srcjar/fr/orsay/lri/varna/applications/SuperpositionDemo.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 import fr.orsay.lri.varna.controlers.ControleurInterpolator;
  36 import fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm;
  37 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  38 import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError;
  39 import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
  40 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  41 import fr.orsay.lri.varna.exceptions.ExceptionParameterError;
  42 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  43 import fr.orsay.lri.varna.exceptions.MappingException;
  44 import fr.orsay.lri.varna.models.VARNAConfig;
  45 import fr.orsay.lri.varna.models.rna.Mapping;
  46 import fr.orsay.lri.varna.models.rna.ModeleBase;
  47 import fr.orsay.lri.varna.models.rna.ModelBaseStyle;
  48 import fr.orsay.lri.varna.models.rna.RNA;
  49
  50 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;;
  51
  52 public class SuperpositionDemo extends JFrame implements InterfaceVARNAListener {
  53
  54         /**
  55          *
  56          */
  57         private static final long serialVersionUID = -790155708306987257L;
  58
  59         private static final String DEFAULT_SEQUENCE1 = "CGCGCACGCGAUAUUUCGCGUCGCGCAUUUGCGCGUAGCGCG";
  60         private static final String DEFAULT_SEQUENCE2 = "CGCGCACGCGAUAUUUCGCGUCGCGCAUUUGCGCGUAGCGCG";
  61
  62         private static final String DEFAULT_STRUCTURE1 = "(((((.(((((----....----))))).(((((....)))))..)))))";
  63         private static final String DEFAULT_STRUCTURE2 = "(((((.(((((((((....))))))))).--------------..)))))";
  64         // private static final String DEFAULT_STRUCTURE1 = "((((....))))";
  65         // private static final String DEFAULT_STRUCTURE2 =
  66         // "((((..(((....)))..))))";
  67
  68         private VARNAPanel _vpMaster;
  69         private VARNAPanel _vpSlave;
  70
  71         private JPanel _tools = new JPanel();
  72         private JPanel _input = new JPanel();
  73
  74         private JPanel _seqPanel = new JPanel();
  75         private JPanel _struct1Panel = new JPanel();
  76         private JPanel _struct2Panel = new JPanel();
  77         private JLabel _info = new JLabel();
  78         private JTextField _struct1 = new JTextField(DEFAULT_STRUCTURE1);
  79         private JTextField _struct2 = new JTextField(DEFAULT_STRUCTURE2);
  80         private JTextField _seq1 = new JTextField(DEFAULT_SEQUENCE1);
  81         private JTextField _seq2 = new JTextField(DEFAULT_SEQUENCE2);
  82         private JLabel _struct1Label = new JLabel(" Str1:");
  83         private JLabel _struct2Label = new JLabel(" Str2:");
  84         private JLabel _seqLabel = new JLabel(" Seq:");
  85         private JButton _goButton = new JButton("Go");
  86         private JButton _switchButton = new JButton("Switch");
  87
  88         private String _str1Backup = "";
  89         private String _str2Backup = "";
  90         private RNA _RNA1 = new RNA();
  91         private RNA _RNA2 = new RNA();
  92
  93         private static String errorOpt = "error";
  94         @SuppressWarnings("unused")
  95         private boolean _error;
  96
  97         private Color _backgroundColor = Color.white;
  98
  99         @SuppressWarnings("unused")
 100         private int _algoCode;
 101
 102         private int _currentDisplay = 1;
 103
 104         public static ModelBaseStyle createStyle(String txt)
 105         {
 106                 ModelBaseStyle result = new ModelBaseStyle();
 107                 try {
 108                         result.assignParameters(txt);
 109                 } catch (ExceptionModeleStyleBaseSyntaxError e) {
 110                         // TODO Auto-generated catch block
 111                         e.printStackTrace();
 112                 } catch (ExceptionParameterError e) {
 113                         // TODO Auto-generated catch block
 114                         e.printStackTrace();
 115                 }
 116                 return result;
 117         }
 118
 119         public void applyTo(VARNAPanel vp, ModelBaseStyle mb, int[] indices)
 120         {
 121                 for(int i=0;i<indices.length;i++)
 122                 {
 123                         ModeleBase m = vp.getRNA().getBaseAt(indices[i]);
 124                         m.setStyleBase(mb);
 125                         if (m.getElementStructure()!=-1)
 126                         {
 127                                 vp.getRNA().getBaseAt(m.getElementStructure()).setStyleBase(mb);
 128                         }
 129                 }
 130                 vp.repaint();
 131         }
 132
 133
 134         public SuperpositionDemo() {
 135                 super();
 136                 try {
