X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=af25653a997b35c4bf080e0a4c0dcb8cb3297e8e;hb=2783208dc83a836be2cac47efb9877949909e781;hp=2299c2602b767098e161817d5615d4481337545e;hpb=7d34fe9736520832bd6269cf2bbde3a8739e5e82;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 2299c26..af25653 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -21,24 +21,12 @@ 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.gui.StructureViewer.ViewerType; -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.structures.models.AAStructureBindingModel; +import jalview.util.BrowserLauncher; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.dbsources.Pdb; @@ -50,35 +38,24 @@ import java.awt.Font; import java.awt.Graphics; import java.awt.Rectangle; 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.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.List; 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.JPanel; import javax.swing.JSplitPane; import javax.swing.SwingUtilities; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; public class AppJmol extends StructureViewerBase { + // ms to wait for Jmol to load files + private static final int JMOL_LOAD_TIMEOUT = 20000; + private static final String SPACE = " "; private static final String BACKSLASH = "\""; @@ -91,8 +68,6 @@ public class AppJmol extends StructureViewerBase RenderPanel renderPanel; - ViewSelectionMenu seqColourBy; - /** * * @param files @@ -114,8 +89,8 @@ public class AppJmol extends StructureViewerBase */ public AppJmol(String[] files, String[] ids, SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour, boolean useToAlign, - boolean leaveColouringToJmol, String loadStatus, - Rectangle bounds, String viewid) + boolean leaveColouringToJmol, String loadStatus, Rectangle bounds, + String viewid) { PDBEntry[] pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < pdbentrys.length; i++) @@ -128,7 +103,7 @@ public class AppJmol extends StructureViewerBase // / TODO: check if protocol is needed to be set, and if chains are // autodiscovered. jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), - pdbentrys, seqs, null, null); + pdbentrys, seqs, null); jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); @@ -136,6 +111,7 @@ public class AppJmol extends StructureViewerBase { useAlignmentPanelForSuperposition(ap); } + initMenus(); if (leaveColouringToJmol || !usetoColour) { jmb.setColourBySequence(false); @@ -150,7 +126,6 @@ public class AppJmol extends StructureViewerBase viewerColour.setSelected(false); } this.setBounds(bounds); - initMenus(); setViewId(viewid); // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); @@ -158,94 +133,35 @@ public class AppJmol extends StructureViewerBase this.addInternalFrameListener(new InternalFrameAdapter() { @Override - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) + public void internalFrameClosing( + InternalFrameEvent internalFrameEvent) { closeViewer(false); } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! - } - private void initMenus() + @Override + protected void initMenus() { - seqColour.setSelected(jmb.isColourBySequence()); - viewerColour.setSelected(!jmb.isColourBySequence()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (_alignwith == null) - { - _alignwith = new Vector(); - } - - 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 jmol display now. - seqColour_actionPerformed(null); - } - } - }); - viewMenu.add(seqColourBy); - final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu( - MessageManager.getString("label.superpose_with"), this, - _alignwith, handler = new ItemListener() - { + super.initMenus(); - @Override - public void itemStateChanged(ItemEvent e) - { - alignStructs.setEnabled(_alignwith.size() > 0); - alignStructs.setToolTipText(MessageManager - .formatMessage( - "label.align_structures_using_linked_alignment_views", - new String[] { 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 + viewerActionMenu.setText(MessageManager.getString("label.jmol")); - } - }); + viewerColour + .setText(MessageManager.getString("label.colour_with_jmol")); + viewerColour.setToolTipText(MessageManager + .getString("label.let_jmol_manage_structure_colours")); } IProgressIndicator progressBar = null; + @Override + protected IProgressIndicator getIProgressIndicator() + { + return progressBar; + } /** * add a single PDB structure to a new or existing Jmol view * @@ -284,23 +200,15 @@ public class AppJmol extends StructureViewerBase openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); } - /** - * Answers true if this viewer already involves the given PDB ID - */ - @Override - protected boolean hasPdbId(String pdbId) - { - return jmb.hasPdbId(pdbId); - } - private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { progressBar = ap.alignFrame; jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), - pdbentrys, seqs, null, null); + pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length > 1) { alignAddedStructures = true; @@ -309,16 +217,15 @@ public class AppJmol extends StructureViewerBase jmb.setColourBySequence(true); setSize(400, 400); // probably should be a configurable/dynamic default here initMenus(); - worker = null; - { - addingStructures = false; - worker = new Thread(this); - worker.start(); - } + addingStructures = false; + worker = new Thread(this); + worker.start(); + this.addInternalFrameListener(new InternalFrameAdapter() { @Override - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) + public void internalFrameClosing( + InternalFrameEvent internalFrameEvent) { closeViewer(false); } @@ -339,29 +246,6 @@ public class AppJmol extends StructureViewerBase openNewJmol(ap, pe, seqs); } - /** - * Returns a list of any Jmol viewers. The list is restricted to those linked - * to the given alignment panel if it is not null. - */ - @Override - protected List getViewersFor(AlignmentPanel apanel) - { - List result = new ArrayList(); - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (JInternalFrame frame : frames) - { - if (frame instanceof AppJmol) - { - if (apanel == null - || ((StructureViewerBase) frame).isLinkedWith(apanel)) - { - result.add((StructureViewerBase) frame); - } - } - } - return