src/jalview/gui/PymolViewer.java

   1 package jalview.gui;
   2
   3 import java.awt.event.ActionEvent;
   4 import java.awt.event.ActionListener;
   5 import java.io.File;
   6 import java.util.ArrayList;
   7 import java.util.List;
   8 import java.util.Map;
   9
  10 import javax.swing.JInternalFrame;
  11 import javax.swing.JMenuItem;
  12 import javax.swing.event.InternalFrameAdapter;
  13 import javax.swing.event.InternalFrameEvent;
  14
  15 import jalview.api.AlignmentViewPanel;
  16 import jalview.api.FeatureRenderer;
  17 import jalview.bin.Console;
  18 import jalview.datamodel.PDBEntry;
  19 import jalview.datamodel.SequenceI;
  20 import jalview.datamodel.StructureViewerModel;
  21 import jalview.datamodel.StructureViewerModel.StructureData;
  22 import jalview.gui.StructureViewer.ViewerType;
  23 import jalview.io.DataSourceType;
  24 import jalview.io.StructureFile;
  25 import jalview.structures.models.AAStructureBindingModel;
  26 import jalview.util.MessageManager;
  27
  28 public class PymolViewer extends StructureViewerBase
  29 {
  30   private static final int myWidth = 500;
  31
  32   private static final int myHeight = 150;
  33
  34   private PymolBindingModel binding;
  35
  36   private String pymolSessionFile;
  37
  38   public PymolViewer()
  39   {
  40     super();
  41
  42     /*
  43      * closeViewer will decide whether or not to close this frame
  44      * depending on whether user chooses to Cancel or not
  45      */
  46     setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
  47   }
  48
  49   public PymolViewer(PDBEntry pdb, SequenceI[] seqs, Object object,
  50           AlignmentPanel ap)
  51   {
  52     this();
  53     openNewPymol(ap, new PDBEntry[] { pdb }, new SequenceI[][] { seqs });
  54   }
  55
  56   public PymolViewer(PDBEntry[] pe, boolean alignAdded, SequenceI[][] seqs,
  57           AlignmentPanel ap)
  58   {
  59     this();
  60     setAlignAddedStructures(alignAdded);
  61     openNewPymol(ap, pe, seqs);
  62   }
  63
  64   /**
  65    * Constructor given a session file to be restored
  66    *
  67    * @param sessionFile
  68    * @param alignPanel
  69    * @param pdbArray
  70    * @param seqsArray
  71    * @param colourByPymol
  72    * @param colourBySequence
  73    * @param newViewId
  74    */
  75   public PymolViewer(StructureViewerModel viewerModel,
  76           AlignmentPanel alignPanel, String sessionFile, String vid)
  77   {
  78     // TODO convert to base/factory class method
  79     this();
  80     setViewId(vid);
  81     this.pymolSessionFile = sessionFile;
  82     Map<File, StructureData> pdbData = viewerModel.getFileData();
  83     PDBEntry[] pdbArray = new PDBEntry[pdbData.size()];
  84     SequenceI[][] seqsArray = new SequenceI[pdbData.size()][];
  85     int i = 0;
  86     for (StructureData data : pdbData.values())
  87     {
  88       PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
  89               PDBEntry.Type.PDB, data.getFilePath());
  90       pdbArray[i] = pdbentry;
  91       List<SequenceI> sequencesForPdb = data.getSeqList();
  92       seqsArray[i] = sequencesForPdb
  93               .toArray(new SequenceI[sequencesForPdb.size()]);
  94       i++;
  95     }
  96
  97     openNewPymol(alignPanel, pdbArray, seqsArray);
  98     if (viewerModel.isColourByViewer())
  99     {
 100       binding.setColourBySequence(false);
 101       seqColour.setSelected(false);
 102       viewerColour.setSelected(true);
 103     }
 104     else if (viewerModel.isColourWithAlignPanel())
 105     {
 106       binding.setColourBySequence(true);
 107       seqColour.setSelected(true);
 108       viewerColour.setSelected(false);
 109     }
 110   }
 111
 112   private void openNewPymol(AlignmentPanel ap, PDBEntry[] pe,
 113           SequenceI[][] seqs)
 114   {
 115     createProgressBar();
 116     binding = new PymolBindingModel(this, ap.getStructureSelectionManager(),
 117             pe, seqs);
 118     addAlignmentPanel(ap);
 119     useAlignmentPanelForColourbyseq(ap);
 120
 121     if (pe.length > 1)
 122     {
 123       useAlignmentPanelForSuperposition(ap);
