src/jalview/jbgui/GStructureViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.api.structures.JalviewStructureDisplayI;
  24 import jalview.gui.UserDefinedColours;
  25 import jalview.schemes.UserColourScheme;
  26 import jalview.util.MessageManager;
  27
  28 import java.awt.BorderLayout;
  29 import java.awt.GridLayout;
  30 import java.awt.event.ActionEvent;
  31 import java.awt.event.ActionListener;
  32 import java.util.Map;
  33
  34 import javax.swing.ButtonGroup;
  35 import javax.swing.JInternalFrame;
  36 import javax.swing.JLabel;
  37 import javax.swing.JMenu;
  38 import javax.swing.JMenuBar;
  39 import javax.swing.JMenuItem;
  40 import javax.swing.JPanel;
  41 import javax.swing.JRadioButtonMenuItem;
  42
  43 public abstract class GStructureViewer extends JInternalFrame implements
  44         JalviewStructureDisplayI
  45 {
  46   // private AAStructureBindingModel bindingModel;
  47
  48   protected JMenu savemenu;
  49
  50   protected JMenu viewMenu;
  51
  52   protected JMenu colourMenu;
  53
  54   protected JMenu chainMenu;
  55
  56   protected JMenu viewerActionMenu;
  57
  58   protected JMenuItem alignStructs;
  59
  60   protected JMenuItem fitToWindow;
  61
  62   protected JRadioButtonMenuItem seqColour;
  63
  64   protected JRadioButtonMenuItem chainColour;
  65
  66   protected JRadioButtonMenuItem chargeColour;
  67
  68   protected JRadioButtonMenuItem zappoColour;
  69
  70   protected JRadioButtonMenuItem taylorColour;
  71
  72   protected JRadioButtonMenuItem hydroColour;
  73
  74   protected JRadioButtonMenuItem strandColour;
  75
  76   protected JRadioButtonMenuItem helixColour;
  77
  78   protected JRadioButtonMenuItem turnColour;
  79
  80   protected JRadioButtonMenuItem buriedColour;
  81
  82   protected JRadioButtonMenuItem nucleotideColour;
  83
  84   protected JRadioButtonMenuItem purinePyrimidineColour;
  85
  86   protected JRadioButtonMenuItem userColour;
  87
  88   protected JRadioButtonMenuItem viewerColour;
  89
  90   protected JMenuItem helpItem;
  91
  92   protected JLabel statusBar;
  93
  94   protected JPanel statusPanel;
  95
  96   /**
  97    * Constructor
  98    */
  99   public GStructureViewer()
 100   {
 101     try
 102     {
 103       jbInit();
 104     } catch (Exception ex)
 105     {
 106       ex.printStackTrace();
 107     }
 108   }
 109
 110   private void jbInit() throws Exception
 111   {
 112     JMenuBar menuBar = new JMenuBar();
 113     this.setJMenuBar(menuBar);
 114
 115     JMenu fileMenu = new JMenu();
 116     fileMenu.setText(MessageManager.getString("action.file"));
 117
 118     savemenu = new JMenu();
 119     savemenu.setActionCommand(MessageManager.getString("action.save_image"));
 120     savemenu.setText(MessageManager.getString("action.save_as"));
 121
 122     JMenuItem pdbFile = new JMenuItem();
 123     pdbFile.setText(MessageManager.getString("label.pdb_file"));
 124     pdbFile.addActionListener(new ActionListener()
 125     {
 126       @Override
 127       public void actionPerformed(ActionEvent actionEvent)
 128       {
 129         pdbFile_actionPerformed(actionEvent);
 130       }
 131     });
 132
 133     JMenuItem png = new JMenuItem();
 134     png.setText("PNG");
 135     png.addActionListener(new ActionListener()
 136     {
 137       @Override
 138       public void actionPerformed(ActionEvent actionEvent)
 139       {
 140         png_actionPerformed(actionEvent);
 141       }
 142     });
 143
 144     JMenuItem eps = new JMenuItem();
 145     eps.setText("EPS");
 146     eps.addActionListener(new ActionListener()
 147     {
 148       @Override
 149       public void actionPerformed(ActionEvent actionEvent)
 150       {
 151         eps_actionPerformed(actionEvent);
 152       }
 153     });
 154
 155     JMenuItem viewMapping = new JMenuItem();
 156     viewMapping.setText(MessageManager.getString("label.view_mapping"));
 157     viewMapping.addActionListener(new ActionListener()
 158     {
 159       @Override
 160       public void actionPerformed(ActionEvent actionEvent)
 161       {
 162         viewMapping_actionPerformed(actionEvent);
 163       }
 164     });
 165
 166     viewMenu = new JMenu();
 167     viewMenu.setText(MessageManager.getString("action.view"));
 168
