src2/fr/orsay/lri/varna/applications/NussinovDesignDemo.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 import java.awt.event.ItemEvent;
  28 import java.awt.event.ItemListener;
  29 import java.awt.event.MouseEvent;
  30 import java.math.BigInteger;
  31 import java.util.ArrayList;
  32 import java.util.Collections;
  33
  34 import javax.swing.BorderFactory;
  35 import javax.swing.DefaultComboBoxModel;
  36 import javax.swing.JButton;
  37 import javax.swing.JComboBox;
  38 import javax.swing.JFrame;
  39 import javax.swing.JLabel;
  40 import javax.swing.JOptionPane;
  41 import javax.swing.JPanel;
  42 import javax.swing.JSplitPane;
  43 import javax.swing.JTextArea;
  44 import javax.swing.JTextField;
  45 import javax.swing.JTextPane;
  46 import javax.swing.border.BevelBorder;
  47
  48 import fr.orsay.lri.varna.VARNAPanel;
  49 import fr.orsay.lri.varna.controlers.ControleurInterpolator;
  50 import fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm;
  51 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  52 import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError;
  53 import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
  54 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  55 import fr.orsay.lri.varna.exceptions.ExceptionParameterError;
  56 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  57 import fr.orsay.lri.varna.exceptions.MappingException;
  58 import fr.orsay.lri.varna.models.VARNAConfig;
  59 import fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE;
  60 import fr.orsay.lri.varna.models.rna.Mapping;
  61 import fr.orsay.lri.varna.models.rna.ModeleBP;
  62 import fr.orsay.lri.varna.models.rna.ModeleBase;
  63 import fr.orsay.lri.varna.models.rna.ModelBaseStyle;
  64 import fr.orsay.lri.varna.models.rna.RNA;
  65 import fr.orsay.lri.varna.interfaces.InterfaceVARNABasesListener;
  66 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;;
  67
  68 public class NussinovDesignDemo extends JFrame implements InterfaceVARNAListener,InterfaceVARNABasesListener, ItemListener {
  69
  70         /**
  71          *
  72          */
  73         private static final long serialVersionUID = -790155708306987257L;
  74
  75         private static final String SEQUENCE_A =        "AGGCACGUCU";
  76         private static final String SEQUENCE_B =  "GAGUAGCCUC";
  77         private static final String SEQUENCE_C = "GCAUAGCUGC";
  78         private static final String SEQUENCE_INRIA = "CGAUUGCAUCGCAAGU";
  79
  80         private static final String TARGET_STRUCTURE_1 = "(((((((..)))))))";
  81         private static final String TARGET_STRUCTURE_2 = "(((())))(((())))";
  82         private static final String TARGET_STRUCTURE_3 = "(.((.((..).)).))";
  83         private static final String TARGET_STRUCTURE_4 = "((((((())))(((())(()))))))";
  84         private static final String TARGET_STRUCTURE_5 = "(((())))(((())))(((())))(((())))(((())))(((())))";
  85
  86         private static final String SEQUENCE_BIG = "AAAACAAAAACACCAUGGUGUUUUCACCCAAUUGGGUGAAAACAGAGAUCUCGAGAUCUCUGUUUUUGUUUU";
  87
  88         private static final String DEFAULT_STRUCTURE = "..........";
  89         // private static final String DEFAULT_STRUCTURE1 = "((((....))))";
  90         // private static final String DEFAULT_STRUCTURE2 =
  91         // "((((..(((....)))..))))";
  92
  93         private VARNAPanel _vpMaster;
  94         private VARNAPanel _vpTarget;
  95
  96         private InfoPanel _infos = new InfoPanel();
  97         private JPanel _tools = new JPanel();
  98         private JPanel _input = new JPanel();
  99
 100         private JPanel _seqPanel = new JPanel();
 101         private JPanel _structPanel = new JPanel();
 102         private JLabel _actions = new JLabel();
 103         private JComboBox _struct = new JComboBox();
 104         private JLabel _seq1 = new JLabel();
 105         private JLabel _structLabel = new JLabel("Structure Cible");
 106         private JLabel _seqLabel = new JLabel("Sequence d'ARN");
 107         private JButton _switchButton = new JButton("Reset");
 108
 109
 110         private Color _backgroundColor = Color.white;
 111
 112         private Color _okColor = Color.decode("#E33729");
 113         private Color _koColor = new Color(250,200,200);
 114
 115
 116         public static ModelBaseStyle createStyle(String txt)
 117         {
 118                 ModelBaseStyle result = new ModelBaseStyle();
 119                 try {
 120                         result.assignParameters(txt);
 121                 } catch (ExceptionModeleStyleBaseSyntaxError e) {
 122                         // TODO Auto-generated catch block
 123                         e.printStackTrace();
 124                 } catch (ExceptionParameterError e) {
 125                         // TODO Auto-generated catch block
 126                         e.printStackTrace();
 127                 }
 128                 return result;
 129         }
 130
 131         public void applyTo(VARNAPanel vp, ModelBaseStyle mb, int[] indices)
 132         {
 133                 for(int i=0;i<indices.length;i++)
 134                 {
 135                         ModeleBase m = vp.getRNA().getBaseAt(indices[i]);
 136                         m.setStyleBase(mb);
 137                         if (m.getElementStructure()!=-1)
 138                         {
 139                                 vp.getRNA().getBaseAt(m.getElementStructure()).setStyleBase(mb);
