X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=caaffa2869afb277da11d5e06fbf0bf55ee6caf0;hb=11cce1c1e065d4430400ad414460ae643b51fbfe;hp=82dab262028d415cdaa819a837490d9e6125b427;hpb=ddf5e62ae51206236ead85fb2ab6bcf868b48e7e;p=jalview.git diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index 82dab26..caaffa2 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -1,803 +1,940 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.appletgui; - -import java.util.*; -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; -import jalview.structure.*; -import jalview.io.*; - -import org.jmol.api.*; -import org.jmol.adapter.smarter.SmarterJmolAdapter; -import org.jmol.popup.*; -import jalview.schemes.*; - - -public class AppletJmol extends Frame - implements StructureListener, JmolStatusListener, - KeyListener, ActionListener, ItemListener - -{ - Menu fileMenu = new Menu("File"); - Menu viewMenu = new Menu("View"); - Menu coloursMenu = new Menu("Colours"); - Menu chainMenu = new Menu("Show Chain"); - Menu helpMenu = new Menu("Help"); - MenuItem mappingMenuItem = new MenuItem("View Mapping"); - - CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true); - MenuItem chain = new MenuItem("By Chain"); - MenuItem charge = new MenuItem("Charge & Cysteine"); - MenuItem zappo = new MenuItem("Zappo"); - MenuItem taylor = new MenuItem("Taylor"); - MenuItem hydro = new MenuItem("Hydrophobicity"); - MenuItem helix = new MenuItem("Helix Propensity"); - MenuItem strand = new MenuItem("Strand Propensity"); - MenuItem turn = new MenuItem("Turn Propensity"); - MenuItem buried = new MenuItem("Buried Index"); - MenuItem user = new MenuItem("User Defined Colours"); - - MenuItem jmolHelp = new MenuItem("Jmol Help"); - - JmolViewer viewer; - JmolPopup jmolpopup; - - Panel scriptWindow; - TextField inputLine; - TextArea history; - SequenceI[] sequence; - StructureSelectionManager ssm; - RenderPanel renderPanel; - AlignmentPanel ap; - String fileLoadingError; - boolean loadedInline; - PDBEntry pdbentry; - boolean colourBySequence = true; - Vector atomsPicked = new Vector(); - - public AppletJmol(PDBEntry pdbentry, - SequenceI[] seq, - AlignmentPanel ap, - String protocol) - { - this.ap = ap; - this.sequence = seq; - this.pdbentry = pdbentry; - - String alreadyMapped = StructureSelectionManager - .getStructureSelectionManager() - .alreadyMappedToFile(pdbentry.getId()); - - if (alreadyMapped != null) - { - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, pdbentry.getFile(), protocol); - return; - } - - renderPanel = new RenderPanel(); - - this.add(renderPanel, BorderLayout.CENTER); - - viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter()); - - viewer.setAppletContext("jalview", - ap.av.applet.getDocumentBase(), - ap.av.applet.getCodeBase(), - null); - - viewer.setJmolStatusListener(this); - - jmolpopup = JmolPopup.newJmolPopup(viewer); - - this.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent evt) - { - closeViewer(); - } - }); - - MenuBar menuBar = new MenuBar(); - menuBar.add(fileMenu); - fileMenu.add(mappingMenuItem); - menuBar.add(viewMenu); - mappingMenuItem.addActionListener(this); - viewMenu.add(chainMenu); - menuBar.add(coloursMenu); - menuBar.add(helpMenu); - - charge.addActionListener(this); - hydro.addActionListener(this); - chain.addActionListener(this); - seqColour.addItemListener(this); - zappo.addActionListener(this); - taylor.addActionListener(this); - helix.addActionListener(this); - strand.addActionListener(this); - turn.addActionListener(this); - buried.addActionListener(this); - user.addActionListener(this); - - jmolHelp.addActionListener(this); - - coloursMenu.add(seqColour); - coloursMenu.add(chain); - coloursMenu.add(charge); - coloursMenu.add(zappo); - coloursMenu.add(taylor); - coloursMenu.add(hydro); - coloursMenu.add(helix); - coloursMenu.add(strand); - coloursMenu.add(turn); - coloursMenu.add(buried); - coloursMenu.add(user); - - helpMenu.add(jmolHelp); - - this.setMenuBar(menuBar); - - if(pdbentry.getFile()!