srcjar/fr/orsay/lri/varna/controlers/ControleurClicMovement.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.controlers;
  19
  20 import java.awt.Component;
  21 import java.awt.Point;
  22 import java.awt.Rectangle;
  23 import java.awt.event.MouseEvent;
  24 import java.awt.event.MouseListener;
  25 import java.awt.event.MouseMotionListener;
  26 import java.awt.geom.Point2D;
  27 import java.util.ArrayList;
  28 import java.util.Collection;
  29 import java.util.Vector;
  30
  31 import javax.swing.JMenu;
  32 import javax.swing.JMenuItem;
  33 import javax.swing.event.PopupMenuEvent;
  34 import javax.swing.event.PopupMenuListener;
  35
  36 import fr.orsay.lri.varna.VARNAPanel;
  37 import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
  38 import fr.orsay.lri.varna.models.annotations.TextAnnotation;
  39 import fr.orsay.lri.varna.models.rna.ModeleBase;
  40 import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
  41 import fr.orsay.lri.varna.models.rna.ModeleBasesComparison;
  42 import fr.orsay.lri.varna.models.rna.ModeleBP;
  43 import fr.orsay.lri.varna.models.rna.RNA;
  44
  45
  46 /**
  47  * Controller of the mouse click
  48  *
  49  * @author darty
  50  *
  51  */
  52 public class ControleurClicMovement implements MouseListener,
  53                 MouseMotionListener, PopupMenuListener {
  54         private VARNAPanel _vp;
  55         private boolean _presenceMenuSelection;
  56         private JMenu _submenuSelection;
  57         public Point _spawnPoint;
  58         public Point _initialPoint;
  59         public Point _prevPoint;
  60         public Point _currentPoint;
  61
  62         public static final double MIN_SELECTION_DISTANCE = 40.0;
  63         public static final double HYSTERESIS_DISTANCE = 10.0;
  64
  65         private ModeleBase _selectedBase = null;
  66
  67
  68         public enum MouseStates {
  69                 NONE,
  70                 MOVE_ELEMENT,
  71                 MOVE_OR_SELECT_ELEMENT,
  72                 SELECT_ELEMENT,
  73                 SELECT_REGION_OR_UNSELECT,
  74                 SELECT_REGION,
  75                 CREATE_BP,
  76                 POPUP_MENU,
  77                 MOVE_ANNOTATION,
  78         };
  79         private MouseStates _currentState = MouseStates.NONE;
  80
  81
  82
  83         public ControleurClicMovement(VARNAPanel _vuep) {
  84                 _vp = _vuep;
  85                 _vp.getPopup().addPopupMenuListener(this);
  86                 _presenceMenuSelection = false;
  87         }
  88
  89         public void mouseClicked(MouseEvent arg0) {
  90         }
  91
  92         public void mouseEntered(MouseEvent arg0) {
  93         }
  94
  95         public void mouseExited(MouseEvent arg0) {
  96         }
  97
  98         public void mousePressed(MouseEvent arg0)
  99         {
 100                 _vp.requestFocus();
 101                 boolean button1 = (arg0.getButton() == MouseEvent.BUTTON1);
 102                 boolean button2 = (arg0.getButton() == MouseEvent.BUTTON2);
 103                 boolean button3 = (arg0.getButton() == MouseEvent.BUTTON3);
 104                 boolean shift = arg0.isShiftDown();
 105                 boolean ctrl = arg0.isControlDown();
 106                 boolean alt = arg0.isAltDown();
 107                 _vp.removeSelectedAnnotation();
 108                 if (button1 && !ctrl && !alt && !shift)
 109                 {
 110                         if (_vp.isModifiable())
 111                         {
 112                                 _currentState = MouseStates.MOVE_OR_SELECT_ELEMENT;
 113                                 if (_vp.getRealCoords() != null
 114                                                 && _vp.getRealCoords().length != 0
 115                                                 && _vp.getRNA().get_listeBases().size() != 0)
 116                                 {
 117                                         _selectedBase = _vp.getNearestBase(arg0.getX(),arg0.getY(),false,false);
 118                                         TextAnnotation selectedAnnotation = _vp.getNearestAnnotation(arg0.getX(), arg0.getY());
 119                                         _initialPoint = new Point(arg0.getX(),arg0.getY());
 120                                         _currentPoint = new Point(_initialPoint);
 121                                         _prevPoint = new Point(_initialPoint);
 122                                         if (_selectedBase != null)
 123                                         {
 124                                                 if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_RADIATE)
 125                                                 {
