git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-974 - refactor FeatureRenderer constructor to AlignmentPanel (should probably...
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationColourChooser.java
diff --git
a/src/jalview/gui/AnnotationColourChooser.java
b/src/jalview/gui/AnnotationColourChooser.java
index
eca0b4c
..
64b1d19
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.
*
@@
-51,14
+51,11
@@
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();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+ for (SequenceGroup sg:ap.av.getAlignment().getGroups())
{
{
- sg = (SequenceGroup) allGroups.get(g);
if (sg.cs != null)
{
oldgroupColours.put(sg, sg.cs);
if (sg.cs != null)
{
oldgroupColours.put(sg, sg.cs);
@@
-91,7
+88,7
@@
public class AnnotationColourChooser extends JPanel
}
});
}
});
- if (av.alignment.getAlignmentAnnotation() == null)
+ if (av.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
{
return;
}
@@
-113,9
+110,9
@@
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
+375,7
@@
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;
@@
-450,14
+447,11
@@
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();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+
+ for (SequenceGroup sg:ap.av.getAlignment().getGroups())
{
{
- sg = (SequenceGroup) allGroups.get(g);
-
if (sg.cs == null)
{
continue;
if (sg.cs == null)
{
continue;
@@
-508,13
+502,11
@@
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();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+
+ for (SequenceGroup sg:ap.av.getAlignment().getGroups())
{
{
- sg = (SequenceGroup) allGroups.get(g);
sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
}
}
sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
}
}