src2/fr/orsay/lri/varna/controlers/ControleurMenu.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 Universit� 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.controlers;
  19
  20
  21 import java.awt.Color;
  22 import java.awt.event.ActionEvent;
  23 import java.awt.event.ActionListener;
  24 import java.io.File;
  25 import java.text.ParseException;
  26 import java.util.ArrayList;
  27
  28 import javax.swing.JCheckBoxMenuItem;
  29 import javax.swing.JColorChooser;
  30 import javax.swing.JOptionPane;
  31
  32 import fr.orsay.lri.varna.VARNAPanel;
  33 import fr.orsay.lri.varna.exceptions.ExceptionExportFailed;
  34 import fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding;
  35 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  36 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  37 import fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden;
  38 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
  39 import fr.orsay.lri.varna.models.VARNAConfig;
  40 import fr.orsay.lri.varna.models.annotations.TextAnnotation;
  41 import fr.orsay.lri.varna.models.rna.ModeleBase;
  42 import fr.orsay.lri.varna.models.rna.ModeleBP;
  43 import fr.orsay.lri.varna.models.rna.RNA;
  44 import fr.orsay.lri.varna.views.VueBPThickness;
  45 import fr.orsay.lri.varna.views.VueMenu;
  46
  47 /**
  48  * This listener controls menu items
  49  *
  50  * @author darty
  51  *
  52  */
  53 public class ControleurMenu implements InterfaceVARNAListener,
  54                 ActionListener {
  55
  56         private VARNAPanel _vp;
  57         @SuppressWarnings("unused")
  58         private VueMenu _vm;
  59         private String _type;
  60         private String _color;
  61         private Object _source;
  62
  63         /**
  64          * Creates the menu listener
  65          *
  66          * @param _varnaPanel
  67          *            The VARNAPanel
  68          */
  69         public ControleurMenu(VARNAPanel _varnaPanel, VueMenu _vueMenu) {
  70                 _vp = _varnaPanel;
  71                 _vm = _vueMenu;
  72                 _vp.getRNA().addVARNAListener(this);
  73         }
  74
  75         public void actionPerformed(ActionEvent e) {
  76                 String[] temp = e.getActionCommand().split(",");
  77                 _source = e.getSource();
  78                 _type = temp[0];
  79                 if (temp.length > 1)
  80                         _color = temp[1];
  81                 else
  82                         _color = "";
  83                 // selon l'option choisie dans le menu:
  84                 if (!optionRedraw())
  85                         if (!optionExport())
  86                                 if (!optionImport())
  87                                         if (!optionRNADisplay())
  88                                                 if (!optionTitle())
  89                                                         if (!optionColorMap())
  90                                                                 if (!optionView())
  91                                                                         if (!optionBase())
  92                                                                                 if (!optionBasePair())
  93                                                                                         if (!optionLoop())
  94                                                                                                 if (!option3prime())
  95                                                                                                         if (!option5prime())
  96                                                                                                                 if (!optionHelix())
  97                                                                                                                         if (!optionStem())
  98                                                                                                                                 if (!optionBulge())
  99                                                                                                                                         if (!optionAnnotation())
 100                                                                                                                                                 if (!optionEditRNA())
 101                                                                                                                                                         _vp.errorDialog(new Exception("Uknown action command '"+_type+"'"));
 102         }
 103
 104         private boolean optionEditRNA()
 105         {
 106                 if (_type.equals("editallbps")) {
 107                         _vp.getVARNAUI().UIEditAllBasePairs();
