+++ /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