src2/fr/orsay/lri/varna/applications/VARNAConsoleDemo.java

   1 package fr.orsay.lri.varna.applications;
   2
   3 /*
   4 VARNA is a Java library for quick automated drawings RNA secondary structure
   5 Copyright (C) 2007  Yann Ponty
   6
   7 This program is free software:you can redistribute it and/or modify
   8 it under the terms of the GNU General Public License as published by
   9 the Free Software Foundation, either version 3 of the License, or
  10 (at your option) any later version.
  11
  12 This program is distributed in the hope that it will be useful,
  13 but WITHOUT ANY WARRANTY; without even the implied warranty of
  14 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  15 GNU General Public License for more details.
  16
  17 You should have received a copy of the GNU General Public License
  18 along with this program.  If not, see <http://www.gnu.org/licenses/>.
  19 */
  20
  21 import java.awt.BorderLayout;
  22 import java.awt.Color;
  23 import java.awt.Dimension;
  24 import java.awt.Font;
  25 import java.awt.GridLayout;
  26 import java.awt.event.ActionEvent;
  27 import java.awt.event.ActionListener;
  28
  29 import javax.swing.JApplet;
  30 import javax.swing.JButton;
  31 import javax.swing.JLabel;
  32 import javax.swing.JPanel;
  33 import javax.swing.JTextField;
  34
  35 import fr.orsay.lri.varna.VARNAPanel;
  36 import fr.orsay.lri.varna.components.VARNAConsole;
  37 import fr.orsay.lri.varna.controlers.ControleurDemoTextField;
  38 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  39 import fr.orsay.lri.varna.models.rna.RNA;
  40
  41 /**
  42 * An RNA 2d Panel demo applet
  43 *
  44 * @author Yann Ponty & Darty Kévin
  45 *
  46 */
  47
  48 public class VARNAConsoleDemo extends JApplet implements ActionListener  {
  49
  50         /**
  51          *
  52          */
  53         private static final long serialVersionUID = -790155708306987257L;
  54
  55         private static final String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
  56
  57         private static final String DEFAULT_STRUCTURE = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
  58
  59         private VARNAPanel _vp;
  60
  61         private JPanel _tools = new JPanel();
  62         private JPanel _input = new JPanel();
  63
  64         private JPanel _seqPanel = new JPanel();
  65         private JPanel _structPanel = new JPanel();
  66         private JLabel _info = new JLabel();
  67         private JButton _go = new JButton("Go");
  68         private JTextField _struct = new JTextField();
  69         private JTextField _seq = new JTextField();
  70         private JLabel _structLabel = new JLabel(" Str:");
  71         private JLabel _seqLabel = new JLabel(" Seq:");
  72
  73         private VARNAConsole _console;
  74
  75         private static String errorOpt = "error";
  76         private boolean _error;
  77
  78         private Color _backgroundColor = Color.white;
  79
  80         private int _algoCode;
  81
  82         public VARNAConsoleDemo() {
  83                 super();
  84                 try {
  85                         _vp = new VARNAPanel(_seq.getText(), _struct.getText());
  86                         _vp.setErrorsOn(false);
  87                 } catch (ExceptionNonEqualLength e) {
  88                         _vp.errorDialog(e);
  89                 }
  90                 RNAPanelDemoInit();
  91         }
  92
  93         private void RNAPanelDemoInit() {
  94
  95
  96                 int marginTools = 40;
  97
  98                 setBackground(_backgroundColor);
  99                 _vp.setBackground(_backgroundColor);
 100
 101                 try {
 102                         _vp.getRNA().setRNA(_seq.getText(), _struct.getText());
 103                         _vp.setErrorsOn(false);
 104                 } catch (Exception e1) {
 105                         _vp.errorDialog(e1);
 106                 }
 107
 108                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 109
 110                 _console = new VARNAConsole(_vp);
 111
 112
 113                 _go.addActionListener(this);
 114
 115                 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 116                 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 117                 _seq.setFont(textFieldsFont);
 118                 _seq.setText(_vp.getRNA().getSeq());
 119
 120                 _seqPanel.setLayout(new BorderLayout());
 121                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 122                 _seqPanel.add(_seq, BorderLayout.CENTER);
 123
 124                 _structLabel.setPreferredSize(new Dimension(marginTools, 15));
 125                 _structLabel.setHorizontalTextPosition(JLabel.LEFT);
 126                 _struct.setFont(textFieldsFont);
 127                 _struct.setText(_vp.getRNA().getStructDBN());
 128                 _structPanel.setLayout(new BorderLayout());
 129                 _structPanel.add(_structLabel, BorderLayout.WEST);
 130                 _structPanel.add(_struct, BorderLayout.CENTER);
 131
 132
 133                 _input.setLayout(new GridLayout(3, 0));
 134                 _input.add(_seqPanel);
 135                 _input.add(_structPanel);
 136