 169     chainMenu = new JMenu();
 170     chainMenu.setText(MessageManager.getString("action.show_chain"));
 171
 172     fitToWindow = new JMenuItem();
 173     fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
 174     fitToWindow.addActionListener(new ActionListener()
 175     {
 176       @Override
 177       public void actionPerformed(ActionEvent actionEvent)
 178       {
 179         fitToWindow_actionPerformed();
 180       }
 181     });
 182
 183     JMenu helpMenu = new JMenu();
 184     helpMenu.setText(MessageManager.getString("action.help"));
 185     helpItem = new JMenuItem();
 186     helpItem.setText(MessageManager.getString("label.jmol_help"));
 187     helpItem.addActionListener(new ActionListener()
 188     {
 189       @Override
 190       public void actionPerformed(ActionEvent actionEvent)
 191       {
 192         showHelp_actionPerformed(actionEvent);
 193       }
 194     });
 195     alignStructs = new JMenuItem();
 196     alignStructs
 197             .setText(MessageManager.getString("label.align_structures"));
 198     alignStructs.addActionListener(new ActionListener()
 199     {
 200       @Override
 201       public void actionPerformed(ActionEvent actionEvent)
 202       {
 203         alignStructs_actionPerformed(actionEvent);
 204       }
 205     });
 206
 207     viewerActionMenu = new JMenu(MessageManager.getString("label.jmol"));
 208     viewerActionMenu.setVisible(false);
 209     viewerActionMenu.add(alignStructs);
 210     colourMenu = new JMenu();
 211     buildColourMenu();
 212     fileMenu.add(savemenu);
 213     fileMenu.add(viewMapping);
 214     savemenu.add(pdbFile);
 215     savemenu.add(png);
 216     savemenu.add(eps);
 217     viewMenu.add(chainMenu);
 218     helpMenu.add(helpItem);
 219
 220     menuBar.add(fileMenu);
 221     menuBar.add(viewMenu);
 222     menuBar.add(colourMenu);
 223     menuBar.add(viewerActionMenu);
 224     menuBar.add(helpMenu);
 225
 226     statusPanel = new JPanel();
 227     statusPanel.setLayout(new GridLayout());
 228     this.getContentPane().add(statusPanel, BorderLayout.SOUTH);
 229     statusBar = new JLabel();
 230     statusPanel.add(statusBar, null);
 231   }
 232
 233   /**
 234    * Builds the colour menu
 235    */
 236   protected void buildColourMenu()
 237   {
 238     colourMenu.removeAll();
 239     colourMenu.setText(MessageManager.getString("label.colours"));
 240
 241     JMenuItem backGround = new JMenuItem();
 242     backGround
 243             .setText(MessageManager.getString("action.background_colour"));
 244     backGround.addActionListener(new ActionListener()
 245     {
 246       @Override
 247       public void actionPerformed(ActionEvent actionEvent)
 248       {
 249         backGround_actionPerformed(actionEvent);
 250       }
 251     });
 252     seqColour = new JRadioButtonMenuItem();
 253     seqColour.setSelected(false);
 254     seqColour.setText(MessageManager.getString("action.by_sequence"));
 255     seqColour.addActionListener(new ActionListener()
 256     {
 257       @Override
 258       public void actionPerformed(ActionEvent actionEvent)
 259       {
 260         seqColour_actionPerformed(actionEvent);
 261       }
 262     });
 263     chainColour = new JRadioButtonMenuItem();
 264     chainColour.setText(MessageManager.getString("action.by_chain"));
 265     chainColour.addActionListener(new ActionListener()
 266     {
 267       @Override
 268       public void actionPerformed(ActionEvent actionEvent)
 269       {
 270         chainColour_actionPerformed(actionEvent);
 271       }
 272     });
 273     chargeColour = new JRadioButtonMenuItem();
 274     chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
 275     chargeColour.addActionListener(new ActionListener()
 276     {
 277       @Override
 278       public void actionPerformed(ActionEvent actionEvent)
 279       {
 280         chargeColour_actionPerformed(actionEvent);
 281       }
 282     });
 283     zappoColour = new JRadioButtonMenuItem();
 284     zappoColour.setText(MessageManager.getString("label.zappo"));
 285     zappoColour.addActionListener(new ActionListener()
 286     {
 287       @Override
 288       public void actionPerformed(ActionEvent actionEvent)
 289       {
 290         zappoColour_actionPerformed(actionEvent);
