/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
+ * 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
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
private JTextField _seq = new JTextField();
- private JLabel _strLabel = new JLabel(MessageManager.getString("label.str"));
+ private JLabel _strLabel = new JLabel(
+ MessageManager.getString("label.str"));
- private JLabel _seqLabel = new JLabel(MessageManager.getString("label.seq"));
+ private JLabel _seqLabel = new JLabel(
+ MessageManager.getString("label.seq"));
- private JButton _createButton = new JButton(MessageManager.getString("action.create"));
+ private JButton _createButton = new JButton(
+ MessageManager.getString("action.create"));
- private JButton _updateButton = new JButton(MessageManager.getString("action.update"));
+ private JButton _updateButton = new JButton(
+ MessageManager.getString("action.update"));
- private JButton _deleteButton = new JButton(MessageManager.getString("action.delete"));
+ private JButton _deleteButton = new JButton(
+ MessageManager.getString("action.delete"));
- private JButton _duplicateButton = new JButton(MessageManager.getString("action.snapshot"));
+ private JButton _duplicateButton = new JButton(
+ MessageManager.getString("action.snapshot"));
protected JPanel _listPanel = new JPanel();
{
// super("VARNA in Jalview");
initVarna(seq, struc);
-
+
}
public AppVarnaBinding(ArrayList<RNA> rnaList)
private void initVarna(String seq, String str)
{
-
+
DefaultListModel dlm = new DefaultListModel();
DefaultListSelectionModel m = new DefaultListSelectionModel();
try
{
-
+
vp = new VARNAPanel("0", ".");
_RNA1.setRNA(seq, str);
_RNA1.drawRNARadiate(vp.getConfig());
private void initVarnaEdit(ArrayList<RNA> rnaInList)
{
-
+
DefaultListModel dlm = new DefaultListModel();
int marginTools = 40;
FullBackup sel = (FullBackup) _sideList.getSelectedValue();
Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
.getSize(), sel.rna.getSize());
- //vp.showRNAInterpolated(sel.rna, sel.config, map);
+ // vp.showRNAInterpolated(sel.rna, sel.config, map);
vp.showRNA(sel.rna, sel.config);
// _seq.setText(sel.rna.getSeq());
_str.setText(sel.rna.getStructDBN());
try
{
-
+
vp = new VARNAPanel("0", ".");
for (int i = 0; i < rnaInList.size(); i++)
{
rnaInList.get(i).drawRNARadiate(vp.getConfig());
-
+
}
} catch (ExceptionNonEqualLength e)
{
ops.add(_deleteButton);
ops.add(_duplicateButton);
- JLabel j = new JLabel(MessageManager.getString("label.structures_manager"), JLabel.CENTER);
+ JLabel j = new JLabel(
+ MessageManager.getString("label.structures_manager"),
+ JLabel.CENTER);
_listPanel.setLayout(new BorderLayout());
// _listPanel.add(ops, BorderLayout.SOUTH);
public void onUINewStructure(VARNAConfig v, RNA r)
{
// patch to fix infinite loop
- // The problem is that onUINewStructure is called when user clicks
+ // The problem is that onUINewStructure is called when user clicks
// check with Yann about whether Jalview should do anything with this event.
- // e.g. if user has used VARNA's menu to import a structure .. Jalview may need to be told which structure is displayed.
-
+ // e.g. if user has used VARNA's menu to import a structure .. Jalview may
+ // need to be told which structure is displayed.
+
// _rnaList.add(v, r, "", true);
}
public void onZoomLevelChanged()
{
// TODO Auto-generated method stub
-
+
}
@Override
public void onTranslationChanged()
{
// TODO Auto-generated method stub
-
+
}
}