/*
* 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
*
* 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
* 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 .
*/
package jalview.gui;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.Transferable;
import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTarget;
import java.awt.dnd.DropTargetDragEvent;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.dnd.DropTargetEvent;
import java.awt.dnd.DropTargetListener;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ComponentEvent;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.io.File;
import java.text.DateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
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;
import fr.orsay.lri.varna.VARNAPanel;
import fr.orsay.lri.varna.components.ReorderableJList;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
import fr.orsay.lri.varna.models.FullBackup;
import fr.orsay.lri.varna.models.VARNAConfig;
import fr.orsay.lri.varna.models.rna.Mapping;
import fr.orsay.lri.varna.models.rna.RNA;
public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding implements DropTargetListener, InterfaceVARNAListener, MouseListener {
/**
*
*/
//private static final long serialVersionUID = -790155708306987257L;
private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
public VARNAPanel vp;
protected JPanel _tools = new JPanel();
private JPanel _input = new JPanel();
private JPanel _seqPanel = new JPanel();
private JPanel _strPanel = new JPanel();
private JLabel _info = new JLabel();
private JTextField _str = new JTextField();
private JTextField _seq = new JTextField();
private JLabel _strLabel = new JLabel(" Str:");
private JLabel _seqLabel = new JLabel(" Seq:");
private JButton _createButton = new JButton("Create");
private JButton _updateButton = new JButton("Update");
private JButton _deleteButton = new JButton("Delete");
private JButton _duplicateButton = new JButton("Snapshot");
protected JPanel _listPanel = new JPanel();
private ReorderableJList _sideList = null;
private static String errorOpt = "error";
@SuppressWarnings("unused")
private boolean _error;
private Color _backgroundColor = Color.white;
private static int _nextID = 1;
@SuppressWarnings("unused")
private int _algoCode;
private BackupHolder _rnaList;
/*public AppVarnaBinding() {
//super("VARNA in Jalview");
//this.set_seq("ATGC");
//this.set_str(".().");
//RNAPanelDemoInit();
//initVarna("ATGCATGATATATATATAT","....((((...))))....");
initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1);
}*/
public AppVarnaBinding(String seq,String struc){
//super("VARNA in Jalview");
initVarna(seq,struc);
}
public AppVarnaBinding(ArrayList rnaList){
//super("VARNA in Jalview");
initVarnaEdit(rnaList);
}
private void initVarna(String seq, String str){
DefaultListModel dlm = new DefaultListModel();
DefaultListSelectionModel m = new DefaultListSelectionModel();
m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
m.setLeadAnchorNotificationEnabled(false);
_sideList = new ReorderableJList();
_sideList.setModel(dlm);
_sideList.addMouseListener(this);
_sideList.setSelectionModel(m);
_sideList.setPreferredSize(new Dimension(100, 0));
_sideList.addListSelectionListener( new ListSelectionListener(){
public void valueChanged(ListSelectionEvent arg0) {
if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
{
FullBackup sel = (FullBackup) _sideList.getSelectedValue();
Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
vp.showRNAInterpolated(sel.rna,sel.config,map);
_seq.setText(sel.rna.getSeq());
_str.setText(sel.rna.getStructDBN());
}
}
});
_rnaList = new BackupHolder(dlm,_sideList);
RNA _RNA1 = new RNA("User defined 1");
try {
vp = new VARNAPanel("0",".");
_RNA1.setRNA(seq, str);
_RNA1.drawRNARadiate(vp.getConfig());
} catch (ExceptionNonEqualLength e) {
vp.errorDialog(e);
} catch (ExceptionUnmatchedClosingParentheses e2) {
e2.printStackTrace();
} catch (ExceptionFileFormatOrSyntax e3) {
e3.printStackTrace();
}
vp.setPreferredSize(new Dimension(400, 400));
_rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
//TODO setBackground(_backgroundColor);
vp.setBackground(_backgroundColor);
//TODO getContentPane().setLayout(new BorderLayout());
//TODO getContentPane().add(vp, BorderLayout.CENTER);
//setVisible(true);
vp.addVARNAListener(this);
