(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

[jalview.git] / src / jalview / gui / RedundancyPanel.java

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index cb4c595..9f117b6 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 file is part of Jalview.
  * 
- * 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 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.
  * 
- * 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 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/>.
  */
 package jalview.gui;
 
@@ -55,9 +54,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * Creates a new RedundancyPanel object.
    * 
    * @param ap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param af
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
   {
@@ -103,9 +102,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * slider to dynamically hide redundant sequences
    * 
    * @param threshold
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param sel
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -132,15 +131,15 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     if ((sg != null) && (sg.getSize() >= 1))
     {
-      originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+      originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
       start = sg.getStartRes();
       end = sg.getEndRes();
     }
     else
     {
-      originalSequences = ap.av.alignment.getSequencesArray();
+      originalSequences = ap.av.getAlignment().getSequencesArray();
       start = 0;
-      end = ap.av.alignment.getWidth();
+      end = ap.av.getAlignment().getWidth();
     }
 
     height = originalSequences.length;
@@ -151,7 +150,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       redundancy[i] = 0f;
     }
 
-    if (ap.av.hasHiddenColumns)
+    if (ap.av.hasHiddenColumns())
     {
       omitHidden = ap.av.getViewAsString(sg != null);
     }
@@ -237,7 +236,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void applyButton_actionPerformed(ActionEvent e)
   {
@@ -274,11 +273,11 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       }
 
       EditCommand cut = new EditCommand("Remove Redundancy",
-              EditCommand.CUT, deleted, 0, width, ap.av.alignment);
+              EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
 
       for (int i = 0; i < del.size(); i++)
       {
-        ap.av.alignment.deleteSequence(deleted[i]);
+        ap.av.getAlignment().deleteSequence(deleted[i]);
         PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
         if (sg != null)
         {
@@ -300,7 +299,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void undoButton_actionPerformed(ActionEvent e)
   {
@@ -325,7 +324,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void valueField_actionPerformed(ActionEvent e)
   {