X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=83926066c4aa18af9cf55787e7fac4e7f3e69006;hb=refs%2Fheads%2Ffeature%2FJAL-3190jalviewjsChimera;hp=13134762ce1d04001e09238ca6765b957a1b5c96;hpb=521de3345302eb3234996733383b9e810f77699f;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 1313476..8392606 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -20,58 +20,42 @@ */ package jalview.gui; +import jalview.api.FeatureRenderer; 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.AppletFormatAdapter; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -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.io.DataSourceType; +import jalview.io.StructureFile; import jalview.structures.models.AAStructureBindingModel; +import jalview.util.BrowserLauncher; +import jalview.util.ImageMaker.TYPE; 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.io.BufferedReader; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; 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 javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; import javax.swing.JInternalFrame; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; /** * GUI elements for handling an external chimera display @@ -83,8 +67,6 @@ public class ChimeraViewFrame extends StructureViewerBase { private JalviewChimeraBinding jmb; - private boolean allChainsSelected = false; - private IProgressIndicator progressBar = null; /* @@ -96,91 +78,29 @@ public class ChimeraViewFrame extends StructureViewerBase private Random random = new Random(); + private int myWidth = 500; + + private int myHeight = 150; + /** * Initialise menu options. */ - private void initMenus() + @Override + protected void initMenus() { + super.initMenus(); + viewerActionMenu.setText(MessageManager.getString("label.chimera")); - viewerColour.setText(MessageManager - .getString("label.colour_with_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); - - 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); + helpItem.setText(MessageManager.getString("label.chimera_help")); + 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 @@ -194,6 +114,71 @@ public class ChimeraViewFrame extends StructureViewerBase } }); viewerActionMenu.add(writeFeatures); + + final JMenu fetchAttributes = new JMenu( + MessageManager.getString("label.fetch_chimera_attributes")); + fetchAttributes.setToolTipText( + MessageManager.getString("label.fetch_chimera_attributes_tip")); + fetchAttributes.addMouseListener(new MouseAdapter() + { + + @Override + public void mouseEntered(MouseEvent e) + { + buildAttributesMenu(fetchAttributes); + } + }); + viewerActionMenu.add(fetchAttributes); + } + + /** + * Query Chimera 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; + } + attributesMenu.removeAll(); + Collections.sort(atts); + for (String att : 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + getChimeraAttributes(attName); + } + }); + 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()); } /** @@ -205,11 +190,13 @@ public class ChimeraViewFrame extends StructureViewerBase */ protected void sendFeaturesToChimera() { - jmb.sendFeaturesToChimera(getAlignmentPanel()); + int count = jmb.sendFeaturesToViewer(getAlignmentPanel()); + statusBar.setText( + MessageManager.formatMessage("label.attributes_set", count)); } /** - * 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 @@ -220,32 +207,10 @@ 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 }); } /** @@ -259,33 +224,21 @@ public class ChimeraViewFrame extends StructureViewerBase } } - /** - * 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(); - // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs - String[][] chains = extractChains(seqs); jmb = new JalviewChimeraBindingModel(this, - ap.getStructureSelectionManager(), pdbentrys, seqs, chains, - null); + ap.getStructureSelectionManager(), pdbentrys, seqs, null); 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; @@ -295,7 +248,8 @@ public class ChimeraViewFrame extends StructureViewerBase this.addInternalFrameListener(new InternalFrameAdapter() { @Override - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) + public void internalFrameClosing( + InternalFrameEvent internalFrameEvent) { closeViewer(false); } @@ -304,42 +258,6 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * Retrieve chains for sequences by