X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=955ad7be3313eea63ca8ba721b74107deaa4ff95;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=1b0a5cbc9e1d0348fbbe09e59bbf93f7ba800c2c;hpb=4c5b46336a4a57c09b4a1d2ab13c81b0958a6c9e;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 1b0a5cb..955ad7b 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -17,39 +17,33 @@ */ package jalview.gui; -import java.util.regex.*; import java.util.*; import java.awt.*; import javax.swing.*; import javax.swing.event.*; + import java.awt.event.*; import java.io.*; import jalview.jbgui.GStructureViewer; +import jalview.api.AlignmentViewPanel; import jalview.api.SequenceStructureBinding; import jalview.bin.Cache; import jalview.datamodel.*; -import jalview.gui.*; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.structure.*; import jalview.datamodel.PDBEntry; import jalview.io.*; import jalview.schemes.*; -import jalview.ws.ebi.EBIFetchClient; - -import org.jmol.api.*; -import org.jmol.adapter.smarter.SmarterJmolAdapter; -import org.jmol.popup.*; -import org.jmol.viewer.JmolConstants; -import org.openscience.jmol.app.jmolpanel.AppConsole; public class AppJmol extends GStructureViewer implements Runnable, - SequenceStructureBinding + SequenceStructureBinding, ViewSetProvider { AppJmolBinding jmb; JPanel scriptWindow; - + JSplitPane splitPane; RenderPanel renderPanel; @@ -86,22 +80,32 @@ public class AppJmol extends GStructureViewer implements Runnable, this(new String[] { file }, new String[] { id }, new SequenceI[][] - { seq }, ap, loadStatus, bounds, viewid); + { seq }, ap, true, true, false, loadStatus, bounds, viewid); } + ViewSelectionMenu seqColourBy; + /** * * @param files * @param ids * @param seqs * @param ap + * @param usetoColour + * - add the alignment panel to the list used for colouring these + * structures + * @param useToAlign + * - add the alignment panel to the list used for aligning these + * structures + * @param leaveColouringToJmol + * - do not update the colours from any other source. Jmol is handling them * @param loadStatus * @param bounds * @param viewid */ public AppJmol(String[] files, String[] ids, SequenceI[][] seqs, - AlignmentPanel ap, String loadStatus, Rectangle bounds, - String viewid) + AlignmentPanel ap, boolean usetoColour, boolean useToAlign, boolean leaveColouringToJmol, + String loadStatus, Rectangle bounds, String viewid) { PDBEntry[] pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < pdbentrys.length; i++) @@ -113,13 +117,29 @@ public class AppJmol extends GStructureViewer implements Runnable, } // / TODO: check if protocol is needed to be set, and if chains are // autodiscovered. - jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null); + jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); jmb.setLoadingFromArchive(true); - this.ap = ap; + addAlignmentPanel(ap); + if (useToAlign) + { + useAlignmentPanelForSuperposition(ap); + } + if (leaveColouringToJmol || !usetoColour) + { + jmb.setColourBySequence(false); + seqColour.setSelected(false); + jmolColour.setSelected(true); + } + if (usetoColour) + { + useAlignmentPanelForColourbyseq(ap); + jmb.setColourBySequence(true); + seqColour.setSelected(true); + jmolColour.setSelected(false); + } this.setBounds(bounds); - jmb.setColourBySequence(false); - seqColour.setSelected(false); + initMenus(); viewId = viewid; // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); @@ -135,16 +155,93 @@ public class AppJmol extends GStructureViewer implements Runnable, } + private void initMenus() + { + seqColour.setSelected(jmb.isColourBySequence()); + jmolColour.setSelected(!jmb.isColourBySequence()); + if (_colourwith==null) + { + _colourwith=new Vector(); + } + if (_alignwith==null) + { + _alignwith=new Vector(); + } + + seqColourBy = new ViewSelectionMenu("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("Superpose with ..", this, + _alignwith, handler = new ItemListener() + { + + @Override + public void itemStateChanged(ItemEvent e) + { + alignStructs.setEnabled(_alignwith.size() > 0); + alignStructs.setToolTipText("Align structures using " + + _alignwith.size() + " linked alignment views"); + } + }); + handler.itemStateChanged(null); + jmolActionMenu.add(alpanels); + jmolActionMenu.