--- /dev/null
+/*
+ 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 Université 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
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff