src2/fr/orsay/lri/varna/applications/NussinovDemo.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.MouseEvent;
  28 import java.math.BigInteger;
  29 import java.util.ArrayList;
  30 import java.util.Collections;
  31
  32 import javax.swing.BorderFactory;
  33 import javax.swing.DefaultComboBoxModel;
  34 import javax.swing.JButton;
  35 import javax.swing.JComboBox;
  36 import javax.swing.JFrame;
  37 import javax.swing.JLabel;
  38 import javax.swing.JPanel;
  39 import javax.swing.JTextArea;
  40 import javax.swing.JTextField;
  41 import javax.swing.JTextPane;
  42 import javax.swing.border.BevelBorder;
  43
  44 import fr.orsay.lri.varna.VARNAPanel;
  45 import fr.orsay.lri.varna.controlers.ControleurInterpolator;
  46 import fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm;
  47 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  48 import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError;
  49 import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
  50 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  51 import fr.orsay.lri.varna.exceptions.ExceptionParameterError;
  52 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  53 import fr.orsay.lri.varna.exceptions.MappingException;
  54 import fr.orsay.lri.varna.models.VARNAConfig;
  55 import fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE;
  56 import fr.orsay.lri.varna.models.rna.Mapping;
  57 import fr.orsay.lri.varna.models.rna.ModeleBase;
  58 import fr.orsay.lri.varna.models.rna.ModelBaseStyle;
  59 import fr.orsay.lri.varna.models.rna.RNA;
  60 import fr.orsay.lri.varna.interfaces.InterfaceVARNABasesListener;
  61 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;;
  62
  63 public class NussinovDemo extends JFrame implements InterfaceVARNAListener,InterfaceVARNABasesListener {
  64
  65         /**
  66          *
  67          */
  68         private static final long serialVersionUID = -790155708306987257L;
  69
  70         private static final String SEQUENCE_DUMMY =        "AAAAAAAAAA";
  71         private static final String SEQUENCE_A =        "AGGCACGUCU";
  72         private static final String SEQUENCE_B =  "GAGUAGCCUC";
  73         private static final String SEQUENCE_C = "GCAUAGCUGC";
  74         private static final String SEQUENCE_INRIA = "GAGAAGUACUUGAAAUUGGCCUCCUC";
  75
  76
  77         private static final String SEQUENCE_BIG = "AAAACAAAAACACCAUGGUGUUUUCACCCAAUUGGGUGAAAACAGAGAUCUCGAGAUCUCUGUUUUUGUUUU";
  78
  79         private static final String DEFAULT_STRUCTURE = "..........";
  80         // private static final String DEFAULT_STRUCTURE1 = "((((....))))";
  81         // private static final String DEFAULT_STRUCTURE2 =
  82         // "((((..(((....)))..))))";
  83
  84         private VARNAPanel _vpMaster;
  85
  86         private InfoPanel _infos = new InfoPanel();
  87         private JPanel _tools = new JPanel();
  88         private JPanel _input = new JPanel();
  89
  90         private JPanel _seqPanel = new JPanel();
  91         private JPanel _structPanel = new JPanel();
  92         private JLabel _actions = new JLabel();
  93         private JLabel _struct = new JLabel(DEFAULT_STRUCTURE);
  94         private JComboBox _seq1 = new JComboBox();
  95         private JLabel _structLabel = new JLabel("Structure Secondaire");
  96         private JLabel _seqLabel = new JLabel("Sequence d'ARN");
  97         private JButton _goButton = new JButton("Repliement");
  98         private JButton _switchButton = new JButton("Effacer");
  99
 100
 101         private Color _backgroundColor = Color.white;
 102
 103         public static Font textFieldsFont = Font.decode("MonoSpaced-BOLD-16");
 104         public static Font labelsFont = Font.decode("SansSerif-BOLD-20");
 105         public static final int marginTools = 250;
 106         public static String APP_TITLE = "Fête de la science 2015 - Inria AMIB - Repliement d'ARN";
 107
 108
 109         public static ModelBaseStyle createStyle(String txt)
 110         {
 111                 ModelBaseStyle result = new ModelBaseStyle();
 112                 try {
 113                         result.assignParameters(txt);
 114                 } catch (ExceptionModeleStyleBaseSyntaxError e) {
 115                         // TODO Auto-generated catch block
 116                         e.printStackTrace();
 117                 } catch (ExceptionParameterError e) {
 118                         // TODO Auto-generated catch block
 119                         e.printStackTrace();
 120                 }
 121                 return result;
 122         }
 123
 124         public void applyTo(VARNAPanel vp, ModelBaseStyle mb, int[] indices)
 125         {
 126                 for(int i=0;i<indices.length;i++)
 127                 {
 128                         ModeleBase m = vp.getRNA().getBaseAt(indices[i]);
 129                         m.setStyleBase(mb);
 130                         if (m.getElementStructure()!=-1)
 131                         {
 132                                 vp.getRNA().getBaseAt(m.getElementStructure()).setStyleBase(mb);
 133                         }
 134                 }
 135                 vp.repaint();
 136         }
 137
 138
 139         public NussinovDemo() {
 140                 super();
 141                 try {
 142                         _vpMaster = new VARNAPanel(getSeq(), "");
 143                 } catch (ExceptionNonEqualLength e) {
 144                         _vpMaster.errorDialog(e);
 145                 }
 146                 _vpMaster.setPreferredSize(new Dimension(600, 600));
 147                 RNAPanelDemoInit();
 148         }
 149
 150         public static void formatLabel(JLabel j)
 151         {
 152                 j.setHorizontalTextPosition(JLabel.LEFT);
 153                 j.setPreferredSize(new Dimension(marginTools, 15));
 154                 j.setFont(labelsFont);
 155         }
 156
 157         private void RNAPanelDemoInit() {
 158
 159
 160
 161                 _seq1.setFont(textFieldsFont);
 162                 String[] seqs = {SEQUENCE_DUMMY,SEQUENCE_INRIA,SEQUENCE_A,SEQUENCE_B,SEQUENCE_C,SEQUENCE_BIG};
 163                 _seq1.setModel(new DefaultComboBoxModel(seqs));
 164                 _seq1.setEditable(true);
 165
 166
 167                 setBackground(_backgroundColor);
 168                 _vpMaster.setBackground(_backgroundColor);
 169                 _vpMaster.addVARNAListener(this);
 170                 _vpMaster.setFlatExteriorLoop(true);
 171
 172
 173
 174                 formatLabel(_seqLabel);
 175                 formatLabel(_structLabel);
 176
 177                 _goButton.addActionListener(new ActionListener() {
 178                         public void actionPerformed(ActionEvent e) {
 179                                 showSolution();
 180                                 onStructureRedrawn();
 181                         }
 182                 });
 183
 184                 _switchButton.addActionListener(new ActionListener() {
 185                         public void actionPerformed(ActionEvent e) {
 186                                 try {
 187                                                         RNA r = new RNA();
 188                                                         r.setRNA("", "");
 189                                                         _struct.setText("");
 190                                                         _vpMaster.setTitle("");
 191                                                         _vpMaster.showRNA(r);
 192                                                         onStructureRedrawn();
 193                                         }
 194                                 catch (ExceptionFileFormatOrSyntax e2) {
 195                                         e2.printStackTrace();
 196                                 } catch (ExceptionUnmatchedClosingParentheses e2) {
 197                                         // TODO Auto-generated catch block
 198                                         e2.printStackTrace();
 199                                 }
 200                                 _vpMaster.repaint();
 201                         }
 202                 });
 203
 204                 _seqPanel.setLayout(new BorderLayout());
 205                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 206                 _seqPanel.add(_seq1, BorderLayout.CENTER);
 207
 208                 _structLabel.setPreferredSize(new Dimension(marginTools, 15));
 209                 _structLabel.setHorizontalTextPosition(JLabel.LEFT);
 210                 _struct.setFont(textFieldsFont);
 211                 _structPanel.setLayout(new BorderLayout());
 212                 _structPanel.add(_structLabel, BorderLayout.WEST);
 213                 _structPanel.add(_struct, BorderLayout.CENTER);
 214
 215                 _input.setLayout(new GridLayout(0, 1));
 216                 _input.add(_seqPanel);
 217                 _input.add(_structPanel);
 218
 219                 JPanel goPanel = new JPanel();
 220                 goPanel.setLayout(new BorderLayout());
 221
 222                 _infos.setFont(labelsFont);
 223
 224
 225                 _tools.setLayout(new BorderLayout());
 226                 _tools.add(_infos, BorderLayout.SOUTH);
 227                 _tools.add(_input, BorderLayout.CENTER);
 228                 _tools.add(_actions, BorderLayout.NORTH);
 229                 _tools.add(goPanel, BorderLayout.EAST);
 230                 _tools.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
 231
 232                 goPanel.add(_goButton, BorderLayout.CENTER);
 233                 goPanel.add(_switchButton, BorderLayout.SOUTH);
 234
 235                 getContentPane().setLayout(new BorderLayout());
 236                 JPanel VARNAs = new JPanel();
 237                 VARNAs.setLayout(new GridLayout(1,2));
 238                 VARNAs.add(_vpMaster);
 239                 VARNAs.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
 240                 getContentPane().add(VARNAs, BorderLayout.CENTER);
 241                 getContentPane().add(_tools, BorderLayout.SOUTH);
 242
 243                 setVisible(true);
 244
 245                 _vpMaster.getVARNAUI().UIRadiate();
 246                 _vpMaster.setTitleFontSize(26f);
 247                 _vpMaster.setTitleFontStyle(Font.PLAIN);
 248                 _vpMaster.addVARNABasesListener(this);
 249                 _vpMaster.setBackground(Color.decode("#308099"));
 250                 _vpMaster.setModifiable(false);
 251                 _vpMaster.setTitle("Repliement cible");
 252                 _vpMaster.setBPStyle(BP_STYLE.SIMPLE);
 253                 _vpMaster.setBackboneColor(Color.white);
 254                 _vpMaster.setDefaultBPColor(Color.white);
 255                 _vpMaster.setBaseNumbersColor(Color.white);
 256                 _vpMaster.setBaseOutlineColor(Color.white);
 257                 _vpMaster.setTitleColor(Color.white);
 258                 _vpMaster.setTitleFontSize(26f);
 259
 260
 261
 262                 this.setTitle(APP_TITLE);
 263
 264                 showSolution();
 265                 onStructureRedrawn();
 266         }
 267
 268         private synchronized void showSolution()
 269         {
 270                 ArrayList<String> sols = getStructs();
 271                 _infos.setInfo(sols, count(getSeq()));
 272         }
 273
 274
 275
 276
 277         public String getSeq()
 278         {
 279                 return (""+_seq1.getSelectedItem()).toUpperCase();
 280         }
 281
 282
 283         private boolean canBasePairAll(char a, char b)
 284         {
 285                 return true;
 286         }
 287
 288         private boolean canBasePairBasic(char a, char b)
 289         {
 290                 if ((a=='G')&&(b=='C'))
 291                         return true;
 292                 if ((a=='C')&&(b=='G'))
 293                         return true;
 294                 if ((a=='U')&&(b=='A'))
 295                         return true;
 296                 if ((a=='A')&&(b=='U'))
 297                         return true;
 298                 if ((a=='G')&&(b=='U'))
 299                         return true;
 300                 if ((a=='U')&&(b=='G'))
 301                         return true;
 302                 return false;
 303         }
 304
 305         private double basePairScoreBasic(char a, char b)
 306         {
 307                 if ((a=='G')&&(b=='C'))
 308                         return 1.0;
 309                 if ((a=='C')&&(b=='G'))
 310                         return 1.0;
 311                 if ((a=='U')&&(b=='A'))
 312                         return 1.0;
 313                 if ((a=='A')&&(b=='U'))
 314                         return 1.0;
 315                 if ((a=='G')&&(b=='U'))
 316                         return 1.0;
 317                 if ((a=='U')&&(b=='G'))
 318                         return 1.0;
 319                 return Double.NEGATIVE_INFINITY;
 320         }
 321
 322
 323         private boolean canBasePairNussinov(char a, char b)
 324         {
 325                 if ((a=='G')&&(b=='C'))
 326                         return true;
 327                 if ((a=='C')&&(b=='G'))
 328                         return true;
 329                 if ((a=='U')&&(b=='A'))
 330                         return true;
 331                 if ((a=='A')&&(b=='U'))
 332                         return true;
 333                 if ((a=='U')&&(b=='G'))
 334                         return true;
 335                 if ((a=='G')&&(b=='U'))
 336                         return true;
 337                 return false;
 338         }
 339
 340         private double basePairScoreNussinov(char a, char b)
 341         {
 342                 if ((a=='G')&&(b=='C'))
 343                         return 3.0;
 344                 if ((a=='C')&&(b=='G'))
 345                         return 3.0;
 346                 if ((a=='U')&&(b=='A'))
 347                         return 2.0;
 348                 if ((a=='A')&&(b=='U'))
 349                         return 2.0;
 350                 if ((a=='U')&&(b=='G'))
 351                         return 1.0;
 352                 if ((a=='G')&&(b=='U'))
 353                         return 1.0;
 354                 return Double.NEGATIVE_INFINITY;
 355         }
 356
 357         private boolean canBasePairINRIA(char a, char b)
 358         {
 359                 if ((a=='U')&&(b=='A'))
 360                         return true;
 361                 if ((a=='A')&&(b=='U'))
 362                         return true;
 363                 if ((a=='G')&&(b=='C'))
 364                         return true;
 365                 if ((a=='C')&&(b=='G'))
 366                         return true;
 367
 368                 if ((a=='A')&&(b=='G'))
 369                         return true;
 370                 if ((a=='G')&&(b=='A'))
 371                         return true;
