X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=567a14cb80ecaf3d5819d21c9b66eedb5e424331;hb=c66902a9536b10a5477b58aaf7c2d75772890a5d;hp=a3ff00b5198bc0d428fbb03f7892d773fc785023;hpb=ae216fceddd8539d20fa5425cdaef3da73aba8f0;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index a3ff00b..567a14c 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -20,14 +20,13 @@ */ package jalview.gui; -import jalview.api.SequenceStructureBinding; -import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.ext.rbvi.chimera.JalviewChimeraBinding; import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AppletFormatAdapter; import jalview.io.JalviewFileChooser; @@ -42,8 +41,10 @@ import jalview.schemes.StrandColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.ZappoColourScheme; +import jalview.structures.models.AAStructureBindingModel; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.ws.dbsources.Pdb; import java.awt.Component; import java.awt.event.ActionEvent; @@ -54,9 +55,9 @@ import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; import java.io.FileReader; +import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; -import java.util.Enumeration; import java.util.List; import java.util.Vector; @@ -78,73 +79,43 @@ import javax.swing.event.MenuListener; * */ public class ChimeraViewFrame extends GStructureViewer implements Runnable, - ViewSetProvider, JalviewStructureDisplayI - + ViewSetProvider { - JalviewChimeraBindingModel jmb; + private JalviewChimeraBinding jmb; + + private boolean allChainsSelected = false; + + private boolean alignAddedStructures = false; AlignmentPanel ap; - Vector atomsPicked = new Vector(); + /* + * state flag for PDB retrieval thread + */ + private boolean _started = false; private boolean addingStructures = false; - ViewSelectionMenu seqColourBy; + private IProgressIndicator progressBar = null; + + /* + * pdb retrieval thread. + */ + private Thread worker = null; /** - * - * @param files - * @param ids - * @param seqs - * @param ap - * @param usetoColour - * - add the alignment panel to the list used for colouring these - * structures - * @param useToAlign - * - add the alignment panel to the list used for aligning these - * structures - * @param leaveColouringToJmol - * - do not update the colours from any other source. Jmol is - * handling them - * @param loadStatus - * @param bounds - * @param viewid - * - * public ChimeraViewFrame(String[] files, String[] ids, - * SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour, - * boolean useToAlign, boolean leaveColouringToJmol, String - * loadStatus, Rectangle bounds, String viewid) { PDBEntry[] - * pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < - * pdbentrys.length; i++) { PDBEntry pdbentry = new PDBEntry(); - * pdbentry.setFile(files[i]); pdbentry.setId(ids[i]); pdbentrys[i] = - * pdbentry; } // / TODO: check if protocol is needed to be set, and - * if chains are // autodiscovered. jmb = new - * JalviewChimeraBindingModel(this, - * ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); - * - * jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); if - * (useToAlign) { useAlignmentPanelForSuperposition(ap); } if - * (leaveColouringToJmol || !usetoColour) { - * jmb.setColourBySequence(false); seqColour.setSelected(false); - * jmolColour.setSelected(true); } if (usetoColour) { - * useAlignmentPanelForColourbyseq(ap); - * jmb.setColourBySequence(true); seqColour.setSelected(true); - * jmolColour.setSelected(false); } this.setBounds(bounds); - * initMenus(); viewId = viewid; // - * jalview.gui.Desktop.addInternalFrame(this, "Loading File", // - * bounds.width,bounds.height); - * - * this.addInternalFrameListener(new InternalFrameAdapter() { public - * void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - * closeViewer(); } }); initJmol(loadStatus); // pdbentry, seq, - * JBPCHECK! - * - * } + * Initialise menu options. */ private void initMenus() { + viewerActionMenu.setText(MessageManager.getString("label.chimera")); + viewerColour.setText(MessageManager + .getString("label.colour_with_chimera")); + viewerColour.setToolTipText(MessageManager + .getString("label.let_chimera_manage_structure_colours")); + helpItem.setText(MessageManager.getString("label.chimera_help")); seqColour.setSelected(jmb.isColourBySequence()); - jmolColour.setSelected(!jmb.isColourBySequence()); + viewerColour.setSelected(!jmb.isColourBySequence()); if (_colourwith == null) { _colourwith = new Vector(); @@ -154,10 +125,13 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, _alignwith = new Vector(); } - seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith, + // save As not yet implemented + savemenu.setVisible(false); + + ViewSelectionMenu seqColourBy = new ViewSelectionMenu( + MessageManager.getString("label.colour_by"), this, _colourwith, new ItemListener() { - @Override public void itemStateChanged(ItemEvent e) { @@ -167,17 +141,17 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } else { - // update the jmol display now. + // update the Chimera display now. seqColour_actionPerformed(null); } } }); viewMenu.add(seqColourBy); final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this, + JMenu alpanels = new ViewSelectionMenu( + MessageManager.getString("label.superpose_with"), this, _alignwith, handler = new ItemListener() { - @Override public void itemStateChanged(ItemEvent e) { @@ -185,13 +159,13 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, alignStructs.setToolTipText(MessageManager .formatMessage( "label.align_structures_using_linked_alignment_views", - new String[] + new Object[] { new Integer(_alignwith.size()).toString() })); } }); handler.itemStateChanged(null); - jmolActionMenu.add(alpanels); - jmolActionMenu.addMenuListener(new MenuListener() + viewerActionMenu.add(alpanels); + viewerActionMenu.addMenuListener(new MenuListener() { @Override @@ -204,22 +178,18 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, public void menuDeselected(MenuEvent e) { // TODO Auto-generated method stub - } @Override public void menuCanceled(MenuEvent e) { // TODO Auto-generated method stub - } }); } - IProgressIndicator progressBar = null; - /** - * add a single PDB structure to a new or existing Jmol view + * add a single PDB structure to a new or existing Chimera view * * @param pdbentry * @param seq @@ -229,6 +199,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq, String[] chains, final AlignmentPanel ap) { + super(); progressBar = ap.alignFrame; // //////////////////////////////// // Is the pdb file already loaded? @@ -239,42 +210,49 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, { int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, MessageManager.formatMessage( - "label.pdb_entry_is_already_displayed", new String[] + "label.pdb_entry_is_already_displayed", new Object[] { pdbentry.getId() }), MessageManager.formatMessage( - "label.map_sequences_to_visible_window", new String[] - { pdbentry.getId() }), JOptionPane.YES_NO_OPTION); + "label.map_sequences_to_visible_window", new Object[] + { pdbentry.getId() }), + JOptionPane.YES_NO_CANCEL_OPTION); + if (option == JOptionPane.CANCEL_OPTION) + { + return; + } if (option == JOptionPane.YES_OPTION) { // TODO : Fix multiple seq to one chain issue here. ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE); - if (ap.seqPanel.seqCanvas.fr != null) + if (ap.getSeqPanel().seqCanvas.fr != null) { - ap.seqPanel.seqCanvas.fr.featuresAdded(); + ap.getSeqPanel().seqCanvas.fr.featuresAdded(); ap.paintAlignment(true); } - // Now this AppJmol is mapped to new sequences. We must add them to - // the exisiting array + // Now this ChimeraViewFrame is mapped to new sequences. We must add + // them to the existing array JInternalFrame[] frames = Desktop.instance.getAllFrames(); - for (int i = 0; i < frames.length; i++) + for (JInternalFrame frame : frames) { - if (frames[i] instanceof ChimeraViewFrame) + if (frame instanceof ChimeraViewFrame) { - final ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]); + final ChimeraViewFrame topView = ((ChimeraViewFrame) frame); // JBPNOTE: this looks like a binding routine, rather than a gui // routine - for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++) + for (int pe = 0; pe < topView.jmb.getPdbCount(); pe++) { - if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped)) + if (topView.jmb.getPdbEntry(pe).getFile() + .equals( + alreadyMapped)) { - topJmol.jmb.addSequence(pe, seq); - topJmol.addAlignmentPanel(ap); + topView.jmb.addSequence(pe, seq); + topView.addAlignmentPanel(ap); // add