X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPymolViewer.java;h=665b13740b112385410cb8e1e5c1414d0bff12ea;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=8f7f2c1209b1af14734510bf9615309f28fa89a9;hpb=28f21e26830c0df0529e74f8de1019476eaca7bf;p=jalview.git diff --git a/src/jalview/gui/PymolViewer.java b/src/jalview/gui/PymolViewer.java index 8f7f2c1..665b137 100644 --- a/src/jalview/gui/PymolViewer.java +++ b/src/jalview/gui/PymolViewer.java @@ -1,24 +1,30 @@ package jalview.gui; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.io.File; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; + +import javax.swing.JInternalFrame; +import javax.swing.JMenuItem; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.datamodel.StructureViewerModel; +import jalview.datamodel.StructureViewerModel.StructureData; import jalview.gui.StructureViewer.ViewerType; import jalview.io.DataSourceType; import jalview.io.StructureFile; import jalview.structures.models.AAStructureBindingModel; import jalview.util.MessageManager; -import java.io.File; -import java.util.ArrayList; -import java.util.List; - -import javax.swing.JInternalFrame; -import javax.swing.event.InternalFrameAdapter; -import javax.swing.event.InternalFrameEvent; - public class PymolViewer extends StructureViewerBase { private static final int myWidth = 500; @@ -44,9 +50,7 @@ public class PymolViewer extends StructureViewerBase AlignmentPanel ap) { this(); - openNewPymol(ap, new PDBEntry[] { pdb }, - new SequenceI[][] - { seqs }); + openNewPymol(ap, new PDBEntry[] { pdb }, new SequenceI[][] { seqs }); } public PymolViewer(PDBEntry[] pe, boolean alignAdded, SequenceI[][] seqs, @@ -57,6 +61,54 @@ public class PymolViewer extends StructureViewerBase openNewPymol(ap, pe, seqs); } + /** + * Constructor given a session file to be restored + * + * @param sessionFile + * @param alignPanel + * @param pdbArray + * @param seqsArray + * @param colourByPymol + * @param colourBySequence + * @param newViewId + */ + public PymolViewer(StructureViewerModel viewerModel, + AlignmentPanel alignPanel, String sessionFile, String vid) + { + // TODO convert to base/factory class method + this(); + setViewId(vid); + this.pymolSessionFile = sessionFile; + Map pdbData = viewerModel.getFileData(); + PDBEntry[] pdbArray = new PDBEntry[pdbData.size()]; + SequenceI[][] seqsArray = new SequenceI[pdbData.size()][]; + int i = 0; + for (StructureData data : pdbData.values()) + { + PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null, + PDBEntry.Type.PDB, data.getFilePath()); + pdbArray[i] = pdbentry; + List sequencesForPdb = data.getSeqList(); + seqsArray[i] = sequencesForPdb + .toArray(new SequenceI[sequencesForPdb.size()]); + i++; + } + + openNewPymol(alignPanel, pdbArray, seqsArray); + if (viewerModel.isColourByViewer()) + { + binding.setColourBySequence(false); + seqColour.setSelected(false); + viewerColour.setSelected(true); + } + else if (viewerModel.isColourWithAlignPanel()) + { + binding.setColourBySequence(true); + seqColour.setSelected(true); + viewerColour.setSelected(false); + } + } + private void openNewPymol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs) { @@ -107,11 +159,12 @@ public class PymolViewer extends StructureViewerBase public void run() { // todo pull up much of this - + StringBuilder errormsgs = new StringBuilder(128); List filePDB = new ArrayList<>(); List filePDBpos = new ArrayList<>(); - String[] curfiles = binding.getStructureFiles(); // files currently in viewer + String[] curfiles = binding.getStructureFiles(); // files currently in + // viewer for (int pi = 0; pi < binding.getPdbCount(); pi++) { String file = null; @@ -132,8 +185,7 @@ public class PymolViewer extends StructureViewerBase /* * got file already */ - file = new File(thePdbEntry.getFile()).getAbsoluteFile() - .getPath(); + file = new File(thePdbEntry.getFile()).getAbsoluteFile().getPath(); // todo - skip if already loaded in PyMOL } if (file != null) @@ -142,7 +194,7 @@ public class PymolViewer extends StructureViewerBase filePDBpos.add(Integer.valueOf(pi)); } } - + if (!filePDB.isEmpty()) { /* @@ -156,9 +208,19 @@ public class PymolViewer extends StructureViewerBase initPymol(); } catch (Exception ex) { - Cache.log.error("Couldn't open PyMOL viewer!", ex); + Console.error("Couldn't open PyMOL viewer!", ex); + // if we couldn't open Pymol, no point continuing + return; } } + if (!binding.isViewerRunning()) + { + // nothing to do + // TODO: ensure we tidy up JAL-3619 + + return; + } + int num = -1; for (PDBEntry pe : filePDB) { @@ -190,17 +252,15 @@ public class PymolViewer extends StructureViewerBase StructureFile pdb = binding.getSsm().setMapping( binding.getSequence()[pos], binding.getChains()[pos], - pe.getFile(), protocol, - getProgressIndicator()); + pe.getFile(), protocol, getProgressIndicator()); binding.stashFoundChains(pdb, pe.getFile()); } catch (Exception ex) { - Cache.log.error( - "Couldn't open " + pe.getFile() + " in Chimera viewer!", - ex); + Console.error("Couldn't open " + pe.getFile() + " in " + + getViewerName() + "!", ex); } finally { - // Cache.log.debug("File locations are " + files); + // Cache.debug("File locations are " + files); } } } @@ -256,9 +316,11 @@ public class PymolViewer extends StructureViewerBase if (!binding.launchPymol()) { JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.getString("label.pymol_failed"), + MessageManager.formatMessage("label.open_viewer_failed", + getViewerName()), MessageManager.getString("label.error_loading_file"), JvOptionPane.ERROR_MESSAGE); + binding.closeViewer(true); this.dispose(); return; } @@ -268,7 +330,7 @@ public class PymolViewer extends StructureViewerBase boolean opened = binding.openSession(pymolSessionFile); if (!opened) { - System.err.println("An error occurred opening PyMOL session file " + Console.error("An error occurred opening PyMOL session file " + pymolSessionFile); } } @@ -282,59 +344,54 @@ public class PymolViewer extends StructureViewerBase } @Override - public void closeViewer(boolean closePymol) + public ViewerType getViewerType() { - if (binding != null && binding.isPymolRunning()) - { - if (!closePymol) - { - // TODO i18n (and pull up) - String prompt = MessageManager - .formatMessage("label.confirm_close_pymol", new Object[] - { binding.getViewerTitle(getViewerName(), false) }); - prompt = JvSwingUtils.wrapTooltip(true, prompt); - int confirm = JvOptionPane.showConfirmDialog(this, prompt, - MessageManager.getString("label.close_viewer"), - JvOptionPane.YES_NO_CANCEL_OPTION); - /* - * abort closure if user hits escape or Cancel - */ - if (confirm == JvOptionPane.CANCEL_OPTION - || confirm == JvOptionPane.CLOSED_OPTION) - { - return; - } - closePymol = confirm == JvOptionPane.YES_OPTION; - } - binding.closeViewer(closePymol); - } - setAlignmentPanel(null); - _aps.clear(); - _alignwith.clear(); - _colourwith.clear(); - // TODO: check for memory leaks where instance isn't finalised because - // binding - // holds a reference to the window - binding = null; - dispose(); + return ViewerType.PYMOL; } @Override - public String getStateInfo() + protected String getViewerName() { - return null; + return "PyMOL"; } + JMenuItem writeFeatures = null; + @Override - public ViewerType getViewerType() + protected void initMenus() { - return ViewerType.PYMOL; + super.initMenus(); + + savemenu.setVisible(false); // not yet implemented + viewMenu.add(fitToWindow); + + writeFeatures = new JMenuItem( + MessageManager.getString("label.create_viewer_attributes")); + writeFeatures.setToolTipText( + MessageManager.getString("label.create_viewer_attributes_tip")); + writeFeatures.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sendFeaturesToPymol(); + } + }); + viewerActionMenu.add(writeFeatures); } @Override - protected String getViewerName() + protected void buildActionMenu() { - return "PyMOL"; + super.buildActionMenu(); + viewerActionMenu.add(writeFeatures); + } + + protected void sendFeaturesToPymol() + { + int count = binding.sendFeaturesToViewer(getAlignmentPanel()); + statusBar.setText(MessageManager.formatMessage("label.attributes_set", + count, getViewerName())); } }