src/jalview/jbgui/GStructureViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.AlignmentPanel;
  25 import jalview.util.MessageManager;
  26
  27 import java.awt.event.ActionEvent;
  28 import java.awt.event.ActionListener;
  29 import java.util.ArrayList;
  30 import java.util.Vector;
  31
  32 import javax.swing.ButtonGroup;
  33 import javax.swing.JInternalFrame;
  34 import javax.swing.JMenu;
  35 import javax.swing.JMenuBar;
  36 import javax.swing.JMenuItem;
  37 import javax.swing.JRadioButtonMenuItem;
  38
  39 public abstract class GStructureViewer extends JInternalFrame implements
  40         JalviewStructureDisplayI
  41 {
  42   // private AAStructureBindingModel bindingModel;
  43
  44   protected JMenu savemenu = new JMenu();
  45
  46   protected JMenu viewMenu = new JMenu();
  47
  48   protected JMenu chainMenu = new JMenu();
  49
  50   protected JMenu viewerActionMenu = new JMenu();
  51
  52   protected JMenuItem alignStructs = new JMenuItem();
  53
  54   protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
  55
  56   protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
  57
  58   protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
  59
  60   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  61
  62   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  63
  64   protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
  65
  66   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  67
  68   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  69
  70   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  71
  72   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  73
  74   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  75
  76   protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
  77
  78   protected JRadioButtonMenuItem viewerColour = new JRadioButtonMenuItem();
  79
  80   protected JMenuItem helpItem = new JMenuItem();
  81
  82   /**
  83    * list of sequenceSet ids associated with the view
  84    */
  85   protected ArrayList<String> _aps = new ArrayList<String>();
  86
  87   /**
  88    * list of alignment panels to use for superposition
  89    */
  90   protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
  91
  92   /**
  93    * list of alignment panels that are used for colouring structures by aligned
  94    * sequences
  95    */
  96   protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
  97
  98   private String viewId = null;
  99
 100   /**
 101    * Constructor
 102    */
 103   public GStructureViewer()
 104   {
 105     try
 106     {
 107       jbInit();
 108     } catch (Exception ex)
 109     {
 110       ex.printStackTrace();
 111     }
 112   }
 113
 114   private void jbInit() throws Exception
 115   {
 116     JMenuBar menuBar = new JMenuBar();
 117     this.setJMenuBar(menuBar);
 118
 119     JMenu fileMenu = new JMenu();
 120     fileMenu.setText(MessageManager.getString("action.file"));
 121
 122     savemenu.setActionCommand(MessageManager.getString("action.save_image"));
 123     savemenu.setText(MessageManager.getString("action.save_as"));
 124
 125     JMenuItem pdbFile = new JMenuItem();
 126     pdbFile.setText(MessageManager.getString("label.pdb_file"));
 127     pdbFile.addActionListener(new ActionListener()
 128     {
 129       public void actionPerformed(ActionEvent actionEvent)
 130       {
 131         pdbFile_actionPerformed(actionEvent);
 132       }
 133     });
 134
 135     JMenuItem png = new JMenuItem();
 136     png.setText("PNG");
 137     png.addActionListener(new ActionListener()
 138     {
 139       public void actionPerformed(ActionEvent actionEvent)
 140       {
 141         png_actionPerformed(actionEvent);
 142       }
 143     });
 144
 145     JMenuItem eps = new JMenuItem();
 146     eps.setText("EPS");
 147     eps.addActionListener(new ActionListener()
 148     {
 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       public void actionPerformed(ActionEvent actionEvent)
 160       {
 161         viewMapping_actionPerformed(actionEvent);
 162       }
 163     });
 164     viewMenu.setText(MessageManager.getString("action.view"));
 165     chainMenu.setText(MessageManager.getString("action.show_chain"));
 166
 167     JMenu colourMenu = new JMenu();
 168     colourMenu.setText(MessageManager.getString("label.colours"));
 169
 170     JMenuItem backGround = new JMenuItem();
 171     backGround.setText(MessageManager.getString("label.background_colour")
 172             + "...");
 173     backGround.addActionListener(new ActionListener()
 174     {
 175       public void actionPerformed(ActionEvent actionEvent)
 176       {
 177         backGround_actionPerformed(actionEvent);
 178       }
 179     });
 180     seqColour.setSelected(false);
 181     seqColour.setText(MessageManager.getString("action.by_sequence"));
 182     seqColour.addActionListener(new ActionListener()
