src2/fr/orsay/lri/varna/views/VueMenu.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.views;
  19
  20 import java.awt.Color;
  21 import java.awt.Component;
  22 import java.awt.Container;
  23 import java.awt.Font;
  24 import java.awt.Point;
  25 import java.awt.event.KeyEvent;
  26 import java.util.ArrayList;
  27
  28 import javax.swing.JCheckBoxMenuItem;
  29 import javax.swing.JComponent;
  30 import javax.swing.JLabel;
  31 import javax.swing.JMenu;
  32 import javax.swing.JMenuItem;
  33 import javax.swing.JPopupMenu;
  34 import javax.swing.JSeparator;
  35 import javax.swing.KeyStroke;
  36
  37 import fr.orsay.lri.varna.VARNAPanel;
  38 import fr.orsay.lri.varna.controlers.ControleurMenu;
  39 import fr.orsay.lri.varna.models.rna.RNA;
  40
  41 public class VueMenu extends JPopupMenu {
  42         /**
  43          *
  44          */
  45         private static final long serialVersionUID = 1L;
  46
  47         private VARNAPanel _vp;
  48
  49         private ControleurMenu _controlerMenu;
  50
  51         private JCheckBoxMenuItem _itemOptionSpecialBaseColored = new JCheckBoxMenuItem(
  52                         "Custom colored", false);
  53         private JCheckBoxMenuItem _itemShowWarnings = new JCheckBoxMenuItem(
  54                         "Show warnings", false);
  55         private JCheckBoxMenuItem _itemDrawBackbone = new JCheckBoxMenuItem(
  56                         "Draw backbone", true);
  57         private JCheckBoxMenuItem _itemOptionGapsBaseColored = new JCheckBoxMenuItem(
  58                         "Custom colored", false);
  59         private JCheckBoxMenuItem _itemOptionBondsColored = new JCheckBoxMenuItem(
  60                         "Use base color for base-pairs", false);
  61         private JCheckBoxMenuItem _itemShowNCBP = new JCheckBoxMenuItem(
  62                         "Show non-canonical BPs", true);
  63         private JCheckBoxMenuItem _itemShowOnlyPlanar = new JCheckBoxMenuItem(
  64                         "Hide tertiary BPs", false);
  65         private JCheckBoxMenuItem _itemFlatExteriorLoop = new JCheckBoxMenuItem(
  66                         "Flat exterior loop", false);
  67
  68         private JCheckBoxMenuItem _itemShowColorMap = new JCheckBoxMenuItem(
  69                         "Show color map", false);
  70         private JMenuItem _dashBasesColor;
  71
  72         private ArrayList<JComponent> _disabled = new ArrayList<JComponent>();
  73
  74         private JMenuItem _rotation;
  75         private JMenuItem _bpHeightIncrement;
  76
  77         private Point _spawnOrigin = new Point(-1,-1);
  78
  79         public VueMenu(VARNAPanel vp) {
  80                 _vp = vp;
  81                 _controlerMenu = new ControleurMenu(_vp, this);
  82         }
  83
  84         private void addTitle(String title, boolean keep) {
  85                 // TOD BH SwingJS -- this should not be necessary
  86                 JSeparator sep = new JPopupMenu.Separator(); // BH SWingJS needs JPopupMenu.Separator
  87                 //JSeparator sep = new JSeparator();
  88                 JMenuItem titleItem = new JMenuItem(" " + title);//BH SwingJS was JLabel -- need to be able to do this.