 126                                                         _vp.highlightSelectedBase(_selectedBase);
 127                                                 } else {
 128                                                         if (!_vp.getSelectionIndices().contains(_selectedBase.getIndex()))
 129                                                         {
 130                                                                 _vp.highlightSelectedBase(_selectedBase);
 131                                                         }
 132                                                         else
 133                                                         {
 134                                                           // Otherwise, keep current selection as it is and move it
 135                                                         }
 136                                                 }
 137                                         }
 138                                         else
 139                                         {
 140                                                 if (selectedAnnotation != null)
 141                                                 {
 142                                                         _currentState = MouseStates.MOVE_ANNOTATION;
 143                                                         _vp.set_selectedAnnotation(selectedAnnotation);
 144                                                         _vp.highlightSelectedAnnotation();
 145                                                 }
 146                                                 else
 147                                                 {
 148                                                         _vp.clearSelection();
 149                                                         _selectedBase = null;
 150                                                         _currentState = MouseStates.SELECT_REGION_OR_UNSELECT;
 151                                                         _initialPoint = new Point(arg0.getX(),arg0.getY());
 152                                                         _prevPoint = new Point(_initialPoint);
 153                                                         _currentPoint = new Point(_initialPoint);
 154                                                 }
 155                                         }
 156                                 }
 157                         }
 158                 }
 159                 else if (button1 && ctrl && !alt && !shift)
 160                 {
 161                         _selectedBase = _vp.getNearestBase(arg0.getX(),arg0.getY(),false,false);
 162                         if (_selectedBase != null)
 163                         {
 164                                 _vp.clearSelection();
 165                                 _currentState = MouseStates.CREATE_BP;
 166                                 _vp.highlightSelectedBase(_selectedBase);
 167                                 _vp.setOriginLink(_vp.logicToPanel(_selectedBase.getCoords()));
 168                                 _initialPoint = new Point(arg0.getX(),arg0.getY());
 169                                 _currentPoint = new Point(_initialPoint);
 170                         }
 171                 }
 172                 else if (button1 && !ctrl && !alt && shift)
 173                 {
 174                         _currentState = MouseStates.SELECT_ELEMENT;
 175                         _initialPoint = new Point(arg0.getX(),arg0.getY());
 176                         _currentPoint = new Point(_initialPoint);
 177                 }
 178                 else if (button3)
 179                 {
 180                         _currentState = MouseStates.POPUP_MENU;
 181                         if (_presenceMenuSelection) {
 182                                 _vp.getPopupMenu().removeSelectionMenu();
 183                         }
 184                         if ((_vp.getRealCoords() != null) && _vp.getRNA().get_listeBases().size() != 0) {
 185                                 updateNearestBase(arg0);
 186                                 // on insere dans le menu les nouvelles options
 187                                 addMenu(arg0);
 188                                 if (_vp.get_selectedAnnotation() != null)
 189                                         _vp.highlightSelectedAnnotation();
 190                         }
 191                         // affichage du popup menu
 192                         if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_LINEAR) {
 193                                 _vp.getPopup().get_rotation().setEnabled(false);
 194                         } else {
