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