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JAL-958 revised applet parameter documentation to standardise on long form 'normalise...
[jalview.git]
/
src
/
jalview
/
appletgui
/
SliderPanel.java
diff --git
a/src/jalview/appletgui/SliderPanel.java
b/src/jalview/appletgui/SliderPanel.java
index
4e6c2bf
..
2046df6
100755
(executable)
--- a/
src/jalview/appletgui/SliderPanel.java
+++ b/
src/jalview/appletgui/SliderPanel.java
@@
-1,6
+1,6
@@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-18,6
+18,7
@@
package jalview.appletgui;
import java.util.*;
package jalview.appletgui;
import java.util.*;
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
import java.awt.*;
import java.awt.event.*;
@@
-57,7
+58,7
@@
public class SliderPanel extends Panel implements ActionListener,
conservationSlider.setTitle("Conservation Colour Increment (" + source
+ ")");
conservationSlider.setTitle("Conservation Colour Increment (" + source
+ ")");
- if (ap.av.alignment.getGroups() != null)
+ if (ap.av.getAlignment().getGroups() != null)
{
sp.setAllGroupsCheckEnabled(true);
}
{
sp.setAllGroupsCheckEnabled(true);
}
@@
-112,7
+113,7
@@
public class SliderPanel extends Panel implements ActionListener,
}
PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
}
PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
- if (ap.av.alignment.getGroups() != null)
+ if (ap.av.getAlignment().getGroups() != null)
{
pid.setAllGroupsCheckEnabled(true);
}
{
pid.setAllGroupsCheckEnabled(true);
}
@@
-195,24
+196,22
@@
public class SliderPanel extends Panel implements ActionListener,
}
ColourSchemeI toChange = null;
}
ColourSchemeI toChange = null;
- Vector allGroups = null;
- int groupIndex = 0;
+ Iterator<SequenceGroup> allGroups = null;
if (allGroupsCheck.getState())
{
if (allGroupsCheck.getState())
{
- allGroups = ap.av.alignment.getGroups();
- groupIndex = allGroups.size() - 1;
+ allGroups = ap.av.getAlignment().getGroups().listIterator();
}
else
{
toChange = cs;
}
}
else
{
toChange = cs;
}
- while (groupIndex > -1)
+ do
{
if (allGroups != null)
{
{
if (allGroups != null)
{
- toChange = ((SequenceGroup) allGroups.elementAt(groupIndex)).cs;
+ toChange = allGroups.next().cs;
}
if (forConservation)
}
if (forConservation)
@@
-224,8
+223,7
@@
public class SliderPanel extends Panel implements ActionListener,
toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
}
toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
}
- groupIndex--;
- }
+ } while (allGroups!=null && allGroups.hasNext());
ap.seqPanel.seqCanvas.repaint();
ap.seqPanel.seqCanvas.repaint();