X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=67eddcac4a21b8c0a0e25564c74374e12d70011b;hb=20bb45279db7745e7d0062c1084f97644c60db19;hp=048f441f7cc3c49d8b5ffa3d1d5a12245ca7b081;hpb=b0cee3aaf7d8873910939f97b6acb217d518968d;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 048f441..67eddca 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -21,57 +21,39 @@ 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.UserColourScheme; -import jalview.schemes.ZappoColourScheme; import jalview.structures.models.AAStructureBindingModel; +import jalview.util.BrowserLauncher; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.dbsources.Pdb; -import java.awt.Color; import java.awt.event.ActionEvent; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.io.BufferedReader; +import java.awt.event.ActionListener; +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.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 +65,6 @@ public class ChimeraViewFrame extends StructureViewerBase { private JalviewChimeraBinding jmb; - private boolean allChainsSelected = false; - private IProgressIndicator progressBar = null; /* @@ -99,88 +79,113 @@ public class ChimeraViewFrame extends StructureViewerBase /** * 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.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() + JMenuItem writeFeatures = new JMenuItem( + MessageManager.getString("label.create_chimera_attributes")); + writeFeatures.setToolTipText(MessageManager + .getString("label.create_chimera_attributes_tip")); + writeFeatures.addActionListener(new ActionListener() { - @Override - public void menuSelected(MenuEvent e) + public void actionPerformed(ActionEvent e) { - handler.itemStateChanged(null); + sendFeaturesToChimera(); } + }); + 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 menuDeselected(MenuEvent e) + public void mouseEntered(MouseEvent e) { - // TODO Auto-generated method stub + buildAttributesMenu(fetchAttributes); } + }); + viewerActionMenu.add(fetchAttributes); - @Override - public void menuCanceled(MenuEvent e) + } + + /** + * 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)) { - // TODO Auto-generated method stub + 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()); + } + + /** + * 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 + */ + protected void sendFeaturesToChimera() + { + jmb.sendFeaturesToViewer(getAlignmentPanel()); } /** @@ -234,24 +239,15 @@ 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 jmb = new JalviewChimeraBindingModel(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length > 1) { alignAddedStructures = true; @@ -276,8 +272,6 @@ public class ChimeraViewFrame extends StructureViewerBase } - - /** * Create a new viewer from saved session state data including Chimera session * file @@ -372,8 +366,8 @@ public class ChimeraViewFrame extends StructureViewerBase 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()) @@ -396,12 +390,10 @@ public class ChimeraViewFrame extends StructureViewerBase + chimeraSessionFile); } } - jmb.setFinishedInit(true); jmb.startChimeraListener(); } - /** * Show only the selected chain(s) in the viewer */ @@ -440,7 +432,8 @@ public class ChimeraViewFrame extends StructureViewerBase { String prompt = MessageManager.formatMessage( "label.confirm_close_chimera", - new Object[] { jmb.getViewerTitle("Chimera", false) }); + new Object[] { jmb.getViewerTitle(getViewerName(), + false) }); prompt = JvSwingUtils.wrapTooltip(true, prompt); int confirm = JvOptionPane.showConfirmDialog(this, prompt, MessageManager.getString("label.close_viewer"), @@ -551,6 +544,7 @@ public class ChimeraViewFrame extends StructureViewerBase if (files.length() > 0) { + jmb.setFinishedInit(false); if (!addingStructures) { try @@ -570,7 +564,7 @@ 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); @@ -608,6 +602,7 @@ public class ChimeraViewFrame extends StructureViewerBase } } } + jmb.refreshGUI(); jmb.setFinishedInit(true); jmb.setLoadingFromArchive(false); @@ -735,76 +730,6 @@ public class ChimeraViewFrame extends StructureViewerBase } @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( @@ -821,246 +746,17 @@ public class ChimeraViewFrame extends StructureViewerBase } @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 e) - { - if (e.getActionCommand().equals( - MessageManager.getString("action.user_defined"))) - { - new UserDefinedColours(this, null); - } - else - { - UserColourScheme udc = UserDefinedColours.getUserColourSchemes().get( - e.getActionCommand()); - jmb.setJalviewColourScheme(udc); - } - } - - @Override - public void backGround_actionPerformed(ActionEvent actionEvent) - { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_background_colour"), - null); - if (col != null) - { - jmb.setBackgroundColour(col); - } - } - - @Override public void showHelp_actionPerformed(ActionEvent actionEvent) { try { - jalview.util.BrowserLauncher + BrowserLauncher .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"); - } catch (Exception ex) + } catch (IOException 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(); - } - @Override public AAStructureBindingModel getBinding() { @@ -1150,8 +846,25 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override - protected AAStructureBindingModel getBindingModel() + protected String getViewerName() { - return jmb; + return "Chimera"; + } + + /** + * Override superclass method to make the 'Chimera' menu always visible, but + * 'Superpose with...' only enabled if there is more than one structure shown + */ + @Override + public void updateTitleAndMenus() + { + super.updateTitleAndMenus(); + viewerActionMenu.setVisible(true); + viewSelectionMenu.setEnabled(false); + if (getBinding().getPdbFile().length > 1 + && getBinding().getSequence().length > 1) + { + viewSelectionMenu.setEnabled(true); + } } }