 108                 }
 109                 else if (_type.equals("editallbases")) {
 110                         _vp.getVARNAUI().UIEditAllBases();
 111                 }
 112                 else return false;
 113                 return true;
 114         }
 115
 116         private boolean optionAnnotation() {
 117                 if (!_type.contains("annotation"))
 118                         return false;
 119                 // a partir du menu principale (gestion des annotations)
 120                 if (_type.equals("annotationsaddPosition")) {
 121                         _vp.getVARNAUI().UIAnnotationsAddPosition(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y);
 122                 } else if (_type.equals("annotationsaddBase")) {
 123                         _vp.getVARNAUI().UIAnnotationsAddBase(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y);
 124                 } else if (_type.equals("annotationsaddLoop")) {
 125                         _vp.getVARNAUI().UIAnnotationsAddLoop(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y);
 126                 } else if (_type.equals("annotationsaddChemProb")) {
 127                         _vp.getVARNAUI().UIAnnotationsAddChemProb(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y);
 128                 } else if (_type.equals("annotationsaddRegion")) {
 129                         _vp.getVARNAUI().UIAnnotationsAddRegion(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y);
 130                 } else if (_type.equals("annotationsaddHelix")) {
 131                         _vp.getVARNAUI().UIAnnotationsAddHelix(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y);
 132                 } else if (_type.equals("annotationsautohelices")) {
 133                         _vp.getVARNAUI().UIAutoAnnotateHelices();
 134                 } else if (_type.equals("annotationsautointerior")) {
 135                         _vp.getVARNAUI().UIAutoAnnotateInteriorLoops();
 136                 } else if (_type.equals("annotationsautoterminal")) {
 137                         _vp.getVARNAUI().UIAutoAnnotateTerminalLoops();
 138                 } else if (_type.equals("annotationsautohelices")) {
 139                         _vp.getVARNAUI().UIAutoAnnotateHelices();
 140                 } else if (_type.equals("annotationsremove")) {
 141                         _vp.getVARNAUI().UIAnnotationsRemove();
 142                 } else if (_type.equals("annotationsautoextremites")) {
 143                         _vp.getVARNAUI().UIAutoAnnotateStrandEnds();
 144                 } else if (_type.equals("annotationsedit")) {
 145                         _vp.getVARNAUI().UIAnnotationsEdit();
 146                         // a partir du menu selection (annotation la plus proche)
 147                 } else if (_type.equals("Selectionannotationremove")) {
 148                         _vp.getVARNAUI().UIAnnotationRemoveFromAnnotation(_vp.get_selectedAnnotation());
 149                 } else if (_type.equals("Selectionannotationedit")) {
 150                         _vp.getVARNAUI().UIAnnotationEditFromAnnotation(_vp.get_selectedAnnotation());
 151
 152                         // a partir d'une structure(base, loop, helix) dans l'arn
 153                         // (annotation li� a la structure)
 154                 } else if (_type.endsWith("annotationadd")||_type.contains("annotationremove")||_type.contains("annotationedit"))
 155                 {
 156                         try {
 157                                 TextAnnotation.AnchorType type = trouverAncrage();
 158                                  ArrayList<Integer> listeIndex = new ArrayList<Integer>();
 159                                 switch(type)
 160                                 {
 161                                         case BASE:
 162                                                 listeIndex.add(_vp.getNearestBase());
 163                                         case LOOP:
 164                                                 if (_type.startsWith("loop1"))
 165                                                         listeIndex = _vp.getRNA().findLoopForward(_vp.getNearestBase());
 166                                                 else if (_type.startsWith("loop2"))
 167                                                         listeIndex = _vp.getRNA().findLoopBackward(_vp.getNearestBase());
 168                                                 else
 169                                                         listeIndex = _vp.getRNA().findLoop(_vp.getNearestBase());
 170                                         break;
 171                                         case HELIX:
 172                                                 listeIndex = _vp.getRNA().findHelix(_vp.getNearestBase());