=null) - { - if (protocol.equals(AppletFormatAdapter.PASTE)) - loadInline(pdbentry.getFile()); - else - viewer.openFile(pdbentry.getFile()); - } - - this.setBounds(400, 400, 400, 400); - - this.setVisible(true); - } - - public void loadInline(String string) - { - loadedInline = true; - viewer.openStringInline(string); - } - - - void setChainMenuItems(Vector chains) - { - chainMenu.removeAll(); - - MenuItem menuItem = new MenuItem("All"); - menuItem.addActionListener(this); - - chainMenu.add(menuItem); - - CheckboxMenuItem menuItemCB; - for (int c = 0; c < chains.size(); c++) - { - menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), true); - menuItemCB.addItemListener(this); - chainMenu.add(menuItemCB); - } - } - - boolean allChainsSelected = false; - void centerViewer() - { - StringBuffer cmd = new StringBuffer(); - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof CheckboxMenuItem) - { - CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i); - if (item.getState()) - cmd.append(":" + item.getLabel() + " or "); - } - } - - if (cmd.length() > 0) - cmd.setLength(cmd.length() - 4); - - viewer.evalString("select *;restrict " - + cmd + ";cartoon;center " + cmd); - } - - - void closeViewer() - { - viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); - viewer.evalStringQuiet("zap"); - viewer.setJmolStatusListener(null); - viewer = null; - - //We'll need to find out what other - // listeners need to be shut down in Jmol - StructureSelectionManager - .getStructureSelectionManager() - .removeStructureViewerListener(this, pdbentry.getId()); - - this.setVisible(false); - } - - public void actionPerformed(ActionEvent evt) - { - if(evt.getSource()==mappingMenuItem) - { - jalview.appletgui.CutAndPasteTransfer cap - = new jalview.appletgui.CutAndPasteTransfer(false, null); - Frame frame = new Frame(); - frame.add(cap); - - jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 550, - 600); - cap.setText( - StructureSelectionManager.getStructureSelectionManager().printMapping( - pdbentry.getFile()) - ); - } - else if (evt.getSource() == charge) - { - colourBySequence = false; - seqColour.setState(false); - viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;" - +"select LYS,ARG;color blue;select CYS;color yellow"); - } - - else if (evt.getSource() == chain) - { - colourBySequence = false; - seqColour.setState(false); - viewer.evalStringQuiet("select *;color chain"); - } - else if (evt.getSource() == zappo) - { - setJalviewColourScheme(new ZappoColourScheme()); - } - else if (evt.getSource() == taylor) - { - setJalviewColourScheme(new TaylorColourScheme()); - } - else if (evt.getSource() == hydro) - { - setJalviewColourScheme(new HydrophobicColourScheme()); - } - else if (evt.getSource() == helix) - { - setJalviewColourScheme(new HelixColourScheme()); - } - else if (evt.getSource() == strand) - { - setJalviewColourScheme(new StrandColourScheme()); - } - else if (evt.getSource() == turn) - { - setJalviewColourScheme(new TurnColourScheme()); - } - else if (evt.getSource() == buried) - { - setJalviewColourScheme(new BuriedColourScheme()); - } - else if (evt.getSource() == user) - { - new UserDefinedColours(this); - } - else if(evt.getSource() == jmolHelp) - { - try{ - ap.av.applet.getAppletContext().showDocument( - new java.net.URL("http://jmol.sourceforge.net/docs/JmolUserGuide/"), - "jmolHelp"); - }catch(java.net.MalformedURLException