JAL-1432 updated copyright notices

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

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 8c290b5..b9596b4 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,20 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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.
+ *  
+ * 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
+ * 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.gui;
 
@@ -50,13 +50,13 @@ public class SliderPanel extends GSliderPanel
    * Creates a new SliderPanel object.
    * 
    * @param ap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param value
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param forConserve
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param cs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public SliderPanel(final AlignmentPanel ap, int value,
           boolean forConserve, ColourSchemeI cs)
@@ -105,11 +105,11 @@ public class SliderPanel extends GSliderPanel
    * DOCUMENT ME!
    * 
    * @param ap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param cs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param source
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -134,7 +134,7 @@ public class SliderPanel extends GSliderPanel
     conservationSlider.setTitle("Conservation Colour Increment  (" + source
             + ")");
 
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       sp.setAllGroupsCheckEnabled(true);
     }
@@ -161,8 +161,8 @@ public class SliderPanel extends GSliderPanel
 
     if (!conservationSlider.isVisible())
     {
-      Desktop.addInternalFrame(conservationSlider, conservationSlider
-              .getTitle(), 420, 90, false);
+      Desktop.addInternalFrame(conservationSlider,
+              conservationSlider.getTitle(), 420, 90, false);
       conservationSlider
               .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
               {
@@ -180,11 +180,11 @@ public class SliderPanel extends GSliderPanel
    * DOCUMENT ME!
    * 
    * @param ap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param cs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param source
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -210,7 +210,7 @@ public class SliderPanel extends GSliderPanel
 
     PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
 
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       pid.setAllGroupsCheckEnabled(true);
     }
@@ -257,7 +257,7 @@ public class SliderPanel extends GSliderPanel
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void valueChanged(int i)
   {
@@ -267,12 +267,12 @@ public class SliderPanel extends GSliderPanel
     }
 
     ColourSchemeI toChange = null;
-    Vector allGroups = null;
+    List<SequenceGroup> allGroups = null;
     int groupIndex = 0;
 
     if (allGroupsCheck.isSelected())
     {
-      allGroups = ap.av.alignment.getGroups();
+      allGroups = ap.av.getAlignment().getGroups();
       groupIndex = allGroups.size() - 1;
     }
     else
@@ -316,7 +316,7 @@ public class SliderPanel extends GSliderPanel
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setAllGroupsCheckEnabled(boolean b)
   {
@@ -327,7 +327,7 @@ public class SliderPanel extends GSliderPanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void valueField_actionPerformed(ActionEvent e)
   {
@@ -345,7 +345,7 @@ public class SliderPanel extends GSliderPanel
    * DOCUMENT ME!
    * 
    * @param value
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setValue(int value)
   {