 372                 if ((a=='U')&&(b=='C'))
 373                         return true;
 374                 if ((a=='C')&&(b=='U'))
 375                         return true;
 376                 if ((a=='A')&&(b=='A'))
 377                         return true;
 378                 if ((a=='U')&&(b=='U'))
 379                         return true;
 380
 381                 if ((a=='U')&&(b=='G'))
 382                         return true;
 383                 if ((a=='G')&&(b=='U'))
 384                         return true;
 385                 if ((a=='A')&&(b=='C'))
 386                         return true;
 387                 if ((a=='C')&&(b=='A'))
 388                         return true;
 389                 return false;
 390         }
 391
 392         private double basePairScoreINRIA(char a, char b)
 393         {
 394                 if ((a=='U')&&(b=='A'))
 395                         return 3;
 396                 if ((a=='A')&&(b=='U'))
 397                         return 3;
 398                 if ((a=='G')&&(b=='C'))
 399                         return 3;
 400                 if ((a=='C')&&(b=='G'))
 401                         return 3;
 402
 403                 if ((a=='A')&&(b=='G'))
 404                         return 2;
 405                 if ((a=='G')&&(b=='A'))
 406                         return 2;
 407                 if ((a=='U')&&(b=='C'))
 408                         return 2;
 409                 if ((a=='C')&&(b=='U'))
 410                         return 2;
 411                 if ((a=='A')&&(b=='A'))
 412                         return 2;
 413                 if ((a=='U')&&(b=='U'))
 414                         return 2;
 415
 416                 if ((a=='U')&&(b=='G'))
 417                         return 1;
 418                 if ((a=='G')&&(b=='U'))
 419                         return 1;
 420                 if ((a=='A')&&(b=='C'))
 421                         return 1;
 422                 if ((a=='C')&&(b=='A'))
 423                         return 1;
 424                 return Double.NEGATIVE_INFINITY;
 425         }
 426
 427         private boolean canBasePair(char a, char b)
 428         {
 429                 return canBasePairBasic(a,b);
 430                 //return canBasePairNussinov(a,b);
 431                 //return canBasePairINRIA(a,b);
 432         }
 433
 434         private double basePairScore(char a, char b)
 435         {
 436                 return basePairScoreBasic(a,b);
 437                 //return basePairScoreNussinov(a,b);
 438                 //return basePairScoreINRIA(a,b);
 439         }
 440
 441         public double[][] fillMatrix(String seq)
 442         {
 443                 int n = seq.length();
 444                 double[][] tab = new double[n][n];
 445                 for(int m=1;m<=n;m++)
 446                 {
 447                         for(int i=0;i<n-m+1;i++)
 448                         {
 449                                 int j = i+m-1;
 450                                 tab[i][j] = 0;
 451                                 if (i<j)
 452                                 {
 453                                         tab[i][j] = Math.max(tab[i][j], tab[i+1][j]);
 454                                         for (int k=i+1;k<=j;k++)
 455                                         {
 456                                                 if (canBasePair(seq.charAt(i),seq.charAt(k)))
 457                                                 {
 458                                                         double fact1 = 0;
 459                                                         if (k>i+1)
 460                                                         {
 461                                                                 fact1 = tab[i+1][k-1];
 462                                                         }
 463                                                         double fact2 = 0;
 464                                                         if (k<j)
 465                                                         {
 466                                                                 fact2 = tab[k+1][j];
 467                                                         }
 468                                                         tab[i][j] = Math.max(tab[i][j],basePairScore(seq.charAt(i),seq.charAt(k))+fact1+fact2);
 469                                                 }
 470                                         }
 471                                 }
 472                         }
 473                 }
 474                 return tab;
 475         }
 476
 477         public static ArrayList<Double> combine(double bonus, ArrayList<Double> part1, ArrayList<Double> part2)
 478         {
 479                 ArrayList<Double> base = new ArrayList<Double>();
 480                 for(double d1: part1)
 481                 {
 482                         for(double d2: part2)
 483                         {
 484                                 base.add(bonus+d1+d2);
