X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSliderPanel.java;h=d25caa4fe3308c0f69a81a3aa5d429cff19f188b;hb=8e2df4a7b64214a0d1a3b613ab2fec04d451b1d7;hp=a05bbf0d9e2859472801a07d0ecef8a3d60bc432;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index a05bbf0..d25caa4 100755
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/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.appletgui;
@@ -58,7 +57,7 @@ public class SliderPanel extends Panel implements ActionListener,
conservationSlider.setTitle("Conservation Colour Increment (" + source
+ ")");
- if (ap.av.alignment.getGroups() != null)
+ if (ap.av.getAlignment().getGroups() != null)
{
sp.setAllGroupsCheckEnabled(true);
}
@@ -113,7 +112,7 @@ public class SliderPanel extends Panel implements ActionListener,
}
PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
- if (ap.av.alignment.getGroups() != null)
+ if (ap.av.getAlignment().getGroups() != null)
{
pid.setAllGroupsCheckEnabled(true);
}
@@ -196,24 +195,22 @@ public class SliderPanel extends Panel implements ActionListener,
}
ColourSchemeI toChange = null;
- Vector allGroups = null;
- int groupIndex = 0;
+ Iterator allGroups = null;
if (allGroupsCheck.getState())
{
- allGroups = ap.av.alignment.getGroups();
- groupIndex = allGroups.size() - 1;
+ allGroups = ap.av.getAlignment().getGroups().listIterator();
}
else
{
toChange = cs;
}
- while (groupIndex > -1)
+ do
{
if (allGroups != null)
{
- toChange = ((SequenceGroup) allGroups.elementAt(groupIndex)).cs;
+ toChange = allGroups.next().cs;
}
if (forConservation)
@@ -225,8 +222,7 @@ public class SliderPanel extends Panel implements ActionListener,
toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
}
- groupIndex--;
- }
+ } while (allGroups != null && allGroups.hasNext());
ap.seqPanel.seqCanvas.repaint();