 291       }
 292     });
 293     taylorColour = new JRadioButtonMenuItem();
 294     taylorColour.setText(MessageManager.getString("label.taylor"));
 295     taylorColour.addActionListener(new ActionListener()
 296     {
 297       @Override
 298       public void actionPerformed(ActionEvent actionEvent)
 299       {
 300         taylorColour_actionPerformed(actionEvent);
 301       }
 302     });
 303     hydroColour = new JRadioButtonMenuItem();
 304     hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
 305     hydroColour.addActionListener(new ActionListener()
 306     {
 307       @Override
 308       public void actionPerformed(ActionEvent actionEvent)
 309       {
 310         hydroColour_actionPerformed(actionEvent);
 311       }
 312     });
 313     strandColour = new JRadioButtonMenuItem();
 314     strandColour.setText(MessageManager
 315             .getString("label.strand_propensity"));
 316     strandColour.addActionListener(new ActionListener()
 317     {
 318       @Override
 319       public void actionPerformed(ActionEvent actionEvent)
 320       {
 321         strandColour_actionPerformed(actionEvent);
 322       }
 323     });
 324     helixColour = new JRadioButtonMenuItem();
 325     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 326     helixColour.addActionListener(new ActionListener()
 327     {
 328       @Override
 329       public void actionPerformed(ActionEvent actionEvent)
 330       {
 331         helixColour_actionPerformed(actionEvent);
 332       }
 333     });
 334     turnColour = new JRadioButtonMenuItem();
 335     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 336     turnColour.addActionListener(new ActionListener()
 337     {
 338       @Override
 339       public void actionPerformed(ActionEvent actionEvent)
 340       {
 341         turnColour_actionPerformed(actionEvent);
 342       }
 343     });
 344     buriedColour = new JRadioButtonMenuItem();
 345     buriedColour.setText(MessageManager.getString("label.buried_index"));
 346     buriedColour.addActionListener(new ActionListener()
 347     {
 348       @Override
 349       public void actionPerformed(ActionEvent actionEvent)
 350       {
 351         buriedColour_actionPerformed(actionEvent);
 352       }
 353     });
 354     nucleotideColour = new JRadioButtonMenuItem();
 355     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
 356     nucleotideColour.addActionListener(new ActionListener()
 357     {
 358       @Override
 359       public void actionPerformed(ActionEvent actionEvent)
 360       {
 361         nucleotideColour_actionPerformed(actionEvent);
 362       }
 363     });
 364     purinePyrimidineColour = new JRadioButtonMenuItem();
 365     purinePyrimidineColour.setText(MessageManager
 366             .getString("label.purine_pyrimidine"));
 367     purinePyrimidineColour.addActionListener(new ActionListener()
 368     {
 369       @Override
 370       public void actionPerformed(ActionEvent actionEvent)
 371       {
 372         purinePyrimidineColour_actionPerformed(actionEvent);
 373       }
 374     });
 375     userColour = new JRadioButtonMenuItem();
 376     userColour.setText(MessageManager.getString("action.user_defined"));
 377     userColour.addActionListener(new ActionListener()
 378     {
 379       @Override
 380       public void actionPerformed(ActionEvent actionEvent)
 381       {
 382         userColour_actionPerformed(actionEvent);
 383       }
 384     });
 385     viewerColour = new JRadioButtonMenuItem();
 386     viewerColour.setSelected(false);
 387     viewerColour
 388             .setText(MessageManager.getString("label.colour_with_jmol"));
 389     viewerColour.setToolTipText(MessageManager
 390             .getString("label.let_jmol_manage_structure_colours"));
 391     viewerColour.addActionListener(new ActionListener()
 392     {
 393       @Override
 394       public void actionPerformed(ActionEvent actionEvent)
 395       {
 396         viewerColour_actionPerformed(actionEvent);
 397       }
 398     });
 399
 400     /*
 401      * add colour buttons to a group so their selection
 402      * is mutually exclusive
 403      */
 404     ButtonGroup colourButtons = new ButtonGroup();
 405
 406     colourMenu.add(seqColour);