 140                         }
 141                 }
 142                 vp.repaint();
 143         }
 144
 145
 146         public NussinovDesignDemo() {
 147                 super();
 148                 try {
 149                         _vpMaster = new VARNAPanel(getSeq(), "");
 150                         _vpTarget = new VARNAPanel();
 151                 } catch (ExceptionNonEqualLength e) {
 152                         _vpMaster.errorDialog(e);
 153                 }
 154                 _vpMaster.setPreferredSize(new Dimension(600, 600));
 155                 _vpTarget.setPreferredSize(new Dimension(600, 600));
 156                 RNAPanelDemoInit();
 157         }
 158
 159         static Font labelsFont = Font.decode("Dialog-BOLD-25");
 160
 161         private void RNAPanelDemoInit() {
 162                 int marginTools = 250;
 163                 Font textFieldsFont = Font.decode("MonoSpaced-BOLD-16");
 164
 165
 166
 167                 _seq1.setFont(textFieldsFont.deriveFont(25f));
 168
 169
 170                 setBackground(_backgroundColor);
 171
 172
 173                 _structLabel.setFont(labelsFont.deriveFont(Font.PLAIN));
 174
 175
 176                 String[] secstr = {TARGET_STRUCTURE_1,TARGET_STRUCTURE_2,TARGET_STRUCTURE_3,TARGET_STRUCTURE_4,TARGET_STRUCTURE_5};
 177                 DefaultComboBoxModel cm = new DefaultComboBoxModel(secstr);
 178                 _struct.setModel(cm);
 179                 _struct.addActionListener(new ActionListener() {
 180                         public void actionPerformed(ActionEvent e) {
 181                                 System.out.println(e.getActionCommand());
 182                                 setTarget(((JComboBox)e.getSource()).getSelectedItem().toString());
 183                         }
 184                 });
 185                 _struct.setFont(textFieldsFont);
 186                 _struct.setEnabled(true);
 187                 _struct.setEditable(true);
 188
 189
 190                 _switchButton.addActionListener(new ActionListener() {
 191                         public void actionPerformed(ActionEvent e) {
 192                                 setTarget(_struct.getSelectedItem().toString());
 193                         }
 194                 });
 195
 196                 _seqPanel.setLayout(new BorderLayout());
 197                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 198                 _seqPanel.add(_seq1, BorderLayout.CENTER);
 199
 200                 _seqPanel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
 201
 202                 _structLabel.setPreferredSize(new Dimension(marginTools, 15));
 203                 _structLabel.setHorizontalTextPosition(JLabel.LEFT);
 204                 _structPanel.setLayout(new BorderLayout());
 205                 _structPanel.add(_structLabel, BorderLayout.WEST);
 206                 _structPanel.add(_struct, BorderLayout.CENTER);
 207
 208                 _input.setLayout(new GridLayout(0, 1));
 209                 _input.add(_structPanel);
 210
 211                 JPanel goPanel = new JPanel();
 212                 goPanel.setLayout(new BorderLayout());
 213
 214                 _infos.setFont(labelsFont);
 215
 216
 217                 formatLabel(_seqLabel);
 218                 formatLabel(_seq1);
 219
 220
 221                 _tools.setLayout(new BorderLayout());
 222                 //_tools.add(_infos, BorderLayout.NORTH);
 223                 _tools.add(_input, BorderLayout.CENTER);
 224                 _tools.add(_actions, BorderLayout.SOUTH);
 225                 _tools.add(goPanel, BorderLayout.EAST);
 226
 227                 _tools.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
 228
 229                 //goPanel.add(_goButton, BorderLayout.CENTER);
 230                 goPanel.add(_switchButton, BorderLayout.CENTER);
 231
 232                 getContentPane().setLayout(new BorderLayout());
 233                 JSplitPane VARNAs = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
 234                 VARNAs.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
 235                 //VARNAs.setLayout(new GridLayout(1,2));
 236                 JPanel mast2 = new JPanel();
 237                 mast2.setLayout(new BorderLayout());
 238                 mast2.add(_seqPanel, BorderLayout.NORTH);
 239                 mast2.add(_infos, BorderLayout.SOUTH);
 240
 241                 JPanel mast = new JPanel();
 242                 mast.setLayout(new BorderLayout());
 243                 mast.add(_vpMaster, BorderLayout.CENTER);
 244                 mast.add(mast2,BorderLayout.SOUTH);
 245
 246                 VARNAs.add(mast);
 247                 VARNAs.add(_vpTarget);
 248                 VARNAs.doLayout();
 249                 VARNAs.setDividerSize(5);
 250
 251                 getContentPane().add(VARNAs, BorderLayout.CENTER);
 252                 getContentPane().add(_tools, BorderLayout.NORTH);
 253
 254                 setVisible(true);
 255
 256
 257                 _vpMaster.setBackground(_backgroundColor);
 258                 _vpMaster.addVARNAListener(this);
 259                 _vpMaster.setTitle("Meilleur repliement - Séquence courante");
 260                 _vpMaster.setBPStyle(BP_STYLE.SIMPLE);
 261                 _vpMaster.getVARNAUI().UIRadiate();
 262                 _vpMaster.setTitleFontSize(26f);
 263                 _vpMaster.setTitleFontStyle(Font.PLAIN);