 195                                 _vp.getPopup().get_rotation().setEnabled(true);
 196                         }
 197                         _vp.getPopup().updateDialog();
 198                         _vp.getPopup().show(_vp, arg0.getX(), arg0.getY());
 199                 }
 200                 _vp.repaint();
 201         }
 202
 203         public void mouseDragged(MouseEvent me) {
 204                 if ((_currentState == MouseStates.MOVE_OR_SELECT_ELEMENT)||(_currentState == MouseStates.MOVE_ELEMENT))
 205                 {
 206                         _vp.lockScrolling();
 207
 208                         _currentState = MouseStates.MOVE_ELEMENT;
 209                                 // si on deplace la souris et qu'une base est selectionnée
 210                                 if (_selectedBase != null) {
 211                                         if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_RADIATE) {
 212                                                 _vp.highlightSelectedStem(_selectedBase);
 213                                                 // dans le cas radiale on deplace une helice
 214                                                 _vp.getVARNAUI().UIMoveHelixAtom(_selectedBase.getIndex(), _vp.panelToLogicPoint(new Point2D.Double(me.getX(), me.getY())));
 215                                         } else {
 216                                                 // dans le cas circulaire naview ou line on deplace une base
 217                                                 _currentPoint = new Point(me.getX(), me.getY());
 218                                                 moveSelection(_prevPoint,_currentPoint);
 219                                                 _prevPoint = new Point(_currentPoint);
 220                                         }
 221                                         _vp.repaint();
 222                                 }
 223                 }
 224                 else if (_currentState == MouseStates.MOVE_ANNOTATION)
 225                 {
 226                         if (_vp.get_selectedAnnotation()!=null)
 227                         {
 228                                 Point2D.Double p = _vp.panelToLogicPoint(new Point2D.Double(me.getX(), me.getY()));
 229                                 _vp.get_selectedAnnotation().setAncrage(p.x,p.y);
 230                                 _vp.repaint();
 231                         }
 232                 }
 233                 else if ((_currentState == MouseStates.SELECT_ELEMENT)||(_currentState == MouseStates.SELECT_REGION_OR_UNSELECT))
 234                 {
 235                         if (_initialPoint.distance(me.getX(),me.getY())>HYSTERESIS_DISTANCE)
 236                                 _currentState = MouseStates.SELECT_REGION;
 237                 }
 238                 else if (_currentState == MouseStates.SELECT_REGION)
 239                 {
 240                         _currentPoint = new Point(me.getX(),me.getY());
 241                         int minx = Math.min(_currentPoint.x, _initialPoint.x);
 242                         int miny = Math.min(_currentPoint.y, _initialPoint.y);
 243                         int maxx = Math.max(_currentPoint.x, _initialPoint.x);
 244                         int maxy = Math.max(_currentPoint.y, _initialPoint.y);
 245                         _vp.setSelectionRectangle(new Rectangle(minx,miny,maxx-minx,maxy-miny));
 246                 }
 247                 else if (_currentState == MouseStates.CREATE_BP)
 248                 {
 249                         if (_initialPoint.distance(me.getX(),me.getY())>HYSTERESIS_DISTANCE)
 250                         {
 251                                 ModeleBase newSelectedBase = _vp.getNearestBase(me.getX(),me.getY(),false,false);
 252                                 _vp.setHoverBase(newSelectedBase);
 253                                 if (newSelectedBase==null)
 254                                 {
 255                                         _vp.setDestinationLink(new Point2D.Double(me.getX(),me.getY()));
 256                                         _vp.clearSelection();
 257                                         _vp.addToSelection(_selectedBase.getIndex());
 258                                 }
 259                                 else
 260                                 {
 261                                         ModeleBase mborig = _selectedBase;
 262                                         _vp.clearSelection();
 263                                         _vp.addToSelection(newSelectedBase.getIndex());
 264                                         _vp.addToSelection(mborig.getIndex());