inspecting their PDB refs. The hope is - * that the first will be to the sequence's own chain. Really need a more - * managed way of doing this. - * - * @param seqs - * @return - */ - protected String[][] extractChains(SequenceI[][] seqs) - { - String[][] chains = new String[seqs.length][]; - for (int i = 0; i < seqs.length; i++) - { - chains[i] = new String[seqs[i].length]; - int seqno = 0; - for (SequenceI seq : seqs[i]) - { - String chain = null; - if (seq.getDatasetSequence() != null) - { - Vector pdbrefs = seq.getDatasetSequence() - .getAllPDBEntries(); - if (pdbrefs != null && pdbrefs.size() > 0) - { - // FIXME: SequenceI.PDBEntry[0] chain mapping used for - // ChimeraViewFrame. Is this even used ??? - - chain = pdbrefs.get(0).getChainCode(); - } - } - chains[i][seqno++] = chain; - } - } - return chains; - } - - /** * Create a new viewer from saved session state data including Chimera session * file * @@ -375,17 +293,19 @@ 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, + public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded, + SequenceI[][] seqs, AlignmentPanel ap) { this(); + setAlignAddedStructures(alignAdded); openNewChimera(ap, pe, seqs); } @@ -404,45 +324,22 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * Returns a list of any Chimera viewers in the desktop. The list is - * restricted to those linked to the given alignment panel if it is not null. - */ - @Override - protected List getViewersFor(AlignmentPanel ap) - { - List result = new ArrayList(); - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (JInternalFrame frame : frames) - { - if (frame instanceof ChimeraViewFrame) - { - if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap)) - { - result.add((StructureViewerBase) frame); - } - } - } - return result; - } - - /** * Launch Chimera. If we have a chimera session file name, send Chimera the * command to open its saved session file. */ void initChimera() { jmb.setFinishedInit(false); - jalview.gui.Desktop.addInternalFrame(this, - jmb.getViewerTitle("Chimera", true), getBounds().width, + Desktop.addInternalFrame(this, + jmb.getViewerTitle(getViewerName(), true), getBounds().width, getBounds().height); if (!jmb.launchChimera()) { - JOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager.getString("label.chimera_failed"), MessageManager.getString("label.error_loading_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); this.dispose(); return; } @@ -452,76 +349,24 @@ 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); } } - jmb.setFinishedInit(true); - jmb.startChimeraListener(); - } - - /** - * 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 - */ - void setChainMenuItems(List chainNames) - { - chainMenu.removeAll(); - if (chainNames == null || chainNames.isEmpty()) + if (!Platform.isJS()) { - 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); + jmb.startChimeraListener(); } } /** * Show only the selected chain(s) in the viewer */ + @Override void showSelectedChains() { - List toshow = new ArrayList(); + List toshow = new ArrayList<>(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) @@ -551,22 +396,22 @@ public class ChimeraViewFrame extends StructureViewerBase { if (!closeChimera) { - String prompt = MessageManager.formatMessage( - "label.confirm_close_chimera", - new Object[] { jmb.getViewerTitle("Chimera", false) }); + String prompt = MessageManager + .formatMessage("label.confirm_close_chimera", new Object[] + { jmb.getViewerTitle(getViewerName(), false) }); prompt = JvSwingUtils.wrapTooltip(true, prompt); - int confirm = JOptionPane.showConfirmDialog(this, prompt, + int confirm = JvOptionPane.showConfirmDialog(this, prompt, MessageManager.getString("label.close_viewer"), - JOptionPane.YES_NO_CANCEL_OPTION); + JvOptionPane.YES_NO_CANCEL_OPTION); /* * abort closure if user hits escape or Cancel */ - if (confirm == JOptionPane.CANCEL_OPTION - || confirm == JOptionPane.CLOSED_OPTION) + if (confirm == JvOptionPane.CANCEL_OPTION + || confirm == JvOptionPane.CLOSED_OPTION) { return; } - closeChimera = confirm == JOptionPane.YES_OPTION; + closeChimera = confirm == JvOptionPane.YES_OPTION; } jmb.closeViewer(closeChimera); } @@ -591,12 +436,13 @@ 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++) @@ -648,21 +494,23 @@ 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) { - JOptionPane.