/*
* 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.
*
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
oldcs = av.getGlobalColourScheme();
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
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++)
{
}
});
- if (av.alignment.getAlignmentAnnotation() == null)
+ if (av.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
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
return;
}
- currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+ currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
.getSelectedIndex()];
int aboveThreshold = -1;
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++)
{
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++)
{