 265                                         _vp.setDestinationLink(_vp.logicToPanel(newSelectedBase.getCoords()));
 266                                 }
 267                                 _vp.repaint();
 268                         }
 269
 270                 }
 271         }
 272
 273
 274         public void mouseReleased(MouseEvent arg0) {
 275                 if (arg0.getButton() == MouseEvent.BUTTON1)
 276                 {
 277                         _vp.fireBaseClicked(_selectedBase, arg0);
 278                         //System.out.println(""+_currentState);
 279
 280                         if (_currentState == MouseStates.MOVE_ELEMENT)
 281                         {
 282                                 _vp.clearSelection();
 283                                 _selectedBase = null;
 284                                 _vp.unlockScrolling();
 285                                 _vp.removeSelectedAnnotation();
 286                         }
 287                         else if (_currentState == MouseStates.SELECT_REGION_OR_UNSELECT)
 288                         {
 289                                 _vp.clearSelection();
 290                                 _selectedBase = null;
 291                                 _vp.removeSelectedAnnotation();
 292                         }
 293                         else if (_currentState == MouseStates.SELECT_ELEMENT)
 294                         {
 295                                 if (_vp.getRealCoords() != null
 296                                                 && _vp.getRealCoords().length != 0
 297                                                 && _vp.getRNA().get_listeBases().size() != 0)
 298                                         {
 299                                                 int selectedIndex = _vp.getNearestBaseIndex(arg0.getX(),arg0.getY(),false,false);
 300                                                 if (selectedIndex !=-1)
 301                                                 {
 302                                                         _vp.toggleSelection(selectedIndex);
 303                                                 }
 304                                         }
 305                                 _selectedBase = null;
 306                         }
 307                         else if (_currentState == MouseStates.SELECT_REGION)
 308                         {
 309                           _vp.removeSelectionRectangle();
 310                         }
 311                         else if (_currentState == MouseStates.CREATE_BP)
 312                         {
 313                                 if (_initialPoint.distance(arg0.getX(),arg0.getY())>HYSTERESIS_DISTANCE)
 314                                 {
 315                                         int selectedIndex = _vp.getNearestBaseIndex(arg0.getX(),arg0.getY(),false,false);
 316                                         if (selectedIndex>=0)
 317                                         {
 318                                                 ModeleBase mb = _vp.getNearestBase(arg0.getX(),arg0.getY(),false,false);
 319                                                 ModeleBase mborig = _selectedBase;
 320                                                 ModeleBP msbp = new ModeleBP(mb,mborig);
 321                                                 if (mb!=mborig)
 322                                                 {
 323                                                   _vp.getVARNAUI().UIAddBP(mb.getIndex(),mborig.getIndex(),msbp);
 324                                                 }
 325                                         }
 326                                 }
 327                                 _vp.removeLink();
 328                                 _vp.clearSelection();
 329                                 _vp.repaint();
 330                         }
 331                         else
 332                         {
 333                                 _vp.clearSelection();
 334                         }
 335
 336                 }
 337                 _currentState = MouseStates.NONE;
 338                 _vp.repaint();
 339         }
 340
 341
 342         private void addMenu(MouseEvent arg0) {
 343                 // creation du menu
 344                 _submenuSelection = new JMenu("Selection");
 345                 addCurrent();
 346                 // ajout des option sur base
 347                 addMenuBase();
 348                 // ajout des option sur paire de base
 349                 if (_vp.getRNA().get_listeBases().get(_vp.getNearestBase())
 350                                 .getElementStructure() != -1) {
 351                         addMenuBasePair();
 352                 }
 353