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"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } if (files.length() > 0) { + jmb.setFinishedInit(false); if (!addingStructures) { try @@ -674,7 +522,6 @@ public class ChimeraViewFrame extends StructureViewerBase } } int num = -1; - jmb.setFinishedInit(false); for (PDBEntry pe : filePDB) { num++; @@ -683,18 +530,18 @@ 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); jmb.addSequence(pos, jmb.getSequence()[pos]); File fl = new File(pe.getFile()); - String protocol = AppletFormatAdapter.URL; + DataSourceType protocol = DataSourceType.URL; try { if (fl.exists()) { - protocol = AppletFormatAdapter.FILE; + protocol = DataSourceType.FILE; } } catch (Throwable e) { @@ -703,8 +550,12 @@ public class ChimeraViewFrame extends StructureViewerBase stopProgressBar("", startTime); } // Explicitly map to the filename used by Chimera ; - jmb.getSsm().setMapping(jmb.getSequence()[pos], - jmb.getChains()[pos], pe.getFile(), protocol); + + pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos], + jmb.getChains()[pos], pe.getFile(), protocol, + progressBar); + stashFoundChains(pdb, pe.getFile()); + } catch (OutOfMemoryError oomerror) { new OOMWarning( @@ -712,24 +563,37 @@ public class ChimeraViewFrame extends StructureViewerBase oomerror); } catch (Exception ex) { - Cache.log.error("Couldn't open " + pe.getFile() - + " in Chimera viewer!", ex); + Cache.log.error( + "Couldn't open " + pe.getFile() + " in Chimera viewer!", + ex); } finally { Cache.log.debug("File locations are " + files); } } } + + jmb.refreshGUI(); jmb.setFinishedInit(true); jmb.setLoadingFromArchive(false); + /* + * ensure that any newly discovered features (e.g. RESNUM) + * are 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) { jmb.updateColours(ap); } // do superposition if asked to - if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) + if (alignAddedStructures) { new Thread(new Runnable() { @@ -739,7 +603,6 @@ public class ChimeraViewFrame extends StructureViewerBase alignStructs_withAllAlignPanels(); } }).start(); - alignAddedStructures = false; } addingStructures = false; } @@ -749,15 +612,26 @@ public class ChimeraViewFrame extends StructureViewerBase /** * Fetch PDB data and save to a local file. Returns the full path to the file, - * or null if fetch fails. + * or null if fetch fails. TODO: refactor to common with Jmol ? duplication * * @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; @@ -769,7 +643,8 @@ public class ChimeraViewFrame extends StructureViewerBase * Write 'fetching PDB' progress on AlignFrame as we are not yet visible */ String msg = MessageManager.formatMessage("status.fetching_pdb", - new Object[] { pdbid }); + new Object[] + { pdbid }); getAlignmentPanel().alignFrame.setProgressBar(msg, handle); // long hdl = startProgressBar(MessageManager.formatMessage( // "status.fetching_pdb", new Object[] @@ -835,213 +710,10 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override - public void pdbFile_actionPerformed(ActionEvent actionEvent) + public void makePDBImage(TYPE imageType) { - 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) - { - 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); - } + throw new UnsupportedOperationException( + "Image export for Chimera is not implemented"); } @Override @@ -1049,110 +721,14 @@ public class ChimeraViewFrame extends StructureViewerBase { try { - jalview.util.BrowserLauncher + 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 + } catch (IOException ex) { - 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(); - } - - @Override public AAStructureBindingModel getBinding() { return jmb; @@ -1241,8 +817,30 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override - protected AAStructureBindingModel getBindingModel() + protected String getViewerName() { - return jmb; + return "Chimera"; + } + + /** + * Sends commands to align structures according to associated alignment(s). + * + * @return + */ + @Override + protected String alignStructs_withAllAlignPanels() + { + String reply = super.alignStructs_withAllAlignPanels(); + if (reply != null) + { + statusBar.setText("Superposition failed: " + reply); + } + return reply; + } + + @Override + protected IProgressIndicator getIProgressIndicator() + { + return progressBar; } }