ex){} - } - else - { - allChainsSelected = true; - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof CheckboxMenuItem) - ( (CheckboxMenuItem) chainMenu.getItem(i)).setState(true); - } - centerViewer(); - allChainsSelected = false; - } - } - - public void setJalviewColourScheme(ColourSchemeI cs) - { - colourBySequence = false; - seqColour.setState(false); - - if(cs==null) - return; - - String res; - int index; - Color col; - - Enumeration en = ResidueProperties.aa3Hash.keys(); - StringBuffer command = new StringBuffer("select *;color white;"); - while(en.hasMoreElements()) - { - res = en.nextElement().toString(); - index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); - if(index>20) - continue; - - col = cs.findColour(ResidueProperties.aa[index].charAt(0)); - - command.append("select "+res+";color[" - + col.getRed() + "," - + col.getGreen() + "," - + col.getBlue() + "];"); - } - - viewer.evalStringQuiet(command.toString()); - } - - public void itemStateChanged(ItemEvent evt) - { - if (evt.getSource() == seqColour) - { - colourBySequence = seqColour.getState(); - colourBySequence(ap); - } - else if (!allChainsSelected) - centerViewer(); - } - - public void keyPressed(KeyEvent evt) - { - if (evt.getKeyCode() == KeyEvent.VK_ENTER - && scriptWindow.isVisible()) - { - viewer.evalString(inputLine.getText()); - history.append("\n$ "+inputLine.getText()); - inputLine.setText(""); - } - - } - - public void keyTyped(KeyEvent evt) - { } - - public void keyReleased(KeyEvent evt){} - - ////////////////////////////////// - ///StructureListener - public String getPdbFile() - { - return "???"; - } - - - - String lastMessage; - public void mouseOverStructure(int atomIndex, String strInfo) - { - int pdbResNum; - - int chainSeparator = strInfo.indexOf(":"); - - if(chainSeparator==-1) - chainSeparator = strInfo.indexOf("."); - - pdbResNum = Integer.parseInt( - strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator)); - - String chainId; - - if (strInfo.indexOf(":") > -1) - chainId = strInfo.substring - (strInfo.indexOf(":")+1, strInfo.indexOf(".")); - else - { - chainId = " "; - } - - if (lastMessage == null || !lastMessage.equals(strInfo)) - ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile()); - - lastMessage = strInfo; - } - - StringBuffer resetLastRes = new StringBuffer(); - StringBuffer eval = new StringBuffer(); - - public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile) - { - if (!pdbfile.equals(pdbentry.getFile())) - return; - - if (resetLastRes.length() > 0) - { - viewer.evalStringQuiet(resetLastRes.toString()); - } - - eval.setLength(0); - eval.append("select " + pdbResNum); - - resetLastRes.setLength(0); - resetLastRes.append("select " + pdbResNum); - - if (!chain.equals(" ")) - { - eval.append(":" + chain); - resetLastRes.append(":" + chain); - } - - eval.append(";color gold;wireframe 100"); - - Color col = new Color(viewer.getAtomArgb(atomIndex)); - - resetLastRes.append(";color[" - + col.getRed() + "," - + col.getGreen() + "," - + col.getBlue() + "];wireframe 0"); - - viewer.evalStringQuiet(eval.toString()); - - } - - public void updateColours(Object source) - { - colourBySequence( (AlignmentPanel) source); - } - -//End StructureListener -//////////////////////////// - - FeatureRenderer fr; - public void colourBySequence(AlignmentPanel ap) - { - if(!colourBySequence) - return; - - - StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); - - if (mapping.length < 1) - return; - - SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer(); - - boolean showFeatures = false; - if (ap.av.showSequenceFeatures) - { - showFeatures = true; - if (fr == null) - { - fr = new jalview.appletgui.FeatureRenderer(ap.av); - } - - fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); - } - - StringBuffer command = new StringBuffer(); - - int lastPos = -1; - for (int s = 0; s < sequence.length; s++) - { - for (int m = 0; m < mapping.length; m++) - { - if (mapping[m].getSequence() == sequence[s]) - { - for (int r = 0; r < sequence[s].getLength(); r++) - { - int pos = mapping[m].getPDBResNum( - sequence[s].findPosition(r)); - - if (pos < 1 || pos==lastPos) - continue; - - lastPos = pos; - - Color col = sr.getResidueBoxColour(sequence[s], r); - - if (showFeatures) - col = fr.findFeatureColour(col, sequence[s], r); - - if (command.toString().endsWith(":" + mapping[m].getChain()+ - ";color[" - + col.getRed() + "," - + col.getGreen() + "," - + col.getBlue() + "]")) - { - command = condenseCommand(command.toString(), pos); - continue; - } - - command.append(";select " + pos); - - if (!mapping[m].getChain().equals(" ")) - { - command.append(":" + mapping[m].getChain()); - } - - command.append(";color[" - + col.getRed() + "," - + col.getGreen() + "," - + col.getBlue() + "]"); - - } - break; - } - } - } - - viewer.evalStringQuiet(command.toString()); - } - - StringBuffer condenseCommand(String command, int pos) - { - - StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7)); - - command = command.substring(sb.length()); - - String start; - - if (command.indexOf("-") > -1) - { - start = command.substring(0,command.indexOf("-")); - } - else - { - start = command.substring(0, command.indexOf(":")); - } - - sb.append(start+"-"+pos+command.substring(command.indexOf(":"))); - - return sb; - } - - ///////////////////////////////// - //JmolStatusListener - - public String eval(String strEval) - { - // System.out.println(strEval); - //"# 'eval' is implemented only for the applet."; - return null; - } - - public void createImage(String file, String type, int quality) - {} - - public void setCallbackFunction(String callbackType, - String callbackFunction) - {} - - public void notifyFileLoaded(String fullPathName, String fileName, - String modelName, Object clientFile, - String errorMsg) - { - if(errorMsg!=null) - { - fileLoadingError = errorMsg; - repaint(); - return; - } - - fileLoadingError = null; - - if (fileName != null) - { - //FILE LOADED OK - jmolpopup.updateComputedMenus(); - viewer.evalStringQuiet( - "select backbone;restrict;cartoon;wireframe off;spacefill off"); - - ssm = StructureSelectionManager.getStructureSelectionManager(); - - MCview.PDBfile pdb; - if (loadedInline) - { - pdb = ssm.setMapping(sequence, - pdbentry.getFile(), - AppletFormatAdapter.PASTE); - pdbentry.setFile("INLINE"+pdb.id); - } - else - { - pdb = ssm.setMapping(sequence, - pdbentry.getFile(), - AppletFormatAdapter.URL); - } - - pdbentry.setId(pdb.id); - - ssm.addStructureViewerListener(this); - - Vector chains = new Vector(); - for (int i = 0; i < pdb.chains.size(); i++) - { - chains.addElement( ( (MCview.PDBChain) pdb.chains.elementAt(i)).id); - } - setChainMenuItems(chains); - - colourBySequence(ap); - - StringBuffer title = new StringBuffer(sequence[0].getName() + ":" + - pdbentry.getId()); - - if (pdbentry.getProperty() != null) - { - if (pdbentry.getProperty().get("method") != null) - { - title.append(" Method: "); - title.append(pdbentry.getProperty().get("method")); - } - if (pdbentry.getProperty().get("chains") != null) - { - title.append(" Chain:"); - title.append(pdbentry.getProperty().get("chains")); - } - } - - this.setTitle(title.toString()); - - } - else - return; - } - - public void notifyFrameChanged(int frameNo) - { - boolean isAnimationRunning = (frameNo <= -2); - } - - public void notifyScriptStart(String statusMessage, String additionalInfo) - {} - - public void sendConsoleEcho(String strEcho) - { - if (scriptWindow == null) - showConsole(true); - - history.append("\n"+strEcho); - } - - public void sendConsoleMessage(String strStatus) - { - if(history!