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
 285             .getString("label.colourScheme_zappo"));
 286     zappoColour.addActionListener(new ActionListener()
 287     {
 288       @Override
 289       public void actionPerformed(ActionEvent actionEvent)
 290       {
 291         zappoColour_actionPerformed(actionEvent);
 292       }
 293     });
 294     taylorColour = new JRadioButtonMenuItem();
 295     taylorColour.setText(MessageManager
 296             .getString("label.colourScheme_taylor"));
 297     taylorColour.addActionListener(new ActionListener()
 298     {
 299       @Override
 300       public void actionPerformed(ActionEvent actionEvent)
 301       {
 302         taylorColour_actionPerformed(actionEvent);
 303       }
 304     });
 305     hydroColour = new JRadioButtonMenuItem();
 306     hydroColour.setText(MessageManager
 307             .getString("label.colourScheme_hydrophobic"));
 308     hydroColour.addActionListener(new ActionListener()
 309     {
 310       @Override
 311       public void actionPerformed(ActionEvent actionEvent)
 312       {
 313         hydroColour_actionPerformed(actionEvent);
 314       }
 315     });
 316     strandColour = new JRadioButtonMenuItem();
 317     strandColour.setText(MessageManager
 318             .getString("label.colourScheme_strand_propensity"));
 319     strandColour.addActionListener(new ActionListener()
 320     {
 321       @Override
 322       public void actionPerformed(ActionEvent actionEvent)
 323       {
 324         strandColour_actionPerformed(actionEvent);
 325       }
 326     });
 327     helixColour = new JRadioButtonMenuItem();
 328     helixColour.setText(MessageManager
 329             .getString("label.colourScheme_helix_propensity"));
 330     helixColour.addActionListener(new ActionListener()
 331     {
 332       @Override
 333       public void actionPerformed(ActionEvent actionEvent)
 334       {
 335         helixColour_actionPerformed(actionEvent);
 336       }
 337     });
 338     turnColour = new JRadioButtonMenuItem();
 339     turnColour.setText(MessageManager
 340             .getString("label.colourScheme_turn_propensity"));
 341     turnColour.addActionListener(new ActionListener()
 342     {
 343       @Override
 344       public void actionPerformed(ActionEvent actionEvent)
 345       {
 346         turnColour_actionPerformed(actionEvent);
 347       }
 348     });
 349     buriedColour = new JRadioButtonMenuItem();
 350     buriedColour.setText(MessageManager
 351             .getString("label.colourScheme_buried_index"));
 352     buriedColour.addActionListener(new ActionListener()
 353     {
 354       @Override
 355       public void actionPerformed(ActionEvent actionEvent)
 356       {
 357         buriedColour_actionPerformed(actionEvent);
 358       }
 359     });
 360     nucleotideColour = new JRadioButtonMenuItem();
 361     nucleotideColour.setText(MessageManager
 362             .getString("label.colourScheme_nucleotide"));
 363     nucleotideColour.addActionListener(new ActionListener()
 364     {
 365       @Override
 366       public void actionPerformed(ActionEvent actionEvent)
 367       {
 368         nucleotideColour_actionPerformed(actionEvent);
 369       }
 370     });
 371     purinePyrimidineColour = new JRadioButtonMenuItem();
 372     purinePyrimidineColour.setText(MessageManager
 373             .getString("label.colourScheme_purine/pyrimidine"));
 374     purinePyrimidineColour.addActionListener(new ActionListener()
 375     {
 376       @Override
 377       public void actionPerformed(ActionEvent actionEvent)
 378       {
 379         purinePyrimidineColour_actionPerformed(actionEvent);
 380       }
 381     });
 382     userColour = new JRadioButtonMenuItem();
 383     userColour.setText(MessageManager.getString("action.user_defined"));
 384     userColour.addActionListener(new ActionListener()
 385     {
 386       @Override
 387       public void actionPerformed(ActionEvent actionEvent)
 388       {
 389         userColour_actionPerformed(actionEvent);
 390       }
 391     });
 392     viewerColour = new JRadioButtonMenuItem();
 393     viewerColour.setSelected(false);
 394     viewerColour
 395             .setText(MessageManager.getString("label.colour_with_jmol"));
 396     viewerColour.setToolTipText(MessageManager
 397             .getString("label.let_jmol_manage_structure_colours"));
 398     viewerColour.addActionListener(new ActionListener()
 399     {
 400       @Override
 401       public void actionPerformed(ActionEvent actionEvent)
 402       {