it to the set used for colouring - topJmol.useAlignmentPanelForColourbyseq(ap); - topJmol.buildChimeraActionMenu(); + topView.useAlignmentPanelForColourbyseq(ap); + topView.buildChimeraActionMenu(); ap.getStructureSelectionManager() .sequenceColoursChanged(ap); break; @@ -287,40 +265,37 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } } // ///////////////////////////////// - // Check if there are other Jmol views involving this alignment + // Check if there are other Chimera views involving this alignment // and prompt user about adding this molecule to one of them - Vector existingViews = getJmolsFor(ap); - if (existingViews.size() > 0) + List existingViews = getChimeraWindowsFor(ap); + for (ChimeraViewFrame topView : existingViews) { - Enumeration jm = existingViews.elements(); - while (jm.hasMoreElements()) + // TODO: highlight topView in view somehow + int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + MessageManager.formatMessage("label.add_pdbentry_to_view", + new Object[] + { pdbentry.getId(), topView.getTitle() }), + MessageManager + .getString("label.align_to_existing_structure_view"), + JOptionPane.YES_NO_CANCEL_OPTION); + if (option == JOptionPane.CANCEL_OPTION) { - ChimeraViewFrame topJmol = (ChimeraViewFrame) jm.nextElement(); - // TODO: highlight topJmol in view somehow - int option = JOptionPane - .showInternalConfirmDialog( - Desktop.desktop, - MessageManager.formatMessage( - "label.add_pdbentry_to_view", new String[] - { pdbentry.getId(), topJmol.getTitle() }), - MessageManager - .getString("label.align_to_existing_structure_view"), - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) - { - topJmol.useAlignmentPanelForSuperposition(ap); - topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); - return; - } + return; + } + if (option == JOptionPane.YES_OPTION) + { + topView.useAlignmentPanelForSuperposition(ap); + topView.addStructure(pdbentry, seq, chains, true, ap.alignFrame); + return; } } // ///////////////////////////////// - openNewJmol(ap, new PDBEntry[] + openNewChimera(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); } - private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, + private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { progressBar = ap.alignFrame; @@ -353,7 +328,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } /** - * create a new Jmol containing several structures superimposed using the + * create a new viewer containing several structures superimposed using the * given alignPanel. * * @param ap @@ -363,14 +338,10 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs) { - openNewJmol(ap, pe, seqs); + super(); + openNewChimera(ap, pe, seqs); } - /** - * list of sequenceSet ids associated with the view - */ - ArrayList _aps = new ArrayList(); - public AlignmentPanel[] getAllAlignmentPanels() { AlignmentPanel[] t, list = new AlignmentPanel[0]; @@ -390,17 +361,6 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } /** - * list of alignment panels to use for superposition - */ - Vector _alignwith = new Vector(); - - /** - * list of alignment panels that are used for colouring structures by aligned - * sequences - */ - Vector _colourwith = new Vector(); - - /** * set the primary alignmentPanel reference and add another alignPanel to the * list of ones to use for colouring and aligning * @@ -473,7 +433,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, useAlignmentPanelForColourbyseq(nap); jmb.setColourBySequence(enableColourBySeq); seqColour.setSelected(enableColourBySeq); - jmolColour.setSelected(!enableColourBySeq); + viewerColour.setSelected(!enableColourBySeq); } public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) @@ -494,11 +454,6 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } /** - * pdb retrieval thread. - */ - private Thread worker = null; - - /** * add a new structure (with associated sequences and chains) to this viewer, * retrieving it if necessary first. * @@ -554,25 +509,22 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, return; } - private Vector getJmolsFor(AlignmentPanel ap2) + private List getChimeraWindowsFor(AlignmentPanel apanel) { - Vector otherJmols = new Vector(); - // Now this AppJmol