X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FRemoveGapsCommand.java;h=3a485c8ea067c61bffb81a25221827ba361342f0;hb=6f9acb31a9f7c8571273a141583133358a6445ce;hp=8754b513915a2d9c4fae6bb46990b2d4b49f6d13;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index 8754b51..3a485c8 100644
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
@@ -37,7 +39,9 @@ package jalview.commands;
* Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
public class RemoveGapsCommand extends EditCommand
{
@@ -72,7 +76,7 @@ public class RemoveGapsCommand extends EditCommand
int j, jSize;
- edits = new Edit[0];
+ clearEdits();
boolean delete = true;
char[] sequence;
@@ -89,7 +93,7 @@ public class RemoveGapsCommand extends EditCommand
{
delete = true;
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
if (delete)
{
@@ -106,7 +110,7 @@ public class RemoveGapsCommand extends EditCommand
if (!delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, new SequenceI[]
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[]
{ seqs[s] }, start + startCol - deletedCols, endCol - startCol,
al, false, null);
@@ -117,7 +121,7 @@ public class RemoveGapsCommand extends EditCommand
}
if (delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, new SequenceI[]
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[]
{ seqs[s] }, start + startCol - deletedCols, jSize - startCol, al,
false, null);
}