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Merge branch 'JAL-986_idwidthprefs' into JAL-976_jabaws2supp
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationColourChooser.java
diff --git
a/src/jalview/gui/AnnotationColourChooser.java
b/src/jalview/gui/AnnotationColourChooser.java
index
eca0b4c
..
7fb868f
100755
(executable)
--- a/
src/jalview/gui/AnnotationColourChooser.java
+++ b/
src/jalview/gui/AnnotationColourChooser.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.
*
@@
-51,10
+51,10
@@
public class AnnotationColourChooser extends JPanel
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
oldcs = av.getGlobalColourScheme();
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
oldcs = av.getGlobalColourScheme();
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
oldgroupColours = new Hashtable();
{
oldgroupColours = new Hashtable();
- Vector allGroups = ap.av.alignment.getGroups();
+ Vector allGroups = ap.av.getAlignment().getGroups();
SequenceGroup sg;
for (int g = 0; g < allGroups.size(); g++)
{
SequenceGroup sg;
for (int g = 0; g < allGroups.size(); g++)
{
@@
-91,7
+91,7
@@
public class AnnotationColourChooser extends JPanel
}
});
}
});
- if (av.alignment.getAlignmentAnnotation() == null)
+ if (av.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
{
return;
}
@@
-113,9
+113,9
@@
public class AnnotationColourChooser extends JPanel
adjusting = true;
Vector list = new Vector();
int index = 1;
adjusting = true;
Vector list = new Vector();
int index = 1;
- for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
{
{
- String label = av.alignment.getAlignmentAnnotation()[i].label;
+ String label = av.getAlignment().getAlignmentAnnotation()[i].label;
if (!list.contains(label))
list.addElement(label);
else
if (!list.contains(label))
list.addElement(label);
else
@@
-378,7
+378,7
@@
public class AnnotationColourChooser extends JPanel
return;
}
return;
}
- currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+ currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
.getSelectedIndex()];
int aboveThreshold = -1;
.getSelectedIndex()];
int aboveThreshold = -1;
@@
-450,9
+450,9
@@
public class AnnotationColourChooser extends JPanel
av.setGlobalColourScheme(acg);
av.setGlobalColourScheme(acg);
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
{
- Vector allGroups = ap.av.alignment.getGroups();
+ Vector allGroups = ap.av.getAlignment().getGroups();
SequenceGroup sg;
for (int g = 0; g < allGroups.size(); g++)
{
SequenceGroup sg;
for (int g = 0; g < allGroups.size(); g++)
{
@@
-508,9
+508,9
@@
public class AnnotationColourChooser extends JPanel
void reset()
{
av.setGlobalColourScheme(oldcs);
void reset()
{
av.setGlobalColourScheme(oldcs);
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
{
- Vector allGroups = ap.av.alignment.getGroups();
+ Vector allGroups = ap.av.getAlignment().getGroups();
SequenceGroup sg;
for (int g = 0; g < allGroups.size(); g++)
{
SequenceGroup sg;
for (int g = 0; g < allGroups.size(); g++)
{