 183     {
 184       public void actionPerformed(ActionEvent actionEvent)
 185       {
 186         seqColour_actionPerformed(actionEvent);
 187       }
 188     });
 189     chainColour.setText(MessageManager.getString("action.by_chain"));
 190     chainColour.addActionListener(new ActionListener()
 191     {
 192       public void actionPerformed(ActionEvent actionEvent)
 193       {
 194         chainColour_actionPerformed(actionEvent);
 195       }
 196     });
 197     chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
 198     chargeColour.addActionListener(new ActionListener()
 199     {
 200       public void actionPerformed(ActionEvent actionEvent)
 201       {
 202         chargeColour_actionPerformed(actionEvent);
 203       }
 204     });
 205     zappoColour.setText(MessageManager.getString("label.zappo"));
 206     zappoColour.addActionListener(new ActionListener()
 207     {
 208       public void actionPerformed(ActionEvent actionEvent)
 209       {
 210         zappoColour_actionPerformed(actionEvent);
 211       }
 212     });
 213     taylorColour.setText(MessageManager.getString("label.taylor"));
 214     taylorColour.addActionListener(new ActionListener()
 215     {
 216       public void actionPerformed(ActionEvent actionEvent)
 217       {
 218         taylorColour_actionPerformed(actionEvent);
 219       }
 220     });
 221     hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
 222     hydroColour.addActionListener(new ActionListener()
 223     {
 224       public void actionPerformed(ActionEvent actionEvent)
 225       {
 226         hydroColour_actionPerformed(actionEvent);
 227       }
 228     });
 229     strandColour.setText(MessageManager
 230             .getString("label.strand_propensity"));
 231     strandColour.addActionListener(new ActionListener()
 232     {
 233       public void actionPerformed(ActionEvent actionEvent)
 234       {
 235         strandColour_actionPerformed(actionEvent);
 236       }
 237     });
 238     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 239     helixColour.addActionListener(new ActionListener()
 240     {
 241       public void actionPerformed(ActionEvent actionEvent)
 242       {
 243         helixColour_actionPerformed(actionEvent);
 244       }
 245     });
 246     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 247     turnColour.addActionListener(new ActionListener()
 248     {
 249       public void actionPerformed(ActionEvent actionEvent)
 250       {
 251         turnColour_actionPerformed(actionEvent);
 252       }
 253     });
 254     buriedColour.setText(MessageManager.getString("label.buried_index"));
 255     buriedColour.addActionListener(new ActionListener()
 256     {
 257       public void actionPerformed(ActionEvent actionEvent)
 258       {
 259         buriedColour_actionPerformed(actionEvent);
 260       }
 261     });
 262     purinePyrimidineColour.setText(MessageManager
 263             .getString("label.purine_pyrimidine"));
 264     purinePyrimidineColour.addActionListener(new ActionListener()
 265     {
 266       public void actionPerformed(ActionEvent actionEvent)
 267       {
 268         purinePyrimidineColour_actionPerformed(actionEvent);
 269       }
 270     });
 271
 272     userColour.setText(MessageManager.getString("action.user_defined"));
 273     userColour.addActionListener(new ActionListener()
 274     {
 275       public void actionPerformed(ActionEvent actionEvent)
 276       {
 277         userColour_actionPerformed(actionEvent);
 278       }
 279     });
 280     viewerColour.setSelected(false);
 281     viewerColour
 282             .setText(MessageManager.getString("label.colour_with_jmol"));
 283     viewerColour.setToolTipText(MessageManager
 284             .getString("label.let_jmol_manage_structure_colours"));
 285     viewerColour.addActionListener(new ActionListener()
 286     {
 287       public void actionPerformed(ActionEvent actionEvent)
 288       {
 289         viewerColour_actionPerformed(actionEvent);
 290       }
 291     });
 292
 293     JMenu helpMenu = new JMenu();
 294     helpMenu.setText(MessageManager.getString("action.help"));
 295     helpItem.setText(MessageManager.getString("label.jmol_help"));
 296     helpItem.addActionListener(new ActionListener()
 297     {
 298       public void actionPerformed(ActionEvent actionEvent)
 299       {
 300         showHelp_actionPerformed(actionEvent);
 301       }
 302     });
 303     alignStructs
 304             .setText(MessageManager.getString("label.align_structures"));
 305     alignStructs.addActionListener(new ActionListener()
 306     {
 307       public void actionPerformed(ActionEvent actionEvent)
 308       {
 309         alignStructs_actionPerformed(actionEvent);
 310       }
 311     });
 312     viewerActionMenu.setText(MessageManager.getString("label.jmol"));
 313     menuBar.add(fileMenu);
 314     menuBar.add(viewMenu);