}
private void initVarnaEdit(ArrayList rnaInList)
{
DefaultListModel dlm = new DefaultListModel();
int marginTools = 40;
DefaultListSelectionModel m = new DefaultListSelectionModel();
m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
m.setLeadAnchorNotificationEnabled(false);
_sideList = new ReorderableJList();
_sideList.setModel(dlm);
_sideList.addMouseListener(this);
_sideList.setSelectionModel(m);
_sideList.setPreferredSize(new Dimension(100, 0));
_sideList.addListSelectionListener( new ListSelectionListener(){
public void valueChanged(ListSelectionEvent arg0) {
//System.out.println(arg0);
if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
{
FullBackup sel = (FullBackup) _sideList.getSelectedValue();
Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
vp.showRNAInterpolated(sel.rna,sel.config,map);
//_seq.setText(sel.rna.getSeq());
_str.setText(sel.rna.getStructDBN());
}
}
});
_rnaList = new BackupHolder(dlm,_sideList);
try {
vp = new VARNAPanel("0",".");
for(int i=0;i _rnas = new ArrayList();
JList _l;
public BackupHolder(DefaultListModel rnaList, JList l)
{
_rnaList = rnaList;
_l = l;
}
public void add(VARNAConfig c, RNA r)
{
add(c, r, r.getName(),false);
}
public void add(VARNAConfig c, RNA r,boolean select)
{
add(c, r, r.getName(),select);
}
public void add(VARNAConfig c, RNA r, String name)
{
add(c, r, name,false);
}
public void add(VARNAConfig c, RNA r, String name, boolean select)
{
if (select){
_l.removeSelectionInterval(0, _rnaList.size());
}
if (name.equals(""))
{
name = generateDefaultName();
}
FullBackup bck = new FullBackup(c,r,name);
_rnas.add(0, r);
_rnaList.add(0,bck);
if (select){
_l.setSelectedIndex(0);
}
}
public void remove(int i)
{
_rnas.remove(i);
_rnaList.remove(i);
}
public DefaultListModel getModel()
{
return _rnaList;
}
public boolean contains(RNA r)
{
return _rnas.contains(r);
}
/*public int getSize()
{
return _rnaList.getSize();
}*/
public FullBackup getElementAt(int i)
{
return (FullBackup) _rnaList.getElementAt(i);
}
public void removeSelected()
{
int i = _l.getSelectedIndex();
if (i!=-1)
{
if (_rnaList.getSize()==1)
{
RNA r = new RNA();
try {
r.setRNA(" ", ".");
} catch (ExceptionUnmatchedClosingParentheses e1) {
} catch (ExceptionFileFormatOrSyntax e1) {
}
vp.showRNA(r);
vp.repaint();
}
else
{
int newi = i+1;
if (newi==_rnaList.getSize())
{
newi = _rnaList.getSize()-2;
}
FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
_l.setSelectedValue(bck,true);
}
_rnaList.remove(i);
}
}
}
public void onLayoutChanged() {
// TODO Auto-generated method stub
}
public void onUINewStructure(VARNAConfig v, RNA r) {
_rnaList.add(v, r,"",true);
}
public void onWarningEmitted(String s) {
// TODO Auto-generated method stub
}
public void mouseClicked(MouseEvent e) {
if(e.getClickCount() == 2){
int index = _sideList.locationToIndex(e.getPoint());
ListModel dlm = _sideList.getModel();
FullBackup item = (FullBackup) dlm.getElementAt(index);;
_sideList.ensureIndexIsVisible(index);
/*TODO Object newName = JOptionPane.showInputDialog(
this,
"Specify a new name for this RNA",
"Rename RNA",
JOptionPane.QUESTION_MESSAGE,
(Icon)null,
null,
item.toString());
if (newName!=null)
{
item.name = newName.toString();
this._sideList.repaint();
}*/
}
}
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) {
// TODO Auto-generated method stub
return null;
}
@Override
public String[] getPdbFile() {
// TODO Auto-generated method stub
return null;
}
@Override
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbId) {
// TODO Auto-generated method stub
}
@Override
public void mouseOverStructure(int atomIndex, String strInfo) {
// TODO Auto-generated method stub
}
@Override
public void releaseReferences(Object svl) {
// TODO Auto-generated method stub
}
@Override
public void updateColours(Object source) {
// TODO Auto-generated method stub
}
@Override
public void componentHidden(ComponentEvent e) {
// TODO Auto-generated method stub
}
@Override
public void componentMoved(ComponentEvent e) {
// TODO Auto-generated method stub
}
@Override
public void componentResized(ComponentEvent e) {
// TODO Auto-generated method stub
}
@Override
public void componentShown(ComponentEvent e) {
// TODO Auto-generated method stub
}
@Override
public void onStructureRedrawn()
{
// 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);
}
}
*/