src/jalview/gui/PymolViewer.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.gui;
  22
  23 import java.awt.event.ActionEvent;
  24 import java.awt.event.ActionListener;
  25 import java.io.File;
  26 import java.util.ArrayList;
  27 import java.util.List;
  28 import java.util.Map;
  29
  30 import javax.swing.JInternalFrame;
  31 import javax.swing.JMenuItem;
  32 import javax.swing.event.InternalFrameAdapter;
  33 import javax.swing.event.InternalFrameEvent;
  34
  35 import jalview.api.AlignmentViewPanel;
  36 import jalview.api.FeatureRenderer;
  37 import jalview.bin.Console;
  38 import jalview.datamodel.PDBEntry;
  39 import jalview.datamodel.SequenceI;
  40 import jalview.datamodel.StructureViewerModel;
  41 import jalview.datamodel.StructureViewerModel.StructureData;
  42 import jalview.gui.StructureViewer.ViewerType;
  43 import jalview.io.DataSourceType;
  44 import jalview.io.StructureFile;
  45 import jalview.structures.models.AAStructureBindingModel;
  46 import jalview.util.MessageManager;
  47
  48 public class PymolViewer extends StructureViewerBase
  49 {
  50   private static final int myWidth = 500;
  51
  52   private static final int myHeight = 150;
  53
  54   private PymolBindingModel binding;
  55
  56   private String pymolSessionFile;
  57
  58   public PymolViewer()
  59   {
  60     super();
  61
  62     /*
  63      * closeViewer will decide whether or not to close this frame
  64      * depending on whether user chooses to Cancel or not
  65      */
  66     setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
  67   }
  68
  69   public PymolViewer(PDBEntry pdb, SequenceI[] seqs, Object object,
  70           AlignmentPanel ap)
  71   {
  72     this();
  73     openNewPymol(ap, new PDBEntry[] { pdb }, new SequenceI[][] { seqs });
  74   }
  75
  76   public PymolViewer(PDBEntry[] pe, boolean alignAdded, SequenceI[][] seqs,
  77           AlignmentPanel ap)
  78   {
  79     this();
  80     setAlignAddedStructures(alignAdded);
  81     openNewPymol(ap, pe, seqs);
  82   }
  83
  84   /**
  85    * Constructor given a session file to be restored
  86    *
  87    * @param sessionFile
  88    * @param alignPanel
  89    * @param pdbArray
  90    * @param seqsArray
  91    * @param colourByPymol
  92    * @param colourBySequence
  93    * @param newViewId
  94    */
  95   public PymolViewer(StructureViewerModel viewerModel,
  96           AlignmentPanel alignPanel, String sessionFile, String vid)
  97   {
  98     // TODO convert to base/factory class method
  99     this();
 100     setViewId(vid);
 101     this.pymolSessionFile = sessionFile;
 102     Map<File, StructureData> pdbData = viewerModel.getFileData();
 103     PDBEntry[] pdbArray = new PDBEntry[pdbData.size()];
 104     SequenceI[][] seqsArray = new SequenceI[pdbData.size()][];
 105     int i = 0;
 106     for (StructureData data : pdbData.values())
 107     {
 108       PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
 109               PDBEntry.Type.PDB, data.getFilePath());
 110       pdbArray[i] = pdbentry;
 111       List<SequenceI> sequencesForPdb = data.getSeqList();
 112       seqsArray[i] = sequencesForPdb
 113               .toArray(new SequenceI[sequencesForPdb.size()]);
 114       i++;
 115     }
 116
 117     openNewPymol(alignPanel, pdbArray, seqsArray);
 118     if (viewerModel.isColourByViewer())
 119     {
 120       binding.setColourBySequence(false);
 121       seqColour.setSelected(false);
 122       viewerColour.setSelected(true);
 123     }
 124     else if (viewerModel.isColourWithAlignPanel())
 125     {
 126       binding.setColourBySequence(true);
 127       seqColour.setSelected(true);
 128       viewerColour.setSelected(false);
 129     }
 130   }
 131
 132   private void openNewPymol(AlignmentPanel ap, PDBEntry[] pe,
 133           SequenceI[][] seqs)
 134   {
 135     createProgressBar();
 136     binding = new PymolBindingModel(this, ap.getStructureSelectionManager(),
 137             pe, seqs);
 138     addAlignmentPanel(ap);
 139     useAlignmentPanelForColourbyseq(ap);
 140
 141     if (pe.length > 1)
 142     {
 143       useAlignmentPanelForSuperposition(ap);
 144     }
 145     binding.setColourBySequence(true);