 403         viewerColour_actionPerformed(actionEvent);
 404       }
 405     });
 406
 407     /*
 408      * add colour buttons to a group so their selection
 409      * is mutually exclusive
 410      */
 411     ButtonGroup colourButtons = new ButtonGroup();
 412
 413     colourMenu.add(seqColour);
 414     colourMenu.add(chainColour);
 415     colourMenu.add(chargeColour);
 416     colourMenu.add(zappoColour);
 417     colourMenu.add(taylorColour);
 418     colourMenu.add(hydroColour);
 419     colourMenu.add(helixColour);
 420     colourMenu.add(strandColour);
 421     colourMenu.add(turnColour);
 422     colourMenu.add(buriedColour);
 423     colourMenu.add(purinePyrimidineColour);
 424
 425     /*
 426      * add any user-defined colours that are loaded
 427      */
 428     Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
 429             .getUserColourSchemes();
 430     if (userColourSchemes != null)
 431     {
 432       for (String schemeName : userColourSchemes.keySet())
 433       {
 434         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 435                 schemeName);
 436         radioItem.addActionListener(new ActionListener()
 437         {
 438           @Override
 439           public void actionPerformed(ActionEvent evt)
 440           {
 441             userColour_actionPerformed(evt);
 442           }
 443         });
 444         colourMenu.add(radioItem);
 445         colourButtons.add(radioItem);
 446       }
 447     }
 448     colourMenu.add(userColour);
 449     colourMenu.add(viewerColour);
 450     colourMenu.add(backGround);
 451
 452     colourButtons.add(seqColour);
 453     colourButtons.add(chainColour);
 454     colourButtons.add(chargeColour);
 455     colourButtons.add(zappoColour);
 456     colourButtons.add(taylorColour);
 457     colourButtons.add(hydroColour);
 458     colourButtons.add(helixColour);
 459     colourButtons.add(strandColour);
 460     colourButtons.add(turnColour);
 461     colourButtons.add(buriedColour);
 462     colourButtons.add(purinePyrimidineColour);
 463     colourButtons.add(userColour);
 464     colourButtons.add(viewerColour);
 465   }
 466
 467   protected void fitToWindow_actionPerformed()
 468   {
 469   }
 470
 471   protected void highlightSelection_actionPerformed()
 472   {
 473   }
 474
 475   protected void viewerColour_actionPerformed(ActionEvent actionEvent)
 476   {
 477   }
 478
 479   protected void alignStructs_actionPerformed(ActionEvent actionEvent)
 480   {
 481   }
 482
 483   public void pdbFile_actionPerformed(ActionEvent actionEvent)
 484   {
 485
 486   }
 487
 488   public void png_actionPerformed(ActionEvent actionEvent)
 489   {
 490
 491   }
 492
 493   public void eps_actionPerformed(ActionEvent actionEvent)
 494   {
 495
 496   }
 497
 498   public void viewMapping_actionPerformed(ActionEvent actionEvent)
 499   {
 500
 501   }
 502
 503   public void seqColour_actionPerformed(ActionEvent actionEvent)
 504   {
 505
 506   }
 507
 508   public void chainColour_actionPerformed(ActionEvent actionEvent)
 509   {
 510
 511   }
 512
 513   public void chargeColour_actionPerformed(ActionEvent actionEvent)
 514   {
 515
 516   }
 517
 518   public void zappoColour_actionPerformed(ActionEvent actionEvent)
 519   {
 520
 521   }
 522
 523   public void taylorColour_actionPerformed(ActionEvent actionEvent)
 524   {
 525
 526   }
 527
 528   public void hydroColour_actionPerformed(ActionEvent actionEvent)
 529   {
 530
 531   }
 532
 533   public void helixColour_actionPerformed(ActionEvent actionEvent)
 534   {
 535
 536   }
 537
 538   public void strandColour_actionPerformed(ActionEvent actionEvent)
 539   {
 540
 541   }
 542
 543   public void turnColour_actionPerformed(ActionEvent actionEvent)
 544   {
 545
 546   }
 547
 548   public void buriedColour_actionPerformed(ActionEvent actionEvent)
 549   {
 550
 551   }
 552
 553   public void nucleotideColour_actionPerformed(ActionEvent actionEvent)
 554   {
 555
 556   }
 557
 558   public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
 559   {
 560
 561   }
 562
 563   public void userColour_actionPerformed(ActionEvent actionEvent)
 564   {
 565
 566   }
 567
 568   public void backGround_actionPerformed(ActionEvent actionEvent)
 569   {
 570
 571   }
 572
 573   public void showHelp_actionPerformed(ActionEvent actionEvent)
 574   {
 575
 576   }
 577
 578   // {
 579   // return bindingModel;
 580   // }
 581
 582   // public void setBindingModel(AAStructureBindingModel bindingModel)
 583   // {
 584   // this.bindingModel = bindingModel;
 585   // }
 586
 587 }