is mapped to new sequences. We must add them to - // the exisiting array + List result = new ArrayList(); JInternalFrame[] frames = Desktop.instance.getAllFrames(); - for (int i = 0; i < frames.length; i++) + for (JInternalFrame frame : frames) { - if (frames[i] instanceof ChimeraViewFrame) + if (frame instanceof ChimeraViewFrame) { - ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]); - if (topJmol.isLinkedWith(ap2)) + if (((ChimeraViewFrame) frame).isLinkedWith(apanel)) { - otherJmols.addElement(topJmol); + result.add((ChimeraViewFrame) frame); } } } - return otherJmols; + return result; } void initChimera(String command) @@ -580,20 +532,20 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, jmb.setFinishedInit(false); // TODO: consider waiting until the structure/view is fully loaded before // displaying - jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(), + jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true), getBounds().width, getBounds().height); if (command == null) { command = ""; } - jmb.evalStateCommand(command); + jmb.evalStateCommand(command, false); jmb.setFinishedInit(true); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(List chainNames) { chainMenu.removeAll(); - if (chains == null) + if (chainNames == null) { return; } @@ -607,7 +559,9 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) + { ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); + } } centerViewer(); allChainsSelected = false; @@ -616,15 +570,17 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, chainMenu.add(menuItem); - for (int c = 0; c < chains.size(); c++) + for (String chainName : chainNames) { - menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true); + menuItem = new JCheckBoxMenuItem(chainName, true); menuItem.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent evt) { if (!allChainsSelected) + { centerViewer(); + } } }); @@ -632,15 +588,9 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } } - boolean allChainsSelected = false; - - private boolean alignAddedStructures = false; - void centerViewer() { - Vector toshow = new Vector(); - String lbl; - int mlength, p, mnum; + List toshow = new ArrayList(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) @@ -648,16 +598,31 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); if (item.isSelected()) { - toshow.addElement(item.getText()); + toshow.add(item.getText()); } } } jmb.centerViewer(toshow); } + /** + * Close down this instance of Jalview's Chimera viewer, giving the user the + * option to close the associated Chimera window (process). They may wish to + * keep it open until they have had an opportunity to save any work. + */ public void closeViewer() { - jmb.closeViewer(); + if (jmb.isChimeraRunning()) + { + String prompt = MessageManager + .formatMessage("label.confirm_close_chimera", new Object[] + { jmb.getViewerTitle("Chimera", false) }); + prompt = JvSwingUtils.wrapTooltip(true, prompt); + int confirm = JOptionPane.showConfirmDialog(this, prompt, + MessageManager.getString("label.close_viewer"), + JOptionPane.YES_NO_OPTION); + jmb.closeViewer(confirm == JOptionPane.YES_OPTION); + } ap = null; _aps.clear(); _alignwith.clear(); @@ -668,72 +633,45 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } /** - * state flag for PDB retrieval thread + * Open any newly added PDB structures in Chimera, having first fetched data + * from PDB (if not already saved). */ - private boolean _started = false; - public void run() { _started = true; - String pdbid = ""; - // todo - record which pdbids were successfuly imported. - StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer(); - List fileToLoad=new ArrayList(); + // todo - record which pdbids were successfully imported. + StringBuilder errormsgs = new StringBuilder(128); + StringBuilder files = new StringBuilder(128); List filePDB = new ArrayList(); - List filePDBpos =new ArrayList(); + List filePDBpos = new ArrayList(); + PDBEntry thePdbEntry = null; try { String[] curfiles = jmb.getPdbFile(); // files currently in viewer // TODO: replace with reference fetching/transfer code (validate PDBentry // as a DBRef?) - jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb(); - for (int pi = 0; pi < jmb.pdbentry.length; pi++) + for (int pi = 0; pi < jmb.getPdbCount(); pi++) { - String file = new File(jmb.pdbentry[pi].getFile()) - .getAbsoluteFile().getPath(); - if (file == null) + String file = null; + thePdbEntry = jmb.getPdbEntry(pi); + if (thePdbEntry.getFile() == null) { - // retrieve the pdb and store it locally - AlignmentI pdbseq = null; - pdbid = jmb.pdbentry[pi].getId(); - long hdl = pdbid.hashCode() - System.currentTimeMillis(); - if (progressBar != null) + /* + * Retrieve PDB data, save to file, attach to PDBEntry + */ + file = fetchPdbFile(thePdbEntry); + if (file == null) { - progressBar.setProgressBar("Fetching PDB " + pdbid, hdl); - } - try - { - pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi] - .getId()); - } catch (OutOfMemoryError oomerror) - { - new OOMWarning("Retrieving PDB id " + pdbid, oomerror); - } catch (Exception ex) - { - ex.printStackTrace(); - errormsgs.append("'" + pdbid + "'"); - } - if (progressBar != null) - { - progressBar.setProgressBar("Finished.", hdl); - } - if (pdbseq != null) - { - // just transfer the file name from the first sequence's first - // PDBEntry - file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() - .elementAt(0)).getFile()).getAbsolutePath(); - jmb.pdbentry[pi].setFile(file); - - files.append(" \"" + Platform.escapeString(file) + "\""); - } - else - { - errormsgs.append("'" + pdbid + "' "); + errormsgs.append("'" + thePdbEntry.getId() + "' "); } } else { + /* + * Got file already - ignore if already loaded in Chimera. + */ + file = new File(thePdbEntry.getFile()).getAbsoluteFile() + .getPath(); if (curfiles != null && curfiles.length > 0) { addingStructures = true; // already files loaded. @@ -746,37 +684,35 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } } } - - if (file != null) - { - fileToLoad.add(file); - filePDB.add(jmb.pdbentry[pi]); - filePDBpos.add(Integer.valueOf(pi)); - files.append(" \"" + Platform.escapeString(file) + "\""); - } + } + if (file != null) + { + filePDB.add(thePdbEntry); + filePDBpos.add(Integer.valueOf(pi)); + files.append(" \"" + Platform.escapeString(file) + "\""); } } } catch (OutOfMemoryError oomerror) { - new OOMWarning("Retrieving PDB files: " + pdbid, oomerror); + new OOMWarning("Retrieving PDB files: " + thePdbEntry.getId(), + oomerror); } catch (Exception ex) { ex.printStackTrace(); - errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid - + "'"); + errormsgs.append("When retrieving pdbfiles for '" + + thePdbEntry.getId() + "'"); } if (errormsgs.length() > 0) { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", - new String[] + new Object[] { errormsgs.toString() }), MessageManager .getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE); - } - long lastnotify = jmb.getLoadNotifiesHandled(); + if (files.length() > 0) { if (!addingStructures) @@ -788,8 +724,8 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, { Cache.log.error("Couldn't open Chimera viewer!", ex); } - } - int num=-1; + } + int num = -1; for (PDBEntry pe : filePDB) { num++; @@ -797,26 +733,25 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, { try { - int pos=filePDBpos.get(num).intValue(); + int pos = filePDBpos.get(num).intValue(); jmb.openFile(pe); - jmb.addSequence(pos, jmb.sequence[pos]); - File fl=new File(pe.getFile()); + jmb.addSequence(pos, jmb.getSequence()[pos]); + File fl = new File(pe.getFile()); String protocol = AppletFormatAdapter.URL; try { if (fl.exists()) - { - protocol = AppletFormatAdapter.FILE; - } - } catch (Exception e) - { - } catch (Error e) { + protocol = AppletFormatAdapter.FILE; } - // Explicitly map to the filename used by Jmol ; - jmb.ssm.setMapping(jmb.sequence[pos], null, pe.getFile(), - protocol); - // pdbentry[pe].getFile(), protocol); + } catch (Throwable e) + { + } + // Explicitly map to the filename used by Chimera ; + // TODO: use pe.getId() instead of pe.getFile() ? + jmb.getSsm().setMapping(jmb.getSequence()[pos], null, + pe.getFile(), + protocol); } catch (OutOfMemoryError oomerror) { new OOMWarning( @@ -832,10 +767,9 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } } } - // jmb.getPdbFile(); jmb.setFinishedInit(true); jmb.setLoadingFromArchive(false); - + // refresh the sequence colours for the new structure(s) for (AlignmentPanel ap : _colourwith) { @@ -844,13 +778,13 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, // do superposition if asked to if (alignAddedStructures) { - javax.swing.SwingUtilities.invokeLater(new Runnable() + new Thread(new Runnable() { public void run() { alignStructs_withAllAlignPanels(); } - }); + }).start(); alignAddedStructures = false; } addingStructures = false; @@ -859,24 +793,79 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, worker = null; } + /** + * Fetch PDB data and save to a local file. Returns the full path to the file, + * or null if fetch fails. + * + * @param processingEntry + * @return + * @throws Exception + */ + private String fetchPdbFile(PDBEntry processingEntry) throws Exception + { + String filePath = null; + Pdb pdbclient = new Pdb(); + AlignmentI pdbseq = null; + String pdbid = processingEntry.getId(); + long hdl = pdbid.hashCode() - System.currentTimeMillis(); + if (progressBar != null) + { + progressBar.setProgressBar(MessageManager.formatMessage( + "status.fetching_pdb", new Object[] + { pdbid }), hdl); + } + try + { + pdbseq = pdbclient.getSequenceRecords(pdbid); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("Retrieving PDB id " + pdbid, oomerror); + } finally + { + if (progressBar != null) + { + progressBar + .setProgressBar( + pdbid + + " " + + MessageManager + .getString("label.state_completed"), + hdl); + } + } + /* + * If PDB data were saved and are not invalid (empty alignment), return the + * file path. + */ + if (pdbseq != null && pdbseq.getHeight() > 0) + { + // just use the file name from the first sequence's first PDBEntry + filePath = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() + .elementAt(0)).getFile()).getAbsolutePath(); + processingEntry.setFile(filePath); + } + return filePath; + } + + @Override public void pdbFile_actionPerformed(ActionEvent actionEvent) { JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save PDB File"); + chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { + BufferedReader in = null; try { // TODO: cope with multiple PDB files in view - BufferedReader in = new BufferedReader(new FileReader( - jmb.getPdbFile()[0])); + in = new BufferedReader(new FileReader(jmb.getPdbFile()[0])); File outFile = chooser.getSelectedFile(); PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); @@ -892,18 +881,31 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } catch (Exception ex) { ex.printStackTrace(); + } finally + { + if (in != null) + { + try + { + in.close(); + } catch (IOException e) + { + e.printStackTrace(); + } + } } } } + @Override public void viewMapping_actionPerformed(ActionEvent actionEvent) { jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); try { - for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) + for (int pdbe = 0; pdbe < jmb.getPdbCount(); pdbe++) { - cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile())); + cap.appendText(jmb.printMapping(jmb.getPdbEntry(pdbe).getFile())); cap.appendText("\n"); } } catch (OutOfMemoryError e) @@ -919,37 +921,33 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, 600); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ + @Override public void eps_actionPerformed(ActionEvent e) { - throw new Error("EPS Generation not yet implemented."); + throw new Error( + MessageManager + .getString("error.eps_generation_not_implemented")); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ + @Override public void png_actionPerformed(ActionEvent e) { - throw new Error("PNG Generation not yet implemented."); + throw new Error( + MessageManager + .getString("error.png_generation_not_implemented")); } - public void jmolColour_actionPerformed(ActionEvent actionEvent) + @Override + public void viewerColour_actionPerformed(ActionEvent actionEvent) { - if (jmolColour.isSelected()) + if (viewerColour.isSelected()) { // disable automatic sequence colouring. jmb.setColourBySequence(false); } } + @Override public void seqColour_actionPerformed(ActionEvent actionEvent) { jmb.setColourBySequence(seqColour.isSelected()); @@ -975,82 +973,96 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } } + @Override public void chainColour_actionPerformed(ActionEvent actionEvent) { chainColour.setSelected(true); jmb.colourByChain(); } + @Override public