 146     setSize(myWidth, myHeight);
 147     initMenus();
 148     viewerActionMenu.setText("PyMOL");
 149     updateTitleAndMenus();
 150
 151     addingStructures = false;
 152     worker = new Thread(this);
 153     worker.start();
 154
 155     this.addInternalFrameListener(new InternalFrameAdapter()
 156     {
 157       @Override
 158       public void internalFrameClosing(
 159               InternalFrameEvent internalFrameEvent)
 160       {
 161         closeViewer(false);
 162       }
 163     });
 164
 165   }
 166
 167   /**
 168    * Create a helper to manage progress bar display
 169    */
 170   protected void createProgressBar()
 171   {
 172     if (getProgressIndicator() == null)
 173     {
 174       setProgressIndicator(new ProgressBar(statusPanel, statusBar));
 175     }
 176   }
 177
 178   @Override
 179   public void run()
 180   {
 181     // todo pull up much of this
 182
 183     StringBuilder errormsgs = new StringBuilder(128);
 184     List<PDBEntry> filePDB = new ArrayList<>();
 185     List<Integer> filePDBpos = new ArrayList<>();
 186     String[] curfiles = binding.getStructureFiles(); // files currently in
 187                                                      // viewer
 188     for (int pi = 0; pi < binding.getPdbCount(); pi++)
 189     {
 190       String file = null;
 191       PDBEntry thePdbEntry = binding.getPdbEntry(pi);
 192       if (thePdbEntry.getFile() == null)
 193       {
 194         /*
 195          * Retrieve PDB data, save to file, attach to PDBEntry
 196          */
 197         file = fetchPdbFile(thePdbEntry);
 198         if (file == null)
 199         {
 200           errormsgs.append("'" + thePdbEntry.getId() + "' ");
 201         }
 202       }
 203       else
 204       {
 205         /*
 206          * got file already
 207          */
 208         file = new File(thePdbEntry.getFile()).getAbsoluteFile().getPath();
 209         // todo - skip if already loaded in PyMOL
 210       }
 211       if (file != null)
 212       {
 213         filePDB.add(thePdbEntry);
 214         filePDBpos.add(Integer.valueOf(pi));
 215       }
 216     }
 217
 218     if (!filePDB.isEmpty())
 219     {
 220       /*
 221        * at least one structure to add to viewer
 222        */
 223       binding.setFinishedInit(false);
 224       if (!addingStructures)
 225       {
 226         try
 227         {
 228           initPymol();
 229         } catch (Exception ex)
 230         {
 231           Console.error("Couldn't open PyMOL viewer!", ex);
 232           // if we couldn't open Pymol, no point continuing
 233           return;
 234         }
 235       }
 236       if (!binding.isViewerRunning())
 237       {
 238         // nothing to do
 239         // TODO: ensure we tidy up JAL-3619
 240
 241         return;
 242       }
 243
 244       int num = -1;
 245       for (PDBEntry pe : filePDB)
 246       {
 247         num++;
 248         if (pe.getFile() != null)
 249         {
 250           try
 251           {
 252             int pos = filePDBpos.get(num).intValue();
 253             long startTime = startProgressBar(getViewerName() + " "
 254                     + MessageManager.getString("status.opening_file_for")
 255                     + " " + pe.getId());
 256             binding.openFile(pe);
 257             binding.addSequence(pos, binding.getSequence()[pos]);
 258             File fl = new File(pe.getFile());
 259             DataSourceType protocol = DataSourceType.URL;
 260             try
 261             {
 262               if (fl.exists())
 263               {
 264                 protocol = DataSourceType.FILE;
 265               }
 266             } catch (Throwable e)
 267             {
 268             } finally
 269             {
 270               stopProgressBar("", startTime);
 271             }
 272
 273             StructureFile pdb = null;
 274             if (pe.hasStructureFile())
 275             {
 276               pdb = pe.getStructureFile();
 277               Console.debug("(Re)Using StructureFile " + pdb.getId());
 278             }
 279             else
 280             {
 281               pdb = binding.getSsm().setMapping(binding.getSequence()[pos],
 282                       binding.getChains()[pos], pe.getFile(), protocol,