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 + + } + }); + } IProgressIndicator progressBar = null; + /** + * add a single PDB structure to a new or existing Jmol view + * @param pdbentry + * @param seq + * @param chains + * @param ap + */ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, - AlignmentPanel ap) + final AlignmentPanel ap) { progressBar = ap.alignFrame; // //////////////////////////////// // Is the pdb file already loaded? - String alreadyMapped = StructureSelectionManager - .getStructureSelectionManager().alreadyMappedToFile( + String alreadyMapped = ap.getStructureSelectionManager().alreadyMappedToFile( pdbentry.getId()); if (alreadyMapped != null) @@ -157,8 +254,8 @@ public class AppJmol extends GStructureViewer implements Runnable, if (option == JOptionPane.YES_OPTION) { - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, chains, alreadyMapped, + // TODO : Fix multiple seq to one chain issue here. + ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE); if (ap.seqPanel.seqCanvas.fr != null) { @@ -174,7 +271,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { if (frames[i] instanceof AppJmol) { - AppJmol topJmol = ((AppJmol) frames[i]); + final AppJmol topJmol = ((AppJmol) frames[i]); // JBPNOTE: this looks like a binding routine, rather than a gui // routine for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++) @@ -182,6 +279,11 @@ public class AppJmol extends GStructureViewer implements Runnable, if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped)) { topJmol.jmb.addSequence(pe, seq); + topJmol.addAlignmentPanel(ap); + // add it to the set used for colouring + topJmol.useAlignmentPanelForColourbyseq(ap); + topJmol.buildJmolActionMenu(); + ap.getStructureSelectionManager().sequenceColoursChanged(ap); break; } } @@ -209,30 +311,48 @@ public class AppJmol extends GStructureViewer implements Runnable, JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { + topJmol.useAlignmentPanelForSuperposition(ap); topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); return; } } } // ///////////////////////////////// - - jmb = new AppJmolBinding(this, new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }, null, null); - this.ap = ap; - setSize(400, 400); // probably should be a configurable/dynamic default here - - if (pdbentry.getFile() != null) + openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); + } + private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { + boolean promptUser=pdbentrys.length==1; + progressBar = ap.alignFrame; + jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); + addAlignmentPanel(ap); + useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length>1) { - initJmol("load \"" + pdbentry.getFile() + "\""); + alignAddedStructures=true; + useAlignmentPanelForSuperposition(ap); } - else + jmb.setColourBySequence(true); + setSize(400, 400); // probably should be a configurable/dynamic default here + initMenus(); + worker=null; + String filelist=""; +// for (PDBEntry pe: pdbentrys) +// { +// if (pe.getFile()==null) + { + addingStructures = false; + worker = new Thread(this); + worker.start(); +// break; + } +// filelist+=" \""+pe.getFile()+"\""; + +/* } + if (worker==null) { - addingStructures = false; - worker = new Thread(this); - worker.start(); + initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist); } - +*/ this.addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) @@ -244,6 +364,142 @@ public class AppJmol extends GStructureViewer implements Runnable, } /** + * create a new Jmol containing several structures superimposed using the given alignPanel. + * @param ap + * @param pe + * @param seqs + */ + public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs) + { + openNewJmol(ap, pe, seqs); + } + + /** + * list of sequenceSet ids associated with the view + */ + ArrayList _aps = new ArrayList(); + + public AlignmentPanel[] getAllAlignmentPanels() + { + AlignmentPanel[] t, list = new AlignmentPanel[0]; + for (String setid : _aps) + { + AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid); + if (panels != null) + { + t = new AlignmentPanel[list.length + panels.length]; + System.arraycopy(list, 0, t, 0, list.length); + System.arraycopy(panels, 0, t, list.length, panels.length); + list = t; + } + } + + return list; + } + + /** + * list of alignment panels to use for superposition + */ + Vector _alignwith = new Vector(); + + /** + * list of alignment panels that are used for colouring structures by aligned + * sequences + */ + Vector _colourwith = new Vector(); + + /** + * set the primary alignmentPanel reference and add another alignPanel to the + * list of ones to use for colouring and aligning + * + * @param nap + */ + public void addAlignmentPanel(AlignmentPanel nap) + { + if (ap == null) + { + ap = nap; + } + if (!_aps.contains(nap.av.getSequenceSetId())) + { + _aps.add(nap.av.getSequenceSetId()); + } + } + + /** + * remove any references held to the given alignment panel + * + * @param nap + */ + public void removeAlignmentPanel(AlignmentPanel nap) + { + try + { + _alignwith.remove(nap); + _colourwith.remove(nap); + if (ap == nap) + { + ap = null; + for (AlignmentPanel aps : getAllAlignmentPanels()) + { + if (aps != nap) + { + ap = aps; + break; + } + } + } + } catch (Exception ex) + { + } + if (ap != null) + { + buildJmolActionMenu(); + } + } + + public void useAlignmentPanelForSuperposition(AlignmentPanel nap) + { + addAlignmentPanel(nap); + if (!