  89                 // titleItem.setAlignmentX(0.5f);
  90                 Font previousFont = titleItem.getFont();
  91                 Font futureFont = previousFont.deriveFont(Font.BOLD).deriveFont(
  92                                 (float) previousFont.getSize() + 1.0f);
  93
  94                 titleItem.setFont(futureFont);
  95                 Color current = titleItem.getForeground();
  96                 Color future = current.brighter().brighter();
  97                 // titleItem.setBackground(future);
  98                 titleItem.setForeground(future);
  99                 add(titleItem);
 100                 add(sep);
 101                 if (!keep) {
 102                         _disabled.add(sep);
 103                         _disabled.add(titleItem);
 104                 }
 105         }
 106
 107         private void configMenuItem(JMenuItem mi, String command, String keyStroke, Container par)
 108         { configMenuItem(mi,command,keyStroke,par,false); }
 109
 110         private void configMenuItem(JMenuItem mi, String command, String keyStroke, Container par, boolean disabled)
 111         {
 112                 mi.setActionCommand(command);
 113                 mi.addActionListener(_controlerMenu);
 114                 if (keyStroke!=null)
 115                         if (!keyStroke.equals(""))
 116                                 mi.setAccelerator(KeyStroke.getKeyStroke(keyStroke));
 117                 if (disabled)
 118                 { _disabled.add(mi);}
 119                 par.add(mi);
 120         }
 121
 122         private JMenuItem createMenuItem(String caption, String command, String keyStroke, Container par, boolean disabled)
 123         {
 124                 JMenuItem mi = new JMenuItem(caption);
 125                 configMenuItem(mi, command,keyStroke, par, disabled);
 126                 return mi;
 127         }
 128
 129         private JMenuItem createMenuItem(String caption, String command, String keyStroke, Container par)
 130         { return createMenuItem(caption, command, keyStroke, par,false); }
 131
 132
 133         public void updateDialog() {
 134                 for (int i = 0; i < _disabled.size(); i++) {
 135                         JComponent j = _disabled.get(i);
 136                         j.setVisible(_vp.isModifiable());
 137                 }
 138                 _itemOptionSpecialBaseColored.setState(_vp.getColorSpecialBases());
 139                 _itemShowWarnings.setState(_vp.getShowWarnings());
 140                 _itemOptionGapsBaseColored.setState(_vp.getColorGapsBases());
 141                 _itemOptionGapsBaseColored.setEnabled(_vp.isComparisonMode());
 142                 _dashBasesColor.setEnabled(_vp.isComparisonMode());
 143
 144                 _rotation.setEnabled(_vp.getDrawMode() != RNA.DRAW_MODE_LINEAR);
 145                 _bpHeightIncrement.setEnabled(_vp.getDrawMode() == RNA.DRAW_MODE_LINEAR);
 146
 147                 _itemOptionBondsColored.setState(_vp.getUseBaseColorsForBPs());
 148                 _itemShowNCBP.setState(_vp.getShowNonCanonicalBP());
 149                 _itemShowOnlyPlanar.setState(!_vp.getShowNonPlanarBP());
 150                 _itemShowColorMap.setState(_vp.getColorMapVisible());
 151                 _itemFlatExteriorLoop.setState(_vp.getFlatExteriorLoop());
 152                 _itemFlatExteriorLoop.setEnabled(_vp.getDrawMode() == RNA.DRAW_MODE_RADIATE);
 153         }
 154
 155         /**
 156          * Builds the popup menu
 157          */
 158         public void buildPopupMenu() {
 159                 addTitle("File", true);
 160                 fileMenu();
 161                 exportMenu();
 162                 createMenuItem("Print...", "print", "control P", this);
 163                 addSeparator();
 164
 165                 addTitle("Display", true);
 166                 viewMenu();
 167                 displayMenu();
 168                 //JSeparator sep = new JSeparator();
 169                 // TODO BH SwingJS - this should not be necessary
 170                 JSeparator sep = new JPopupMenu.Separator(); // BH SWingJS needs JPopupMenu.Separator