 407     colourMenu.add(chainColour);
 408     colourMenu.add(chargeColour);
 409     colourMenu.add(zappoColour);
 410     colourMenu.add(taylorColour);
 411     colourMenu.add(hydroColour);
 412     colourMenu.add(helixColour);
 413     colourMenu.add(strandColour);
 414     colourMenu.add(turnColour);
 415     colourMenu.add(buriedColour);
 416     colourMenu.add(purinePyrimidineColour);
 417
 418     /*
 419      * add any user-defined colours that are loaded
 420      */
 421     Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
 422             .getUserColourSchemes();
 423     if (userColourSchemes != null)
 424     {
 425       for (String schemeName : userColourSchemes.keySet())
 426       {
 427         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 428                 schemeName);
 429         radioItem.addActionListener(new ActionListener()
 430         {
 431           @Override
 432           public void actionPerformed(ActionEvent evt)
 433           {
 434             userColour_actionPerformed(evt);
 435           }
 436         });
 437         colourMenu.add(radioItem);
 438         colourButtons.add(radioItem);
 439       }
 440     }
 441     colourMenu.add(userColour);
 442     colourMenu.add(viewerColour);
 443     colourMenu.add(backGround);
 444
 445     colourButtons.add(seqColour);
 446     colourButtons.add(chainColour);
 447     colourButtons.add(chargeColour);
 448     colourButtons.add(zappoColour);
 449     colourButtons.add(taylorColour);
 450     colourButtons.add(hydroColour);
 451     colourButtons.add(helixColour);
 452     colourButtons.add(strandColour);
 453     colourButtons.add(turnColour);
 454     colourButtons.add(buriedColour);
 455     colourButtons.add(purinePyrimidineColour);
 456     colourButtons.add(userColour);
 457     colourButtons.add(viewerColour);
 458   }
 459
 460   protected void fitToWindow_actionPerformed()
 461   {
 462   }
 463
 464   protected void highlightSelection_actionPerformed()
 465   {
 466   }
 467
 468   protected void viewerColour_actionPerformed(ActionEvent actionEvent)
 469   {
 470   }
 471
 472   protected void alignStructs_actionPerformed(ActionEvent actionEvent)
 473   {
 474   }
 475
 476   public void pdbFile_actionPerformed(ActionEvent actionEvent)
 477   {
 478
 479   }
 480
 481   public void png_actionPerformed(ActionEvent actionEvent)
 482   {
 483
 484   }
 485
 486   public void eps_actionPerformed(ActionEvent actionEvent)
 487   {
 488
 489   }
 490
 491   public void viewMapping_actionPerformed(ActionEvent actionEvent)
 492   {
 493
 494   }
 495
 496   public void seqColour_actionPerformed(ActionEvent actionEvent)
 497   {
 498
 499   }
 500
 501   public void chainColour_actionPerformed(ActionEvent actionEvent)
 502   {
 503
 504   }
 505
 506   public void chargeColour_actionPerformed(ActionEvent actionEvent)
 507   {
 508
 509   }
 510
 511   public void zappoColour_actionPerformed(ActionEvent actionEvent)
 512   {
 513
 514   }
 515
 516   public void taylorColour_actionPerformed(ActionEvent actionEvent)
 517   {
 518
 519   }
 520
 521   public void hydroColour_actionPerformed(ActionEvent actionEvent)
 522   {
 523
 524   }
 525
 526   public void helixColour_actionPerformed(ActionEvent actionEvent)
 527   {
 528
 529   }
 530
 531   public void strandColour_actionPerformed(ActionEvent actionEvent)
 532   {
 533
 534   }
 535
 536   public void turnColour_actionPerformed(ActionEvent actionEvent)
 537   {
 538
 539   }
 540
 541   public void buriedColour_actionPerformed(ActionEvent actionEvent)
 542   {
 543
 544   }
 545
 546   public void nucleotideColour_actionPerformed(ActionEvent actionEvent)
 547   {
 548
 549   }
 550
 551   public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
 552   {
 553
 554   }
 555
 556   public void userColour_actionPerformed(ActionEvent actionEvent)
 557   {
 558
 559   }
 560
 561   public void backGround_actionPerformed(ActionEvent actionEvent)
 562   {
 563
 564   }
 565
 566   public void showHelp_actionPerformed(ActionEvent actionEvent)
 567   {
 568
 569   }
 570
 571   // {
 572   // return bindingModel;
 573   // }
 574
 575   // public void setBindingModel(AAStructureBindingModel bindingModel)
 576   // {
 577   // this.bindingModel = bindingModel;
 578   // }
 579
 580 }