X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=f3d7fa7b1f1f0ec9618a1facb72c6375c26e9234;hb=2026a420963f094072607c0495b6369ba96e60c0;hp=fb15c8253e57fd50706a67d52be19cae61f67b2a;hpb=b32b824388dea3107cd1598d63f8759f00b75e1f;p=jalview.git diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index fb15c82..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 2.5) - * 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, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -33,7 +33,7 @@ import org.jmol.viewer.JmolConstants; import jalview.schemes.*; -public class AppletJmol extends EmbmenuFrame implements +public class AppletJmol extends EmbmenuFrame implements // StructureListener, KeyListener, ActionListener, ItemListener, SequenceStructureBinding @@ -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; @@ -99,12 +104,40 @@ public class AppletJmol extends EmbmenuFrame implements */ 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 + */ + 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 }, seq, 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) { @@ -126,12 +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 @@ -149,14 +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); @@ -169,18 +204,37 @@ 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()); setMenuBar(menuBar); renderPanel = new RenderPanel(); embedMenuIfNeeded(renderPanel); this.add(renderPanel, BorderLayout.CENTER); - jmb.allocateViewer(renderPanel, - "jalviewJmol", ap.av.applet.getDocumentBase(), ap.av.applet - .getCodeBase(), ""); + 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); + } catch (Exception e) + { + System.err + .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase=" + + ap.av.applet.getDocumentBase() + + "\nCodebase=" + + ap.av.applet.getCodeBase()); + e.printStackTrace(); + dispose(); + return; + } jmb.newJmolPopup(true, "Jmol", true); this.addWindowListener(new WindowAdapter() @@ -190,12 +244,18 @@ public class AppletJmol extends EmbmenuFrame implements closeViewer(); } }); - + if (pdbentry.getProperty() == null) + { + pdbentry.setProperty(new Hashtable()); + pdbentry.getProperty().put("protocol", protocol); + } if (pdbentry.getFile() != null) { // import structure data from pdbentry.getFile based on given protocol if (protocol.equals(AppletFormatAdapter.PASTE)) { + // TODO: JAL-623 : correctly record file contents for matching up later + // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode()); loadInline(pdbentry.getFile()); } else if (protocol.equals(AppletFormatAdapter.FILE) @@ -244,7 +304,8 @@ public class AppletJmol extends EmbmenuFrame implements throw new Exception( "Invalid datasource. Could not obtain Reader."); } - jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader); + jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(), + freader); } catch (Exception e) { // give up! @@ -259,28 +320,10 @@ public class AppletJmol extends EmbmenuFrame implements jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400); } - /** - * create a new binding between structures in an existing jmol viewer instance - * and an alignpanel with sequences that have existing PDBFile entries. Note, - * this does not open a new Jmol window, or modify the display of the - * structures in the original jmol window. - * - * @param viewer2 - * @param alignPanel - * @param seqs - * - sequences to search for associations - */ - public AppletJmol(JmolViewer viewer2, AlignmentPanel alignPanel, - SequenceI[] seqs) - { - - // TODO Auto-generated constructor stub - } - public void loadInline(String string) { loadedInline = true; - jmb.viewer.openStringInline(string); + jmb.loadInline(string); } void setChainMenuItems(Vector chains) @@ -339,15 +382,25 @@ public class AppletJmol extends EmbmenuFrame implements Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", - 550, 600); StringBuffer sb = new StringBuffer(); - for (int s = 0; s < jmb.pdbentry.length; s++) + try + { + 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) { - sb.append(StructureSelectionManager.getStructureSelectionManager() - .printMapping(jmb.pdbentry[s].getFile())); - sb.append("\n"); + frame.dispose(); + 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", + 550, 600); } else if (evt.getSource() == charge) { @@ -395,6 +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); @@ -427,23 +484,29 @@ public class AppletJmol extends EmbmenuFrame implements } /** - * tick or untick the seqColour menu entry depending upon if it was selected or not. + * 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) { - seqColour.setState(itm==seqColour); - jmb.setColourBySequence(itm==seqColour); + 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(); @@ -471,7 +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() @@ -482,7 +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()); } @@ -498,22 +561,30 @@ public class AppletJmol extends EmbmenuFrame implements } } + Panel splitPane = null; + public void showConsole(boolean showConsole) { - if (scriptWindow == null) - { - scriptWindow = new Panel(new BorderLayout()); - inputLine = new TextField(); - history = new TextArea(5, 40); - scriptWindow.add(history, BorderLayout.CENTER); - scriptWindow.add(inputLine, BorderLayout.SOUTH); - add(scriptWindow, BorderLayout.SOUTH); + if (showConsole) + { + remove(renderPanel); + splitPane = new Panel(); + + 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 + { scriptWindow.setVisible(false); - history.setEditable(false); - inputLine.addKeyListener(this); + remove(splitPane); + add(renderPanel, BorderLayout.CENTER); + splitPane = null; } - - scriptWindow.setVisible(!scriptWindow.isVisible()); validate(); } @@ -555,37 +626,39 @@ public class AppletJmol extends EmbmenuFrame implements } } } -/* - @Override - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbId) - { - return jmb.getColour(atomIndex, pdbResNum, chain, pdbId); - } - - @Override - public String[] getPdbFile() - { - return jmb.getPdbFile(); - } - @Override - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbId) + /* + * @Override public Color getColour(int atomIndex, int pdbResNum, String + * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain, + * pdbId); } + * + * @Override public String[] getPdbFile() { return jmb.getPdbFile(); } + * + * @Override public void highlightAtom(int atomIndex, int pdbResNum, String + * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain, + * pdbId); + * + * } + * + * @Override public void mouseOverStructure(int atomIndex, String strInfo) { + * jmb.mouseOverStructure(atomIndex, strInfo); + * + * } + */ + public void setJalviewColourScheme(UserColourScheme ucs) { - jmb.highlightAtom(atomIndex, pdbResNum, chain, pdbId); - + jmb.setJalviewColourScheme(ucs); } - @Override - public void mouseOverStructure(int atomIndex, String strInfo) - { - jmb.mouseOverStructure(atomIndex, strInfo); - - } -*/ - public void setJalviewColourScheme(UserColourScheme ucs) + public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) { - jmb.setJalviewColourScheme(ucs); + for (int i=0;i<_aps.size();i++) + { + if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment) + { + return ((AlignmentPanel)_aps.get(i)); + } + } + return ap; } }