 354                 // detection renflement
 355                 detectBulge();
 356                 // detection 3'
 357                 detect3Prime();
 358                 // detection 5'
 359                 detect5Prime();
 360                 // detection boucle
 361                 detectLoop();
 362                 // detection d'helice
 363                 detectHelix();
 364                 // detection tige
 365                 detectStem();
 366                 // Ajout de toutes bases
 367                 addAllBase();
 368                 // detection d'annotation
 369                 detectAnnotation(arg0);
 370
 371                 _vp.getPopup().addSelectionMenu(_submenuSelection);
 372                 _presenceMenuSelection = true;
 373         }
 374
 375         private void detectAnnotation(MouseEvent arg0) {
 376                 if (_vp.getListeAnnotations().size() != 0) {
 377                         double dist = Double.MAX_VALUE;
 378                         double d2;
 379                         Point2D.Double position;
 380                         for (TextAnnotation textAnnot : _vp.getListeAnnotations()) {
 381                                 // calcul de la distance
 382                                 position = textAnnot.getCenterPosition();
 383                                 position = _vp.transformCoord(position);
 384                                 d2 = Math.sqrt(Math.pow((position.x - arg0.getX()), 2)
 385                                                 + Math.pow((position.y - arg0.getY()), 2));
 386                                 // si la valeur est inferieur au minimum actuel
 387                                 if (dist > d2) {
 388                                         _vp.set_selectedAnnotation(textAnnot);
 389                                         dist = d2;
 390                                 }
 391                         }
 392                         _submenuSelection.addSeparator();
 393                         _vp.getPopup().addAnnotationMenu(_submenuSelection,true);
 394                 }
 395         }
 396
 397         private void detectBulge() {
 398                 int indiceB = _vp.getNearestBase();
 399                 ArrayList<Integer> indices = _vp.getRNA().findBulge(indiceB);
 400                 if ((indices.size() > 0)
 401                                 && (_vp.getRNA().getHelixCountOnLoop(_vp.getNearestBase()) == 2)) {
 402                         JMenu submenuBulge = new JMenu("Bulge");
 403                         submenuBulge.addChangeListener(new ControleurSelectionHighlight(
 404                                         new Vector<Integer>(indices), _vp, submenuBulge));
 405                         submenuBulge.setActionCommand("bulge");
 406                         if (!_vp.isModifiable())
 407                                 submenuBulge.setEnabled(false);
 408                         _vp.getPopupMenu().addColorOptions(submenuBulge);
 409                         _submenuSelection.add(submenuBulge);
 410                 }
 411         }
 412
 413         private void detectHelix() {
 414                 int indiceH = _vp.getNearestBase();
 415                 ArrayList<Integer> indices = _vp.getRNA().findHelix(indiceH);
 416                 if (indices.size() != 0) {
 417                         // ajout menu helice
 418                         JMenu submenuHelix = new JMenu("Helix");
 419                         submenuHelix.addChangeListener(new ControleurSelectionHighlight(
 420                                         new Vector<Integer>(indices), _vp, submenuHelix));
 421                         submenuHelix.setActionCommand("helix");
 422                         if (!_vp.isModifiable())
 423                                 submenuHelix.setEnabled(false);
 424                         _vp.getPopupMenu().addColorOptions(submenuHelix);
 425                         submenuHelix.addSeparator();
 426                         _vp.getPopupMenu().addAnnotationMenu(submenuHelix);
 427                         _submenuSelection.add(submenuHelix);
 428                 }
 429         }
 430
 431         private void detectStem() {
 432                 int indiceS = _vp.getNearestBase();
 433                 ArrayList<Integer> indices = _vp.getRNA().findStem(indiceS);
 434                 if (indices.size() > 0) {
 435                         JMenu submenuStem = new JMenu("Stem");
 436                         submenuStem.addChangeListener(new ControleurSelectionHighlight(
 437                                         new Vector<Integer>(indices), _vp, submenuStem));
 438                         submenuStem.setActionCommand("stem");
 439                         if (!_vp.isModifiable())
