/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
+import jalview.structure.AtomSpec;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import javax.swing.DefaultListModel;
import javax.swing.DefaultListSelectionModel;
-import javax.swing.Icon;
import javax.swing.JButton;
-import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
import javax.swing.JTextField;
import javax.swing.ListModel;
import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
private JTextField _seq = new JTextField();
- private JLabel _strLabel = new JLabel(" Str:");
+ private JLabel _strLabel = new JLabel(
+ MessageManager.getString("label.str"));
- private JLabel _seqLabel = new JLabel(" Seq:");
+ private JLabel _seqLabel = new JLabel(
+ MessageManager.getString("label.seq"));
- private JButton _createButton = new JButton("Create");
+ private JButton _createButton = new JButton(
+ MessageManager.getString("action.create"));
- private JButton _updateButton = new JButton("Update");
+ private JButton _updateButton = new JButton(
+ MessageManager.getString("action.update"));
- private JButton _deleteButton = new JButton("Delete");
+ private JButton _deleteButton = new JButton(
+ MessageManager.getString("action.delete"));
- private JButton _duplicateButton = new JButton("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)
{
+
// super("VARNA in Jalview");
initVarnaEdit(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("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)
{
- _rnaList.add(v, r, "", true);
+ // patch to fix infinite loop
+ // 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.
+
+ // _rnaList.add(v, r, "", true);
}
public void onWarningEmitted(String s)
{
- // TODO Auto-generated method stub
-
}
public void mouseClicked(MouseEvent e)
public void mouseEntered(MouseEvent arg0)
{
- // TODO Auto-generated method stub
-
}
public void mouseExited(MouseEvent arg0)
{
- // TODO Auto-generated method stub
-
}
public void mousePressed(MouseEvent arg0)
{
- // TODO Auto-generated method stub
-
}
public void mouseReleased(MouseEvent arg0)
{
- // TODO Auto-generated method stub
-
}
@Override
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbId)
+ public String[] getPdbFile()
{
- // TODO Auto-generated method stub
return null;
}
@Override
- public String[] getPdbFile()
+ public void releaseReferences(Object svl)
{
- // TODO Auto-generated method stub
- return null;
}
@Override
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbId)
+ public void updateColours(Object source)
{
- // TODO Auto-generated method stub
-
}
@Override
- public void mouseOverStructure(int atomIndex, String strInfo)
+ public void componentHidden(ComponentEvent e)
{
- // TODO Auto-generated method stub
-
}
@Override
- public void releaseReferences(Object svl)
+ public void componentMoved(ComponentEvent e)
{
- // TODO Auto-generated method stub
-
}
@Override
- public void updateColours(Object source)
+ public void componentResized(ComponentEvent e)
{
- // TODO Auto-generated method stub
-
}
@Override
- public void componentHidden(ComponentEvent e)
+ public void componentShown(ComponentEvent e)
{
- // TODO Auto-generated method stub
-
}
@Override
- public void componentMoved(ComponentEvent e)
+ public void onStructureRedrawn()
{
- // TODO Auto-generated method stub
-
}
@Override
- public void componentResized(ComponentEvent e)
+ public void onZoomLevelChanged()
{
- // TODO Auto-generated method stub
-
}
@Override
- public void componentShown(ComponentEvent e)
+ public void onTranslationChanged()
{
- // TODO Auto-generated method stub
-
}
@Override
- public void onStructureRedrawn()
+ public void highlightAtoms(List<AtomSpec> atoms)
{
- // TODO Auto-generated method stub
-
}
}
-
-/*
- * public static void main(String[] args) { JTextField str = new
- * JTextField("ATGC");
- *
- * AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str);
- * vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- * vab.varnagui.pack(); vab.varnagui.setVisible(true); } }
- */
git://source.jalview.org / jalview.git / blobdiff