 485                         }
 486                 }
 487                 return base;
 488         }
 489
 490         public static ArrayList<Double> selectBests(ArrayList<Double> base)
 491         {
 492                 ArrayList<Double> result = new ArrayList<Double>();
 493                 double best = Double.NEGATIVE_INFINITY;
 494                 for(double val: base)
 495                 {
 496                         best = Math.max(val, best);
 497                 }
 498                 for(double val: base)
 499                 {
 500                         if (val == best)
 501                                 result.add(val);
 502                 }
 503                 return result;
 504         }
 505
 506
 507         private ArrayList<String> backtrack(double[][] tab, String seq)
 508         {
 509                 return backtrack(tab,seq, 0, seq.length()-1);
 510         }
 511
 512         private ArrayList<String> backtrack(double[][] tab, String seq, int i, int j)
 513         {
 514                 ArrayList<String> result = new ArrayList<String>();
 515                 if (i<j)
 516                 {
 517                         ArrayList<Integer> indices = new ArrayList<Integer>();
 518                         indices.add(-1);
 519                         for (int k=i+1;k<=j;k++)
 520                         {
 521                                 indices.add(k);
 522                         }
 523                         for (int k : indices)
 524                         {
 525                                 if (k==-1)
 526                                 {
 527                                         if (tab[i][j] == tab[i+1][j])
 528                                         {
 529                                                 for (String s:backtrack(tab, seq, i+1,j))
 530                                                 {
 531                                                         result.add("."+s);
 532                                                 }
 533                                         }
 534                                 }
 535                                 else
 536                                 {
 537                                         if (canBasePair(seq.charAt(i),seq.charAt(k)))
 538                                         {
 539                                                 double fact1 = 0;
 540                                                 if (k>i+1)
 541                                                 {
 542                                                         fact1 = tab[i+1][k-1];
 543                                                 }
 544                                                 double fact2 = 0;
 545                                                 if (k<j)
 546                                                 {
 547                                                         fact2 = tab[k+1][j];
 548                                                 }
 549                                                 if (tab[i][j]==basePairScore(seq.charAt(i),seq.charAt(k))+fact1+fact2)
 550                                                 {
 551                                                         for (String s1:backtrack(tab, seq, i+1,k-1))
 552                                                         {
 553                                                                 for (String s2:backtrack(tab, seq, k+1,j))
 554                                                                 {
 555                                                                         result.add("("+s1+")"+s2);
 556                                                                 }
 557                                                         }
 558                                                 }
 559                                         }
 560                                 }
 561                         }
 562                 }
 563                 else if  (i==j)
 564                 {
 565                         result.add(".");
 566                 }
 567                 else
 568                 {
 569                         result.add("");
 570                 }
 571                 return result;
 572         }
 573
 574         public BigInteger count(String seq)
 575         {
 576                 int n = seq.length();
 577
 578                 BigInteger[][] tab = new BigInteger[n][n];
 579                 for(int m=1;m<=n;m++)
 580                 {
 581                         for(int i=0;i<n-m+1;i++)
 582                         {
 583                                 int j = i+m-1;
 584                                 tab[i][j] = BigInteger.ZERO;
 585                                 if (i<j)
 586                                 {
 587                                         tab[i][j] = tab[i][j].add(tab[i+1][j]);
 588                                         for (int k=i+1;k<=j;k++)
 589                                         {