 264
 265                 _vpTarget.setBackground(Color.decode("#308099"));
 266                 _vpTarget.setModifiable(false);
 267                 _vpTarget.setTitle("Repliement cible");
 268                 _vpTarget.setBPStyle(BP_STYLE.SIMPLE);
 269                 _vpTarget.setBackboneColor(Color.white);
 270                 _vpTarget.setDefaultBPColor(Color.white);
 271                 _vpTarget.setBaseNumbersColor(Color.white);
 272                 _vpTarget.setBaseOutlineColor(Color.white);
 273                 _vpTarget.setTitleColor(Color.white);
 274                 _vpTarget.setTitleFontSize(26f);
 275
 276
 277                 _okColor = Color.decode("#F39126");
 278                 _koColor = new Color(250,200,200);
 279
 280                 _seqPanel.setBackground(Color.decode("#E33729"));
 281                 _infos.setBackground(Color.decode("#E33729"));
 282
 283
 284
 285                 _vpMaster.addVARNABasesListener(this);
 286                 setTitle("Fête de la science 2015 - Inria AMIB - Design d'ARN");
 287
 288                 setTarget(secstr[0]);
 289
 290         }
 291
 292         private synchronized void showSolution()
 293         {
 294                 ArrayList<String> sols = getStructs();
 295                 _infos.setInfo(sols, count(getSeq()));
 296                 if ((sols.size()==1)&&(sols.get(0).equals(_struct.getSelectedItem().toString())))
 297                 {
 298                         /*JOptionPane.showMessageDialog(null,
 299                                         "Vous avez trouvé une séquence pour cette structure !!!\n Saurez vous faire le design de molécules plus complexes ?",
 300                                         "Félicitations !",
 301                                         JOptionPane.INFORMATION_MESSAGE);*/
 302
 303                 }
 304                 else
 305                 {
 306                         this._vpMaster.setTitle("Meilleur repliement - Séquence courante");
 307                 }
 308         }
 309
 310
 311         public void setTarget(String target)
 312         {
 313                 try {
 314                         _vpTarget.drawRNA(String.format("%"+target.length()+"s", ""),target);
 315                         _vpTarget.setBaseNumbersColor(Color.white);
 316                         _vpTarget.setBaseOutlineColor(Color.white);
 317                         //_vpTarget.toggleDrawOutlineBases();
 318                         createDummySeq();
 319                         showSolution();
 320                         onStructureRedrawn();
 321                 } catch (ExceptionNonEqualLength e) {
 322                         // TODO Auto-generated catch block
 323                         e.printStackTrace();
 324                 }
 325         }
 326
 327         private void createDummySeq()
 328         {
 329                 RNA r = _vpTarget.getRNA();
 330                 String seq = new String();
 331                 for (int i=0;i<r.getSize();i++)
 332                 {
 333                         seq += 'A';
 334                 }
 335                 try {
 336                 RNA rn = new RNA();
 337                         rn.setRNA(seq,r.getStructDBN());
 338                 for(ModeleBP mbp: r.getAllBPs())
 339                 {
 340                         rn.getBaseAt(mbp.getIndex5()).setContent("A");
 341                         rn.getBaseAt(mbp.getIndex3()).setContent("U");
 342                 }
 343                 _vpMaster.drawRNA(rn);
 344                 _vpMaster.repaint();
 345                 _seq1.setText(_vpMaster.getRNA().getSeq());
 346                 } catch (ExceptionUnmatchedClosingParentheses e) {
 347                         // TODO Auto-generated catch block
 348                         e.printStackTrace();
 349                 } catch (ExceptionFileFormatOrSyntax e) {
 350                         // TODO Auto-generated catch block
 351                         e.printStackTrace();
 352                 }
 353         }
 354
 355
 356         public String getSeq()
 357         {
 358                 return (""+_seq1.getText()).toUpperCase();
 359         }
 360
 361
 362         private boolean canBasePairAll(char a, char b)
 363         {
 364                 return true;
 365         }
 366
 367         private boolean canBasePairBasic(char a, char b)
 368         {
 369                 if ((a=='G')&&(b=='C'))
 370                         return true;
 371                 if ((a=='C')&&(b=='G'))
 372                         return true;
 373                 if ((a=='U')&&(b=='A'))
 374                         return true;
 375                 if ((a=='A')&&(b=='U'))
 376                         return true;
 377                 return false;
 378         }
 379
 380         private double basePairScoreBasic(char a, char b)
 381         {
 382                 if ((a=='G')&&(b=='C'))
 383                         return 1.0;
 384                 if ((a=='C')&&(b=='G'))
 385                         return 1.0;
 386                 if ((a=='U')&&(b=='A'))
 387                         return 1.0;
 388                 if ((a=='A')&&(b=='U'))
 389                         return 1.0;
 390                 return Double.NEGATIVE_INFINITY;
 391         }
 392
 393
 394         private boolean canBasePairNussinov(char a, char b)
 395         {
 396                 if ((a=='G')&&(b=='C'))
 397                         return true;
