X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=367ca7f5c6f1baa071ab1a8f0358f662939ab51b;hb=f96e6a945e2df8a844f428c08cfc08210d937fc0;hp=bc247cad7c77ad662110e7b258e2ba75ae0d6f4c;hpb=fd9e6f7e0424bb69e46443d7d96237d99e792c03;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index bc247ca..367ca7f 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -20,62 +20,37 @@ */ package jalview.gui; -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.ChimeraCommands; -import jalview.ext.rbvi.chimera.JalviewChimeraBinding; -import jalview.gui.StructureViewer.ViewerType; -import jalview.io.DataSourceType; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.io.StructureFile; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.HelixColourScheme; -import jalview.schemes.HydrophobicColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -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.event.ActionEvent; import java.awt.event.ActionListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; -import java.io.BufferedReader; import java.io.File; -import java.io.FileInputStream; -import java.io.FileOutputStream; -import java.io.FileReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.PrintWriter; import java.util.ArrayList; import java.util.Collections; import java.util.List; -import java.util.Random; -import java.util.Vector; +import java.util.Map; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; import javax.swing.JInternalFrame; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; + +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.bin.Console; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.datamodel.StructureViewerModel; +import jalview.datamodel.StructureViewerModel.StructureData; +import jalview.ext.rbvi.chimera.JalviewChimeraBinding; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.DataSourceType; +import jalview.io.StructureFile; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.ImageMaker.TYPE; +import jalview.util.MessageManager; +import jalview.util.Platform; /** * GUI elements for handling an external chimera display @@ -87,10 +62,6 @@ public class ChimeraViewFrame extends StructureViewerBase { private JalviewChimeraBinding jmb; - private boolean allChainsSelected = false; - - private IProgressIndicator progressBar = null; - /* * Path to Chimera session file. This is set when an open Jalview/Chimera * session is saved, or on restore from a Jalview project (if it holds the @@ -98,98 +69,29 @@ public class ChimeraViewFrame extends StructureViewerBase */ private String chimeraSessionFile = null; - private Random random = new Random(); + private int myWidth = 500; + + private int myHeight = 150; + + private JMenuItem writeFeatures = null; + + private JMenu fetchAttributes = null; /** * Initialise menu options. */ - private void initMenus() + @Override + protected 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()); - viewerColour.setSelected(!jmb.isColourBySequence()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (_alignwith == null) - { - _alignwith = new Vector(); - } - - // save As not yet implemented - savemenu.setVisible(false); + super.initMenus(); - ViewSelectionMenu seqColourBy = new ViewSelectionMenu( - MessageManager.getString("label.colour_by"), this, _colourwith, - new ItemListener() - { - @Override - public void itemStateChanged(ItemEvent e) - { - if (!seqColour.isSelected()) - { - seqColour.doClick(); - } - else - { - // update the Chimera display now. - seqColour_actionPerformed(null); - } - } - }); - viewMenu.add(seqColourBy); + savemenu.setVisible(false); // not yet implemented viewMenu.add(fitToWindow); - final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu( - MessageManager.getString("label.superpose_with"), this, - _alignwith, handler = new ItemListener() - { - @Override - public void itemStateChanged(ItemEvent e) - { - alignStructs.setEnabled(_alignwith.size() > 0); - alignStructs.setToolTipText(MessageManager - .formatMessage( - "label.align_structures_using_linked_alignment_views", - new Object[] { new Integer(_alignwith - .size()).toString() })); - } - }); - handler.itemStateChanged(null); - viewerActionMenu.add(alpanels); - viewerActionMenu.addMenuListener(new