 440                                 submenuStem.setEnabled(false);
 441                         _vp.getPopupMenu().addColorOptions(submenuStem);
 442                         _submenuSelection.add(submenuStem);
 443                 }
 444         }
 445
 446         private void detect3Prime() {
 447                 // detection 3'
 448                 int indice3 = _vp.getNearestBase();
 449                 ArrayList<Integer> indices = _vp.getRNA().find3Prime(indice3);
 450                 if (indices.size() != 0) {
 451                         JMenu submenu3Prime = new JMenu("3'");
 452                         submenu3Prime.addChangeListener(new ControleurSelectionHighlight(
 453                                         new Vector<Integer>(indices), _vp, submenu3Prime));
 454                         submenu3Prime.setActionCommand("3'");
 455                         if (!_vp.isModifiable())
 456                                 submenu3Prime.setEnabled(false);
 457                         _vp.getPopupMenu().addColorOptions(submenu3Prime);
 458                         _submenuSelection.add(submenu3Prime);
 459                 }
 460         }
 461
 462         private void detect5Prime() {
 463                 int indice5 = _vp.getNearestBase();
 464                 ArrayList<Integer> indices = _vp.getRNA().find5Prime(indice5);
 465                 if (indices.size() != 0) {
 466                         JMenu submenu5Prime = new JMenu("5'");
 467                         submenu5Prime.addChangeListener(new ControleurSelectionHighlight(
 468                                         new Vector<Integer>(indices), _vp, submenu5Prime));
 469                         submenu5Prime.setActionCommand("5'");
 470                         if (!_vp.isModifiable())
 471                                 submenu5Prime.setEnabled(false);
 472                         _vp.getPopupMenu().addColorOptions(submenu5Prime);
 473                         _submenuSelection.add(submenu5Prime);
 474                 }
 475         }
 476
 477         private void detectLoop() {
 478                 int indexL = _vp.getNearestBase();
 479                 if (_vp.getRNA().get_listeBases().get(indexL).getElementStructure() == -1) {
 480                         ArrayList<Integer> listLoop = _vp.getRNA().findLoop(indexL);
 481                         JMenu submenuLoop = new JMenu("Loop");
 482                         submenuLoop.addChangeListener(new ControleurSelectionHighlight(
 483                                         listLoop, _vp, submenuLoop));
 484                         submenuLoop.setActionCommand("loop1");
 485                         if (!_vp.isModifiable())
 486                                 submenuLoop.setEnabled(false);
 487                         _vp.getPopupMenu().addColorOptions(submenuLoop);
 488                         submenuLoop.addSeparator();
 489                         _vp.getPopupMenu().addAnnotationMenu(submenuLoop);
 490                         _submenuSelection.add(submenuLoop);
 491                 } else {
 492                         ArrayList<Integer> listLoop1 = _vp.getRNA().findLoopForward(indexL);
 493                         if (listLoop1.size() > 0) {
 494                                 JMenu submenuLoop1 = new JMenu("Forward loop");
 495                                 submenuLoop1
 496                                                 .addChangeListener(new ControleurSelectionHighlight(
 497                                                                 listLoop1, _vp, submenuLoop1));
 498                                 submenuLoop1.setActionCommand("loop1");
 499                                 if (!_vp.isModifiable())
 500                                         submenuLoop1.setEnabled(false);
 501                                 _vp.getPopupMenu().addColorOptions(submenuLoop1);
 502                                 submenuLoop1.addSeparator();
 503                                 _vp.getPopupMenu().addAnnotationMenu(submenuLoop1);
 504                                 _submenuSelection.add(submenuLoop1);
 505                         }
 506                         ArrayList<Integer> listLoop2 = _vp.getRNA()
 507                                         .findLoopBackward(indexL);
 508                         if (listLoop2.size() > 0) {
 509                                 JMenu submenuLoop2 = new JMenu("Backward loop");
 510                                 submenuLoop2
 511                                                 .addChangeListener(new ControleurSelectionHighlight(
 512                                                                 listLoop2, _vp, submenuLoop2));