 283                       getProgressIndicator());
 284             }
 285             binding.stashFoundChains(pdb, pe.getFile());
 286           } catch (Exception ex)
 287           {
 288             Console.error("Couldn't open " + pe.getFile() + " in "
 289                     + getViewerName() + "!", ex);
 290           } finally
 291           {
 292             // Cache.debug("File locations are " + files);
 293           }
 294         }
 295       }
 296
 297       binding.refreshGUI();
 298       binding.setFinishedInit(true);
 299       binding.setLoadingFromArchive(false);
 300
 301       /*
 302        * ensure that any newly discovered features (e.g. RESNUM)
 303        * are added to any open feature settings dialog
 304        */
 305       FeatureRenderer fr = getBinding().getFeatureRenderer(null);
 306       if (fr != null)
 307       {
 308         fr.featuresAdded();
 309       }
 310
 311       // refresh the sequence colours for the new structure(s)
 312       for (AlignmentViewPanel ap : _colourwith)
 313       {
 314         binding.updateColours(ap);
 315       }
 316       // do superposition if asked to
 317       if (alignAddedStructures)
 318       {
 319         new Thread(new Runnable()
 320         {
 321           @Override
 322           public void run()
 323           {
 324             alignStructsWithAllAlignPanels();
 325           }
 326         }).start();
 327       }
 328       addingStructures = false;
 329     }
 330     _started = false;
 331     worker = null;
 332
 333   }
 334
 335   /**
 336    * Launch PyMOL. If we have a session file name, send PyMOL the command to
 337    * open its saved session file.
 338    */
 339   void initPymol()
 340   {
 341     Desktop.addInternalFrame(this,
 342             binding.getViewerTitle(getViewerName(), true),
 343             getBounds().width, getBounds().height);
 344
 345     if (!binding.launchPymol())
 346     {
 347       JvOptionPane.showMessageDialog(Desktop.desktop,
 348               MessageManager.formatMessage("label.open_viewer_failed",
 349                       getViewerName()),
 350               MessageManager.getString("label.error_loading_file"),
 351               JvOptionPane.ERROR_MESSAGE);
 352       binding.closeViewer(true);
 353       this.dispose();
 354       return;
 355     }
 356
 357     if (this.pymolSessionFile != null)
 358     {
 359       boolean opened = binding.openSession(pymolSessionFile);
 360       if (!opened)
 361       {
 362         Console.error("An error occurred opening PyMOL session file "
 363                 + pymolSessionFile);
 364       }
 365     }
 366     // binding.startPymolListener();
 367   }
 368
 369   @Override
 370   public AAStructureBindingModel getBinding()
 371   {
 372     return binding;
 373   }
 374
 375   @Override
 376   public ViewerType getViewerType()
 377   {
 378     return ViewerType.PYMOL;
 379   }
 380
 381   @Override
 382   protected String getViewerName()
 383   {
 384     return "PyMOL";
 385   }
 386
 387   JMenuItem writeFeatures = null;
 388
 389   @Override
 390   protected void initMenus()
 391   {
 392     super.initMenus();
 393
 394     savemenu.setVisible(false); // not yet implemented
 395     viewMenu.add(fitToWindow);
 396
 397     writeFeatures = new JMenuItem(
 398             MessageManager.getString("label.create_viewer_attributes"));
 399     writeFeatures.setToolTipText(
 400             MessageManager.getString("label.create_viewer_attributes_tip"));
 401     writeFeatures.addActionListener(new ActionListener()
 402     {
 403       @Override
 404       public void actionPerformed(ActionEvent e)
 405       {
 406         sendFeaturesToPymol();
 407       }
 408     });
 409     viewerActionMenu.add(writeFeatures);
 410   }
 411
 412   @Override
 413   protected void buildActionMenu()
 414   {
 415     super.buildActionMenu();
 416     viewerActionMenu.add(writeFeatures);
 417   }
 418
 419   protected void sendFeaturesToPymol()
 420   {
 421     int count = binding.sendFeaturesToViewer(getAlignmentPanel());
 422     statusBar.setText(MessageManager.formatMessage("label.attributes_set",
 423             count, getViewerName()));
 424   }
 425
 426 }