MenuListener() - { - - @Override - public void menuSelected(MenuEvent e) - { - handler.itemStateChanged(null); - } - - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - } - - @Override - public void menuCanceled(MenuEvent e) - { - // TODO Auto-generated method stub - } - }); - - JMenuItem writeFeatures = new JMenuItem( - MessageManager.getString("label.create_chimera_attributes")); - writeFeatures.setToolTipText(MessageManager - .getString("label.create_chimera_attributes_tip")); + writeFeatures = new JMenuItem( + MessageManager.getString("label.create_viewer_attributes")); + writeFeatures.setToolTipText( + MessageManager.getString("label.create_viewer_attributes_tip")); writeFeatures.addActionListener(new ActionListener() { @Override @@ -200,9 +102,10 @@ public class ChimeraViewFrame extends StructureViewerBase }); viewerActionMenu.add(writeFeatures); - final JMenu fetchAttributes = new JMenu("Fetch Chimera attributes"); - fetchAttributes - .setToolTipText("Copy Chimera attribute to Jalview feature"); + fetchAttributes = new JMenu(MessageManager.formatMessage( + "label.fetch_viewer_attributes", getViewerName())); + fetchAttributes.setToolTipText(MessageManager.formatMessage( + "label.fetch_viewer_attributes_tip", getViewerName())); fetchAttributes.addMouseListener(new MouseAdapter() { @@ -213,73 +116,62 @@ public class ChimeraViewFrame extends StructureViewerBase } }); viewerActionMenu.add(fetchAttributes); - } + @Override + protected void buildActionMenu() + { + super.buildActionMenu(); + // add these back in after menu is refreshed + viewerActionMenu.add(writeFeatures); + viewerActionMenu.add(fetchAttributes); + + }; + /** - * Query Chimera for its residue attribute names and add them as items off the - * attributes menu + * Query the structure viewer for its residue attribute names and add them as + * items off the attributes menu * * @param attributesMenu */ protected void buildAttributesMenu(JMenu attributesMenu) { - List atts = jmb.sendChimeraCommand("list resattr", true); - if (atts == null) - { - return; - } + List atts = jmb.getChimeraAttributes(); attributesMenu.removeAll(); Collections.sort(atts); - for (String att : atts) + for (String attName : atts) { - final String attName = att.split(" ")[1]; - - /* - * ignore 'jv_*' attributes, as these are Jalview features that have - * been transferred to residue attributes in Chimera! - */ - if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX)) + JMenuItem menuItem = new JMenuItem(attName); + menuItem.addActionListener(new ActionListener() { - JMenuItem menuItem = new JMenuItem(attName); - menuItem.addActionListener(new ActionListener() + @Override + public void actionPerformed(ActionEvent e) { - @Override - public void actionPerformed(ActionEvent e) + if (getBinding().copyStructureAttributesToFeatures(attName, + getAlignmentPanel()) > 0) { - getChimeraAttributes(attName); + getAlignmentPanel().getFeatureRenderer().featuresAdded(); } - }); - attributesMenu.add(menuItem); - } + } + }); + attributesMenu.add(menuItem); } } /** - * Read residues in Chimera with the given attribute name, and set as features - * on the corresponding sequence positions (if any) - * - * @param attName - */ - protected void getChimeraAttributes(String attName) - { - jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel()); - } - - /** - * Send a command to Chimera to create residue attributes for Jalview features - *

- * The syntax is: setattr r - *

- * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A + * Sends command(s) to the structure viewer to create residue attributes for + * visible Jalview features */ protected void sendFeaturesToChimera() { - jmb.sendFeaturesToViewer(getAlignmentPanel()); + // todo pull up? + int count = jmb.sendFeaturesToViewer(getAlignmentPanel()); + statusBar.setText(MessageManager.formatMessage("label.attributes_set", + count, getViewerName())); } /** - * add a single PDB structure to a new or existing Chimera view + * open a single PDB structure in a new Chimera view * * @param pdbentry * @param seq @@ -290,32 +182,10 @@ public class ChimeraViewFrame extends StructureViewerBase String[] chains, final