 137                 _tools.setLayout(new BorderLayout());
 138                 _tools.add(_input, BorderLayout.CENTER);
 139                 _tools.add(_info, BorderLayout.SOUTH);
 140                 _tools.add(_go, BorderLayout.EAST);
 141
 142                 getContentPane().setLayout(new BorderLayout());
 143                 getContentPane().add(_vp, BorderLayout.CENTER);
 144                 getContentPane().add(_tools, BorderLayout.SOUTH);
 145
 146                 _vp.getVARNAUI().UIRadiate();
 147                 setPreferredSize(new Dimension(400,400));
 148
 149                 setVisible(true);
 150
 151                 _console.setVisible(true);
 152
 153         }
 154
 155         public String[][] getParameterInfo() {
 156                 String[][] info = {
 157                                 // Parameter Name Kind of Value Description,
 158                                 { "sequenceDBN", "String", "A raw RNA sequence" },
 159                                 { "structureDBN", "String",
 160                                                 "An RNA structure in dot bracket notation (DBN)" },
 161                                 { errorOpt, "boolean", "To show errors" }, };
 162                 return info;
 163         }
 164
 165         public void init() {
 166                 retrieveParametersValues();
 167                 _vp.setBackground(_backgroundColor);
 168                 _error = true;
 169         }
 170
 171         private Color getSafeColor(String col, Color def) {
 172                 Color result;
 173                 try {
 174                         result = Color.decode(col);
 175                 } catch (Exception e) {
 176                         try {
 177                                 result = Color.getColor(col, def);
 178                         } catch (Exception e2) {
 179                                 return def;
 180                         }
 181                 }
 182                 return result;
 183         }
 184
 185         private String getParameterValue(String key, String def) {
 186                 String tmp;
 187                 tmp = getParameter(key);
 188                 if (tmp == null) {
 189                         return def;
 190                 } else {
 191                         return tmp;
 192                 }
 193         }
 194
 195         private void retrieveParametersValues() {
 196                 _error = Boolean.parseBoolean(getParameterValue(errorOpt, "false"));
 197                 _vp.setErrorsOn(_error);
 198                 _backgroundColor = getSafeColor(getParameterValue("background",
 199                                 _backgroundColor.toString()), _backgroundColor);
 200                 _vp.setBackground(_backgroundColor);
 201                 _seq.setText(getParameterValue("sequenceDBN", ""));
 202                 _struct.setText(getParameterValue("structureDBN", ""));
 203                 String _algo = getParameterValue("algorithm", "radiate");
 204                 if (_algo.equals("circular"))
 205                         _algoCode = RNA.DRAW_MODE_CIRCULAR;
 206                 else if (_algo.equals("naview"))
 207                         _algoCode = RNA.DRAW_MODE_NAVIEW;
 208                 else if (_algo.equals("line"))
 209                         _algoCode = RNA.DRAW_MODE_LINEAR;
 210                 else
 211                         _algoCode = RNA.DRAW_MODE_RADIATE;
 212                 if (_seq.getText().equals("") && _struct.getText().equals("")) {
 213                         _seq.setText(DEFAULT_SEQUENCE);
 214                         _struct.setText(DEFAULT_STRUCTURE);
 215                 }
 216                 try {
 217                         _vp.drawRNA(_seq.getText(), _struct.getText(), _algoCode);
 218                 } catch (ExceptionNonEqualLength e) {
 219                         e.printStackTrace();
 220                 }
 221
 222         }
 223
 224         public VARNAPanel get_varnaPanel() {
 225                 return _vp;
 226         }
 227
 228         public void set_varnaPanel(VARNAPanel surface) {
 229                 _vp = surface;
 230         }
 231
 232         public JTextField get_struct() {
 233                 return _struct;
 234         }
 235
 236         public void set_struct(JTextField _struct) {
 237                 this._struct = _struct;
 238         }
 239
 240         public JTextField get_seq() {
 241                 return _seq;
 242         }
 243
 244         public void set_seq(JTextField _seq) {
 245                 this._seq = _seq;
 246         }
 247
 248         public JLabel get_info() {
 249                 return _info;
 250         }
 251
 252         public void set_info(JLabel _info) {
 253                 this._info = _info;
 254         }
 255
 256         public void actionPerformed(ActionEvent arg0) {
 257                   RNA r = new RNA();
 258                   try {
 259                         _vp.drawRNAInterpolated(_seq.getText(), _struct.getText());
 260                 } catch (ExceptionNonEqualLength e) {
 261                         // TODO Auto-generated catch block
 262                         e.printStackTrace();
 263                 }
 264                   _vp.repaint();
 265         }
 266 }