/*
VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
electronic mail : Yann.Ponty@lri.fr
paper mail : LRI, bat 490 University Paris-Sud 91405 Orsay Cedex France
This file is part of VARNA version 3.1.
VARNA version 3.1 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.
VARNA version 3.1 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 VARNA version 3.1.
If not, see http://www.gnu.org/licenses.
*/
package fr.orsay.lri.varna.applications;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JButton;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTextField;
import fr.orsay.lri.varna.VARNAPanel;
import fr.orsay.lri.varna.models.rna.RNA;
public class AlignmentDemo extends JFrame{
/**
*
*/
private static final long serialVersionUID = -790155708306987257L;
private static final String DEFAULT_SEQUENCE1 = "CGCGCACGCGA----UAUU----UCGCGUCGCGCAUUUGCGCGUAGCGCG";
private static final String DEFAULT_STRUCTURE1 = "(((((.(((((----....----))))).(((((....)))))..)))))";
private static final String DEFAULT_SEQUENCE2 = "CGCGCACGCGSGCGCGUUUGCGCUCGCGU---------------AGCGCG";
private static final String DEFAULT_STRUCTURE2 = "(((((.(((((((((....))))))))).--------------..)))))";
// private static final String DEFAULT_STRUCTURE1 = "((((....))))";
// private static final String DEFAULT_STRUCTURE2 =
// "((((..(((....)))..))))";
private VARNAPanel _vpMaster;
private JPanel _tools = new JPanel();
private JPanel _input = new JPanel();
private JPanel _seq1Panel = new JPanel();
private JPanel _seq2Panel = new JPanel();
private JPanel _struct1Panel = new JPanel();
private JPanel _struct2Panel = new JPanel();
private JLabel _info = new JLabel();
private JTextField _struct1 = new JTextField(DEFAULT_STRUCTURE1);
private JTextField _struct2 = new JTextField(DEFAULT_STRUCTURE2);
private JTextField _seq1 = new JTextField(DEFAULT_SEQUENCE1);
private JTextField _seq2 = new JTextField(DEFAULT_SEQUENCE2);
private JLabel _struct1Label = new JLabel(" Str1:");
private JLabel _struct2Label = new JLabel(" Str2:");
private JLabel _seq1Label = new JLabel(" Seq1:");
private JLabel _seq2Label = new JLabel(" Seq2:");
private JButton _goButton = new JButton("Go");
private String _str1Backup = "";
private String _str2Backup = "";
private String _seq1Backup = "";
private String _seq2Backup = "";
private RNA _RNA = new RNA();
private static String errorOpt = "error";
@SuppressWarnings("unused")
private boolean _error;
private Color _backgroundColor = Color.white;
@SuppressWarnings("unused")
private int _algoCode;
public AlignmentDemo() {
super();
_vpMaster = new VARNAPanel(getSeq1(), getStruct1(), getSeq2(), getStruct2(), RNA.DRAW_MODE_RADIATE,"");
_vpMaster.setPreferredSize(new Dimension(600, 400));
RNAPanelDemoInit();
}
private void RNAPanelDemoInit() {
int marginTools = 40;
setBackground(_backgroundColor);
_vpMaster.setBackground(_backgroundColor);
Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
_goButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
_vpMaster.drawRNA(getSeq1(), getStruct1(), getSeq2(), getStruct2(), _vpMaster.getDrawMode());
_vpMaster.repaint();
}
});
_seq1Label.setHorizontalTextPosition(JLabel.LEFT);
_seq1Label.setPreferredSize(new Dimension(marginTools, 15));
_seq1.setFont(textFieldsFont);
_seq1Panel.setLayout(new BorderLayout());
_seq1Panel.add(_seq1Label, BorderLayout.WEST);
_seq1Panel.add(_seq1, BorderLayout.CENTER);
_seq2Label.setHorizontalTextPosition(JLabel.LEFT);
_seq2Label.setPreferredSize(new Dimension(marginTools, 15));
_seq2.setFont(textFieldsFont);
_seq2Panel.setLayout(new BorderLayout());
