srcjar/fr/orsay/lri/varna/applications/AlignmentDemo.java

   1 /*
   2  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.
   3  Copyright (C) 2008  Kevin Darty, Alain Denise and Yann Ponty.
   4  electronic mail : Yann.Ponty@lri.fr
   5  paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
   6
   7  This file is part of VARNA version 3.1.
   8  VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
   9  as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10
  11  VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
  12  without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
  13  See the GNU General Public License for more details.
  14
  15  You should have received a copy of the GNU General Public License along with VARNA version 3.1.
  16  If not, see http://www.gnu.org/licenses.
  17  */
  18 package fr.orsay.lri.varna.applications;
  19
  20 import java.awt.BorderLayout;
  21 import java.awt.Color;
  22 import java.awt.Dimension;
  23 import java.awt.Font;
  24 import java.awt.GridLayout;
  25 import java.awt.event.ActionEvent;
  26 import java.awt.event.ActionListener;
  27
  28 import javax.swing.JButton;
  29 import javax.swing.JFrame;
  30 import javax.swing.JLabel;
  31 import javax.swing.JPanel;
  32 import javax.swing.JTextField;
  33
  34 import fr.orsay.lri.varna.VARNAPanel;
  35
  36 import fr.orsay.lri.varna.models.rna.RNA;
  37
  38
  39 public class AlignmentDemo extends JFrame{
  40
  41         /**
  42          *
  43          */
  44         private static final long serialVersionUID = -790155708306987257L;
  45
  46         private static final String DEFAULT_SEQUENCE1 =  "CGCGCACGCGA----UAUU----UCGCGUCGCGCAUUUGCGCGUAGCGCG";
  47         private static final String DEFAULT_STRUCTURE1 = "(((((.(((((----....----))))).(((((....)))))..)))))";
  48
  49         private static final String DEFAULT_SEQUENCE2 =  "CGCGCACGCGSGCGCGUUUGCGCUCGCGU---------------AGCGCG";
  50         private static final String DEFAULT_STRUCTURE2 = "(((((.(((((((((....))))))))).--------------..)))))";
  51         // private static final String DEFAULT_STRUCTURE1 = "((((....))))";
  52         // private static final String DEFAULT_STRUCTURE2 =
  53         // "((((..(((....)))..))))";
  54
  55         private VARNAPanel _vpMaster;
  56
  57         private JPanel _tools = new JPanel();
  58         private JPanel _input = new JPanel();
  59
  60         private JPanel _seq1Panel = new JPanel();
  61         private JPanel _seq2Panel = new JPanel();
  62         private JPanel _struct1Panel = new JPanel();
  63         private JPanel _struct2Panel = new JPanel();
  64         private JLabel _info = new JLabel();
  65         private JTextField _struct1 = new JTextField(DEFAULT_STRUCTURE1);
  66         private JTextField _struct2 = new JTextField(DEFAULT_STRUCTURE2);
  67         private JTextField _seq1 = new JTextField(DEFAULT_SEQUENCE1);
  68         private JTextField _seq2 = new JTextField(DEFAULT_SEQUENCE2);
  69         private JLabel _struct1Label = new JLabel(" Str1:");
  70         private JLabel _struct2Label = new JLabel(" Str2:");
  71         private JLabel _seq1Label = new JLabel(" Seq1:");
  72         private JLabel _seq2Label = new JLabel(" Seq2:");
  73         private JButton _goButton = new JButton("Go");
  74
  75         private String _str1Backup = "";
  76         private String _str2Backup = "";
  77         private String _seq1Backup = "";
  78         private String _seq2Backup = "";
  79         private RNA _RNA = new RNA();
  80
  81         private static String errorOpt = "error";
  82         @SuppressWarnings("unused")
  83         private boolean _error;
  84
  85         private Color _backgroundColor = Color.white;
  86
  87         @SuppressWarnings("unused")
  88         private int _algoCode;
  89
  90
  91         public AlignmentDemo() {
  92                 super();
  93                         _vpMaster = new VARNAPanel(getSeq1(), getStruct1(), getSeq2(), getStruct2(), RNA.DRAW_MODE_RADIATE,"");
  94                 _vpMaster.setPreferredSize(new Dimension(600, 400));
  95                 RNAPanelDemoInit();
  96         }
  97
  98         private void RNAPanelDemoInit() {
  99                 int marginTools = 40;
 100
 101                 setBackground(_backgroundColor);
 102                 _vpMaster.setBackground(_backgroundColor);
 103
 104                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 105
 106
 107                 _goButton.addActionListener(new ActionListener() {
 108
 109                         public void actionPerformed(ActionEvent e) {
 110                                         _vpMaster.drawRNA(getSeq1(), getStruct1(), getSeq2(), getStruct2(), _vpMaster.getDrawMode());
 111                                 _vpMaster.repaint();
 112                         }
 113                 });
 114
 115
 116                 _seq1Label.setHorizontalTextPosition(JLabel.LEFT);
 117                 _seq1Label.setPreferredSize(new Dimension(marginTools, 15));
 118                 _seq1.setFont(textFieldsFont);
 119
 120                 _seq1Panel.setLayout(new BorderLayout());
 121                 _seq1Panel.add(_seq1Label, BorderLayout.WEST);
 122                 _seq1Panel.add(_seq1, BorderLayout.CENTER);
 123
 124                 _seq2Label.setHorizontalTextPosition(JLabel.LEFT);
 125                 _seq2Label.setPreferredSize(new Dimension(marginTools, 15));
 126                 _seq2.setFont(textFieldsFont);
 127
 128                 _seq2Panel.setLayout(new BorderLayout());
 129                 _seq2Panel.add(_seq2Label, BorderLayout.WEST);
 130                 _seq2Panel.add(_seq2, BorderLayout.CENTER);
 131
 132                 _struct1Label.setPreferredSize(new Dimension(marginTools, 15));
 133                 _struct1Label.setHorizontalTextPosition(JLabel.LEFT);
 134                 _struct1.setFont(textFieldsFont);
