X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=be11d44706d8adfc9555250d5d15e3874f6423e6;hb=5951e3b0b9faea1c8b54914cb64ff3a08ba27cb6;hp=7218115323f4e4994994b814cd173b1ccbe42560;hpb=91d2b7cf873f1437a3e21049c5aa6c7a7117e820;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 7218115..be11d44 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -37,10 +37,10 @@ import jalview.datamodel.*;
  */
 public class EditCommand implements CommandI
 {
-  public static String INSERT_GAP = "InsertGap";
-  public static String DELETE_GAP = "DeleteGap";
-  public static String CUT = "Cut";
-  public static String PASTE = "Paste";
+  public static final int INSERT_GAP = 0;
+  public static final int DELETE_GAP = 1;
+  public static final int CUT = 2;
+  public static final int PASTE = 3;
 
   Edit[] edits;
 
@@ -55,7 +55,7 @@ public class EditCommand implements CommandI
   }
 
   public EditCommand(String description,
-                     String command,
+                     int command,
                      SequenceI[] seqs,
                      int position,
                      int number,
@@ -63,8 +63,7 @@ public class EditCommand implements CommandI
   {
     this.description = description;
 
-    if (command.equalsIgnoreCase(INSERT_GAP)
-        || command.equalsIgnoreCase(DELETE_GAP))
+    if (command==INSERT_GAP || command==DELETE_GAP)
     {
       edits = new Edit[] { new Edit(command, seqs, position, number, gapChar)};
     }
@@ -73,14 +72,14 @@ public class EditCommand implements CommandI
   }
 
   public EditCommand( String description,
-                      String command,
+                      int command,
                       SequenceI[] seqs,
                       int position,
                       int number,
                       AlignmentI al)
    {
      this.description = description;
-     if ( command.equalsIgnoreCase(CUT) || command.equalsIgnoreCase(PASTE))
+     if ( command==CUT || command==PASTE)
      {
        edits = new Edit[]{new Edit(command, seqs, position, number, al)};
      }
@@ -99,8 +98,13 @@ public class EditCommand implements CommandI
     return edits==null?0:edits.length;
   }
 
+  public AlignmentI getAlignment()
+  {
+    return edits[0].al;
+  }
+
 
-  public void appendEdit(String command,
+  public void appendEdit(int command,
                          SequenceI[] seqs,
                          int position,
                          int number,
@@ -128,19 +132,19 @@ public class EditCommand implements CommandI
     int eSize = edits.length;
     for (int e = commandIndex; e < eSize; e++)
     {
-      if (edits[e].command.equals(INSERT_GAP))
+      if (edits[e].command==INSERT_GAP)
       {
         insertGap(edits[e]);
       }
-      else if (edits[e].command.equals(DELETE_GAP))
+      else if (edits[e].command==DELETE_GAP)
       {
         deleteGap(edits[e]);
       }
-      else if(edits[e].command.equals(CUT))
+      else if(edits[e].command==CUT)
       {
         cut(edits[e]);
       }
-      else if(edits[e].command.equals(PASTE))
+      else if(edits[e].command==PASTE)
       {
         paste(edits[e]);
       }
@@ -157,19 +161,19 @@ public class EditCommand implements CommandI
     int e = 0, eSize = edits.length;
     for (e = eSize-1; e > -1; e--)
     {
-      if (edits[e].command.equals(INSERT_GAP))
+      if (edits[e].command==INSERT_GAP)
       {
         deleteGap(edits[e]);
       }
-      else if (edits[e].command.equals(DELETE_GAP))
+      else if (edits[e].command==DELETE_GAP)
       {
         insertGap(edits[e]);
       }
-      else if (edits[e].command.equals(CUT))
+      else if (edits[e].command==CUT)
       {
         paste(edits[e]);
       }
-      else if (edits[e].command.equals(PASTE))
+      else if (edits[e].command==PASTE)
       {
         cut(edits[e]);
       }
@@ -196,7 +200,7 @@ public class EditCommand implements CommandI
 
   void cut(Edit command)
   {
-    command.string = new String [command.seqs.length];
+    command.string = new char [command.seqs.length][];
 
     for(int i=0; i<command.seqs.length; i++)
     {
@@ -231,10 +235,22 @@ public class EditCommand implements CommandI
         else
           command.al.addSequence(command.seqs[i]);
       }
-      tmp = new StringBuffer(command.seqs[i].getSequence());
+      tmp = new StringBuffer();
+      tmp.append(command.seqs[i].getSequence());
 
       if(command.string!=null && command.string[i]!=null)
       {
+        if(command.position>=tmp.length())
+        {
+          //This occurs if padding is on, and residues
+          //are removed from end of alignment
+          int length = command.position-tmp.length();
+          while (length > 0)
+          {
+            tmp.append(command.gapChar);
+            length--;
+          }
+        }
         tmp.insert(command.position, command.string[i]);
         command.string[i] = null;
       }
@@ -247,14 +263,14 @@ public class EditCommand implements CommandI
   class Edit
   {
     AlignmentI al;
-    String command;
-    String [] string;
+    int command;
+    char [][] string;
     SequenceI[] seqs;
     int [] alIndex;
     int position, number;
     char gapChar;
 
-    Edit(String command,
+    Edit(int command,
          SequenceI[] seqs,
          int position,
          int number,
@@ -268,12 +284,13 @@ public class EditCommand implements CommandI
     }
 
 
-    Edit(String command,
+    Edit(int command,
          SequenceI[] seqs,
          int position,
          int number,
          AlignmentI al)
     {
+      this.gapChar = al.getGapCharacter();
       this.command = command;
       this.seqs = seqs;
       this.position = position;