AlignmentPanel ap) { this(); - String pdbId = pdbentry.getId(); - /* - * If the PDB file is already loaded, the user may just choose to add to an - * existing viewer (or cancel) - */ - if (addAlreadyLoadedFile(seq, chains, ap, pdbId)) - { - return; - } - - /* - * Check if there are other Chimera views involving this alignment and give - * user the option to add and align this molecule to one of them (or cancel) - */ - if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId)) - { - return; - } - - /* - * If the options above are declined or do not apply, show the structure in - * a new viewer - */ openNewChimera(ap, new PDBEntry[] { pdbentry }, - new SequenceI[][] { seq }); + new SequenceI[][] + { seq }); } /** @@ -323,46 +193,37 @@ public class ChimeraViewFrame extends StructureViewerBase */ protected void createProgressBar() { - if (progressBar == null) + if (getProgressIndicator() == null) { - progressBar = new ProgressBar(statusPanel, statusBar); + setProgressIndicator(new ProgressBar(statusPanel, statusBar)); } } - /** - * Answers true if this viewer already involves the given PDB ID - */ - @Override - protected boolean hasPdbId(String pdbId) - { - return jmb.hasPdbId(pdbId); - } - private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { createProgressBar(); - jmb = new JalviewChimeraBindingModel(this, - ap.getStructureSelectionManager(), pdbentrys, seqs, null); + jmb = newBindingModel(ap, pdbentrys, seqs); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length > 1) { - alignAddedStructures = true; useAlignmentPanelForSuperposition(ap); } jmb.setColourBySequence(true); - setSize(400, 400); // probably should be a configurable/dynamic default here + setSize(myWidth, myHeight); initMenus(); addingStructures = false; - worker = new Thread(this); + worker = new Thread(this, "OpenChimeraThread"); worker.start(); this.addInternalFrameListener(new InternalFrameAdapter() { @Override - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) + public void internalFrameClosing( + InternalFrameEvent internalFrameEvent) { closeViewer(false); } @@ -370,6 +231,13 @@ public class ChimeraViewFrame extends StructureViewerBase } + protected JalviewChimeraBindingModel newBindingModel(AlignmentPanel ap, + PDBEntry[] pdbentrys, SequenceI[][] seqs) + { + return new JalviewChimeraBindingModel(this, + ap.getStructureSelectionManager(), pdbentrys, seqs, null); + } + /** * Create a new viewer from saved session state data including Chimera session * file @@ -382,22 +250,34 @@ public class ChimeraViewFrame extends StructureViewerBase * @param colourBySequence * @param newViewId */ - public ChimeraViewFrame(String chimeraSessionFile, - AlignmentPanel alignPanel, PDBEntry[] pdbArray, - SequenceI[][] seqsArray, boolean colourByChimera, - boolean colourBySequence, String newViewId) + public ChimeraViewFrame(StructureViewerModel viewerData, + AlignmentPanel alignPanel, String sessionFile, String vid) { this(); - setViewId(newViewId); - this.chimeraSessionFile = chimeraSessionFile; + setViewId(vid); + this.chimeraSessionFile = sessionFile; + Map pdbData = viewerData.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++; + } openNewChimera(alignPanel, pdbArray, seqsArray); - if (colourByChimera) + if (viewerData.isColourByViewer()) { jmb.setColourBySequence(false); seqColour.setSelected(false); viewerColour.setSelected(true); } - else if (colourBySequence) + else if (viewerData.isColourWithAlignPanel()) { jmb.setColourBySequence(true); seqColour.setSelected(true); @@ -406,17 +286,18 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * create a new viewer containing several structures superimposed using the - * given alignPanel. + * create a new viewer containing several structures, optionally superimposed + * using the given alignPanel. * * @param pe * @param seqs * @param ap */ - public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs, - AlignmentPanel ap) + public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded, + SequenceI[][] seqs, AlignmentPanel ap) { this(); + setAlignAddedStructures(alignAdded); openNewChimera(ap, pe, seqs); } @@ -434,22 +315,25 @@ public class ChimeraViewFrame extends