X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=d7e452a962f5fd9ffa77c6fd08f2d9e0e8200507;hb=f3df97a8d39f8124610d661f8c141677f73d86b0;hp=a20069956ed6851fedcbba7571d31b66405c1178;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index a200699..d7e452a 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.
+ *
+ * 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 .
*/
package jalview.gui;
@@ -50,13 +49,13 @@ 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 +104,11 @@ 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 +133,7 @@ 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 +160,8 @@ 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 +179,11 @@ 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 +209,7 @@ 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 +256,7 @@ public class SliderPanel extends GSliderPanel
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void valueChanged(int i)
{
@@ -267,12 +266,12 @@ public class SliderPanel extends GSliderPanel
}
ColourSchemeI toChange = null;
- Vector allGroups = null;
+ List 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 +315,7 @@ public class SliderPanel extends GSliderPanel
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setAllGroupsCheckEnabled(boolean b)
{
@@ -327,7 +326,7 @@ public class SliderPanel extends GSliderPanel
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void valueField_actionPerformed(ActionEvent e)
{
@@ -345,7 +344,7 @@ public class SliderPanel extends GSliderPanel
* DOCUMENT ME!
*
* @param value
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setValue(int value)
{