=null && strStatus!=null - && !strStatus.equals("Script completed")) - { - history.append("\n"+strStatus); - } - } - - public void notifyScriptTermination(String strStatus, int msWalltime) - { } - - public void handlePopupMenu(int x, int y) - { - jmolpopup.show(x, y); - } - - public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) - { - notifyAtomPicked(iatom, strMeasure); - } - - public void notifyNewDefaultModeMeasurement(int count, String strInfo) - {} - - public void notifyAtomPicked(int atomIndex, String strInfo) - { - - int chainSeparator = strInfo.indexOf(":"); - - if(chainSeparator==-1) - chainSeparator = strInfo.indexOf("."); - - String picked = - strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator); - - - if (strInfo.indexOf(":") > -1) - picked+=strInfo.substring(strInfo.indexOf(":")+1, - strInfo.indexOf(".")); - - picked+=".C"; - - if (!atomsPicked.contains(picked)) - { - viewer.evalString("select "+picked+";label %n %r:%c"); - atomsPicked.addElement(picked); - } - else - { - viewer.evalString("select "+picked+";label off"); - atomsPicked.removeElement(picked); - } - } - - public void notifyAtomHovered(int atomIndex, String strInfo) - { - mouseOverStructure(atomIndex, strInfo); - } - - public void sendSyncScript(String script, String appletName) - {} - - public void showUrl(String url) - { - try{ - ap.av.applet.getAppletContext().showDocument(new java.net.URL(url), - "jmolOutput"); - }catch(java.net.MalformedURLException ex) - {} - } - - 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); - scriptWindow.setVisible(false); - history.setEditable(false); - inputLine.addKeyListener(this); - } - - scriptWindow.setVisible(!scriptWindow.isVisible()); - validate(); - } - - public float functionXY(String functionName, int x, int y) - { - return 0; - } - - ///End JmolStatusListener - /////////////////////////////// - - - class RenderPanel - extends Panel - { - Dimension currentSize = new Dimension(); - Rectangle rectClip = new Rectangle(); - - public void update(Graphics g) { - paint(g); - } - public void paint(Graphics g) - { - currentSize = this.getSize(); - rectClip = g.getClipBounds(); - - if (viewer == null) - { - g.setColor(Color.black); - g.fillRect(0, 0, currentSize.width, currentSize.height); - g.setColor(Color.white); - g.setFont(new Font("Verdana", Font.BOLD, 14)); - g.drawString("Retrieving PDB data....", 20, currentSize.height / 2); - } - else - { - viewer.renderScreenImage(g, currentSize, rectClip); - } - } - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + */ +package jalview.appletgui; + +import java.util.*; +import java.awt.*; +import java.awt.event.*; + +import jalview.datamodel.*; +import jalview.structure.*; +import jalview.io.*; + +import org.jmol.api.*; +import org.jmol.adapter.smarter.SmarterJmolAdapter; + +import org.jmol.popup.*; +import jalview.schemes.*; + +public class AppletJmol extends EmbmenuFrame implements StructureListener, + JmolStatusListener, KeyListener, ActionListener, ItemListener + +{ + Menu fileMenu = new Menu("File"); + + Menu viewMenu = new Menu("View"); + + Menu coloursMenu = new Menu("Colours"); + + Menu chainMenu = new Menu("Show Chain"); + + Menu helpMenu = new Menu("Help"); + + MenuItem mappingMenuItem = new MenuItem("View Mapping"); + + CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true); + + MenuItem chain = new MenuItem("By Chain"); + + MenuItem charge = new