 590                                                 if (canBasePair(seq.charAt(i),seq.charAt(k)))
 591                                                 {
 592                                                         BigInteger fact1 = BigInteger.ONE;
 593                                                         if (k>i+1)
 594                                                         {
 595                                                                 fact1 = tab[i+1][k-1];
 596                                                         }
 597                                                         BigInteger fact2 = BigInteger.ONE;
 598                                                         if (k<j)
 599                                                         {
 600                                                                 fact2 = tab[k+1][j];
 601                                                         }
 602                                                         tab[i][j] = tab[i][j].add(fact1.multiply(fact2));
 603                                                 }
 604                                         }
 605                                 }
 606                                 else
 607                                 {
 608                                         tab[i][j] = BigInteger.ONE;
 609                                 }
 610                         }
 611                 }
 612                 return tab[0][n-1];
 613         }
 614
 615         private String _cache = "";
 616         ArrayList<String> _cacheStructs = new ArrayList<String>();
 617
 618         public ArrayList<String> getStructs() {
 619                 String seq = getSeq();
 620                 seq = seq.toUpperCase();
 621                 if (!_cache.equals(seq))
 622                 {
 623                         double[][] mfe = fillMatrix(seq);
 624                         _cacheStructs = backtrack(mfe,seq);
 625                         _cache = seq;
 626                 }
 627                 return _cacheStructs;
 628         }
 629
 630         public VARNAPanel get_varnaPanel() {
 631                 return _vpMaster;
 632         }
 633
 634         public void set_varnaPanel(VARNAPanel surface) {
 635                 _vpMaster = surface;
 636         }
 637
 638
 639         public JLabel get_info() {
 640                 return _actions;
 641         }
 642
 643         public void set_info(JLabel _info) {
 644                 this._actions = _info;
 645         }
 646
 647         public static void main(String[] args) {
 648                 NussinovDemo d = new NussinovDemo();
 649                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 650                 d.pack();
 651                 d.setVisible(true);
 652         }
 653
 654         public void onStructureRedrawn() {
 655                 _vpMaster.repaint();
 656         }
 657
 658         public void onWarningEmitted(String s) {
 659                 // TODO Auto-generated method stub
 660
 661         }
 662
 663         public void onLoad(String path) {
 664                 // TODO Auto-generated method stub
 665
 666         }
 667
 668         public void onLoaded() {
 669                 // TODO Auto-generated method stub
 670
 671         }
 672
 673         public void onUINewStructure(VARNAConfig v, RNA r) {
 674                 // TODO Auto-generated method stub
 675
 676         }
 677
 678         static final String[] _bases =     {"A","C","G","U"};
 679         static final String[] _basesComp = {"U","G","C","A"};
 680
 681         public void onBaseClicked(ModeleBase mb, MouseEvent e) {
 682         }
 683
 684         public void onZoomLevelChanged() {
 685                 // TODO Auto-generated method stub
 686
 687         }
 688
 689         public void onTranslationChanged() {
 690                 // TODO Auto-generated method stub
 691
 692         }
 693         private class InfoPanel extends JPanel
 694         {
 695                 ArrayList<String> _sols = new ArrayList<String>();
 696                 BigInteger _nbFolds = BigInteger.ZERO;
 697                 JTextArea _text = new JTextArea("");
 698                 JTextArea _subopts = new JTextArea("");
 699                 JPanel _suboptBrowser = new JPanel();
 700                 JPanel _suboptCount = new JPanel();
 701                 int _selectedIndex = 0;
 702                 JButton next = new JButton(">");
 703                 JButton previous = new JButton("<");
 704
 705                 InfoPanel()
 706                 {
 707                         setLayout(new BorderLayout());
 708                         add(_suboptBrowser,BorderLayout.SOUTH);
 709                         add(_suboptCount,BorderLayout.NORTH);
 710
 711                         next.addActionListener(new ActionListener(){
 712                                 public void actionPerformed(ActionEvent arg0) {
 713                                         if (_sols.size()>0)