_seq2Panel.add(_seq2Label, BorderLayout.WEST);
_seq2Panel.add(_seq2, BorderLayout.CENTER);
_struct1Label.setPreferredSize(new Dimension(marginTools, 15));
_struct1Label.setHorizontalTextPosition(JLabel.LEFT);
_struct1.setFont(textFieldsFont);
_struct1Panel.setLayout(new BorderLayout());
_struct1Panel.add(_struct1Label, BorderLayout.WEST);
_struct1Panel.add(_struct1, BorderLayout.CENTER);
_struct2Label.setPreferredSize(new Dimension(marginTools, 15));
_struct2Label.setHorizontalTextPosition(JLabel.LEFT);
_struct2.setFont(textFieldsFont);
_struct2Panel.setLayout(new BorderLayout());
_struct2Panel.add(_struct2Label, BorderLayout.WEST);
_struct2Panel.add(_struct2, BorderLayout.CENTER);
_input.setLayout(new GridLayout(4, 0));
_input.add(_seq1Panel);
_input.add(_struct1Panel);
_input.add(_seq2Panel);
_input.add(_struct2Panel);
JPanel goPanel = new JPanel();
goPanel.setLayout(new BorderLayout());
_tools.setLayout(new BorderLayout());
_tools.add(_input, BorderLayout.CENTER);
_tools.add(_info, BorderLayout.SOUTH);
_tools.add(goPanel, BorderLayout.EAST);
goPanel.add(_goButton, BorderLayout.CENTER);
getContentPane().setLayout(new BorderLayout());
JPanel VARNAs = new JPanel();
VARNAs.setLayout(new GridLayout(1,1));
VARNAs.add(_vpMaster);
getContentPane().add(VARNAs, BorderLayout.CENTER);
getContentPane().add(_tools, BorderLayout.SOUTH);
setVisible(true);
_vpMaster.getVARNAUI().UIRadiate();
}
public RNA getRNA() {
if (!( _str1Backup.equals(getStruct1())
&& _str2Backup.equals(getStruct2())
&& _seq1Backup.equals(getSeq1())
&& _seq2Backup.equals(getSeq2())
)) {
_vpMaster.drawRNA(getSeq1(), getStruct1(), getSeq2(), getStruct2(), _vpMaster.getDrawMode());
_RNA = _vpMaster.getRNA();
_str1Backup = getStruct1();
_str2Backup = getStruct2();
_seq1Backup = getSeq1();
_seq2Backup = getSeq2();
}
return _RNA;
}
public String getStruct1() {
return cleanStruct(_struct1.getText());
}
public String getStruct2() {
return cleanStruct(_struct2.getText());
}
public String getSeq1() {
return cleanStruct(_seq1.getText());
}
public String getSeq2() {
return cleanStruct(_seq2.getText());
}
private String cleanStruct(String struct) {
//struct = struct.replaceAll("[:-]", "");
return struct;
}
public String[][] getParameterInfo() {
String[][] info = {
// Parameter Name Kind of Value Description,
{ "sequenceDBN", "String", "A raw RNA sequence" },
{ "structureDBN", "String",
"An RNA structure in dot bracket notation (DBN)" },
{ errorOpt, "boolean", "To show errors" }, };
return info;
}
public void init() {
_vpMaster.setBackground(_backgroundColor);
_error = true;
}
@SuppressWarnings("unused")
private Color getSafeColor(String col, Color def) {
Color result;
try {
result = Color.decode(col);
} catch (Exception e) {
try {
result = Color.getColor(col, def);
} catch (Exception e2) {
return def;
}
}
return result;
}
public VARNAPanel get_varnaPanel() {
return _vpMaster;
}
public void set_varnaPanel(VARNAPanel surface) {
_vpMaster = surface;
}
public JTextField get_struct() {
return _struct1;
}
public void set_struct(JTextField _struct) {
this._struct1 = _struct;
}
public JTextField get_seq() {
return _seq1;
}
public void set_seq(JTextField _seq) {
this._seq1 = _seq;
}
public JLabel get_info() {
return _info;
}
public void set_info(JLabel _info) {
this._info = _info;
}
public static void main(String[] args) {
AlignmentDemo d = new AlignmentDemo();
d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
d.pack();
d.setVisible(true);
}
public void onWarningEmitted(String s) {
// TODO Auto-generated method stub
}
}