.commands;
 \r
 import jalview.datamodel.*;\r
 \r
+import java.util.Hashtable;\r
+\r
 /**\r
  *\r
  * <p>Title: EditCommmand</p>\r
@@ -54,23 +56,6 @@ public class EditCommand implements CommandI
     this.description = description;\r
   }\r
 \r
-  public EditCommand(String description,\r
-                     int command,\r
-                     SequenceI[] seqs,\r
-                     int position,\r
-                     int number,\r
-                     char gapChar)\r
-  {\r
-    this.description = description;\r
-\r
-    if (command==INSERT_GAP || command==DELETE_GAP)\r
-    {\r
-      edits = new Edit[] { new Edit(command, seqs, position, number, gapChar)};\r
-    }\r
-\r
-    performEdit(0);\r
-  }\r
-\r
   public EditCommand( String description,\r
                       int command,\r
                       SequenceI[] seqs,\r
@@ -108,10 +93,15 @@ public class EditCommand implements CommandI
                          SequenceI[] seqs,\r
                          int position,\r
                          int number,\r
-                         char gapChar,\r
+                         AlignmentI al,\r
                          boolean performEdit)\r
   {\r
-    Edit edit = new Edit(command, seqs, position, number, gapChar);\r
+    Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());\r
+    if(al.getHeight()==seqs.length)\r
+    {\r
+      edit.al = al;\r
+      edit.fullAlignmentHeight = true;\r
+    }\r
 \r
     if (edits != null)\r
     {\r
@@ -188,6 +178,11 @@ public class EditCommand implements CommandI
                                      command.number,\r
                                      command.gapChar);\r
     }\r
+\r
+    if (command.fullAlignmentHeight)\r
+    {\r
+      adjustAnnotations(command, true);\r
+    }\r
   }\r
 \r
   void deleteGap(Edit command)\r
@@ -196,6 +191,11 @@ public class EditCommand implements CommandI
     {\r
       command.seqs[s].deleteChars(command.position, command.position+command.number);\r
     }\r
+\r
+    if (command.fullAlignmentHeight)\r
+    {\r
+      adjustAnnotations(command, false);\r
+    }\r
   }\r
 \r
   void cut(Edit command)\r
@@ -218,6 +218,12 @@ public class EditCommand implements CommandI
         command.al.deleteSequence(command.seqs[i]);\r
       }\r
     }\r
+\r
+    if (command.fullAlignmentHeight)\r
+    {\r
+      adjustAnnotations(command, false);\r
+    }\r
+\r
   }\r
 \r
   void paste(Edit command)\r
@@ -257,11 +263,97 @@ public class EditCommand implements CommandI
       command.seqs[i].setSequence(tmp.toString());\r
     }\r
 \r
+    if (command.fullAlignmentHeight)\r
+    {\r
+      adjustAnnotations(command, true);\r
+    }\r
+\r
     command.string = null;\r
   }\r
 \r
+\r
+  void adjustAnnotations(Edit command, boolean insert)\r
+  {\r
+    AlignmentAnnotation [] annotations = command.al.getAlignmentAnnotation();\r
+    if(annotations!=null)\r
+    {\r
+      if(!insert)\r
+        command.deletedAnnotations = new Hashtable();\r
+\r
+      int aSize, tSize;\r
+      Annotation [] temp;\r
+      for (int a = 0; a < annotations.length; a++)\r
+      {\r
+        if(annotations[a].autoCalculated)\r
+        {\r
+          continue;\r
+        }\r
+\r
+        aSize = annotations[a].annotations.length;\r
+        if(insert)\r
+          tSize = aSize + command.number;\r
+        else\r
+          tSize = aSize - command.number;\r
+\r
+        temp = new Annotation[tSize];\r
+\r
+        if(insert)\r
+        {\r
+          System.arraycopy(annotations[a].annotations,\r
+              0, temp, 0, command.position);\r
+\r
+          if(command.deletedAnnotations!=null\r
+             && command.deletedAnnotations.containsKey(annotations[a].annotationId))\r
+          {\r
+            Annotation [] restore = (Annotation [])\r
+                command.deletedAnnotations.get(annotations[a].annotationId);\r
+\r
+            System.arraycopy(restore,\r
+                             0,\r
+                             temp,\r
+                             command.position,\r
+                             command.number);\r
+\r
+          }\r
+\r
+          System.arraycopy(annotations[a].annotations,\r
+              command.position, temp,\r
+              command.position+command.number,\r
+              aSize - command.position);\r
+        }\r
+        else\r
+        {\r
+          if(command.position < annotations[a].annotations.length)\r
+          {\r
+            System.arraycopy(annotations[a].annotations,\r
+                             0, temp, 0, command.position);\r
+\r
+            Annotation[] deleted = new Annotation[command.number];\r
+            System.arraycopy(annotations[a].annotations,\r
+                             command.position, deleted, 0, command.number);\r
+\r
+            command.deletedAnnotations.put(annotations[a].annotationId,\r
+                                           deleted);\r
+\r
+            System.arraycopy(annotations[a].annotations,\r
+                             command.position + command.number,\r
+                             temp, command.position,\r
+                             aSize - command.position - command.number);\r
+          }\r
+          else\r
+            temp = annotations[a].annotations;\r
+        }\r
+\r
+        annotations[a].annotations = temp;\r
+     }\r
+    }\r
+  }\r
+\r
+\r
   class Edit\r
   {\r
+    boolean fullAlignmentHeight = false;\r
+    Hashtable deletedAnnotations;\r
     AlignmentI al;\r
     int command;\r
     char [][] string;\r
@@ -296,9 +388,13 @@ public class EditCommand implements CommandI
       this.position = position;\r
       this.number = number;\r
       this.al = al;\r
+\r
       alIndex = new int[seqs.length];\r
       for(int i=0; i<seqs.length; i++)\r
         alIndex[i] = al.findIndex(seqs[i]);\r
+\r
+      fullAlignmentHeight = (al.getHeight()==seqs.length);\r
+\r
     }\r
 \r
   }\r