 513                                 submenuLoop2.setActionCommand("loop2");
 514                                 if (!_vp.isModifiable())
 515                                         submenuLoop2.setEnabled(false);
 516                                 _vp.getPopupMenu().addColorOptions(submenuLoop2);
 517                                 submenuLoop2.addSeparator();
 518                                 _vp.getPopupMenu().addAnnotationMenu(submenuLoop2);
 519                                 _submenuSelection.add(submenuLoop2);
 520                         }
 521                 }
 522         }
 523
 524         private void addCurrent() {
 525                 Collection<? extends ModeleBase> mbs = _vp.getSelection().getBases();
 526                 if (mbs.size()>0)
 527                 {
 528                 JMenu submenuAll = new JMenu("Current");
 529                 submenuAll.addChangeListener(new ControleurSelectionHighlight(
 530                                 mbs, _vp, submenuAll));
 531                 submenuAll.setActionCommand("current");
 532                 if (!_vp.isModifiable())
 533                         submenuAll.setEnabled(false);
 534                 _vp.getPopupMenu().addColorOptions(submenuAll);
 535                 _submenuSelection.add(submenuAll);
 536                 }
 537         }
 538
 539
 540         private void addMenuBase() {
 541                 JMenu submenuBase = new JMenu();
 542                 ModeleBase mb = _vp.getRNA().get_listeBases().get(_vp.getNearestBase());
 543                 if (mb instanceof ModeleBasesComparison) {
 544                         submenuBase.setText("Base #" + (mb.getBaseNumber()) + ":"
 545                                         + ((ModeleBasesComparison) mb).getBases());
 546                 } else {
 547                         submenuBase.setText("Base #" + (mb.getBaseNumber()) + ":"
 548                                         + ((ModeleBaseNucleotide) mb).getBase());
 549                 }
 550                 submenuBase.addChangeListener(new ControleurSelectionHighlight(mb
 551                                 .getIndex(), _vp, submenuBase));
 552                 submenuBase.setActionCommand("base");
 553                 // option disponible seulement en mode modifiable
 554                 if (!_vp.isModifiable())
 555                         submenuBase.setEnabled(false);
 556
 557                 JMenuItem baseChar = new JMenuItem("Edit base");
 558                 baseChar.setActionCommand("baseChar");
 559                 baseChar.addActionListener(_vp.getPopupMenu().get_controleurMenu());
 560                 submenuBase.add(baseChar);
 561                 _vp.getPopupMenu().addColorOptions(submenuBase);
 562                 submenuBase.addSeparator();
 563                 _vp.getPopupMenu().addAnnotationMenu(submenuBase);
 564                 _submenuSelection.add(submenuBase);
 565         }
 566
 567         private void addAllBase() {
 568                 ArrayList<Integer> indices = _vp.getRNA().findAll();
 569                 JMenu submenuAll = new JMenu("All");
 570                 submenuAll.addChangeListener(new ControleurSelectionHighlight(
 571                                 new Vector<Integer>(indices), _vp, submenuAll));
 572                 submenuAll.setActionCommand("all");
 573                 if (!_vp.isModifiable())
 574                         submenuAll.setEnabled(false);
 575                 _vp.getPopupMenu().addColorOptions(submenuAll);
 576                 _submenuSelection.add(submenuAll);
 577         }
 578
 579         private void addMenuBasePair() {
 580                         int indiceBP = _vp.getNearestBase();
 581                         ArrayList<Integer> indices = _vp.getRNA().findPair(indiceBP);
 582                         ModeleBase base = _vp.getRNA()
 583                                         .get_listeBases().get(_vp.getNearestBase());
 584                         if (base.getElementStructure() != -1) {
 585                                 JMenu submenuBasePair = new JMenu();
 586                                 ModeleBase partner = _vp
 587                                                 .getRNA().get_listeBases().get(
 588                                                                 base.getElementStructure());
 589                                 submenuBasePair
 590                                                 .addChangeListener(new ControleurSelectionHighlight(
 591                                                                 indices, _vp, submenuBasePair));
 592                                 submenuBasePair.setText("Base pair #("
 593                                                 + (Math.min(base.getBaseNumber(), partner