 398                 if ((a=='C')&&(b=='G'))
 399                         return true;
 400                 if ((a=='U')&&(b=='A'))
 401                         return true;
 402                 if ((a=='A')&&(b=='U'))
 403                         return true;
 404                 if ((a=='U')&&(b=='G'))
 405                         return true;
 406                 if ((a=='G')&&(b=='U'))
 407                         return true;
 408                 return false;
 409         }
 410
 411         private double basePairScoreNussinov(char a, char b)
 412         {
 413                 if ((a=='G')&&(b=='C'))
 414                         return 3.0;
 415                 if ((a=='C')&&(b=='G'))
 416                         return 3.0;
 417                 if ((a=='U')&&(b=='A'))
 418                         return 2.0;
 419                 if ((a=='A')&&(b=='U'))
 420                         return 2.0;
 421                 if ((a=='U')&&(b=='G'))
 422                         return 1.0;
 423                 if ((a=='G')&&(b=='U'))
 424                         return 1.0;
 425                 return Double.NEGATIVE_INFINITY;
 426         }
 427
 428         private boolean canBasePairINRIA(char a, char b)
 429         {
 430                 if ((a=='U')&&(b=='A'))
 431                         return true;
 432                 if ((a=='A')&&(b=='U'))
 433                         return true;
 434                 if ((a=='G')&&(b=='C'))
 435                         return true;
 436                 if ((a=='C')&&(b=='G'))
 437                         return true;
 438
 439                 if ((a=='A')&&(b=='G'))
 440                         return true;
 441                 if ((a=='G')&&(b=='A'))
 442                         return true;
 443                 if ((a=='U')&&(b=='C'))
 444                         return true;
 445                 if ((a=='C')&&(b=='U'))
 446                         return true;
 447                 if ((a=='A')&&(b=='A'))
 448                         return true;
 449                 if ((a=='U')&&(b=='U'))
 450                         return true;
 451
 452                 if ((a=='U')&&(b=='G'))
 453                         return true;
 454                 if ((a=='G')&&(b=='U'))
 455                         return true;
 456                 if ((a=='A')&&(b=='C'))
 457                         return true;
 458                 if ((a=='C')&&(b=='A'))
 459                         return true;
 460                 return false;
 461         }
 462
 463         private double basePairScoreINRIA(char a, char b)
 464         {
 465                 if ((a=='U')&&(b=='A'))
 466                         return 3;
 467                 if ((a=='A')&&(b=='U'))
 468                         return 3;
 469                 if ((a=='G')&&(b=='C'))
 470                         return 3;
 471                 if ((a=='C')&&(b=='G'))
 472                         return 3;
 473
 474                 if ((a=='A')&&(b=='G'))
 475                         return 2;
 476                 if ((a=='G')&&(b=='A'))
 477                         return 2;
 478                 if ((a=='U')&&(b=='C'))
 479                         return 2;
 480                 if ((a=='C')&&(b=='U'))
 481                         return 2;
 482                 if ((a=='A')&&(b=='A'))
 483                         return 2;
 484                 if ((a=='U')&&(b=='U'))
 485                         return 2;
 486
 487                 if ((a=='U')&&(b=='G'))
 488                         return 1;
 489                 if ((a=='G')&&(b=='U'))
 490                         return 1;
 491                 if ((a=='A')&&(b=='C'))
 492                         return 1;
 493                 if ((a=='C')&&(b=='A'))
 494                         return 1;
 495                 return Double.NEGATIVE_INFINITY;
 496         }
 497
 498         private boolean canBasePair(char a, char b)
 499         {
 500                 return canBasePairBasic(a,b);
 501                 //return canBasePairNussinov(a,b);
 502                 //return canBasePairINRIA(a,b);
 503         }
 504
 505         private double basePairScore(char a, char b)
 506         {
 507                 return basePairScoreBasic(a,b);
 508                 //return basePairScoreNussinov(a,b);
 509                 //return basePairScoreINRIA(a,b);
 510         }
 511
 512         public double[][] fillMatrix(String seq)
 513         {
 514                 int n = seq.length();
 515                 double[][] tab = new double[n][n];
 516                 for(int m=1;m<=n;m++)
 517                 {
 518                         for(int i=0;i<n-m+1;i++)
 519                         {
 520                                 int j = i+m-1;
 521                                 tab[i][j] = 0;
 522                                 if (i<j)
 523                                 {
 524                                         tab[i][j] = Math.max(tab[i][j], tab[i+1][j]);
 525                                         for (int k=i+1;k<=j;k++)
 526                                         {
 527                                                 if (canBasePair(seq.charAt(i),seq.charAt(k)))
 528                                                 {
 529                                                         double fact1 = 0;
 530                                                         if (k>i+1)
 531                                                         {