void chargeColour_actionPerformed(ActionEvent actionEvent) { chargeColour.setSelected(true); jmb.colourByCharge(); } + @Override public void zappoColour_actionPerformed(ActionEvent actionEvent) { zappoColour.setSelected(true); jmb.setJalviewColourScheme(new ZappoColourScheme()); } + @Override public void taylorColour_actionPerformed(ActionEvent actionEvent) { taylorColour.setSelected(true); jmb.setJalviewColourScheme(new TaylorColourScheme()); } + @Override public void hydroColour_actionPerformed(ActionEvent actionEvent) { hydroColour.setSelected(true); jmb.setJalviewColourScheme(new HydrophobicColourScheme()); } + @Override public void helixColour_actionPerformed(ActionEvent actionEvent) { helixColour.setSelected(true); jmb.setJalviewColourScheme(new HelixColourScheme()); } + @Override public void strandColour_actionPerformed(ActionEvent actionEvent) { strandColour.setSelected(true); jmb.setJalviewColourScheme(new StrandColourScheme()); } + @Override public void turnColour_actionPerformed(ActionEvent actionEvent) { turnColour.setSelected(true); jmb.setJalviewColourScheme(new TurnColourScheme()); } + @Override public void buriedColour_actionPerformed(ActionEvent actionEvent) { buriedColour.setSelected(true); jmb.setJalviewColourScheme(new BuriedColourScheme()); } + @Override public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new PurinePyrimidineColourScheme()); } + @Override public void userColour_actionPerformed(ActionEvent actionEvent) { userColour.setSelected(true); new UserDefinedColours(this, null); } + @Override public void backGround_actionPerformed(ActionEvent actionEvent) { - java.awt.Color col = JColorChooser.showDialog(this, - "Select Background Colour", null); + java.awt.Color col = JColorChooser + .showDialog(this, MessageManager + .getString("label.select_backgroud_colour"), null); if (col != null) { jmb.setBackgroundColour(col); } } - public void jmolHelp_actionPerformed(ActionEvent actionEvent) + @Override + public void showHelp_actionPerformed(ActionEvent actionEvent) { try { @@ -1061,17 +1073,6 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } } - String viewId = null; - - public String getViewId() - { - if (viewId == null) - { - viewId = System.currentTimeMillis() + "." + this.hashCode(); - } - return viewId; - } - public void updateTitleAndMenus() { if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) @@ -1081,10 +1082,10 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } setChainMenuItems(jmb.chainNames); - this.setTitle(jmb.getViewerTitle()); - if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) + this.setTitle(jmb.getViewerTitle("Chimera", true)); + if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) { - jmolActionMenu.setVisible(true); + viewerActionMenu.setVisible(true); } if (!jmb.isLoadingFromArchive()) { @@ -1103,14 +1104,13 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, _alignwith.add(ap); } ; - for (Component c : jmolActionMenu.getMenuComponents()) + for (Component c : viewerActionMenu.getMenuComponents()) { if (c != alignStructs) { - jmolActionMenu.remove((JMenuItem) c); + viewerActionMenu.remove((JMenuItem) c); } } - final ItemListener handler; } /* @@ -1190,39 +1190,20 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, return ap; } - /** - * - * @param ap2 - * @return true if this Jmol instance is linked with the given alignPanel - */ - public boolean isLinkedWith(AlignmentPanel ap2) - { - return _aps.contains(ap2.av.getSequenceSetId()); - } - - public boolean isUsedforaligment(AlignmentPanel ap2) - { - - return (_alignwith != null) && _alignwith.contains(ap2); - } - - public boolean isUsedforcolourby(AlignmentPanel ap2) + @Override + public AAStructureBindingModel getBinding() { - return (_colourwith != null) && _colourwith.contains(ap2); + return jmb; } /** + * Ask Chimera to save its session to the designated file path. Returns true + * if successful, else false. * - * @return TRUE if the view is NOT being coloured by sequence associations. + * @param filepath */ - public boolean isColouredByJmol() + public boolean saveSession(String filepath) { - return !jmb.isColourBySequence(); + return jmb.saveSession(filepath); } - - public SequenceStructureBinding getBinding() - { - return jmb; - } - }