JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java
index 9b9c99e..153371a 100644 (file)
--- a/src/jalview/commands/SlideSequencesCommand.java
+++ b/src/jalview/commands/SlideSequencesCommand.java
@@ -1,36 +1,33 @@
-
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.commands;
 
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceI;
 
 public class SlideSequencesCommand extends EditCommand
 {
   boolean gapsInsertedBegin = false;
 
-  public SlideSequencesCommand(String description,
-                               SequenceI[] seqsLeft,
-                               SequenceI[] seqsRight,
-                               int slideSize,
-                               char gapChar)
+  public SlideSequencesCommand(String description, SequenceI[] seqsLeft,
+          SequenceI[] seqsRight, int slideSize, char gapChar)
   {
     this.description = description;
 
@@ -40,21 +37,29 @@ public class SlideSequencesCommand extends EditCommand
     for (i = 0; i < lSize; i++)
     {
       for (j = 0; j < slideSize; j++)
+      {
         if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))
         {
           gapsInsertedBegin = true;
           break;
         }
+      }
     }
 
+    Edit e = null;
+
     if (!gapsInsertedBegin)
-      edits = new Edit[]
-          {  new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)};
+    {
+      e = new Edit(Action.DELETE_GAP, seqsLeft, 0, slideSize, gapChar);
+      setEdit(e);
+    }
     else
-      edits = new Edit[]
-          {  new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)};
+    {
+      e = new Edit(Action.INSERT_GAP, seqsRight, 0, slideSize, gapChar);
+      setEdit(e);
+    }
 
-    performEdit(0,null);
+    performEdit(e, null);
   }
 
   public boolean getGapsInsertedBegin()
@@ -66,28 +71,23 @@ public class SlideSequencesCommand extends EditCommand
   {
     boolean same = false;
 
-    if(command.edits[0].seqs.length==edits[0].seqs.length)
+    if (command.getEdit(0).seqs.length == getEdit(0).seqs.length)
     {
       same = true;
-      for (int i = 0; i < command.edits[0].seqs.length; i++)
+      for (int i = 0; i < command.getEdit(0).seqs.length; i++)
       {
-        if (edits[0].seqs[i] != command.edits[0].seqs[i])
+        if (getEdit(0).seqs[i] != command.getEdit(0).seqs[i])
         {
           same = false;
         }
       }
     }
 
-    if(same)
+    if (same)
     {
-      Edit[] temp = new Edit[command.edits.length + 1];
-      System.arraycopy(command.edits, 0, temp, 0, command.edits.length);
-      command.edits = temp;
-      command.edits[command.edits.length - 1] = edits[0];
+      command.addEdit(getEdit(0));
     }
 
     return same;
   }
 }
-
-