 315     menuBar.add(colourMenu);
 316     menuBar.add(viewerActionMenu);
 317     viewerActionMenu.setVisible(false);
 318     menuBar.add(helpMenu);
 319     fileMenu.add(savemenu);
 320     fileMenu.add(viewMapping);
 321     savemenu.add(pdbFile);
 322     savemenu.add(png);
 323     savemenu.add(eps);
 324     viewMenu.add(chainMenu);
 325
 326     colourMenu.add(seqColour);
 327     colourMenu.add(chainColour);
 328     colourMenu.add(chargeColour);
 329     colourMenu.add(zappoColour);
 330     colourMenu.add(taylorColour);
 331     colourMenu.add(hydroColour);
 332     colourMenu.add(helixColour);
 333     colourMenu.add(strandColour);
 334     colourMenu.add(turnColour);
 335     colourMenu.add(buriedColour);
 336     colourMenu.add(purinePyrimidineColour);
 337     colourMenu.add(userColour);
 338     colourMenu.add(viewerColour);
 339     colourMenu.add(backGround);
 340
 341     ButtonGroup colourButtons = new ButtonGroup();
 342
 343     colourButtons.add(seqColour);
 344     colourButtons.add(chainColour);
 345     colourButtons.add(chargeColour);
 346     colourButtons.add(zappoColour);
 347     colourButtons.add(taylorColour);
 348     colourButtons.add(hydroColour);
 349     colourButtons.add(helixColour);
 350     colourButtons.add(strandColour);
 351     colourButtons.add(turnColour);
 352     colourButtons.add(buriedColour);
 353     colourButtons.add(userColour);
 354     colourButtons.add(viewerColour);
 355
 356     helpMenu.add(helpItem);
 357     viewerActionMenu.add(alignStructs);
 358   }
 359
 360   protected void viewerColour_actionPerformed(ActionEvent actionEvent)
 361   {
 362   }
 363
 364   protected void alignStructs_actionPerformed(ActionEvent actionEvent)
 365   {
 366   }
 367
 368   public void pdbFile_actionPerformed(ActionEvent actionEvent)
 369   {
 370
 371   }
 372
 373   public void png_actionPerformed(ActionEvent actionEvent)
 374   {
 375
 376   }
 377
 378   public void eps_actionPerformed(ActionEvent actionEvent)
 379   {
 380
 381   }
 382
 383   public void viewMapping_actionPerformed(ActionEvent actionEvent)
 384   {
 385
 386   }
 387
 388   public void seqColour_actionPerformed(ActionEvent actionEvent)
 389   {
 390
 391   }
 392
 393   public void chainColour_actionPerformed(ActionEvent actionEvent)
 394   {
 395
 396   }
 397
 398   public void chargeColour_actionPerformed(ActionEvent actionEvent)
 399   {
 400
 401   }
 402
 403   public void zappoColour_actionPerformed(ActionEvent actionEvent)
 404   {
 405
 406   }
 407
 408   public void taylorColour_actionPerformed(ActionEvent actionEvent)
 409   {
 410
 411   }
 412
 413   public void hydroColour_actionPerformed(ActionEvent actionEvent)
 414   {
 415
 416   }
 417
 418   public void helixColour_actionPerformed(ActionEvent actionEvent)
 419   {
 420
 421   }
 422
 423   public void strandColour_actionPerformed(ActionEvent actionEvent)
 424   {
 425
 426   }
 427
 428   public void turnColour_actionPerformed(ActionEvent actionEvent)
 429   {
 430
 431   }
 432
 433   public void buriedColour_actionPerformed(ActionEvent actionEvent)
 434   {
 435
 436   }
 437
 438   public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
 439   {
 440
 441   }
 442
 443   public void userColour_actionPerformed(ActionEvent actionEvent)
 444   {
 445
 446   }
 447
 448   public void backGround_actionPerformed(ActionEvent actionEvent)
 449   {
 450
 451   }
 452
 453   public void showHelp_actionPerformed(ActionEvent actionEvent)
 454   {
 455
 456   }
 457
 458   // {
 459   // return bindingModel;
 460   // }
 461
 462   // public void setBindingModel(AAStructureBindingModel bindingModel)
 463   // {
 464   // this.bindingModel = bindingModel;
 465   // }
 466
 467   /**
 468    *
 469    * @param ap2
 470    * @return true if this Jmol instance is linked with the given alignPanel
 471    */
 472   public boolean isLinkedWith(AlignmentPanel ap2)
 473   {
 474     return _aps.contains(ap2.av.getSequenceSetId());
 475   }
 476
 477   public boolean isUsedforaligment(AlignmentPanel ap2)
 478   {
 479
 480     return (_alignwith != null) && _alignwith.contains(ap2);
 481   }
 482
 483   public boolean isUsedforcolourby(AlignmentPanel ap2)
 484   {
 485     return (_colourwith != null) && _colourwith.contains(ap2);
 486   }
 487
 488   /**
 489    *
 490    * @return TRUE if the view is NOT being coloured by the alignment colours.
 491    */
 492   public boolean isColouredByViewer()
 493   {
 494     return !getBinding().isColourBySequence();
 495   }
 496
 497   public String getViewId()
 498   {
 499     if (viewId == null)
 500     {
 501       viewId = System.currentTimeMillis() + "." + this.hashCode();
 502     }
 503     return viewId;
 504   }
 505
 506   protected void setViewId(String viewId)
 507   {
 508     this.viewId = viewId;
 509   }
 510
 511   public String getStateInfo()
 512   {
 513     return null;
 514   }
 515 }