StructureViewerBase setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE); } - /** * Launch Chimera. If we have a chimera session file name, send Chimera the * command to open its saved session file. */ void initChimera() { - Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true), - getBounds().width, getBounds().height); + jmb.setFinishedInit(false); + Desktop.addInternalFrame(this, + jmb.getViewerTitle(getViewerName(), true), getBounds().width, + getBounds().height); if (!jmb.launchChimera()) { JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.getString("label.chimera_failed"), + MessageManager.formatMessage("label.open_viewer_failed", + getViewerName()), MessageManager.getString("label.error_loading_file"), JvOptionPane.ERROR_MESSAGE); + jmb.closeViewer(true); this.dispose(); return; } @@ -459,9 +343,8 @@ public class ChimeraViewFrame extends StructureViewerBase boolean opened = jmb.openSession(chimeraSessionFile); if (!opened) { - System.err - .println("An error occurred opening Chimera session file " - + chimeraSessionFile); + System.err.println("An error occurred opening Chimera session file " + + chimeraSessionFile); } } @@ -469,138 +352,6 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * If the list is not empty, add menu items for 'All' and each individual - * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed. - * - * @param chainNames - */ - @Override - void setChainMenuItems(List chainNames) - { - chainMenu.removeAll(); - if (chainNames == null || chainNames.isEmpty()) - { - return; - } - JMenuItem menuItem = new JMenuItem( - MessageManager.getString("label.all")); - menuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - allChainsSelected = true; - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) - { - ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); - } - } - showSelectedChains(); - allChainsSelected = false; - } - }); - - chainMenu.add(menuItem); - - for (String chainName : chainNames) - { - menuItem = new JCheckBoxMenuItem(chainName, true); - menuItem.addItemListener(new ItemListener() - { - @Override - public void itemStateChanged(ItemEvent evt) - { - if (!allChainsSelected) - { - showSelectedChains(); - } - } - }); - - chainMenu.add(menuItem); - } - } - - /** - * Show only the selected chain(s) in the viewer - */ - @Override - void showSelectedChains() - { - List toshow = new ArrayList(); - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) - { - JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); - if (item.isSelected()) - { - toshow.add(item.getText()); - } - } - } - jmb.showChains(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. - * - * @param forceCloseChimera - * if true, close any linked Chimera process; if false, prompt first - */ - @Override - public void closeViewer(boolean forceCloseChimera) - { - if (jmb != null) - { - if (jmb.isChimeraRunning()) - { - /* - * force close, or prompt to close, Chimera - */ - if (!forceCloseChimera) - { - String prompt = MessageManager.formatMessage( - "label.confirm_close_chimera", - new Object[] { jmb.getViewerTitle("Chimera", 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; - } - forceCloseChimera = confirm == JvOptionPane.YES_OPTION; - } - } - - /* - * close the viewer plus any side-effects e.g. remove mappings - * note we do this also if closing Chimera triggered this method - */ - jmb.closeViewer(forceCloseChimera); - } - - setAlignmentPanel(null); - _aps.clear(); - _alignwith.clear(); - _colourwith.clear(); - // TODO: check for memory leaks where instance isn't finalised because jmb - // holds a reference to the window - jmb = null; - dispose(); - } - - /** * Open any newly added PDB structures in Chimera, having first fetched data * from PDB (if not already saved). */ @@ -611,13 +362,13 @@ public class ChimeraViewFrame extends StructureViewerBase // 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 filePDB = new ArrayList<>(); + List filePDBpos = new ArrayList<>(); PDBEntry thePdbEntry = null; StructureFile pdb = null; try { - String[] curfiles = jmb.getPdbFile(); // files currently in viewer + String[] curfiles = jmb.getStructureFiles(); // files currently in viewer // TODO: replace with reference fetching/transfer code (validate PDBentry // as a DBRef?) for (int pi = 0; pi < jmb.getPdbCount(); pi++) @@ -659,7 +410,7 @@ public class ChimeraViewFrame extends StructureViewerBase { filePDB.add(thePdbEntry); filePDBpos.add(Integer.valueOf(pi)); - files.append(" \"" + Platform.escapeString(file) + "\""); + files.append(" \"" + Platform.escapeBackslashes(file) + "\""); } } } catch (OutOfMemoryError oomerror) @@ -669,15 +420,16 @@ public class ChimeraViewFrame extends StructureViewerBase } catch (Exception ex) { ex.printStackTrace(); - errormsgs.append("When retrieving pdbfiles for '" - + thePdbEntry.getId() + "'"); + errormsgs.append( + "When retrieving pdbfiles for '" + thePdbEntry.getId() + "'"); } if (errormsgs.length() > 0) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .formatMessage("label.pdb_entries_couldnt_be_retrieved", - new Object[] { errormsgs.toString() }), + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.pdb_entries_couldnt_be_retrieved", new Object[] + { errormsgs.toString() }), MessageManager.getString("label.couldnt_load_file"), JvOptionPane.ERROR_MESSAGE); } @@ -692,9 +444,15 @@ public class ChimeraViewFrame extends StructureViewerBase initChimera(); } catch (Exception ex) { - Cache.log.error("Couldn't open Chimera viewer!", ex); + Console.error("Couldn't open Chimera viewer!", ex); } } + if (!jmb.isViewerRunning()) + { + // nothing to do + // TODO: ensure we tidy up JAL-3619 + return; + } int num = -1; for (PDBEntry pe : filePDB) { @@ -704,7 +462,7 @@ public class ChimeraViewFrame extends StructureViewerBase try { int pos = filePDBpos.get(num).intValue(); - long startTime = startProgressBar("Chimera " + long startTime = startProgressBar(getViewerName() + " " + MessageManager.getString("status.opening_file_for") + " " + pe.getId()); jmb.openFile(pe); @@ -724,9 +482,12 @@ public class ChimeraViewFrame extends StructureViewerBase stopProgressBar("", startTime); } // Explicitly map to the filename used by Chimera ; + pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos], - jmb.getChains()[pos], pe.getFile(), protocol); - stashFoundChains(pdb, pe.getFile()); + jmb.getChains()[pos], pe.getFile(), protocol, + getProgressIndicator()); + jmb.stashFoundChains(pdb, pe.getFile()); + } catch (OutOfMemoryError oomerror) { new OOMWarning( @@ -734,11 +495,12 @@ public class ChimeraViewFrame extends StructureViewerBase oomerror); } catch (Exception ex) { - Cache.log.error("Couldn't open " + pe.getFile() - + " in Chimera viewer!", ex); + Console.error( + "Couldn't open " + pe.getFile() + " in Chimera viewer!", + ex); } finally { - Cache.log.debug("File locations are " + files); + Console.debug("File locations are " + files); } } } @@ -747,23 +509,33 @@ public class ChimeraViewFrame extends StructureViewerBase jmb.setFinishedInit(true); jmb.setLoadingFromArchive(false); + /* + * ensure that any newly discovered features (e.g. RESNUM) + * are notified to the FeatureRenderer (and added to any + * open feature settings dialog) + */ + FeatureRenderer fr = getBinding().getFeatureRenderer(null); + if (fr != null) + { + fr.featuresAdded(); + } + // refresh the sequence colours for the new structure(s) - for (AlignmentPanel ap : _colourwith) + for (AlignmentViewPanel ap : _colourwith) { jmb.updateColours(ap); } // do superposition if asked to - if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) + if (alignAddedStructures) { new Thread(new Runnable() { @Override public void run() { - alignStructs_withAllAlignPanels(); + alignStructsWithAllAlignPanels(); } }).start(); - alignAddedStructures = false; } addingStructures = false; } @@ -771,420 +543,11 @@ public class ChimeraViewFrame extends StructureViewerBase 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 void stashFoundChains(StructureFile pdb, String file) - { - for (int i = 0; i < pdb.getChains().size(); i++) - { - String chid = new String(pdb.getId() + ":" - + pdb.getChains().elementAt(i).id); - jmb.getChainNames().add(chid); - jmb.getChainFile().put(chid, file); - } - } - private String fetchPdbFile(PDBEntry processingEntry) throws Exception - { - // FIXME: this is duplicated code with Jmol frame ? - String