X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=f3d7fa7b1f1f0ec9618a1facb72c6375c26e9234;hb=2026a420963f094072607c0495b6369ba96e60c0;hp=55df1940a468bb6061010968b2f44b671c701aa4;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index 55df194..f3d7fa7 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.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, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -52,6 +52,8 @@ public class AppletJmol extends EmbmenuFrame implements CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true); + CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false); + MenuItem chain = new MenuItem("By Chain"); MenuItem charge = new MenuItem("Charge & Cysteine"); @@ -69,6 +71,8 @@ public class AppletJmol extends EmbmenuFrame implements MenuItem turn = new MenuItem("Turn Propensity"); MenuItem buried = new MenuItem("Buried Index"); + + MenuItem purinepyrimidine = new MenuItem("Purine/Pyrimidine"); MenuItem user = new MenuItem("User Defined Colours"); @@ -83,6 +87,7 @@ public class AppletJmol extends EmbmenuFrame implements RenderPanel renderPanel; AlignmentPanel ap; + ArrayList _aps = new ArrayList(); String fileLoadingError; @@ -98,25 +103,41 @@ public class AppletJmol extends EmbmenuFrame implements * datasource protocol for access to PDBEntry */ String protocol = null; + /** - * Load a bunch of pdb entries associated with sequences in the alignment and display them - aligning them if necessary. - * @param pdbentries each pdb file (at least one needed) - * @param boundseqs each set of sequences for each pdb file (must match number of pdb files) - * @param boundchains the target pdb chain corresponding with each sequence associated with each pdb file (may be null at any level) - * @param align true/false - * @param ap associated alignment - * @param protocol how to get pdb data + * Load a bunch of pdb entries associated with sequences in the alignment and + * display them - aligning them if necessary. + * + * @param pdbentries + * each pdb file (at least one needed) + * @param boundseqs + * each set of sequences for each pdb file (must match number of pdb + * files) + * @param boundchains + * the target pdb chain corresponding with each sequence associated + * with each pdb file (may be null at any level) + * @param align + * true/false + * @param ap + * associated alignment + * @param protocol + * how to get pdb data */ - public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, String[][] boundchains, boolean align, AlignmentPanel ap, String protocol) + public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, + String[][] boundchains, boolean align, AlignmentPanel ap, + String protocol) { throw new Error("Not yet implemented."); } + public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, AlignmentPanel ap, String protocol) { this.ap = ap; - jmb = new AppletJmolBinding(this, new PDBEntry[] - { pdbentry }, new SequenceI[][]{seq}, new String[][]{ chains }, protocol); + jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[] + { pdbentry }, new SequenceI[][] + { seq }, new String[][] + { chains }, protocol); jmb.setColourBySequence(true); if (pdbentry.getId() == null || pdbentry.getId().length() < 1) { @@ -138,12 +159,12 @@ public class AppletJmol extends EmbmenuFrame implements } String alreadyMapped = StructureSelectionManager - .getStructureSelectionManager().alreadyMappedToFile( + .getStructureSelectionManager(ap.av.applet).alreadyMappedToFile( pdbentry.getId()); MCview.PDBfile reader = null; if (alreadyMapped != null) { - reader = StructureSelectionManager.getStructureSelectionManager() + reader = StructureSelectionManager.getStructureSelectionManager(ap.av.applet) .setMapping(seq, chains, pdbentry.getFile(), protocol); // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW? // FOR NOW, LETS JUST OPEN A NEW WINDOW @@ -161,14 +182,16 @@ public class AppletJmol extends EmbmenuFrame implements hydro.addActionListener(this); chain.addActionListener(this); seqColour.addItemListener(this); + jmolColour.addItemListener(this); zappo.addActionListener(this); taylor.addActionListener(this); helix.addActionListener(this); strand.addActionListener(this); turn.addActionListener(this); buried.addActionListener(this); + purinepyrimidine.addActionListener(this); user.addActionListener(this); - + jmolHelp.addActionListener(this); coloursMenu.add(seqColour); @@ -181,8 +204,9 @@ public class AppletJmol extends EmbmenuFrame implements coloursMenu.add(strand); coloursMenu.add(turn); coloursMenu.add(buried); + coloursMenu.add(purinepyrimidine); coloursMenu.add(user); - + coloursMenu.add(jmolColour); helpMenu.add(jmolHelp); this.setLayout(new