 173                                         break;
 174                                 }
 175                                 if (_type.endsWith("annotationadd"))
 176                                 { _vp.getVARNAUI().UIAnnotationAddFromStructure(type,listeIndex); }
 177                                 else if (_type.contains("annotationremove"))
 178                                 { _vp.getVARNAUI().UIAnnotationRemoveFromStructure(trouverAncrage(),listeIndex); }
 179                                 else if (_type.contains("annotationedit"))
 180                                 { _vp.getVARNAUI().UIAnnotationEditFromStructure(trouverAncrage(),listeIndex); }
 181
 182                         } catch (Exception e2) {
 183                                 e2.printStackTrace();
 184                         }
 185                         } else
 186                         return false;
 187                 return true;
 188         }
 189
 190         private TextAnnotation.AnchorType trouverAncrage() {
 191                 if (_type.contains("loop"))
 192                         return TextAnnotation.AnchorType.LOOP;
 193                 if (_type.contains("helix"))
 194                         return TextAnnotation.AnchorType.HELIX;
 195                 if (_type.contains("base"))
 196                         return TextAnnotation.AnchorType.BASE;
 197                 errorDialog(new Exception("probleme d'identification de l'ancrage"));
 198                 return TextAnnotation.AnchorType.POSITION;
 199         }
 200
 201         private boolean option5prime() {
 202                 return colorBases();
 203         }
 204
 205         private boolean option3prime() {
 206                 return colorBases();
 207         }
 208
 209         private boolean optionBulge() {
 210                 return colorBases();
 211         }
 212
 213         private boolean optionStem() {
 214                 return colorBases();
 215         }
 216
 217         private boolean optionHelix() {
 218                 return colorBases();
 219         }
 220
 221         private boolean colorBases() {
 222                 // System.out.println(_type);
 223                 ArrayList<Integer> listBase = new ArrayList<Integer>();
 224                 String phrase = "Choose new " + _type;
 225                 if (_color.equals("InnerColor")) {
 226                         phrase += " inner color";
 227                         Color c = JColorChooser.showDialog(_vp, phrase,
 228                                         VARNAConfig.BASE_INNER_COLOR_DEFAULT);
 229                         if (c != null) {
 230                                 listBase = listSwitchType(_type);
 231                                 for (int i = 0; i < listBase.size(); i++) {
 232                                         _vp.getRNA().get_listeBases().get(listBase.get(i))
 233                                                         .getStyleBase().setBaseInnerColor(c);
 234                                 }
 235                                 _vp.repaint();
 236                         }
 237                 } else if (_color.equals("OutlineColor")) {
 238                         phrase += " outline color";
 239                         Color c = JColorChooser.showDialog(_vp, phrase,
 240                                         VARNAConfig.BASE_OUTLINE_COLOR_DEFAULT);
 241                         if (c != null) {
 242                                 listBase = listSwitchType(_type);
 243                                 for (int i = 0; i < listBase.size(); i++) {
 244                                         _vp.getRNA().get_listeBases().get(listBase.get(i))
 245                                                         .getStyleBase().setBaseOutlineColor(c);
 246                                 }
 247                                 _vp.repaint();
 248                         }
 249                 } else if (_color.equals("NameColor")) {
 250                         phrase += " name color";
 251                         Color c = JColorChooser.showDialog(_vp, phrase,
 252                                         VARNAConfig.BASE_NAME_COLOR_DEFAULT);
 253                         if (c != null) {
 254                                 listBase = listSwitchType(_type);
 255                                 for (int i = 0; i < listBase.size(); i++) {
 256                                         _vp.getRNA().get_listeBases().get(listBase.get(i))
 257                                                         .getStyleBase().setBaseNameColor(c);
 258                                 }
 259                                 _vp.repaint();
 260                         }
 261                 } else if (_color.equals("NumberColor")) {