 532                                                                 fact1 = tab[i+1][k-1];
 533                                                         }
 534                                                         double fact2 = 0;
 535                                                         if (k<j)
 536                                                         {
 537                                                                 fact2 = tab[k+1][j];
 538                                                         }
 539                                                         tab[i][j] = Math.max(tab[i][j],basePairScore(seq.charAt(i),seq.charAt(k))+fact1+fact2);
 540                                                 }
 541                                         }
 542                                 }
 543                         }
 544                 }
 545                 return tab;
 546         }
 547
 548         public static ArrayList<Double> combine(double bonus, ArrayList<Double> part1, ArrayList<Double> part2)
 549         {
 550                 ArrayList<Double> base = new ArrayList<Double>();
 551                 for(double d1: part1)
 552                 {
 553                         for(double d2: part2)
 554                         {
 555                                 base.add(bonus+d1+d2);
 556                         }
 557                 }
 558                 return base;
 559         }
 560
 561         public static ArrayList<Double> selectBests(ArrayList<Double> base)
 562         {
 563                 ArrayList<Double> result = new ArrayList<Double>();
 564                 double best = Double.NEGATIVE_INFINITY;
 565                 for(double val: base)
 566                 {
 567                         best = Math.max(val, best);
 568                 }
 569                 for(double val: base)
 570                 {
 571                         if (val == best)
 572                                 result.add(val);
 573                 }
 574                 return result;
 575         }
 576
 577
 578         private ArrayList<String> backtrack(double[][] tab, String seq)
 579         {
 580                 return backtrack(tab,seq, 0, seq.length()-1);
 581         }
 582
 583         private ArrayList<String> backtrack(double[][] tab, String seq, int i, int j)
 584         {
 585                 ArrayList<String> result = new ArrayList<String>();
 586                 if (i<j)
 587                 {
 588                         ArrayList<Integer> indices = new ArrayList<Integer>();
 589                         indices.add(-1);
 590                         for (int k=i+1;k<=j;k++)
 591                         {
 592                                 indices.add(k);
 593                         }
 594                         for (int k : indices)
 595                         {
 596                                 if (k==-1)
 597                                 {
 598                                         if (tab[i][j] == tab[i+1][j])
 599                                         {
 600                                                 for (String s:backtrack(tab, seq, i+1,j))
 601                                                 {
 602                                                         result.add("."+s);
 603                                                 }
 604                                         }
 605                                 }
 606                                 else
 607                                 {
 608                                         if (canBasePair(seq.charAt(i),seq.charAt(k)))
 609                                         {
 610                                                 double fact1 = 0;
 611                                                 if (k>i+1)
 612                                                 {
 613                                                         fact1 = tab[i+1][k-1];
 614                                                 }
 615                                                 double fact2 = 0;
 616                                                 if (k<j)
 617                                                 {
 618                                                         fact2 = tab[k+1][j];
 619                                                 }
 620                                                 if (tab[i][j]==basePairScore(seq.charAt(i),seq.charAt(k))+fact1+fact2)
 621                                                 {
 622                                                         for (String s1:backtrack(tab, seq, i+1,k-1))
 623                                                         {
 624                                                                 for (String s2:backtrack(tab, seq, k+1,j))
 625                                                                 {
 626                                                                         result.add("("+s1+")"+s2);
 627                                                                 }
 628                                                         }
 629                                                 }
 630                                         }
 631                                 }
 632                         }
 633                 }
 634                 else if  (i==j)
 635                 {
 636                         result.add(".");
 637                 }
 638                 else
 639                 {
 640                         result.add("");