 135                 _struct1Panel.setLayout(new BorderLayout());
 136                 _struct1Panel.add(_struct1Label, BorderLayout.WEST);
 137                 _struct1Panel.add(_struct1, BorderLayout.CENTER);
 138
 139                 _struct2Label.setPreferredSize(new Dimension(marginTools, 15));
 140                 _struct2Label.setHorizontalTextPosition(JLabel.LEFT);
 141                 _struct2.setFont(textFieldsFont);
 142                 _struct2Panel.setLayout(new BorderLayout());
 143                 _struct2Panel.add(_struct2Label, BorderLayout.WEST);
 144                 _struct2Panel.add(_struct2, BorderLayout.CENTER);
 145
 146                 _input.setLayout(new GridLayout(4, 0));
 147                 _input.add(_seq1Panel);
 148                 _input.add(_struct1Panel);
 149                 _input.add(_seq2Panel);
 150                 _input.add(_struct2Panel);
 151
 152                 JPanel goPanel = new JPanel();
 153                 goPanel.setLayout(new BorderLayout());
 154
 155                 _tools.setLayout(new BorderLayout());
 156                 _tools.add(_input, BorderLayout.CENTER);
 157                 _tools.add(_info, BorderLayout.SOUTH);
 158                 _tools.add(goPanel, BorderLayout.EAST);
 159
 160                 goPanel.add(_goButton, BorderLayout.CENTER);
 161
 162                 getContentPane().setLayout(new BorderLayout());
 163                 JPanel VARNAs = new JPanel();
 164                 VARNAs.setLayout(new GridLayout(1,1));
 165                 VARNAs.add(_vpMaster);
 166                 getContentPane().add(VARNAs, BorderLayout.CENTER);
 167                 getContentPane().add(_tools, BorderLayout.SOUTH);
 168
 169                 setVisible(true);
 170                 _vpMaster.getVARNAUI().UIRadiate();
 171         }
 172
 173         public RNA getRNA() {
 174
 175                 if (!( _str1Backup.equals(getStruct1())
 176                         && _str2Backup.equals(getStruct2())
 177                         && _seq1Backup.equals(getSeq1())
 178                         && _seq2Backup.equals(getSeq2())
 179                 )) {
 180                         _vpMaster.drawRNA(getSeq1(), getStruct1(), getSeq2(), getStruct2(), _vpMaster.getDrawMode());
 181                         _RNA = _vpMaster.getRNA();
 182                         _str1Backup = getStruct1();
 183                         _str2Backup = getStruct2();
 184                         _seq1Backup = getSeq1();
 185                         _seq2Backup = getSeq2();
 186                 }
 187                 return _RNA;
 188         }
 189
 190
 191         public String getStruct1() {
 192                 return cleanStruct(_struct1.getText());
 193         }
 194
 195         public String getStruct2() {
 196                 return cleanStruct(_struct2.getText());
 197         }
 198
 199         public String getSeq1() {
 200                 return cleanStruct(_seq1.getText());
 201         }
 202
 203         public String getSeq2() {
 204                 return cleanStruct(_seq2.getText());
 205         }
 206
 207
 208         private String cleanStruct(String struct) {
 209                 struct = struct.replaceAll("[:-]", "-");
 210                 return struct;
 211         }
 212
 213         public String[][] getParameterInfo() {
 214                 String[][] info = {
 215                                 // Parameter Name Kind of Value Description,
 216                                 { "sequenceDBN", "String", "A raw RNA sequence" },
 217                                 { "structureDBN", "String",
 218                                                 "An RNA structure in dot bracket notation (DBN)" },
 219                                 { errorOpt, "boolean", "To show errors" }, };
 220                 return info;
 221         }
 222
 223         public void init() {
 224                 _vpMaster.setBackground(_backgroundColor);
 225                 _error = true;
 226         }
 227
 228         @SuppressWarnings("unused")
 229         private Color getSafeColor(String col, Color def) {
 230                 Color result;
 231                 try {
 232                         result = Color.decode(col);
 233                 } catch (Exception e) {
 234                         try {
 235                                 result = Color.getColor(col, def);
 236                         } catch (Exception e2) {
 237                                 return def;
 238                         }
 239                 }
 240                 return result;
 241         }
 242
 243         public VARNAPanel get_varnaPanel() {
 244                 return _vpMaster;
 245         }
 246
 247         public void set_varnaPanel(VARNAPanel surface) {
 248                 _vpMaster = surface;
 249         }
 250
 251         public JTextField get_struct() {
 252                 return _struct1;
 253         }
 254
 255         public void set_struct(JTextField _struct) {
 256                 this._struct1 = _struct;
 257         }
 258
 259         public JTextField get_seq() {
 260                 return _seq1;
 261         }
 262
 263         public void set_seq(JTextField _seq) {
 264                 this._seq1 = _seq;
 265         }
 266
 267         public JLabel get_info() {
 268                 return _info;
 269         }
 270
 271         public void set_info(JLabel _info) {
 272                 this._info = _info;
 273         }
 274
 275         public static void main(String[] args) {
 276                 AlignmentDemo d = new AlignmentDemo();
 277                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 278                 d.pack();
 279                 d.setVisible(true);
 280         }
 281
 282         public void onWarningEmitted(String s) {
 283                 // TODO Auto-generated method stub
 284
 285         }
 286 }