 262                         phrase += " number color";
 263                         Color c = JColorChooser.showDialog(_vp, phrase,
 264                                         VARNAConfig.BASE_NUMBER_COLOR_DEFAULT);
 265                         if (c != null) {
 266                                 listBase = listSwitchType(_type);
 267                                 for (int i = 0; i < listBase.size(); i++) {
 268                                         _vp.getRNA().get_listeBases().get(listBase.get(i))
 269                                                         .getStyleBase().setBaseNumberColor(c);
 270                                 }
 271                                 _vp.repaint();
 272                         }
 273                 } else if (_color.equals("BPColor")) {
 274                         phrase += " base-pair color";
 275                         Color c = JColorChooser.showDialog(_vp, phrase,
 276                                         VARNAConfig.BASE_NUMBER_COLOR_DEFAULT);
 277                         if (c != null) {
 278                                 listBase = listSwitchType(_type);
 279                                 for (int i = 0; i < listBase.size(); i++)
 280                                 {
 281                                         for (ModeleBP msbp:_vp.getRNA().getBPsAt(listBase.get(i)))
 282                                         {
 283                                                 if (msbp!=null) {
 284                                                         msbp.getStyle().setCustomColor(c);
 285                                                 }
 286                                         }
 287                                 }
 288                                 _vp.repaint();
 289                         }
 290                 } else if (_color.equals("BPColor")) {
 291                         phrase += " base-pair color";
 292                         Color c = JColorChooser.showDialog(_vp, phrase,
 293                                         VARNAConfig.BASE_NUMBER_COLOR_DEFAULT);
 294                         if (c != null) {
 295                                 listBase = listSwitchType(_type);
 296                                 for (int i = 0; i < listBase.size(); i++) {
 297                                         ModeleBase mb = _vp.getRNA().get_listeBases().get(
 298                                                         listBase.get(i));
 299                                         if (mb.getElementStructure() != -1) {
 300                                                 mb.getStyleBP().getStyle().setCustomColor(c);
 301                                         }
 302                                 }
 303                                 _vp.repaint();
 304                         }
 305                 } else if (_color.equals("BPThickness")) {
 306                         listBase = listSwitchType(_type);
 307                         // System.out.println(listBase.size());
 308                         ArrayList<ModeleBP> styleBPs = new ArrayList<ModeleBP>();
 309                         for (int i = 0; i < listBase.size(); i++) {
 310                                 ModeleBase mb = _vp.getRNA().get_listeBases().get(
 311                                                 listBase.get(i));
 312                                 if (mb.getElementStructure() != -1) {
 313                                         styleBPs.add(mb.getStyleBP());
 314                                 }
 315                         }
 316                         VueBPThickness vbpt = new VueBPThickness(_vp, styleBPs);
 317                         if (JOptionPane.showConfirmDialog(_vp, vbpt.getPanel(),
 318                                         "Set base pair(s) thickness", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) {
 319                                 vbpt.restoreThicknesses();
 320                                 _vp.repaint();
 321                         }
 322                 } else
 323                         return false;
 324                 return true;
 325         }
 326
 327         private ArrayList<Integer> listSwitchType(String _type) {
 328                 if (_type.equals("helix"))
 329                         return _vp.getRNA().findHelix(_vp.getNearestBase());
 330                 if (_type.equals("current")) {
 331                         return _vp.getSelectionIndices();
 332                 }
 333                 if (_type.equals("allBases")) {
 334                         return _vp.getRNA().findAll();
 335                 }
 336                 if (_type.equals("loop1")) {
 337                         return _vp.getRNA().findLoopForward(_vp.getNearestBase());
 338                 }
 339                 if (_type.equals("loop2")) {