 641                 }
 642                 return result;
 643         }
 644
 645         public BigInteger count(String seq)
 646         {
 647                 int n = seq.length();
 648
 649                 BigInteger[][] tab = new BigInteger[n][n];
 650                 for(int m=1;m<=n;m++)
 651                 {
 652                         for(int i=0;i<n-m+1;i++)
 653                         {
 654                                 int j = i+m-1;
 655                                 tab[i][j] = BigInteger.ZERO;
 656                                 if (i<j)
 657                                 {
 658                                         tab[i][j] = tab[i][j].add(tab[i+1][j]);
 659                                         for (int k=i+1;k<=j;k++)
 660                                         {
 661                                                 if (canBasePair(seq.charAt(i),seq.charAt(k)))
 662                                                 {
 663                                                         BigInteger fact1 = BigInteger.ONE;
 664                                                         if (k>i+1)
 665                                                         {
 666                                                                 fact1 = tab[i+1][k-1];
 667                                                         }
 668                                                         BigInteger fact2 = BigInteger.ONE;
 669                                                         if (k<j)
 670                                                         {
 671                                                                 fact2 = tab[k+1][j];
 672                                                         }
 673                                                         tab[i][j] = tab[i][j].add(fact1.multiply(fact2));
 674                                                 }
 675                                         }
 676                                 }
 677                                 else
 678                                 {
 679                                         tab[i][j] = BigInteger.ONE;
 680                                 }
 681                         }
 682                 }
 683                 return tab[0][n-1];
 684         }
 685
 686         private String _cache = "";
 687         ArrayList<String> _cacheStructs = new ArrayList<String>();
 688
 689         public ArrayList<String> getStructs() {
 690                 String seq = getSeq();
 691                 seq = seq.toUpperCase();
 692                 if (!_cache.equals(seq))
 693                 {
 694                         double[][] mfe = fillMatrix(seq);
 695                         _cacheStructs = backtrack(mfe,seq);
 696                         _cache = seq;
 697                 }
 698                 return _cacheStructs;
 699         }
 700
 701         public VARNAPanel get_varnaPanel() {
 702                 return _vpMaster;
 703         }
 704
 705         public void set_varnaPanel(VARNAPanel surface) {
 706                 _vpMaster = surface;
 707         }
 708
 709
 710         public JLabel get_info() {
 711                 return _actions;
 712         }
 713
 714         public void set_info(JLabel _info) {
 715                 this._actions = _info;
 716         }
 717
 718         public static void main(String[] args) {
 719                 NussinovDesignDemo d = new NussinovDesignDemo();
 720                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 721                 d.pack();
 722                 d.setVisible(true);
 723         }
 724
 725         public void onStructureRedrawn() {
 726                 _vpMaster.repaint();
 727         }
 728
 729         public void onWarningEmitted(String s) {
 730                 // TODO Auto-generated method stub
 731
 732         }
 733
 734         public void onLoad(String path) {
 735                 // TODO Auto-generated method stub
 736
 737         }
 738
 739         public void onLoaded() {
 740                 // TODO Auto-generated method stub
 741
 742         }
 743
 744         public void onUINewStructure(VARNAConfig v, RNA r) {
 745                 // TODO Auto-generated method stub
 746
 747         }
 748
 749         static final String[] _bases =     {"A","C","G","U"};
 750         static final String[] _basesComp = {"U","G","C","A"};
 751
 752         public void onBaseClicked(ModeleBase mb, MouseEvent e) {
 753                 int index = -1;
 754                 for(int i =0;i<_bases.length;i++)
 755                 {
 756                         if (mb.getContent().equalsIgnoreCase(_bases[i]))
 757                         {
 758                                 index = i;
 759                         }
 760                 }
 761                 index = (index+1)%_bases.length;
 762                 mb.setContent(_bases[index].toUpperCase());
 763                 ArrayList<ModeleBase> partners =_vpTarget.getRNA().getAllPartners(mb.getIndex());
 764                 if (partners.size()!=0)
 765                 {
 766                         ModeleBase mbPartner = _vpMaster.getRNA().getBaseAt(partners.get(0).getIndex());
 767                         mbPartner.setContent(_basesComp[index].toUpperCase());
 768                 }
 769                 _vpMaster.repaint();
 770                 _seq1.setText(_vpMaster.getRNA().getSeq());
 771                 new Temporizer(_vpMaster.getRNA().getSeq()).start();
