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