 340                         return _vp.getRNA().findLoopBackward(_vp.getNearestBase());
 341                 }
 342                 if (_type.equals("stem"))
 343                         return _vp.getRNA().findStem(_vp.getNearestBase());
 344                 if (_type.equals("base")) {
 345                         ArrayList<Integer> list = new ArrayList<Integer>();
 346                         list.add(_vp.getNearestBase());
 347                         return list;
 348                 }
 349                 if (_type.equals("basepair") || _type.equals("bpcolor")
 350                                 || _type.equals("bp")) {
 351                         ArrayList<Integer> list = new ArrayList<Integer>();
 352                         int i = _vp.getNearestBase();
 353                         list.add(i);
 354                         ModeleBase mb = _vp.getRNA().get_listeBases().get(i);
 355                         int j = mb.getElementStructure();
 356                         if (mb.getElementStructure() != -1) {
 357                                 list.add(i);
 358                                 list.add(j);
 359                         }
 360                         return list;
 361                 }
 362                 if (_type.equals("5'"))
 363                         return _vp.getRNA().findNonPairedBaseGroup(_vp.getNearestBase());
 364                 if (_type.equals("3'"))
 365                         return _vp.getRNA().findNonPairedBaseGroup(_vp.getNearestBase());
 366                 if (_type.equals("bulge"))
 367                         return _vp.getRNA().findNonPairedBaseGroup(_vp.getNearestBase());
 368                 if (_type.equals("all"))
 369                         return _vp.getRNA().findAll();
 370                 return new ArrayList<Integer>();
 371         }
 372
 373         private boolean optionLoop() {
 374                 return colorBases();
 375         }
 376
 377         private boolean optionBase() {
 378                 if (_type.equals("baseChar")) {
 379                         _vp.getVARNAUI().UISetBaseCharacter();
 380                         return true;
 381                 } else {
 382                         return colorBases();
 383                 }
 384         }
 385
 386         private boolean optionBasePair() {
 387                 if (_type.equals("basepair")) {
 388                         _vp.getVARNAUI().UIEditBasePair();
 389                         return true;
 390                 } else if (_type.equals("bpcolor")) {
 391                         _vp.getVARNAUI().UIColorBasePair();
 392                         return true;
 393                 } else if (_type.equals("thickness")) {
 394                         _vp.getVARNAUI().UIThicknessBasePair();
 395                         return true;
 396                 }
 397                 return false;
 398         }
 399
 400
 401
 402         private boolean optionView() {
 403                 if (_type.equals("background")) {
 404                         _vp.getVARNAUI().UISetBackground();
 405                 } else if (_type.equals("shownc")) {
 406                         _vp.getVARNAUI().UIToggleShowNCBP();
 407                 } else if (_type.equals("showbackbone")) {
 408                         _vp.getVARNAUI().UIToggleDrawBackbone();
 409                 } else if (_type.equals("shownp")) {
 410                         _vp.getVARNAUI().UIToggleShowNonPlanar();
 411                 } else if (_type.equals("spaceBetweenBases")) {
 412                         _vp.getVARNAUI().UISetSpaceBetweenBases();
 413                 } else if (_type.equals("bpheightincrement")) {
 414                         _vp.getVARNAUI().UISetBPHeightIncrement();
 415                 } else if (_type.equals("borderSize")) {
 416                         _vp.getVARNAUI().UISetBorder();
 417                 } else if (_type.startsWith("zoom")) {
 418                         if (_type.equals("zoom")) {
 419                                 _vp.getVARNAUI().UICustomZoom();
 420                         } else {
 421                                 String factor = _type.substring("zoom".length());
 422                                 double pc = Integer.parseInt(factor);
 423                                 pc /= 100.0;
 424                                 _vp.setZoom(new Double(pc));
 425                                 _vp.repaint();
 426                         }
 427                 } else if (_type.equals("rotation")) {
 428                         _vp.getVARNAUI().UIGlobalRotation();
 429                 } else if (_type.equals("rescale")) {
 430                         _vp.getVARNAUI().UIGlobalRescale();
 431                 } else
 432                         return false;
 433                 return true;
 434         }
 435
 436