 772         }
 773
 774         private class Temporizer extends Thread{
 775                 String _seq;
 776                 public Temporizer(String seq)
 777                 {
 778                         _seq = seq;
 779                 }
 780                 public void run() {
 781             try {
 782                                 this.sleep(1000);
 783                                 if (_vpMaster.getRNA().getSeq().equalsIgnoreCase(_seq))
 784                                 {
 785                                         showSolution();
 786                                 }
 787                         } catch (InterruptedException e) {
 788                                 // TODO Auto-generated catch block
 789                                 e.printStackTrace();
 790                         }
 791         }
 792         }
 793         public void onZoomLevelChanged() {
 794                 // TODO Auto-generated method stub
 795
 796         }
 797
 798         public void onTranslationChanged() {
 799                 // TODO Auto-generated method stub
 800
 801         }
 802
 803         public void itemStateChanged(ItemEvent arg0) {
 804                 // TODO Auto-generated method stub
 805                 System.out.println();
 806         }
 807
 808
 809         public static void formatLabel(JLabel j)
 810         {
 811                 j.setHorizontalTextPosition(JLabel.LEFT);
 812                 j.setPreferredSize(new Dimension(NussinovDemo.marginTools, 25));
 813                 j.setFont(labelsFont);
 814                 j.setForeground(Color.white);
 815         }
 816
 817         public static void formatLabel(JTextArea j)
 818         {
 819                 j.setPreferredSize(new Dimension(NussinovDemo.marginTools, 25));
 820                 j.setFont(labelsFont);
 821                 j.setForeground(Color.white);
 822         }
 823
 824         public class InfoPanel extends JPanel
 825         {
 826                 ArrayList<String> _sols = new ArrayList<String>();
 827                 BigInteger _nbFolds = BigInteger.ZERO;
 828                 JLabel _text = new JLabel("");
 829                 JLabel _subopts = new JLabel("");
 830                 JPanel _suboptBrowser = new JPanel();
 831                 JPanel _suboptCount = new JPanel();
 832                 int _selectedIndex = 0;
 833                 JButton next = new JButton(">");
 834                 JButton previous = new JButton("<");
 835
 836                 InfoPanel()
 837                 {
 838                         this.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
 839                         setLayout(new BorderLayout());
 840                         add(_suboptBrowser,BorderLayout.SOUTH);
 841                         add(_suboptCount,BorderLayout.NORTH);
 842
 843                         next.addActionListener(new ActionListener(){
 844                                 public void actionPerformed(ActionEvent arg0) {
 845                                         if (_sols.size()>0)
 846                                         {
 847                                                 setSelectedIndex((_selectedIndex+1)%_sols.size());
 848                                         }
 849                                 }
 850                         });
 851
 852                         previous.addActionListener(new ActionListener(){
 853                                 public void actionPerformed(ActionEvent arg0) {
 854                                         if (_sols.size()>0)
 855                                         {
 856                                                 setSelectedIndex((_selectedIndex+_sols.size()-1)%_sols.size());
 857                                         }
 858                                 }
 859                         });
 860                         next.setEnabled(false);
 861                         previous.setEnabled(false);
 862
 863                         JLabel nbLab = new JLabel("#Repliements");
 864                         NussinovDesignDemo.formatLabel(nbLab);
 865
 866
 867                         JLabel cooptlab = new JLabel("#Co-optimaux");
 868                         NussinovDesignDemo.formatLabel(cooptlab);
 869
 870                         NussinovDesignDemo.formatLabel(_text);
 871                         NussinovDesignDemo.formatLabel(_subopts);
 872
 873
 874                         _suboptCount.setLayout(new BorderLayout());
 875                         _suboptCount.add(nbLab,BorderLayout.WEST);
 876                         _suboptCount.add(_text,BorderLayout.CENTER);
 877                         _suboptCount.setBackground(Color.decode("#E33729"));
 878
 879
 880                         JPanel commands = new JPanel();
 881                         commands.add(previous);
 882                         commands.add(next);
 883                         commands.setBackground(Color.decode("#E33729"));
 884
 885                         JPanel jp = new JPanel();
 886                         jp.setLayout(new BorderLayout());
 887                         jp.add(_subopts,BorderLayout.WEST);
 888                         jp.add(commands,BorderLayout.CENTER);
 889                         jp.setBackground(Color.decode("#E33729"));
 890
 891                         _suboptBrowser.setLayout(new BorderLayout());
 892                         _suboptBrowser.add(cooptlab,BorderLayout.WEST);