 137                         _vpMaster = new VARNAPanel(getText1(), getStruct1());
 138                         _vpSlave = new VARNAPanel(getText2(), getStruct2());
 139                 } catch (ExceptionNonEqualLength e) {
 140                         _vpMaster.errorDialog(e);
 141                 }
 142                 _vpMaster.setPreferredSize(new Dimension(400, 400));
 143                 RNAPanelDemoInit();
 144         }
 145
 146         private void RNAPanelDemoInit() {
 147                 int marginTools = 40;
 148
 149                 setBackground(_backgroundColor);
 150                 _vpMaster.setBackground(_backgroundColor);
 151                 _vpMaster.addVARNAListener(this);
 152                 //_vpSlave.setModifiable(false);
 153                 _vpSlave.setBackground(Color.decode("#F0F0F0"));
 154
 155                 _vpMaster.drawRNA(getRNA((_currentDisplay)%2));
 156                 _vpSlave.drawRNA(getRNA((_currentDisplay+1)%2));
 157
 158                 /*ModeleStyleBase red = createStyle("label=#ff4d4d,fill=#ffdddd,outline=#ff4d4d");
 159                 int[] ired = {6,7,8,9,10};
 160                 applyTo(_vpMaster, red, ired);
 161                 applyTo(_vpSlave, red, ired);
 162                 ModeleStyleBase blue = createStyle("label=#0000ff,fill=#ddddff,outline=#0000ff");
 163                 int[] iblue = {0,1,2,3,4};
 164                 applyTo(_vpMaster, blue, iblue);
 165                 applyTo(_vpSlave, blue, iblue);
 166                 ModeleStyleBase purple = createStyle("label=#cc00cc,fill=#ffddff,outline=#cc00cc");
 167                 int[] ipurple = {21,22,23,24,25};
 168                 applyTo(_vpMaster, purple, ipurple);
 169                 ModeleStyleBase green = createStyle("label=#009900,fill=#aaeeaa,outline=#009900");
 170                 int[] igreen = {11,12,13,14};
 171                 applyTo(_vpSlave, green, igreen);*/
 172
 173                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 174
 175                 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 176                 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 177                 _seq1.setFont(textFieldsFont);
 178                 _seq1.setText(getRNA1().getSeq());
 179                 _seq2.setFont(textFieldsFont);
 180                 _seq2.setText(getRNA2().getSeq());
 181
 182                 _goButton.addActionListener(new ActionListener() {
 183
 184                         public void actionPerformed(ActionEvent e) {
 185                                 _currentDisplay = (_currentDisplay + 1) % 2;
 186                                 _vpMaster.drawRNA(getRNA(_currentDisplay));
 187                                 _vpSlave.drawRNA(getRNA((_currentDisplay + 1) % 2));
 188                                 onStructureRedrawn();
 189                         }
 190                 });
 191
 192                 _switchButton.addActionListener(new ActionListener() {
 193                         public void actionPerformed(ActionEvent e) {
 194                                 try {
 195                                         _currentDisplay = (_currentDisplay + 1) % 2;
 196
 197                                                         Mapping m = Mapping.readMappingFromAlignment(
 198                                                                         getStruct(_currentDisplay), getStruct((_currentDisplay+1)%2));
 199                                                         Mapping m2 = Mapping.readMappingFromAlignment(
 200                                                                         getStruct((_currentDisplay+1)%2), getStruct(_currentDisplay));
 201                                                         _vpMaster.showRNAInterpolated(getRNA(_currentDisplay), m);
 202                                                         _vpSlave.showRNAInterpolated(getRNA((_currentDisplay+1)%2), m2);
 203                                                         onStructureRedrawn();
 204                                         }
 205                                 catch (MappingException e3)
 206                                 {
 207                                                         try {
 208                                                                 _vpMaster.drawRNAInterpolated(getText(_currentDisplay),getStruct(_currentDisplay));
 209                                                         } catch (ExceptionNonEqualLength e1) {
 210                                                                 // TODO Auto-generated catch block
 211                                                                 e1.printStackTrace();
 212                                                         }
 213                                                 }
 214                                 _vpMaster.repaint();