 437         private boolean optionTitle() {
 438                 if (_type.equals("titleDisplay")) {
 439                         _vp.getVARNAUI().UISetTitleFont();
 440                 } else if (_type.equals("setTitle")) {
 441                         _vp.getVARNAUI().UISetTitle();
 442                 } else if (_type.equals("titleColor")) {
 443                         _vp.getVARNAUI().UISetTitleColor();
 444                 } else
 445                         return false;
 446                 return true;
 447         }
 448
 449
 450         private boolean optionColorMap() {
 451                 if (_type.equals("toggleshowcolormap")) {
 452                         _vp.getVARNAUI().UIToggleColorMap();
 453                 } else  if (_type.equals("colormapcaption")) {
 454                         _vp.getVARNAUI().UISetColorMapCaption();
 455                 } else  if (_type.equals("colormapstyle")) {
 456                         _vp.getVARNAUI().UISetColorMapStyle();
 457                 } else  if (_type.equals("colormaploadvalues")) {
 458                         _vp.getVARNAUI().UILoadColorMapValues();
 459                 } else  if (_type.equals("colormapvalues")) {
 460                         _vp.getVARNAUI().UISetColorMapValues();
 461                 } else
 462                         return false;
 463                 return true;
 464         }
 465
 466         private boolean optionRNADisplay() {
 467                 // les options d'affichages generales
 468                 if (_type.equals("gaspin")) {
 469                         _vp.getVARNAUI().UIToggleGaspinMode();
 470                 } else if (_type.equals("backbone")) {
 471                         _vp.getVARNAUI().UISetBackboneColor();
 472                 } else if (_type.equals("bonds")) {
 473                         Color c = JColorChooser.showDialog(_vp, "Choose new bonds color",
 474                                         _vp.getBackground());
 475                         if (c != null) {
 476                                 _vp.setDefaultBPColor(c);
 477                                 _vp.repaint();
 478                         }
 479                 } else if (_type.equals("basecolorforBP")) {
 480                         if (_source != null) {
 481                                 if (_source instanceof JCheckBoxMenuItem) {
 482                                         JCheckBoxMenuItem check = (JCheckBoxMenuItem) _source;
 483                                         _vp.setUseBaseColorsForBPs(check.getState());
 484                                         _vp.repaint();
 485                                 }
 486                         }
 487                 } else if (_type.equals("bpstyle")) {
 488                         _vp.getVARNAUI().UISetBPStyle();
 489                 } else if (_type.equals("specialbasecolored")) {
 490                         _vp.getVARNAUI().UIToggleColorSpecialBases();
 491                 } else if (_type.equals("showwarnings")) {
 492                         _vp.getVARNAUI().UIToggleShowWarnings();
 493                 } else if (_type.equals("dashbasecolored")) {
 494                         _vp.getVARNAUI().UIToggleColorGapsBases();
 495                 } else if (_type.equals("numPeriod")) {
 496                         _vp.getVARNAUI().UISetNumPeriod();
 497                 } else if (_type.equals("eachKind")) {
 498                         if (_vp.getRNA().get_listeBases() != null) {
 499                                 _vp.getVARNAUI().UIBaseTypeColor();
 500                         } else {
 501                                 _vp.emitWarning("No base");
 502                         }
 503                 } else if (_type.equals("eachCouple")) {
 504                         if (_vp.getRNA().get_listeBases() != null
 505                                         && _vp.getRNA().get_listeBases().size() != 0) {
 506                                 _vp.getVARNAUI().UIBasePairTypeColor();
 507                         } else {
 508                                 _vp.emitWarning("No base");
 509                         }
 510                 } else if (_type.equals("eachBase")) {
 511                         if (_vp.getRNA().get_listeBases() != null
 512                                         && _vp.getRNA().get_listeBases().size() != 0) {
 513                                 _vp.getVARNAUI().UIBaseAllColor();
 514                         } else {
 515                                 _vp.emitWarning("No base");
 516                         }
 517                 } else if (_type.equals("specialBasesColor")) {
 518                         _vp.getVARNAUI().UIPickSpecialBasesColor();
 519                 } else if (_type.equals("dashBasesColor")) {
 520                         _vp.getVARNAUI().UIPickGapsBasesColor();