filePath = null; - Pdb pdbclient = new Pdb(); - AlignmentI pdbseq = null; - String pdbid = processingEntry.getId(); - long handle = System.currentTimeMillis() - + Thread.currentThread().hashCode(); - - /* - * Write 'fetching PDB' progress on AlignFrame as we are not yet visible - */ - String msg = MessageManager.formatMessage("status.fetching_pdb", - new Object[] { pdbid }); - getAlignmentPanel().alignFrame.setProgressBar(msg, handle); - // long hdl = startProgressBar(MessageManager.formatMessage( - // "status.fetching_pdb", new Object[] - // { pdbid })); - try - { - pdbseq = pdbclient.getSequenceRecords(pdbid); - } catch (OutOfMemoryError oomerror) - { - new OOMWarning("Retrieving PDB id " + pdbid, oomerror); - } finally - { - msg = pdbid + " " + MessageManager.getString("label.state_completed"); - getAlignmentPanel().alignFrame.setProgressBar(msg, handle); - // stopProgressBar(msg, 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(pdbseq.getSequenceAt(0).getAllPDBEntries() - .elementAt(0).getFile()).getAbsolutePath(); - processingEntry.setFile(filePath); - } - return filePath; - } - - /** - * Convenience method to update the progress bar if there is one. Be sure to - * call stopProgressBar with the returned handle to remove the message. - * - * @param msg - * @param handle - */ - public long startProgressBar(String msg) - { - // TODO would rather have startProgress/stopProgress as the - // IProgressIndicator interface - long tm = random.nextLong(); - if (progressBar != null) - { - progressBar.setProgressBar(msg, tm); - } - return tm; - } - - /** - * End the progress bar with the specified handle, leaving a message (if not - * null) on the status bar - * - * @param msg - * @param handle - */ - public void stopProgressBar(String msg, long handle) - { - if (progressBar != null) - { - progressBar.setProgressBar(msg, handle); - } - } - - @Override - public void pdbFile_actionPerformed(ActionEvent actionEvent) - { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - 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 - in = new BufferedReader(new FileReader(jmb.getPdbFile()[0])); - File outFile = chooser.getSelectedFile(); - - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; - while ((data = in.readLine()) != null) - { - if (!(data.indexOf("

") > -1 || data.indexOf("
") > -1)) - { - out.println(data); - } - } - out.close(); - } 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 - { - cap.appendText(jmb.printMappings()); - } catch (OutOfMemoryError e) - { - new OOMWarning( - "composing sequence-structure alignments for display in text box.", - e); - cap.dispose(); - return; - } - jalview.gui.Desktop.addInternalFrame(cap, - MessageManager.getString("label.pdb_sequence_mapping"), 550, - 600); - } - - @Override - public void eps_actionPerformed(ActionEvent e) - { - throw new Error( - MessageManager - .getString("error.eps_generation_not_implemented")); - } - - @Override - public void png_actionPerformed(ActionEvent e) - { - throw new Error( - MessageManager - .getString("error.png_generation_not_implemented")); - } - - @Override - public void viewerColour_actionPerformed(ActionEvent actionEvent) - { - if (viewerColour.isSelected()) - { - // disable automatic sequence colouring. - jmb.setColourBySequence(false); - } - } - - @Override - public void seqColour_actionPerformed(ActionEvent actionEvent) - { - jmb.setColourBySequence(seqColour.isSelected()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (jmb.isColourBySequence()) - { - if (!jmb.isLoadingFromArchive()) - { - if (_colourwith.size() == 0 && getAlignmentPanel() != null) - { - // Make the currently displayed alignment panel the associated view - _colourwith.add(getAlignmentPanel().alignFrame.alignPanel); - } - } - // Set the colour using the current view for the associated alignframe - for (AlignmentPanel ap : _colourwith) - { - jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap); - } - } - } - - @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) + public void makePDBImage(TYPE imageType) { - 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, MessageManager - .getString("label.select_backgroud_colour"), null); - if (col != null) - { - jmb.setBackgroundColour(col); - } - } - - @Override - public void showHelp_actionPerformed(ActionEvent actionEvent) - { - try - { - jalview.util.BrowserLauncher - .