result; - } void initJmol(String command) { @@ -381,11 +265,8 @@ public class AppJmol extends StructureViewerBase scriptWindow.setVisible(false); } - /* - * -i for no info logging (less verbose) - */ - jmb.allocateViewer(renderPanel, true, "", null, null, "-i", - scriptWindow, null); + jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, + null); // jmb.newJmolPopup("Jmol"); if (command == null) { @@ -396,59 +277,12 @@ public class AppJmol extends StructureViewerBase jmb.setFinishedInit(true); } - void setChainMenuItems(Vector chains) - { - chainMenu.removeAll(); - if (chains == null) - { - 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); - } - } - centerViewer(); - allChainsSelected = false; - } - }); - - chainMenu.add(menuItem); - - for (String chain : chains) - { - menuItem = new JCheckBoxMenuItem(chain, true); - menuItem.addItemListener(new ItemListener() - { - @Override - public void itemStateChanged(ItemEvent evt) - { - if (!allChainsSelected) - { - centerViewer(); - } - } - }); - - chainMenu.add(menuItem); - } - } - boolean allChainsSelected = false; - void centerViewer() + @Override + void showSelectedChains() { - Vector toshow = new Vector(); + Vector toshow = new Vector<>(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) @@ -511,8 +345,8 @@ public class AppJmol extends StructureViewerBase StringBuilder fileList = new StringBuilder(); for (String s : files) { - fileList.append(SPACE).append(BACKSLASH).append(Platform.escapeString(s)) - .append(BACKSLASH); + fileList.append(SPACE).append(BACKSLASH) + .append(Platform.escapeString(s)).append(BACKSLASH); } String filesString = fileList.toString(); @@ -544,8 +378,7 @@ public class AppJmol extends StructureViewerBase jmb.evalStateCommand(command); } catch (OutOfMemoryError oomerror) { - new OOMWarning( - "When trying to add structures to the Jmol viewer!", + new OOMWarning("When trying to add structures to the Jmol viewer!", oomerror); Cache.log.debug("File locations are " + filesString); } catch (Exception ex) @@ -555,12 +388,12 @@ public class AppJmol extends StructureViewerBase } // need to wait around until script has finished - int waitMax = 5000; // give up after 5 seconds + int waitMax = JMOL_LOAD_TIMEOUT; int waitFor = 35; int waitTotal = 0; while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() - : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb - .getPdbFile().length == files.size())) + : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null + && jmb.getStructureFiles().length == files.size())) { try { @@ -572,7 +405,12 @@ public class AppJmol extends StructureViewerBase } if (waitTotal > waitMax) { - System.err.println("Timed out waiting for Jmol to load files"); + System.err.println("Timed out waiting for Jmol to load files after " + + waitTotal + "ms"); + // System.err.println("finished: " + jmb.isFinishedInit() + // + "; loaded: " + Arrays.toString(jmb.getPdbFile()) + // + "; files: " + files.toString()); + jmb.getStructureFiles(); break; } } @@ -633,11 +471,11 @@ public class AppJmol extends StructureViewerBase // todo - record which pdbids were successfully imported. StringBuilder errormsgs = new StringBuilder(); - List files = new ArrayList(); + List files = new ArrayList<>(); String pdbid = ""; try { - String[] filesInViewer = jmb.getPdbFile(); + String[] filesInViewer = jmb.getStructureFiles(); // TODO: replace with reference fetching/transfer code (validate PDBentry // as a DBRef?) Pdb pdbclient = new Pdb(); @@ -652,8 +490,9 @@ public class AppJmol extends StructureViewerBase long hdl = pdbid.hashCode() - System.currentTimeMillis(); if (progressBar != null) { - progressBar.setProgressBar(MessageManager.formatMessage( - "status.fetching_pdb", new String[] { pdbid }), hdl); + progressBar.setProgressBar(MessageManager + .formatMessage("status.fetching_pdb", new String[] + { pdbid }), hdl); } try { @@ -719,86 +558,17 @@ public class AppJmol extends StructureViewerBase } if (errormsgs.length() > 0) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .formatMessage("label.pdb_entries_couldnt_be_retrieved", - new String[] { errormsgs.toString() }), + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.pdb_entries_couldnt_be_retrieved", new String[] + { errormsgs.toString() }), MessageManager.getString("label.couldnt_load_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } return files; } @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) - { - // ignore - } - } - } - } - } - - @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) { makePDBImage(jalview.util.ImageMaker.TYPE.EPS); @@ -845,135 +615,11 @@ public class AppJmol 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); - } - } - } - - @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); - } - } - - @Override public void showHelp_actionPerformed(ActionEvent actionEvent) { try { - jalview.util.BrowserLauncher + BrowserLauncher .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/"); } catch (Exception ex) { @@ -1022,7 +668,7 @@ public class AppJmol extends StructureViewerBase { getSize(currentSize); - if (jmb != null && jmb.fileLoadingError != null) + if (jmb != null && jmb.hasFileLoadingError()) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -1043,8 +689,8 @@ public class AppJmol extends StructureViewerBase if (e == jmb.getPdbCount() - 1 || sb.length() > 20) { lines++; - g.drawString(sb.toString(), 20, currentSize.height / 2 - lines - * g.getFontMetrics().getHeight()); + g.drawString(sb.toString(), 20, currentSize.height / 2 + - lines * g.getFontMetrics().getHeight()); } } } @@ -1065,104 +711,6 @@ public class AppJmol extends StructureViewerBase } } - public void updateTitleAndMenus() - { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) - { - repaint(); - return; - } - setChainMenuItems(jmb.chainNames); - - this.setTitle(jmb.getViewerTitle()); - 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() { @@ -1182,9 +730,8 @@ public class AppJmol extends StructureViewerBase } @Override - protected AAStructureBindingModel getBindingModel() + protected String getViewerName() { - return jmb; + return "Jmol"; } - }