 171                 add(sep);
 172                 _disabled.add(sep);
 173
 174                 addTitle("Edit", false);
 175                 editRNAMenu();
 176                 redrawMenu();
 177                 colorClassesMenu();
 178                 annotationMenu();
 179                 _disabled.add(_itemShowNCBP);
 180                 _disabled.add(_itemShowOnlyPlanar);
 181                 aboutMenu();
 182         }
 183
 184         private void annotationMenu() {
 185                 JMenu submenuAnnotations = new JMenu("Annotations");
 186                 JMenu addAnnotations = new JMenu("New");
 187                 createMenuItem("Here", "annotationsaddPosition", "", addAnnotations);
 188                 createMenuItem("Base", "annotationsaddBase", "", addAnnotations);
 189                 createMenuItem("Loop", "annotationsaddLoop", "", addAnnotations);
 190                 createMenuItem("Helix", "annotationsaddHelix", "", addAnnotations);
 191                 //JSeparator sep = new JSeparator();
 192                 JSeparator sep = new JPopupMenu.Separator(); // BH SWingJS needs JPopupMenu.Separator
 193
 194                 addAnnotations.add(sep);
 195                 createMenuItem("Region", "annotationsaddRegion", "", addAnnotations);
 196                 createMenuItem("Chem. prob.", "annotationsaddChemProb", "", addAnnotations);
 197                 submenuAnnotations.add(addAnnotations);
 198                 createMenuItem("Edit from list...", "annotationsedit", "", submenuAnnotations);
 199                 createMenuItem("Remove from list...", "annotationsremove", "", submenuAnnotations);
 200                 submenuAnnotations.addSeparator();
 201                 createMenuItem("Auto 5'/3'", "annotationsautoextremites", "control alt Q", submenuAnnotations);
 202                 createMenuItem("Auto helices", "annotationsautohelices", "control Q", submenuAnnotations);
 203                 createMenuItem("Auto interior loops", "annotationsautointerior", "alt shift Q", submenuAnnotations);
 204                 createMenuItem("Auto terminal loops", "annotationsautoterminal", "control shift Q", submenuAnnotations);
 205                 add(submenuAnnotations);
 206         }
 207
 208         private void fileMenu() {
 209                 createMenuItem("New...", "userInput", "control N", this,true);
 210                 createMenuItem("Open...", "file", "control O", this,true);
 211                 createMenuItem("Save...", "saveas", "control S", this,true);
 212                 JMenu submenuSave = new JMenu("Save as");
 213                 createMenuItem("DBN (Vienna)", "dbn", "", submenuSave);
 214                 createMenuItem("BPSEQ", "bpseq", "", submenuSave);
 215                 createMenuItem("CT", "ct", "", submenuSave);
 216                 add(submenuSave);
 217         }
 218
 219         private void exportMenu() {
 220                 // Export menu
 221                 JMenu submenuExport = new JMenu("Export");
 222                 createMenuItem("SVG", "svg", "", submenuExport);
 223                 createMenuItem("PGF/TIKZ", "tikz", "", submenuExport);
 224                 createMenuItem("XFIG", "xfig", "", submenuExport);
 225                 submenuExport.addSeparator();
 226                 createMenuItem("EPS", "eps", "", submenuExport);
 227                 submenuExport.addSeparator();
 228                 createMenuItem("PNG", "png", "", submenuExport);
 229                 createMenuItem("JPEG", "jpeg", "", submenuExport);
 230                 add(submenuExport);
 231         }
 232
 233
 234         private void displayMenu() {
 235
 236                 // SubMenu Base-pairs
 237                 JMenu subMenuBasePairs = new JMenu("Base Pairs");
 238                 createMenuItem("BP style...", "bpstyle", "control shift P", subMenuBasePairs);
 239                 configMenuItem(_itemShowNCBP, "shownc", "control W", subMenuBasePairs);
 240                 configMenuItem(_itemShowOnlyPlanar, "shownp", "control E", subMenuBasePairs);