_alignwith.contains(nap)) + { + _alignwith.add(nap); + } + } + + public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap) + { + if (_alignwith.contains(nap)) + { + _alignwith.remove(nap); + } + } + + public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq) + { + useAlignmentPanelForColourbyseq(nap); + jmb.setColourBySequence(enableColourBySeq); + seqColour.setSelected(enableColourBySeq); + jmolColour.setSelected(!enableColourBySeq); + } + public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) + { + addAlignmentPanel(nap); + if (!_colourwith.contains(nap)) + { + _colourwith.add(nap); + } + } + + public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap) + { + if (_colourwith.contains(nap)) + { + _colourwith.remove(nap); + } + } + + /** * pdb retrieval thread. */ private Thread worker = null; @@ -255,12 +511,13 @@ public class AppJmol extends GStructureViewer implements Runnable, * @param pdbentry * @param seq * @param chains - * @param alignFrame + * @param alignFrame * @param align * if true, new structure(s) will be align using associated alignment */ private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq, - final String[] chains, final boolean b, final IProgressIndicator alignFrame) + final String[] chains, final boolean b, + final IProgressIndicator alignFrame) { if (pdbentry.getFile() == null) { @@ -298,7 +555,7 @@ public class AppJmol extends GStructureViewer implements Runnable, addingStructures = true; _started = false; alignAddedStructures = b; - progressBar = alignFrame; // visual indication happens on caller frame. + progressBar = alignFrame; // visual indication happens on caller frame. (worker = new Thread(this)).start(); return; } @@ -315,7 +572,7 @@ public class AppJmol extends GStructureViewer implements Runnable, if (frames[i] instanceof AppJmol) { AppJmol topJmol = ((AppJmol) frames[i]); - if (topJmol.ap == ap2) + if (topJmol.isLinkedWith(ap2)) { otherJmols.addElement(topJmol); } @@ -340,9 +597,15 @@ public class AppJmol extends GStructureViewer implements Runnable, bl.setVgap(0); scriptWindow = new JPanel(bl); scriptWindow.setVisible(false); - }; - jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null); + } + ; + jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, + null); jmb.newJmolPopup(true, "Jmol", true); + if (command==null) + { + command=""; + } jmb.evalStateCommand(command); jmb.setFinishedInit(true); } @@ -414,6 +677,10 @@ public class AppJmol extends GStructureViewer implements Runnable, void closeViewer() { jmb.closeViewer(); + ap = 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; @@ -444,11 +711,10 @@ public class AppJmol extends GStructureViewer implements Runnable, // retrieve the pdb and store it locally AlignmentI pdbseq = null; pdbid = jmb.pdbentry[pi].getId(); - long hdl=pdbid.hashCode()-System.currentTimeMillis(); + long hdl = pdbid.hashCode() - System.currentTimeMillis(); if (progressBar != null) { - progressBar.setProgressBar("Fetching PDB " + pdbid, - hdl); + progressBar.setProgressBar("Fetching PDB " + pdbid, hdl); } try { @@ -518,6 +784,7 @@ public class AppJmol extends GStructureViewer implements Runnable, "Couldn't load file", JOptionPane.ERROR_MESSAGE); } + long lastnotify = jmb.getLoadNotifiesHandled(); if (files.length() > 0) { if (!addingStructures) @@ -543,6 +810,8 @@ public class AppJmol extends GStructureViewer implements Runnable, cmd.append("\nloadingJalviewdata=null"); final String command = cmd.toString(); cmd = null; + lastnotify = jmb.getLoadNotifiesHandled(); + try { jmb.evalStateCommand(command); @@ -556,33 +825,40 @@ public class AppJmol extends GStructureViewer implements Runnable, { Cache.log.error("Couldn't add files to Jmol viewer!", ex); } - long lastnotify=jmb.getLoadNotifiesHandled(); - // need to wait around until script has finished - while (lastnotify>=jmb.getLoadNotifiesHandled()); + } + + // need to wait around until script has finished + while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() + : (jmb.isFinishedInit() && jmb.getPdbFile().length!=jmb.pdbentry.length)) + { + try + { + Cache.log.debug("Waiting around for jmb notify."); + Thread.sleep(35); + } catch (Exception e) + { + } + } + // refresh the sequence colours for the new structure(s) + for (AlignmentPanel ap : _colourwith) + { + jmb.updateColours(ap); + } + // do superposition if asked to + if (alignAddedStructures) + { + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() { - try - { - Thread.sleep(35); - } catch (Exception e) - { - } + alignStructs_withAllAlignPanels(); + // jmb.superposeStructures(ap.av.getAlignment(), -1, null); } - // refresh the sequence colours for the new structure(s) - jmb.updateColours(ap); - // do superposition if asked to - if (alignAddedStructures) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - jmb.superposeStructures(ap.av.getAlignment(), -1, null); - } - }); - alignAddedStructures = false; - } - addingStructures = false; + }); + alignAddedStructures = false; } + addingStructures = false; + } _started = false; worker = null; @@ -632,8 +908,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) { - cap.appendText(StructureSelectionManager - .getStructureSelectionManager().printMapping( + cap.appendText(jmb.printMapping( jmb.pdbentry[pdbe].getFile())); cap.appendText("\n"); } @@ -697,13 +972,35 @@ public class AppJmol extends GStructureViewer implements Runnable, im.writeImage(); } } - + public void jmolColour_actionPerformed(ActionEvent actionEvent) + { + if (jmolColour.isSelected()) { + // disable automatic sequence colouring. + jmb.setColourBySequence(false); + } + } public void seqColour_actionPerformed(ActionEvent actionEvent) { jmb.setColourBySequence(seqColour.isSelected()); - // Set the colour using the current view for the associated alignframe - jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures, - ap.alignFrame.viewport.alignment); + if (_colourwith == null) + { + _colourwith = new Vector(); + } + if (jmb.isColourBySequence()) + { + if (!jmb.isLoadingFromArchive()) + { + if (_colourwith.size()==0 && ap!=null) { + // Make the currently displayed alignment panel the associated view + _colourwith.add(ap.alignFrame.alignPanel); + } + } + // Set the colour using the current view for the associated alignframe + for (AlignmentPanel ap : _colourwith) + { + jmb.colourBySequence(ap.av.showSequenceFeatures, ap); + } + } } public void chainColour_actionPerformed(ActionEvent actionEvent) @@ -759,7 +1056,12 @@ public class AppJmol extends GStructureViewer implements Runnable, buriedColour.setSelected(true); jmb.setJalviewColourScheme(new BuriedColourScheme()); } - + + public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new PurinePyrimidineColourScheme()); + } + public void userColour_actionPerformed(ActionEvent actionEvent) { userColour.setSelected(true); @@ -786,7 +1088,8 @@ public class AppJmol extends GStructureViewer implements Runnable, { } } -public void showConsole(boolean showConsole) + + public void showConsole(boolean showConsole) { if (showConsole) @@ -807,9 +1110,9 @@ public void showConsole(boolean showConsole) else { if (splitPane != null) - { - splitPane.setVisible(false); - } + { + splitPane.setVisible(false); + } splitPane = null; @@ -818,6 +1121,7 @@ public void showConsole(boolean showConsole) validate(); } + class RenderPanel extends JPanel { final Dimension currentSize = new Dimension(); @@ -888,13 +1192,37 @@ public void showConsole(boolean showConsole) return; } setChainMenuItems(jmb.chainNames); - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); this.setTitle(jmb.getViewerTitle()); if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) { jmolActionMenu.setVisible(true); } + if (!jmb.isLoadingFromArchive()) + { + seqColour_actionPerformed(null); + } + } + + protected void buildJmolActionMenu() + { + if (_alignwith == null) + { + _alignwith = new Vector(); + } + if (_alignwith.size() == 0 && ap != null) + { + _alignwith.add(ap); + } + ; + for (Component c : jmolActionMenu.getMenuComponents()) + { + if (c != alignStructs) + { + jmolActionMenu.remove((JMenuItem) c); + } + } + final ItemListener handler; } /* @@ -907,17 +1235,47 @@ public void showConsole(boolean showConsole) @Override protected void alignStructs_actionPerformed(ActionEvent actionEvent) { + alignStructs_withAllAlignPanels(); + } + private void alignStructs_withAllAlignPanels() + { + if (ap == null) + { + return; + } + ; + if (_alignwith.size() == 0) + { + _alignwith.add(ap); + } + ; try { - jmb.superposeStructures(ap.av.getAlignment(), -1, - ap.av.getColumnSelection()); + 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) { - Cache.log.info("Couldn't align structures in alignframe " - + ap.alignFrame.getTitle(), 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); } + } public void setJalviewColourScheme(ColourSchemeI ucs) @@ -926,4 +1284,53 @@ public void showConsole(boolean showConsole) } + /** + * + * @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 ap; + } + + /** + * + * @param ap2 + * @return true if this Jmol instance is linked with the given alignPanel + */ + public boolean isLinkedWith(AlignmentPanel ap2) + { + return _aps.contains(ap2.av.getSequenceSetId()); + } + + public boolean isUsedforaligment(AlignmentPanel ap2) + { + + return (_alignwith != null) && _alignwith.contains(ap2); + } + + public boolean isUsedforcolourby(AlignmentPanel ap2) + { + return (_colourwith != null) && _colourwith.contains(ap2); + } + + /** + * + * @return TRUE if the view is NOT being coloured by sequence associations. + */ + public boolean isColouredByJmol() + { + return !jmb.isColourBySequence(); + } + + }