 215                                 _vpSlave.repaint();
 216                         }
 217                 });
 218
 219                 _seqPanel.setLayout(new BorderLayout());
 220                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 221                 _seqPanel.add(_seq1, BorderLayout.CENTER);
 222
 223                 _struct1Label.setPreferredSize(new Dimension(marginTools, 15));
 224                 _struct1Label.setHorizontalTextPosition(JLabel.LEFT);
 225                 _struct1.setFont(textFieldsFont);
 226                 _struct1Panel.setLayout(new BorderLayout());
 227                 _struct1Panel.add(_struct1Label, BorderLayout.WEST);
 228                 _struct1Panel.add(_struct1, BorderLayout.CENTER);
 229
 230                 _struct2Label.setPreferredSize(new Dimension(marginTools, 15));
 231                 _struct2Label.setHorizontalTextPosition(JLabel.LEFT);
 232                 _struct2.setFont(textFieldsFont);
 233                 _struct2Panel.setLayout(new BorderLayout());
 234                 _struct2Panel.add(_struct2Label, BorderLayout.WEST);
 235                 _struct2Panel.add(_struct2, BorderLayout.CENTER);
 236
 237                 _input.setLayout(new GridLayout(3, 0));
 238                 _input.add(_seqPanel);
 239                 _input.add(_struct1Panel);
 240                 _input.add(_struct2Panel);
 241
 242                 JPanel goPanel = new JPanel();
 243                 goPanel.setLayout(new BorderLayout());
 244
 245                 _tools.setLayout(new BorderLayout());
 246                 _tools.add(_input, BorderLayout.CENTER);
 247                 _tools.add(_info, BorderLayout.SOUTH);
 248                 _tools.add(goPanel, BorderLayout.EAST);
 249
 250                 goPanel.add(_goButton, BorderLayout.CENTER);
 251                 goPanel.add(_switchButton, BorderLayout.SOUTH);
 252
 253                 getContentPane().setLayout(new BorderLayout());
 254                 JPanel VARNAs = new JPanel();
 255                 VARNAs.setLayout(new GridLayout(1,2));
 256                 VARNAs.add(_vpMaster);
 257                 VARNAs.add(_vpSlave);
 258                 getContentPane().add(VARNAs, BorderLayout.CENTER);
 259                 getContentPane().add(_tools, BorderLayout.SOUTH);
 260
 261                 setVisible(true);
 262
 263                 _vpMaster.getVARNAUI().UIRadiate();
 264                 _vpSlave.getVARNAUI().UIRadiate();
 265
 266                 onStructureRedrawn();
 267         }
 268
 269         public RNA getMasterRNA()
 270         {
 271                 return getRNA(_currentDisplay);
 272         }
 273
 274         public RNA getSlaveRNA1()
 275         {
 276                 return getRNA((_currentDisplay+1)%2);
 277         }
 278
 279         public RNA getSlaveRNA2()
 280         {
 281                 return getRNA((_currentDisplay+2)%2);
 282         }
 283
 284
 285         public RNA getRNA(int i) {
 286           if (i==0)
 287           {  return getRNA1();  }
 288           else
 289           {  return getRNA2();  }
 290         }
 291
 292
 293         public RNA getRNA1() {
 294                 if (!_str1Backup.equals(getStruct1())) {
 295                         try {
 296                                 _RNA1.setRNA(getText1(), getStruct1());
 297                                 _RNA1.drawRNA(_vpMaster.getDrawMode(),_vpMaster.getConfig());
 298                         } catch (ExceptionUnmatchedClosingParentheses e) {
 299                                 e.printStackTrace();
 300                         } catch (ExceptionFileFormatOrSyntax e1) {
 301                                 _vpMaster.errorDialog(e1);
 302                         } catch (ExceptionDrawingAlgorithm e) {
 303                                 // TODO Auto-generated catch block
 304                                 e.printStackTrace();
 305                         }
 306                         _str1Backup = getStruct1();
 307                 }
 308                 return _RNA1;
 309         }
 310
 311         public RNA getRNA2() {
 312                 if (!_str2Backup.equals(getStruct2())) {
 313                         try {
 314                                 _RNA2.setRNA(getText2(), getStruct2());
 315                                 _RNA2.drawRNA(_vpMaster.getDrawMode(),_vpMaster.getConfig());
 316                         } catch (ExceptionUnmatchedClosingParentheses e) {
 317                                 e.printStackTrace();
 318                         } catch (ExceptionFileFormatOrSyntax e1) {
 319                                 _vpMaster.errorDialog(e1);
 320                         } catch (ExceptionDrawingAlgorithm e) {
 321                                 // TODO Auto-generated catch block
 322                                 e.printStackTrace();
 323                         }