 124     }
 125     binding.setColourBySequence(true);
 126     setSize(myWidth, myHeight);
 127     initMenus();
 128     viewerActionMenu.setText("PyMOL");
 129     updateTitleAndMenus();
 130
 131     addingStructures = false;
 132     worker = new Thread(this);
 133     worker.start();
 134
 135     this.addInternalFrameListener(new InternalFrameAdapter()
 136     {
 137       @Override
 138       public void internalFrameClosing(
 139               InternalFrameEvent internalFrameEvent)
 140       {
 141         closeViewer(false);
 142       }
 143     });
 144
 145   }
 146
 147   /**
 148    * Create a helper to manage progress bar display
 149    */
 150   protected void createProgressBar()
 151   {
 152     if (getProgressIndicator() == null)
 153     {
 154       setProgressIndicator(new ProgressBar(statusPanel, statusBar));
 155     }
 156   }
 157
 158   @Override
 159   public void run()
 160   {
 161     // todo pull up much of this
 162
 163     StringBuilder errormsgs = new StringBuilder(128);
 164     List<PDBEntry> filePDB = new ArrayList<>();
 165     List<Integer> filePDBpos = new ArrayList<>();
 166     String[] curfiles = binding.getStructureFiles(); // files currently in
 167                                                      // viewer
 168     for (int pi = 0; pi < binding.getPdbCount(); pi++)
 169     {
 170       String file = null;
 171       PDBEntry thePdbEntry = binding.getPdbEntry(pi);
 172       if (thePdbEntry.getFile() == null)
 173       {
 174         /*
 175          * Retrieve PDB data, save to file, attach to PDBEntry
 176          */
 177         file = fetchPdbFile(thePdbEntry);
 178         if (file == null)
 179         {
 180           errormsgs.append("'" + thePdbEntry.getId() + "' ");
 181         }
 182       }
 183       else
 184       {
 185         /*
 186          * got file already
 187          */
 188         file = new File(thePdbEntry.getFile()).getAbsoluteFile().getPath();
 189         // todo - skip if already loaded in PyMOL
 190       }
 191       if (file != null)
 192       {
 193         filePDB.add(thePdbEntry);
 194         filePDBpos.add(Integer.valueOf(pi));
 195       }
 196     }
 197
 198     if (!filePDB.isEmpty())
 199     {
 200       /*
 201        * at least one structure to add to viewer
 202        */
 203       binding.setFinishedInit(false);
 204       if (!addingStructures)
 205       {
 206         try
 207         {
 208           initPymol();
 209         } catch (Exception ex)
 210         {
 211           Console.error("Couldn't open PyMOL viewer!", ex);
 212           // if we couldn't open Pymol, no point continuing
 213           return;
 214         }
 215       }
 216       if (!binding.isViewerRunning())
 217       {
 218         // nothing to do
 219         // TODO: ensure we tidy up JAL-3619
 220
 221         return;
 222       }
 223
 224       int num = -1;
 225       for (PDBEntry pe : filePDB)
 226       {
 227         num++;
 228         if (pe.getFile() != null)
 229         {
 230           try
 231           {
 232             int pos = filePDBpos.get(num).intValue();
 233             long startTime = startProgressBar(getViewerName() + " "
 234                     + MessageManager.getString("status.opening_file_for")
 235                     + " " + pe.getId());
 236             binding.openFile(pe);
 237             binding.addSequence(pos, binding.getSequence()[pos]);
 238             File fl = new File(pe.getFile());
 239             DataSourceType protocol = DataSourceType.URL;
 240             try
 241             {
 242               if (fl.exists())
 243               {
 244                 protocol = DataSourceType.FILE;
 245               }
 246             } catch (Throwable e)
 247             {
 248             } finally
 249             {
 250               stopProgressBar("", startTime);
 251             }
 252
 253             StructureFile pdb = binding.getSsm().setMapping(
 254                     binding.getSequence()[pos], binding.getChains()[pos],
 255                     pe.getFile(), protocol, getProgressIndicator());
