/*
* 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.
*
import java.awt.*;
import java.awt.event.*;
-import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
Vector allGroups = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
+ if (af.getViewport().getAlignment().getSequenceAt(i).getDatasetSequence()
.getSequenceFeatures() == null)
{
continue;
}
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
int index = 0;
// Find out which features should be visible depending on which groups
// are selected / deselected
// and recompute average width ordering
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
if (tmpfeatures == null)
{
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(choice), "UTF-8"));
- Enumeration e = fr.featureColours.keys();
+ Iterator e = fr.featureColours.keySet().iterator();
float[] sortOrder = new float[fr.featureColours.size()];
String[] sortTypes = new String[fr.featureColours.size()];
int i = 0;
- while (e.hasMoreElements())
+ while (e.hasNext())
{
- sortTypes[i] = e.nextElement().toString();
+ sortTypes[i] = e.next().toString();
sortOrder[i] = fr.getOrder(sortTypes[i]);
i++;
}
if (fr.featureGroups != null)
{
- Enumeration en = fr.featureGroups.keys();
+ Iterator en = fr.featureGroups.keySet().iterator();
gps = new String[fr.featureColours.size()];
int g = 0;
boolean valid = false;
- while (en.hasMoreElements())
+ while (en.hasNext())
{
- String gp = (String) en.nextElement();
+ String gp = (String) en.next();
Boolean on = (Boolean) fr.featureGroups.get(gp);
if (on != null && on.booleanValue())
{