/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
if (groupPanel != null)
{
- groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
- 4));
+ groupPanel
+ .setLayout(new GridLayout(
+ (fr.featureGroups.size() - fr.hiddenGroups.size()) / 4 + 1,
+ 4));
groupPanel.validate();
add(groupPanel, BorderLayout.NORTH);
rdrw = true;
groupPanel.removeAll();
}
-
+ // TODO: JAL-964 - smoothly incorporate new group entries if panel already
+ // displayed and new groups present
Enumeration gps = fr.featureGroups.keys();
while (gps.hasMoreElements())
{
check.addMouseListener(this);
check.setFont(new Font("Serif", Font.BOLD, 12));
check.addItemListener(this);
+ check.setVisible(fr.hiddenGroups.contains(group));
groupPanel.add(check);
}
if (rdrw)
SequenceFeature[] tmpfeatures;
String group = null, type;
Vector visibleChecks = new Vector();
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{