 893                         _suboptBrowser.add(jp,BorderLayout.CENTER);
 894                         _suboptBrowser.setBackground(Color.decode("#E33729"));
 895
 896                 }
 897
 898
 899                 /*public void setSelectedIndex(int i)
 900                 {
 901                         _selectedIndex = i;
 902                         RNA rfolded = new RNA();
 903                         try {
 904                                 rfolded.setRNA(getSeq(), _sols.get(i));
 905                                 rfolded.drawRNARadiate(_vpMaster.getConfig());
 906                         _vpMaster.showRNAInterpolated(rfolded);
 907                         } catch (ExceptionUnmatchedClosingParentheses e) {
 908                                 // TODO Auto-generated catch block
 909                                 e.printStackTrace();
 910                         } catch (ExceptionFileFormatOrSyntax e) {
 911                                 // TODO Auto-generated catch block
 912                                 e.printStackTrace();
 913                         }
 914                         //_struct.setText(_sols.get(i));
 915                         formatDescription();
 916                 }*/
 917
 918                 public void setSelectedIndex(int i)
 919                 {
 920                         _selectedIndex = i;
 921                         RNA rfolded = new RNA();
 922                         try {
 923                                 rfolded.setRNA(getSeq(), _sols.get(i));
 924                                 RNA target = _vpTarget.getRNA();
 925                                 for(ModeleBase mb: rfolded.get_listeBases())
 926                                 {
 927                                         ModeleBase mbref = target.getBaseAt(mb.getIndex());
 928                                         if (mb.getElementStructure()==mbref.getElementStructure())
 929                                         {
 930                                                 mb.getStyleBase().setBaseInnerColor(_okColor);
 931                                                 mb.getStyleBase().setBaseNameColor(Color.white);
 932                                         }
 933                                 }
 934                                 for(ModeleBase mb: target.get_listeBases())
 935                                 {
 936                                         ModeleBase mbref = rfolded.getBaseAt(mb.getIndex());
 937                                         if (mb.getElementStructure()==mbref.getElementStructure())
 938                                         {
 939                                                 mb.getStyleBase().setBaseInnerColor(_okColor);
 940                                         }
 941                                         else
 942                                         {
 943                                                 mb.getStyleBase().setBaseInnerColor(Color.white);
 944                                         }
 945                                 }
 946                                 rfolded.drawRNARadiate(_vpMaster.getConfig());
 947                                 if ((_sols.size()==1)&& (target.getStructDBN().equals(_sols.get(0))))
 948                                         rfolded.setName("Félicitations !");
 949                                 else
 950                                         rfolded.setName("Repliement stable - "+(i+1)+"/"+_sols.size());
 951                         _vpMaster.showRNAInterpolated(rfolded);
 952                         _vpTarget.repaint();
 953                         } catch (ExceptionUnmatchedClosingParentheses e) {
 954                                 // TODO Auto-generated catch block
 955                                 e.printStackTrace();
 956                         } catch (ExceptionFileFormatOrSyntax e) {
 957                                 // TODO Auto-generated catch block
 958                                 e.printStackTrace();
 959                         }
 960                         //_struct.setSelectedItem(_sols.get(i));
 961                         formatDescription();
 962                 }
 963
 964 //              public void setFont(Font f)
 965 //              {
 966 //                      super.setFont(f);
 967 //                      if(_text!=null)
 968 //                      {
 969 //                              _text.setFont(f);
 970 //                              _text.setOpaque(false);
 971 //                      }
 972 //                      if(_subopts!=null)
 973 //                      {
 974 //                      _subopts.setFont(f);
 975 //                      _subopts.setOpaque(false);
 976 //                      }
 977 //              }
 978                 public void setInfo(ArrayList<String> sols, BigInteger nbFolds)
 979                 {
 980                         _sols = sols;
 981                         _nbFolds = nbFolds;
 982                         formatDescription();
 983                         setSelectedIndex(0);
 984                 }
 985
 986                 private void formatDescription()
 987                 {
 988                         _text.setText(""+_nbFolds);
 989                         _subopts.setText(""+_sols.size());
 990                         next.setEnabled(_sols.size()>1);
 991                         previous.setEnabled(_sols.size()>1);
 992
 993                 }
 994
 995         }
 996
 997 }