X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FAlignmentDemo.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FAlignmentDemo.java;h=0000000000000000000000000000000000000000;hb=a1225b9392dc7657d5cef12907385b07527d6122;hp=18c328cbf5cdf7f42db60938e303048e4a82bfbb;hpb=b513684c725997c77341f30ce4e584cf9f7cdfed;p=jalview.git diff --git a/src2/fr/orsay/lri/varna/applications/AlignmentDemo.java b/src2/fr/orsay/lri/varna/applications/AlignmentDemo.java deleted file mode 100644 index 18c328c..0000000 --- a/src2/fr/orsay/lri/varna/applications/AlignmentDemo.java +++ /dev/null @@ -1,286 +0,0 @@ -/* - 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 - - } -}