BorderLayout()); @@ -194,12 +218,12 @@ public class AppletJmol extends EmbmenuFrame implements scriptWindow = new Panel(); scriptWindow.setVisible(false); // this.add(scriptWindow, BorderLayout.SOUTH); - + try { - jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()+"_jmol_", - ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(), - "-applet", scriptWindow, null); + jmb.allocateViewer(renderPanel, true, ap.av.applet.getName() + + "_jmol_", ap.av.applet.getDocumentBase(), + ap.av.applet.getCodeBase(), "-applet", scriptWindow, null); } catch (Exception e) { System.err @@ -220,7 +244,7 @@ public class AppletJmol extends EmbmenuFrame implements closeViewer(); } }); - if (pdbentry.getProperty()==null) + if (pdbentry.getProperty() == null) { pdbentry.setProperty(new Hashtable()); pdbentry.getProperty().put("protocol", protocol); @@ -359,19 +383,20 @@ public class AppletJmol extends EmbmenuFrame implements frame.add(cap); StringBuffer sb = new StringBuffer(); - try { - for (int s = 0; s < jmb.pdbentry.length; s++) + try { - sb.append(StructureSelectionManager.getStructureSelectionManager() - .printMapping(jmb.pdbentry[s].getFile())); - sb.append("\n"); - } - cap.setText(sb.toString()); - } - catch (OutOfMemoryError ex) + for (int s = 0; s < jmb.pdbentry.length; s++) + { + sb.append(jmb.printMapping( + jmb.pdbentry[s].getFile())); + sb.append("\n"); + } + cap.setText(sb.toString()); + } catch (OutOfMemoryError ex) { frame.dispose(); - System.err.println("Out of memory when trying to create dialog box with sequence-structure mapping."); + System.err + .println("Out of memory when trying to create dialog box with sequence-structure mapping."); return; } jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", @@ -423,6 +448,10 @@ public class AppletJmol extends EmbmenuFrame implements setEnabled(buried); jmb.setJalviewColourScheme(new BuriedColourScheme()); } + else if(evt.getSource() == purinepyrimidine) + { + jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme()); + } else if (evt.getSource() == user) { setEnabled(user); @@ -455,23 +484,29 @@ public class AppletJmol extends EmbmenuFrame implements } /** - * tick or untick the seqColour menu entry depending upon if it was selected + * tick or untick the seqColour menu entry or jmoColour entry depending upon if it was selected * or not. * * @param itm */ private void setEnabled(MenuItem itm) { + jmolColour.setState(itm == jmolColour); seqColour.setState(itm == seqColour); jmb.setColourBySequence(itm == seqColour); } public void itemStateChanged(ItemEvent evt) { + if (evt.getSource() == jmolColour) + { + setEnabled(jmolColour); + jmb.setColourBySequence(false); + } else if (evt.getSource() == seqColour) { setEnabled(seqColour); - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); + jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap); } else if (!allChainsSelected) centerViewer(); @@ -499,7 +534,7 @@ public class AppletJmol extends EmbmenuFrame implements public void updateColours(Object source) { AlignmentPanel ap = (AlignmentPanel) source; - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); + jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap); } public void updateTitleAndMenus() @@ -510,7 +545,7 @@ public class AppletJmol extends EmbmenuFrame implements return; } setChainMenuItems(jmb.chainNames); - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); + jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap); setTitle(jmb.getViewerTitle()); } @@ -525,26 +560,30 @@ public class AppletJmol extends EmbmenuFrame implements { } } - Panel splitPane=null; + + Panel splitPane = null; + public void showConsole(boolean showConsole) { if (showConsole) { remove(renderPanel); splitPane = new Panel(); - - splitPane.setLayout(new java.awt.GridLayout(2,1)); + + splitPane.setLayout(new java.awt.GridLayout(2, 1)); splitPane.add(renderPanel); splitPane.add(scriptWindow); scriptWindow.setVisible(true); this.add(splitPane, BorderLayout.CENTER); splitPane.setVisible(true); splitPane.validate(); - } else { + } + else + { scriptWindow.setVisible(false); remove(splitPane); add(renderPanel, BorderLayout.CENTER); - splitPane=null; + splitPane = null; } validate(); } @@ -610,4 +649,16 @@ public class AppletJmol extends EmbmenuFrame implements { jmb.setJalviewColourScheme(ucs); } + + public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) + { + for (int i=0;i<_aps.size();i++) + { + if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment) + { + return ((AlignmentPanel)_aps.get(i)); + } + } + return ap; + } }