 521                 } else
 522                         return colorBases();
 523                 return true;
 524         }
 525
 526         private boolean optionImport() {
 527                 if (_type.equals("userInput")) {
 528                         try {
 529                                 _vp.getVARNAUI().UIManualInput();
 530                         } catch (ParseException e1) {
 531                                 errorDialog(e1);
 532                         } catch (ExceptionNonEqualLength e2) {
 533                                 errorDialog(e2);
 534                         }
 535                 } else if (_type.equals("file")) {
 536                         try {
 537                                 _vp.getVARNAUI().UIFile();
 538                         } catch (ExceptionNonEqualLength e1) {
 539                                 errorDialog(e1);
 540                         }
 541                 } else if (_type.equals("print")) {
 542                         _vp.getVARNAUI().UIPrint();
 543                 } else if (_type.equals("about")) {
 544                         _vp.getVARNAUI().UIAbout();
 545                 } else
 546                         return false;
 547                 return true;
 548         }
 549
 550         private boolean optionRedraw() {
 551                 if (_type.equals("reset")) {
 552                         _vp.getVARNAUI().UIReset();
 553                 } else if (_type.equals("circular")) {
 554                         _vp.getVARNAUI().UICircular();
 555                 } else if (_type.equals("radiate")) {
 556                         _vp.getVARNAUI().UIRadiate();
 557                 } else if (_type.equals("naview")) {
 558                         _vp.getVARNAUI().UINAView();
 559                 } else if (_type.equals("varnaview")) {
 560                         _vp.getVARNAUI().UIVARNAView();
 561                 } else if (_type.equals("motifview")) {
 562                         _vp.getVARNAUI().UIMOTIFView();
 563                 } else if (_type.equals("line")) {
 564                         _vp.getVARNAUI().UILine();
 565                 } else if (_type.equals("flat")) {
 566                         _vp.getVARNAUI().UIToggleFlatExteriorLoop();
 567                 } else
 568                         return false;
 569                 return true;
 570         }
 571
 572         private boolean optionExport() {
 573                 if (_type.equals("saveas")) {
 574                         try {
 575                                 _vp.getVARNAUI().UISaveAs();
 576                         } catch (ExceptionExportFailed e1) {
 577                                 errorDialog(e1);
 578                         } catch (ExceptionPermissionDenied e1) {
 579                                 errorDialog(e1);
 580                         }
 581                 } else if (_type.equals("dbn")) {
 582                         try {
 583                                 _vp.getVARNAUI().UISaveAsDBN();
 584                         } catch (ExceptionExportFailed e) {
 585                                 errorDialog(e);
 586                         } catch (ExceptionPermissionDenied e) {
 587                                 errorDialog(e);
 588                         }
 589                 } else if (_type.equals("bpseq")) {
 590                         try {
 591                                 _vp.getVARNAUI().UISaveAsBPSEQ();
 592                         } catch (ExceptionExportFailed e) {
 593                                 errorDialog(e);
 594                         } catch (ExceptionPermissionDenied e) {
 595                                 errorDialog(e);
 596                         }
 597                 } else if (_type.equals("ct")) {
 598                         try {
 599                                 _vp.getVARNAUI().UISaveAsCT();
 600                         } catch (ExceptionExportFailed e) {
 601                                 errorDialog(e);
 602                         } catch (ExceptionPermissionDenied e) {
 603                                 errorDialog(e);
 604                         }
 605                 } else if (_type.equals("eps")) {
 606                         try {
 607                                 _vp.getVARNAUI().UIExportEPS();
 608                         } catch (ExceptionWritingForbidden e1) {
 609                                 errorDialog(e1);
 610                         } catch (ExceptionExportFailed e) {
 611                                 errorDialog(e);
 612                         }
 613                 } else if (_type.equals("tikz")) {
 614                         try {
 615                                 _vp.getVARNAUI().UIExportTIKZ();