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"); - } catch (Exception ex) - { - } - } - - public void updateTitleAndMenus() - { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) - { - repaint(); - return; - } - setChainMenuItems(jmb.getChainNames()); - - this.setTitle(jmb.getViewerTitle("Chimera", true)); - // if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) - // { - viewerActionMenu.setVisible(true); - // } - if (!jmb.isLoadingFromArchive()) - { - seqColour_actionPerformed(null); - } - } - - /* - * (non-Javadoc) - * - * @see - * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event - * .ActionEvent) - */ - @Override - protected void alignStructs_actionPerformed(ActionEvent actionEvent) - { - alignStructs_withAllAlignPanels(); - } - - private void alignStructs_withAllAlignPanels() - { - if (getAlignmentPanel() == null) - { - return; - } - - if (_alignwith.size() == 0) - { - _alignwith.add(getAlignmentPanel()); - } - - try - { - AlignmentI[] als = new Alignment[_alignwith.size()]; - ColumnSelection[] alc = new ColumnSelection[_alignwith.size()]; - int[] alm = new int[_alignwith.size()]; - int a = 0; - - for (AlignmentPanel ap : _alignwith) - { - als[a] = ap.av.getAlignment(); - alm[a] = -1; - alc[a++] = ap.av.getColumnSelection(); - } - jmb.superposeStructures(als, alm, alc); - } catch (Exception e) - { - StringBuffer sp = new StringBuffer(); - for (AlignmentPanel ap : _alignwith) - { - sp.append("'" + ap.alignFrame.getTitle() + "' "); - } - Cache.log.info("Couldn't align structures with the " + sp.toString() - + "associated alignment panels.", e); - } - } - - @Override - public void setJalviewColourScheme(ColourSchemeI ucs) - { - jmb.setJalviewColourScheme(ucs); - - } - - /** - * - * @param alignment - * @return first alignment panel displaying given alignment, or the default - * alignment panel - */ - public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) - { - for (AlignmentPanel ap : getAllAlignmentPanels()) - { - if (ap.av.getAlignment() == alignment) - { - return ap; - } - } - return getAlignmentPanel(); + throw new UnsupportedOperationException( + "Image export for Chimera is not implemented"); } @Override @@ -1193,82 +556,6 @@ public class ChimeraViewFrame extends StructureViewerBase return jmb; } - /** - * Ask Chimera to save its session to the designated file path, or to a - * temporary file if the path is null. Returns the file path if successful, - * else null. - * - * @param filepath - * @see getStateInfo - */ - protected String saveSession(String filepath) - { - String pathUsed = filepath; - try - { - if (pathUsed == null) - { - File tempFile = File.createTempFile("chimera", ".py"); - tempFile.deleteOnExit(); - pathUsed = tempFile.getPath(); - } - boolean result = jmb.saveSession(pathUsed); - if (result) - { - this.chimeraSessionFile = pathUsed; - return pathUsed; - } - } catch (IOException e) - { - } - return null; - } - - /** - * Returns a string representing the state of the Chimera session. This is - * done by requesting Chimera to save its session to a temporary file, then - * reading the file contents. Returns an empty string on any error. - */ - @Override - public String getStateInfo() - { - String sessionFile = saveSession(null); - if (sessionFile == null) - { - return ""; - } - InputStream is = null; - try - { - File f = new File(sessionFile); - byte[] bytes = new byte[(int) f.length()]; - is = new FileInputStream(sessionFile); - is.read(bytes); - return new String(bytes); - } catch (IOException e) - { - return ""; - } finally - { - if (is != null) - { - try - { - is.close(); - } catch (IOException e) - { - // ignore - } - } - } - } - - @Override - protected void fitToWindow_actionPerformed() - { - jmb.focusView(); - } - @Override public ViewerType getViewerType() { @@ -1276,8 +563,8 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override - protected AAStructureBindingModel getBindingModel() + protected String getViewerName() { - return jmb; + return "Chimera"; } }