 594                                                                 .getBaseNumber()))
 595                                                 + ","
 596                                                 + (Math.max(base.getBaseNumber(), partner
 597                                                                 .getBaseNumber())) + ")");
 598                                 submenuBasePair.setActionCommand("bp");
 599                                 // option disponible seulement en mode modifiable
 600                                 if (!_vp.isModifiable())
 601                                         submenuBasePair.setEnabled(false);
 602
 603                                 JMenuItem basepair = new JMenuItem("Edit BP");
 604                                 basepair.setActionCommand("basepair");
 605                                 basepair.addActionListener(_vp.getPopupMenu()
 606                                                 .get_controleurMenu());
 607
 608                                 _vp.getPopupMenu().addColorOptions(submenuBasePair);
 609                                 Component[] comps = submenuBasePair.getMenuComponents();
 610                                 int offset = -1;
 611                                 for (int i = 0; i < comps.length; i++) {
 612                                         Component c = comps[i];
 613                                         if (c instanceof JMenuItem) {
 614                                                 JMenuItem jmi = (JMenuItem) c;
 615                                                 if (jmi.getActionCommand().contains(",BPColor")) {
 616                                                         offset = i;
 617                                                 }
 618                                         }
 619                                 }
 620                                 if (offset != -1) {
 621                                         submenuBasePair.insert(basepair, offset);
 622                                 } else {
 623                                         submenuBasePair.add(basepair);
 624                                 }
 625                                 _submenuSelection.add(submenuBasePair);
 626                         }
 627                 }
 628
 629         private void updateNearestBase(MouseEvent arg0) {
 630                 int i = _vp.getNearestBaseIndex(arg0.getX(),arg0.getY(),true,false);
 631                 if (i!=-1)
 632                         _vp.setNearestBase(i);
 633         }
 634
 635
 636
 637
 638         public void mouseMoved(MouseEvent arg0) {
 639                 _selectedBase = _vp.getNearestBase(arg0.getX(),arg0.getY());
 640                 TextAnnotation selectedAnnotation = _vp.getNearestAnnotation(arg0.getX(),arg0.getY());
 641                 _vp.setHoverBase(_selectedBase);
 642                 if (_selectedBase != null)
 643                 {
 644                 }
 645                 else if (selectedAnnotation!=null)
 646                 {
 647                         _vp.set_selectedAnnotation(selectedAnnotation);
 648                         _vp.highlightSelectedAnnotation();
 649                         _vp.repaint();
 650                 }
 651                 _vp.setLastSelectedPosition(new Point2D.Double(arg0.getX(),arg0.getY()));
 652         }
 653
 654
 655
 656         private void moveSelection(Point prev, Point cur)
 657         {
 658                 Point2D.Double p1 =  _vp.panelToLogicPoint(new Point2D.Double(prev.x,prev.y));
 659                 Point2D.Double p2 =  _vp.panelToLogicPoint(new Point2D.Double(cur.x,cur.y));
 660                 double dx = (p2.x - p1.x);
 661                 double dy = (p2.y - p1.y);
 662
 663                 if (_vp.isModifiable())
 664                 {
 665                         double ndx = dx;
 666                         double ndy = dy;
 667                         if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_LINEAR)
 668                         {
 669                                 ndy=0.0;
 670                         }
 671                         _vp.getVARNAUI().UIShiftBaseCoord(_vp.getSelectionIndices(), ndx, ndy);
 672                         _vp.fireLayoutChanged();
 673
 674                 }
 675         }
 676
 677
 678         public void popupMenuCanceled(PopupMenuEvent arg0) {
 679         }
 680
 681         public void popupMenuWillBecomeInvisible(PopupMenuEvent arg0) {
 682                 _vp.resetAnnotationHighlight();
 683                 _selectedBase = null;
 684         }
 685
 686         public void popupMenuWillBecomeVisible(PopupMenuEvent arg0) {
 687         }
 688 }