 324                         _str2Backup = getStruct2();
 325                 }
 326                 return _RNA2;
 327         }
 328
 329     public String getText(int i)
 330     {
 331         return "";
 332     }
 333
 334     public String getStruct(int i)
 335     {
 336         if (i==0)
 337                 return _struct1.getText();
 338         else
 339                 return _struct2.getText();
 340     }
 341
 342
 343         public String getText1()
 344         {
 345                 return _seq1.getText();
 346         }
 347
 348         public String getText2()
 349         {
 350                 return _seq2.getText();
 351         }
 352
 353         public String getStruct1() {
 354                 return cleanStruct(_struct1.getText());
 355         }
 356
 357         public String getStruct2() {
 358                 return cleanStruct(_struct2.getText());
 359         }
 360
 361         private String cleanStruct(String struct) {
 362                 struct = struct.replaceAll("[:-]", "");
 363                 return struct;
 364         }
 365
 366         public String[][] getParameterInfo() {
 367                 String[][] info = {
 368                                 // Parameter Name Kind of Value Description,
 369                                 { "sequenceDBN", "String", "A raw RNA sequence" },
 370                                 { "structureDBN", "String",
 371                                                 "An RNA structure in dot bracket notation (DBN)" },
 372                                 { errorOpt, "boolean", "To show errors" }, };
 373                 return info;
 374         }
 375
 376         public void init() {
 377                 _vpMaster.setBackground(_backgroundColor);
 378                 _error = true;
 379         }
 380
 381         @SuppressWarnings("unused")
 382         private Color getSafeColor(String col, Color def) {
 383                 Color result;
 384                 try {
 385                         result = Color.decode(col);
 386                 } catch (Exception e) {
 387                         try {
 388                                 result = Color.getColor(col, def);
 389                         } catch (Exception e2) {
 390                                 return def;
 391                         }
 392                 }
 393                 return result;
 394         }
 395
 396         public VARNAPanel get_varnaPanel() {
 397                 return _vpMaster;
 398         }
 399
 400         public void set_varnaPanel(VARNAPanel surface) {
 401                 _vpMaster = surface;
 402         }
 403
 404         public JTextField get_struct() {
 405                 return _struct1;
 406         }
 407
 408         public void set_struct(JTextField _struct) {
 409                 this._struct1 = _struct;
 410         }
 411
 412         public JLabel get_info() {
 413                 return _info;
 414         }
 415
 416         public void set_info(JLabel _info) {
 417                 this._info = _info;
 418         }
 419
 420         public static void main(String[] args) {
 421                 SuperpositionDemo d = new SuperpositionDemo();
 422                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 423                 d.pack();
 424                 d.setVisible(true);
 425         }
 426
 427         public void onStructureRedrawn() {
 428                 try{
 429                                         Mapping m = Mapping.readMappingFromAlignment(
 430                                                         this.getStruct((_currentDisplay+1)%2), getStruct((_currentDisplay)%2));
 431                                         ControleurInterpolator.moveNearOtherRNA(getRNA((_currentDisplay)%2), getRNA((_currentDisplay+1)%2), m);
 432                                         _vpSlave.repaint();
 433                                         _vpMaster.repaint();
 434                 }
 435                 catch (MappingException e3) {System.out.println(e3.toString());}
 436         }
 437
 438         public void onWarningEmitted(String s) {
 439                 // TODO Auto-generated method stub
 440
 441         }
 442
 443         public void onLoad(String path) {
 444                 // TODO Auto-generated method stub
 445
 446         }
 447
 448         public void onLoaded() {
 449                 // TODO Auto-generated method stub
 450
 451         }
 452
 453         public void onUINewStructure(VARNAConfig v, RNA r) {
 454                 // TODO Auto-generated method stub
 455
 456         }
 457
 458         public void onZoomLevelChanged(){
 459                 // TODO Auto-generated method stub
 460
 461         }
 462
 463         public void onTranslationChanged() {
 464                 // TODO Auto-generated method stub
 465
 466         }
 467 }