 256             binding.stashFoundChains(pdb, pe.getFile());
 257           } catch (Exception ex)
 258           {
 259             Console.error("Couldn't open " + pe.getFile() + " in "
 260                     + getViewerName() + "!", ex);
 261           } finally
 262           {
 263             // Cache.debug("File locations are " + files);
 264           }
 265         }
 266       }
 267
 268       binding.refreshGUI();
 269       binding.setFinishedInit(true);
 270       binding.setLoadingFromArchive(false);
 271
 272       /*
 273        * ensure that any newly discovered features (e.g. RESNUM)
 274        * are added to any open feature settings dialog
 275        */
 276       FeatureRenderer fr = getBinding().getFeatureRenderer(null);
 277       if (fr != null)
 278       {
 279         fr.featuresAdded();
 280       }
 281
 282       // refresh the sequence colours for the new structure(s)
 283       for (AlignmentViewPanel ap : _colourwith)
 284       {
 285         binding.updateColours(ap);
 286       }
 287       // do superposition if asked to
 288       if (alignAddedStructures)
 289       {
 290         new Thread(new Runnable()
 291         {
 292           @Override
 293           public void run()
 294           {
 295             alignStructsWithAllAlignPanels();
 296           }
 297         }).start();
 298       }
 299       addingStructures = false;
 300     }
 301     _started = false;
 302     worker = null;
 303
 304   }
 305
 306   /**
 307    * Launch PyMOL. If we have a session file name, send PyMOL the command to
 308    * open its saved session file.
 309    */
 310   void initPymol()
 311   {
 312     Desktop.addInternalFrame(this,
 313             binding.getViewerTitle(getViewerName(), true),
 314             getBounds().width, getBounds().height);
 315
 316     if (!binding.launchPymol())
 317     {
 318       JvOptionPane.showMessageDialog(Desktop.desktop,
 319               MessageManager.formatMessage("label.open_viewer_failed",
 320                       getViewerName()),
 321               MessageManager.getString("label.error_loading_file"),
 322               JvOptionPane.ERROR_MESSAGE);
 323       binding.closeViewer(true);
 324       this.dispose();
 325       return;
 326     }
 327
 328     if (this.pymolSessionFile != null)
 329     {
 330       boolean opened = binding.openSession(pymolSessionFile);
 331       if (!opened)
 332       {
 333         Console.error("An error occurred opening PyMOL session file "
 334                 + pymolSessionFile);
 335       }
 336     }
 337     // binding.startPymolListener();
 338   }
 339
 340   @Override
 341   public AAStructureBindingModel getBinding()
 342   {
 343     return binding;
 344   }
 345
 346   @Override
 347   public ViewerType getViewerType()
 348   {
 349     return ViewerType.PYMOL;
 350   }
 351
 352   @Override
 353   protected String getViewerName()
 354   {
 355     return "PyMOL";
 356   }
 357
 358   JMenuItem writeFeatures = null;
 359
 360   @Override
 361   protected void initMenus()
 362   {
 363     super.initMenus();
 364
 365     savemenu.setVisible(false); // not yet implemented
 366     viewMenu.add(fitToWindow);
 367
 368     writeFeatures = new JMenuItem(
 369             MessageManager.getString("label.create_viewer_attributes"));
 370     writeFeatures.setToolTipText(
 371             MessageManager.getString("label.create_viewer_attributes_tip"));
 372     writeFeatures.addActionListener(new ActionListener()
 373     {
 374       @Override
 375       public void actionPerformed(ActionEvent e)
 376       {
 377         sendFeaturesToPymol();
 378       }
 379     });
 380     viewerActionMenu.add(writeFeatures);
 381   }
 382
 383   @Override
 384   protected void buildActionMenu()
 385   {
 386     super.buildActionMenu();
 387     viewerActionMenu.add(writeFeatures);
 388   }
 389
 390   protected void sendFeaturesToPymol()
 391   {
 392     int count = binding.sendFeaturesToViewer(getAlignmentPanel());
 393     statusBar.setText(MessageManager.formatMessage("label.attributes_set",
 394             count, getViewerName()));
 395   }
 396
 397 }