X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=955ad7be3313eea63ca8ba721b74107deaa4ff95;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=fd7e297d0e4e6ea69b34132475a80e3eeacaf9ad;hpb=2997ebc41fa9f1da29bdac06323036678cb4d1c7;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index fd7e297..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 2.6) - * 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. * @@ -26,6 +26,7 @@ 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.*; @@ -79,7 +80,7 @@ public class AppJmol extends GStructureViewer implements Runnable, this(new String[] { file }, new String[] { id }, new SequenceI[][] - { seq }, ap, true,true, loadStatus, bounds, viewid); + { seq }, ap, true, true, false, loadStatus, bounds, viewid); } ViewSelectionMenu seqColourBy; @@ -90,15 +91,21 @@ public class AppJmol extends GStructureViewer implements Runnable, * @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 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, boolean usetoColour,boolean useToAlign, 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++) @@ -110,7 +117,7 @@ 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); addAlignmentPanel(ap); @@ -118,13 +125,20 @@ public class AppJmol extends GStructureViewer implements Runnable, { 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", @@ -140,7 +154,20 @@ public class AppJmol extends GStructureViewer implements Runnable, initJmol(loadStatus); // pdbentry, seq, JBPCHECK! } - private void initMenus() { + + 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() { @@ -162,7 +189,7 @@ public class AppJmol extends GStructureViewer implements Runnable, viewMenu.add(seqColourBy); final ItemListener handler; JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this, - _alignwith, handler=new ItemListener() + _alignwith, handler = new ItemListener() { @Override @@ -177,39 +204,44 @@ public class AppJmol extends GStructureViewer implements Runnable, 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) @@ -222,8 +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) { @@ -239,7 +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++) @@ -248,7 +280,10 @@ public class AppJmol extends GStructureViewer implements Runnable, { 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; } } @@ -283,25 +318,41 @@ public class AppJmol extends GStructureViewer implements Runnable, } } // ///////////////////////////////// - - jmb = new AppJmolBinding(this, new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }, null, 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); - setSize(400, 400); // probably should be a configurable/dynamic default here - initMenus(); - - if (pdbentry.getFile() != null) + 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) @@ -313,6 +364,17 @@ 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(); @@ -338,13 +400,13 @@ public class AppJmol extends GStructureViewer implements Runnable, /** * list of alignment panels to use for superposition */ - ArrayList _alignwith = new ArrayList(); + Vector _alignwith = new Vector(); /** * list of alignment panels that are used for colouring structures by aligned * sequences */ - ArrayList _colourwith = new ArrayList(); + Vector _colourwith = new Vector(); /** * set the primary alignmentPanel reference and add another alignPanel to the @@ -413,6 +475,13 @@ public class AppJmol extends GStructureViewer implements Runnable, } } + 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); @@ -533,6 +602,10 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null); jmb.newJmolPopup(true, "Jmol", true); + if (command==null) + { + command=""; + } jmb.evalStateCommand(command); jmb.setFinishedInit(true); } @@ -711,6 +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) @@ -736,7 +810,8 @@ public class AppJmol extends GStructureViewer implements Runnable, cmd.append("\nloadingJalviewdata=null"); final String command = cmd.toString(); cmd = null; - long lastnotify = jmb.getLoadNotifiesHandled(); + lastnotify = jmb.getLoadNotifiesHandled(); + try { jmb.evalStateCommand(command); @@ -750,37 +825,40 @@ public class AppJmol extends GStructureViewer implements Runnable, { Cache.log.error("Couldn't add files to Jmol viewer!", ex); } - // 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 { - try - { - Thread.sleep(35); - } catch (Exception e) - { - } - } - // refresh the sequence colours for the new structure(s) - for (AlignmentPanel ap : _colourwith) + Cache.log.debug("Waiting around for jmb notify."); + Thread.sleep(35); + } catch (Exception e) { - jmb.updateColours(ap); } - // do superposition if asked to - if (alignAddedStructures) + } + // 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() { - javax.swing.SwingUtilities.invokeLater(new Runnable() + public void run() { - public void run() - { - alignStructs_withAllAlignPanels(); - // jmb.superposeStructures(ap.av.getAlignment(), -1, null); - } - }); - alignAddedStructures = false; - } - addingStructures = false; + alignStructs_withAllAlignPanels(); + // jmb.superposeStructures(ap.av.getAlignment(), -1, null); + } + }); + alignAddedStructures = false; } + addingStructures = false; + } _started = false; worker = null; @@ -830,8 +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"); } @@ -895,17 +972,34 @@ 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()); - if (_colourwith==null) { _colourwith=new ArrayList();}; - if (_colourwith.size()==0){ _colourwith.add(ap); }; - - // Set the colour using the current view for the associated alignframe - for (AlignmentPanel ap : _colourwith) + if (_colourwith == null) { - jmb.colourBySequence(ap.av.showSequenceFeatures, ap); + _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); + } } } @@ -962,7 +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); @@ -1099,15 +1198,23 @@ public class AppJmol extends GStructureViewer implements Runnable, { jmolActionMenu.setVisible(true); } - if (!jmb.isLoadingFromArchive()) { + if (!jmb.isLoadingFromArchive()) + { seqColour_actionPerformed(null); } } protected void buildJmolActionMenu() { - if (_alignwith==null) { _alignwith=new ArrayList();} - if (_alignwith.size()==0 && ap!=null) { _alignwith.add(ap);}; + if (_alignwith == null) + { + _alignwith = new Vector(); + } + if (_alignwith.size() == 0 && ap != null) + { + _alignwith.add(ap); + } + ; for (Component c : jmolActionMenu.getMenuComponents()) { if (c != alignStructs) @@ -1133,8 +1240,16 @@ public class AppJmol extends GStructureViewer implements Runnable, private void alignStructs_withAllAlignPanels() { - if (ap==null) { return; }; - if (_alignwith.size()==0) { _alignwith.add(ap);}; + if (ap == null) + { + return; + } + ; + if (_alignwith.size() == 0) + { + _alignwith.add(ap); + } + ; try { AlignmentI[] als = new Alignment[_alignwith.size()]; @@ -1208,4 +1323,14 @@ public class AppJmol extends GStructureViewer implements Runnable, return (_colourwith != null) && _colourwith.contains(ap2); } + /** + * + * @return TRUE if the view is NOT being coloured by sequence associations. + */ + public boolean isColouredByJmol() + { + return !jmb.isColourBySequence(); + } + + }