 241                 // SubMenu Non standard Bases
 242                 JMenu subMenuNSBases = new JMenu("Non-standard bases");
 243                 configMenuItem(_itemOptionSpecialBaseColored, "specialbasecolored", "control J", subMenuNSBases);
 244                 createMenuItem("Color", "specialBasesColor", "control shift J", subMenuNSBases);
 245                 // SubMenu Gaps Bases
 246                 JMenu subMenuGapsBases = new JMenu("'Gaps' bases");
 247                 configMenuItem(_itemOptionGapsBaseColored, "dashbasecolored", "control D", subMenuGapsBases);
 248                 _dashBasesColor = createMenuItem("Color", "dashBasesColor", "control shift D", subMenuGapsBases);
 249                 // Removable separator
 250                 //JSeparator sep = new JSeparator();
 251                 JSeparator sep = new JPopupMenu.Separator(); // BH SWingJS needs JPopupMenu.Separator
 252                 _disabled.add(sep);
 253
 254                 // Style menu
 255                 JMenu submenuStyle = new JMenu("RNA style");
 256                 createMenuItem("Toggle draw bases", "gaspin", "alt G", submenuStyle,true);
 257                 submenuStyle.add(subMenuBasePairs);
 258                 submenuStyle.addSeparator();
 259                 submenuStyle.add(subMenuNSBases);
 260                 submenuStyle.add(subMenuGapsBases);
 261                 submenuStyle.add(sep);
 262                 createMenuItem("Backbone color", "backbone", "control K", submenuStyle,true);
 263                 configMenuItem(_itemDrawBackbone, "showbackbone", "alt B", submenuStyle);
 264
 265                 // Submenu Title
 266                 JMenu submenuTitle = new JMenu("Title");
 267                 createMenuItem("Set Title", "setTitle", "control T", submenuTitle, true);
 268                 createMenuItem("Font", "titleDisplay", "control shift T", submenuTitle, true);
 269                 createMenuItem("Color", "titleColor", "control alt T", submenuTitle, true);
 270                 _disabled.add(submenuTitle);
 271
 272                 // Color map menu
 273                 JMenu submenuColorMap = new JMenu("Color map");
 274                 configMenuItem(_itemShowColorMap, "toggleshowcolormap", "control shift L", submenuColorMap, false);
 275                 createMenuItem("Caption", "colormapcaption", "control shift C", submenuColorMap,true);
 276                 createMenuItem("Style...", "colormapstyle", "control L", submenuColorMap,false);
 277                 submenuColorMap.addSeparator();
 278                 createMenuItem("Edit values...", "colormapvalues", "shift L", submenuColorMap,true);
 279                 createMenuItem("Load values...", "colormaploadvalues", "control shift K", submenuColorMap,true);
 280                 _disabled.add(submenuColorMap);
 281
 282                 // Menu Misc
 283                 JMenu submenuMisc = new JMenu("Misc");
 284                 createMenuItem("Num. period.", "numPeriod", "control M", submenuMisc);
 285                 createMenuItem("Background color", "background", "control G", submenuMisc);
 286                 submenuMisc.add(submenuTitle);
 287
 288                 // Main menu
 289                 add(submenuStyle);
 290                 add(submenuColorMap);
 291                 add(submenuMisc);
 292
 293         }
 294
 295         private void editRNAMenu()
 296         {
 297                 createMenuItem("Bases...","editallbases","",this,true);
 298                 createMenuItem("BasePairs...","editallbps","",this,true);
 299         }
 300
 301         private void redrawMenu() {
 302                 JMenu submenuRedraw = new JMenu("Redraw");
 303                 _disabled.add(submenuRedraw);
 304
 305                 JMenu submenuAlgorithms = new JMenu("Algorithm");
 306                 _disabled.add(submenuAlgorithms);
 307
 308                 createMenuItem("Linear","line","control 1",submenuAlgorithms,true);
 309                 createMenuItem("Circular","circular","control 2",submenuAlgorithms,true);
 310                 createMenuItem("Radiate","radiate","control 3",submenuAlgorithms,true);