 714                                         {
 715                                                 setSelectedIndex((_selectedIndex+1)%_sols.size());
 716                                         }
 717                                 }
 718                         });
 719
 720                         previous.addActionListener(new ActionListener(){
 721                                 public void actionPerformed(ActionEvent arg0) {
 722                                         if (_sols.size()>0)
 723                                         {
 724                                                 setSelectedIndex((_selectedIndex+_sols.size()-1)%_sols.size());
 725                                         }
 726                                 }
 727                         });
 728                         next.setEnabled(false);
 729                         previous.setEnabled(false);
 730
 731
 732                         JLabel nbLab = new JLabel("#Repliements");
 733                         NussinovDemo.formatLabel(nbLab);
 734
 735                         _suboptCount.setLayout(new BorderLayout());
 736                         _suboptCount.add(nbLab,BorderLayout.WEST);
 737                         _suboptCount.add(_text,BorderLayout.CENTER);
 738
 739                         JLabel cooptlab = new JLabel("#Co-optimaux");
 740                         NussinovDemo.formatLabel(cooptlab);
 741
 742                         JPanel commands = new JPanel();
 743                         commands.add(previous);
 744                         commands.add(next);
 745
 746                         JPanel jp = new JPanel();
 747                         jp.setLayout(new BorderLayout());
 748                         jp.add(_subopts,BorderLayout.WEST);
 749                         jp.add(commands,BorderLayout.CENTER);
 750
 751                         _suboptBrowser.setLayout(new BorderLayout());
 752                         _suboptBrowser.add(cooptlab,BorderLayout.WEST);
 753                         _suboptBrowser.add(jp,BorderLayout.CENTER);
 754
 755
 756                 }
 757
 758
 759                 public void setSelectedIndex(int i)
 760                 {
 761                         _selectedIndex = i;
 762                         RNA rfolded = new RNA();
 763                         try {
 764                                 rfolded.setRNA(getSeq(), _sols.get(i));
 765                                 rfolded.drawRNARadiate(_vpMaster.getConfig());
 766                                 rfolded.setBaseNameColor(Color.white);
 767                                 rfolded.setBaseOutlineColor(Color.white);
 768                                 rfolded.setBaseNumbersColor(Color.white);
 769                                 _vpMaster.setBaseNumbersColor(Color.white);
 770                                 _vpMaster.setBaseOutlineColor(Color.white);
 771                                 _vpMaster.setFillBases(false);
 772                                 _vpMaster.setBaseNameColor(Color.white);
 773                                 _vpMaster.showRNAInterpolated(rfolded);
 774
 775                         } catch (ExceptionUnmatchedClosingParentheses e) {
 776                                 // TODO Auto-generated catch block
 777                                 e.printStackTrace();
 778                         } catch (ExceptionFileFormatOrSyntax e) {
 779                                 // TODO Auto-generated catch block
 780                                 e.printStackTrace();
 781                         }
 782                         _struct.setText(_sols.get(i));
 783                         formatDescription();
 784                 }
 785
 786                 public void setFont(Font f)
 787                 {
 788                         super.setFont(f);
 789                         if(_text!=null)
 790                         {
 791                                 _text.setFont(f);
 792                                 _text.setOpaque(false);
 793                         }
 794                         if(_subopts!=null)
 795                         {
 796                         _subopts.setFont(f);
 797                         _subopts.setOpaque(false);
 798                         }
 799                 }
 800                 public void setInfo(ArrayList<String> sols, BigInteger nbFolds)
 801                 {
 802                         _sols = sols;
 803                         _nbFolds = nbFolds;
 804                         formatDescription();
 805                         setSelectedIndex(0);
 806                 }
 807
 808                 private void formatDescription()
 809                 {
 810                         _text.setText(""+_nbFolds);
 811                         _subopts.setText(""+_sols.size());
 812                         next.setEnabled(_sols.size()>1);
 813                         previous.setEnabled(_sols.size()>1);
 814
 815                 }
 816
 817         }
 818
 819 }