 616                         } catch (ExceptionWritingForbidden e1) {
 617                                 errorDialog(e1);
 618                         } catch (ExceptionExportFailed e) {
 619                                 errorDialog(e);
 620                         }
 621                 } else if (_type.equals("xfig")) {
 622                         try {
 623                                 _vp.getVARNAUI().UIExportXFIG();
 624                         } catch (ExceptionWritingForbidden e1) {
 625                                 errorDialog(e1);
 626                         } catch (ExceptionExportFailed e) {
 627                                 errorDialog(e);
 628                         }
 629                 } else if (_type.equals("svg")) {
 630                         try {
 631                                 _vp.getVARNAUI().UIExportSVG();
 632                         } catch (ExceptionWritingForbidden e1) {
 633                                 errorDialog(e1);
 634                         } catch (ExceptionExportFailed e) {
 635                                 errorDialog(e);
 636                         }
 637                 } else if (_type.equals("jpeg")) {
 638                         try {
 639                                 _vp.getVARNAUI().UIExportJPEG();
 640                         } catch (ExceptionJPEGEncoding e1) {
 641                                 errorDialog(e1);
 642                         } catch (ExceptionExportFailed e1) {
 643                                 errorDialog(e1);
 644                         }
 645                 } else if (_type.equals("png")) {
 646                         try {
 647                                 _vp.getVARNAUI().UIExportPNG();
 648                         } catch (ExceptionExportFailed e1) {
 649                                 errorDialog(e1);
 650                         }
 651                 } else
 652                         return false;
 653                 return true;
 654         }
 655
 656         /**
 657          * Return the extension of a file, it means the string after the last dot of
 658          * the file name
 659          *
 660          * @param f
 661          *            The file
 662          * @return <code>null</code> if the file name have no dot<br>
 663          *         <code>ext</code> if the file name contains a dot
 664          */
 665         public String getExtension(File f) {
 666                 String s = f.getName();
 667                 return getExtension(s);
 668         }
 669
 670         /**
 671          * Return the extension of a string, it means the string after the last dot
 672          * of the path
 673          *
 674          * @param s
 675          *            The strnig o the path
 676          * @return <code>null</code> if the path have no dot<br>
 677          *         <code>ext</code> if the path contains a dot
 678          */
 679         public String getExtension(String s) {
 680                 String ext = null;
 681                 int i = s.lastIndexOf('.');
 682
 683                 if (i > 0 && i < s.length() - 1) {
 684                         ext = s.substring(i + 1).toLowerCase();
 685                 }
 686                 return ext;
 687         }
 688
 689         /**
 690          * Open an error message dialog with the exception message
 691          *
 692          * @param e1
 693          *            The <code>Exception</code>
 694          */
 695         public void errorDialog(Exception e1) {
 696                 if (_vp.isErrorsOn())
 697                         JOptionPane.showMessageDialog(_vp, e1.getMessage(), "VARNA Error",
 698                                         JOptionPane.ERROR_MESSAGE);
 699         }
 700
 701         public void onStructureRedrawn() {
 702                 // TODO Auto-generated method stub
 703
 704         }
 705
 706         public void onWarningEmitted(String s) {
 707                 if (_vp.isErrorsOn())
 708                         JOptionPane.showMessageDialog(_vp,s, "VARNA Warning",
 709                                         JOptionPane.ERROR_MESSAGE);
 710         }
 711
 712         public void onLoad(String path) {
 713                 // TODO Auto-generated method stub
 714
 715         }
 716
 717         public void onLoaded() {
 718                 // TODO Auto-generated method stub
 719
 720         }
 721
 722         public void onUINewStructure(VARNAConfig v, RNA r) {
 723                 // TODO Auto-generated method stub
 724
 725         }
 726
 727         public void onZoomLevelChanged() {
 728                 // TODO Auto-generated method stub
 729
 730         }
 731
 732         public void onTranslationChanged() {
 733                 // TODO Auto-generated method stub
 734
 735         }
 736
 737
 738 }