 311                 createMenuItem("NAView","naview","control 4",submenuAlgorithms,true);
 312                 //createMenuItem("VARNAView","varnaview","control 5",submenuAlgorithms,true);
 313                 //createMenuItem("MOTIFView","motifview","control 6",submenuAlgorithms,true);
 314                 submenuRedraw.add(submenuAlgorithms);
 315
 316                 // Sets the height increment in LINEAR_MODE type of drawing
 317                 _bpHeightIncrement = createMenuItem("BP height increment","bpheightincrement","control H",submenuRedraw);
 318                 configMenuItem(_itemFlatExteriorLoop, "flat", "control F", submenuRedraw, true);
 319
 320                 // Item pour le r�glage de l'espace entre chaques bases
 321                 createMenuItem("Space between bases","spaceBetweenBases","control shift S",submenuRedraw,true);
 322                 createMenuItem("Reset","reset","control shift R",submenuRedraw,true);
 323
 324                 add(submenuRedraw);
 325         }
 326
 327         @SuppressWarnings("unused")
 328         private void warningMenu() {
 329                 // Menu showWarning
 330                 configMenuItem(_itemShowWarnings, "showwarnings", "", this, true);
 331         }
 332
 333         private void viewMenu() {
 334                 // View menu
 335                 JMenu submenuView = new JMenu("View");
 336
 337                 // Zoom submenu
 338                 JMenu zoomDisplay = new JMenu("Zoom");
 339                 createMenuItem("25%","zoom25","",zoomDisplay);
 340                 createMenuItem("50%","zoom50","",zoomDisplay);
 341                 createMenuItem("100%","zoom100","",zoomDisplay);
 342                 createMenuItem("150%","zoom150","",zoomDisplay);
 343                 createMenuItem("200%","zoom200","",zoomDisplay);
 344                 createMenuItem("Custom","zoom","control Z",zoomDisplay);
 345                 submenuView.add(zoomDisplay);
 346                 _rotation = createMenuItem("Rotation...","rotation","control R",submenuView);
 347                 createMenuItem("Rescale...","rescale","",submenuView);
 348                 submenuView.addSeparator();
 349                 createMenuItem("Border size","borderSize","control B",submenuView);
 350
 351                 add(submenuView);
 352
 353         }
 354
 355         JMenu _subMenuBases;
 356
 357         private Component _selectionMenuIndex = null;
 358
 359         public void addSelectionMenu(JMenuItem s) {
 360                 _selectionMenuIndex = s;
 361                 _disabled.add(s);
 362                 insert(s, getComponentCount() - 2);
 363         }
 364
 365         public void removeSelectionMenu() {
 366                 if (_selectionMenuIndex != null) {
 367                         this.remove(_selectionMenuIndex);
 368                         _selectionMenuIndex = null;
 369                 }
 370         }
 371
 372         private void colorClassesMenu() {
 373                 // Menu Bases
 374                 _subMenuBases = new JMenu("Colors");
 375                 _disabled.add(_subMenuBases);
 376                 createMenuItem("By Base","eachKind","control U",_subMenuBases,true);
 377                 createMenuItem("By BP","eachCouple","shift U",_subMenuBases,true);
 378                 createMenuItem("By Position","eachBase","alt U",_subMenuBases,true);
 379                 add(_subMenuBases);
 380         }
 381
 382         /**
 383          * add default color options to a menu
 384          */
 385         public void addColorOptions(JMenu submenu) {
 386                 createMenuItem("Fill Color",submenu.getActionCommand() + ",InnerColor","",submenu,true);
 387                 createMenuItem("Stroke Color",submenu.getActionCommand() + ",OutlineColor","",submenu,true);
 388                 createMenuItem("Label Color",submenu.getActionCommand() + ",NameColor","",submenu,true);
 389                 submenu.addSeparator();
 390                 createMenuItem("BP Color",submenu.getActionCommand() + ",BPColor","",submenu,true);
