JAL-1620 version bump and release notes

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

diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index 5639fa5..e49d42b 100644 (file)
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -1,31 +1,51 @@
-package jalview.commands;
-
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
- * 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.commands;
+
+/*
+ * 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
  */
 
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 
-public class RemoveGapsCommand
-    extends EditCommand
+public class RemoveGapsCommand extends EditCommand
 {
-  public RemoveGapsCommand(String description,
-                           SequenceI[] seqs, AlignmentI al)
+  public RemoveGapsCommand(String description, SequenceI[] seqs,
+          AlignmentI al)
   {
     this.description = description;
     int width = 0;
@@ -40,9 +60,8 @@ public class RemoveGapsCommand
     findGaps(seqs, 0, width, al);
   }
 
-  public RemoveGapsCommand(String description,
-                           SequenceI[] seqs,
-                           int start, int end, AlignmentI al)
+  public RemoveGapsCommand(String description, SequenceI[] seqs, int start,
+          int end, AlignmentI al)
   {
     this.description = description;
     findGaps(seqs, start, end, al);
@@ -56,7 +75,7 @@ public class RemoveGapsCommand
 
     int j, jSize;
 
-    edits = new Edit[0];
+    clearEdits();
 
     boolean delete = true;
     char[] sequence;
@@ -90,12 +109,9 @@ public class RemoveGapsCommand
 
         if (!delete && startCol > -1)
         {
-          this.appendEdit(DELETE_GAP, new SequenceI[]
-                          {seqs[s]},
-                          start + startCol - deletedCols,
-                          endCol - startCol,
-                          al,
-                          false,null);
+          this.appendEdit(Action.DELETE_GAP, new SequenceI[]
+          { seqs[s] }, start + startCol - deletedCols, endCol - startCol,
+                  al, false, null);
 
           deletedCols += (endCol - startCol);
           startCol = -1;
@@ -104,17 +120,14 @@ public class RemoveGapsCommand
       }
       if (delete && startCol > -1)
       {
-        this.appendEdit(DELETE_GAP, new SequenceI[]
-                        {seqs[s]},
-                        start + startCol - deletedCols,
-                        jSize - startCol,
-                        al,
-                        false,null);
+        this.appendEdit(Action.DELETE_GAP, new SequenceI[]
+        { seqs[s] }, start + startCol - deletedCols, jSize - startCol, al,
+                false, null);
       }
 
     }
 
-    performEdit(0,null);
+    performEdit(0, null);
   }
 
 }