 391                 createMenuItem("BP Thickness",submenu.getActionCommand() + ",BPThickness","",submenu,true);
 392                 submenu.addSeparator();
 393                 createMenuItem("Number Color",submenu.getActionCommand() + ",NumberColor","",submenu,true);
 394         }
 395
 396         private void aboutMenu() {
 397                 addSeparator();
 398                 createMenuItem("About VARNA", "about", "control A", this);
 399         }
 400
 401         public void addAnnotationMenu(JMenu menu) {
 402                 addAnnotationMenu(menu, false);
 403         }
 404
 405         public void addAnnotationMenu(JMenu menu, boolean existingAnnot) {
 406                 String title = "Annotation";
 407                 if (existingAnnot)
 408                 {
 409                         String debut = "";
 410                         String texte = _vp.get_selectedAnnotation().getTexte();
 411                         if (texte.length() < 5)
 412                                 debut = texte;
 413                         else
 414                                 debut = texte.substring(0, 5) + "...";
 415                         title = "Annotation: " + debut;
 416                 }
 417                 JMenu menuAnnotation = new JMenu(title);
 418                 if (!existingAnnot)
 419                         createMenuItem("Add",menu.getActionCommand() + "annotationadd","",menuAnnotation,true);
 420                 createMenuItem("Edit",menu.getActionCommand() + "annotationedit","",menuAnnotation,true);
 421                 createMenuItem("Remove",menu.getActionCommand() + "annotationremove","",menuAnnotation,true);
 422                 menu.add(menuAnnotation);
 423         }
 424
 425
 426         public static long getSerialVersionUID() {
 427                 return serialVersionUID;
 428         }
 429
 430         public VARNAPanel get_vp() {
 431                 return _vp;
 432         }
 433
 434         public ControleurMenu get_controleurMenu() {
 435                 return _controlerMenu;
 436         }
 437
 438         public JCheckBoxMenuItem get_itemOptionSpecialBaseColored() {
 439                 return _itemOptionSpecialBaseColored;
 440         }
 441
 442         public JCheckBoxMenuItem get_itemShowWarnings() {
 443                 return _itemShowWarnings;
 444         }
 445
 446         public JCheckBoxMenuItem get_itemOptionDashBaseColored() {
 447                 return _itemOptionGapsBaseColored;
 448         }
 449
 450         public void set_controleurMenu(ControleurMenu menu) {
 451                 _controlerMenu = menu;
 452         }
 453
 454         public void set_itemOptionSpecialBaseColored(
 455                         JCheckBoxMenuItem optionSpecialBaseColored) {
 456                 _itemOptionSpecialBaseColored = optionSpecialBaseColored;
 457         }
 458
 459         public void set_itemShowWarnings(JCheckBoxMenuItem showWarnings) {
 460                 _itemShowWarnings = showWarnings;
 461         }
 462
 463         public void set_itemOptionDashBaseColored(
 464                         JCheckBoxMenuItem optionDashBaseColored) {
 465                 _itemOptionGapsBaseColored = optionDashBaseColored;
 466         }
 467
 468         public JMenuItem get_rotation() {
 469                 return _rotation;
 470         }
 471
 472         public void set_rotation(JMenuItem _rotation) {
 473                 this._rotation = _rotation;
 474         }
 475
 476         public JCheckBoxMenuItem get_itemOptionBondsColored() {
 477                 return _itemOptionBondsColored;
 478         }
 479
 480         public void set_itemOptionBondsColored(JCheckBoxMenuItem optionBondsColored) {
 481                 _itemOptionBondsColored = optionBondsColored;
 482         }
 483
 484
 485         public void show(Component invoker,int x,int y) {
 486                  _spawnOrigin = new Point(x,y);
 487                  super.show(invoker,x,y);
 488          }
 489
 490         public Point getSpawnPoint()
 491         {
 492                 return _spawnOrigin ;
 493         }
 494
 495 }