MenuItem("Charge & Cysteine"); + + MenuItem zappo = new MenuItem("Zappo"); + + MenuItem taylor = new MenuItem("Taylor"); + + MenuItem hydro = new MenuItem("Hydrophobicity"); + + MenuItem helix = new MenuItem("Helix Propensity"); + + MenuItem strand = new MenuItem("Strand Propensity"); + + MenuItem turn = new MenuItem("Turn Propensity"); + + MenuItem buried = new MenuItem("Buried Index"); + + MenuItem user = new MenuItem("User Defined Colours"); + + MenuItem jmolHelp = new MenuItem("Jmol Help"); + + JmolViewer viewer; + + JmolPopup jmolpopup; + + Panel scriptWindow; + + TextField inputLine; + + TextArea history; + + SequenceI[] sequence; + + String[] chains; + + StructureSelectionManager ssm; + + RenderPanel renderPanel; + + AlignmentPanel ap; + + String fileLoadingError; + + boolean loadedInline; + + PDBEntry pdbentry; + + boolean colourBySequence = true; + + Vector atomsPicked = new Vector(); + + /** + * datasource protocol for access to PDBEntry + */ + String protocol = null; + + public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, + AlignmentPanel ap, String protocol) + { + this.ap = ap; + this.sequence = seq; + this.chains = chains; + this.pdbentry = pdbentry; + this.protocol = protocol; + if (pdbentry.getId() == null || pdbentry.getId().length() < 1) + { + if (protocol.equals(AppletFormatAdapter.PASTE)) + { + pdbentry.setId("PASTED PDB" + + (chains == null ? "_" : chains.toString())); + } + else + { + pdbentry.setId(pdbentry.getFile()); + } + } + + if (jalview.bin.JalviewLite.debug) + { + System.err + .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'"); + } + + String alreadyMapped = StructureSelectionManager + .getStructureSelectionManager().alreadyMappedToFile( + pdbentry.getId()); + MCview.PDBfile reader = null; + if (alreadyMapped != null) + { + reader = StructureSelectionManager.getStructureSelectionManager() + .setMapping(seq, chains, pdbentry.getFile(), protocol); + // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW? + // FOR NOW, LETS JUST OPEN A NEW WINDOW + } + MenuBar menuBar = new MenuBar(); + menuBar.add(fileMenu); + fileMenu.add(mappingMenuItem); + menuBar.add(viewMenu); + mappingMenuItem.addActionListener(this); + viewMenu.add(chainMenu); + menuBar.add(coloursMenu); + menuBar.add(helpMenu); + + charge.addActionListener(this); + hydro.addActionListener(this); + chain.addActionListener(this); + seqColour.addItemListener(this); + zappo.addActionListener(this); + taylor.addActionListener(this); + helix.addActionListener(this); + strand.addActionListener(this); + turn.addActionListener(this); + buried.addActionListener(this); + user.addActionListener(this); + + jmolHelp.addActionListener(this); + + coloursMenu.add(seqColour); + coloursMenu.add(chain); + coloursMenu.add(charge); + coloursMenu.add(zappo); + coloursMenu.add(taylor); + coloursMenu.add(hydro); + coloursMenu.add(helix); + coloursMenu.add(strand); + coloursMenu.add(turn); + coloursMenu.add(buried); + coloursMenu.add(user); + + helpMenu.add(jmolHelp); + + setMenuBar(menuBar); + + renderPanel = new RenderPanel(); + embedMenuIfNeeded(renderPanel); + this.add(renderPanel, BorderLayout.CENTER); + viewer = JmolViewer.allocateViewer(renderPanel, + new SmarterJmolAdapter()); + + viewer.setAppletContext("jalview", ap.av.applet.getDocumentBase(), + ap.av.applet.getCodeBase(), null); + + viewer.setJmolStatusListener(this); + + jmolpopup = JmolPopup.newJmolPopup(viewer); + + this.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent evt) + { + closeViewer(); + } + }); + + if (pdbentry.getFile() != null) + { + // import structure data from pdbentry.getFile based on given protocol + if (protocol.equals(AppletFormatAdapter.PASTE)) + { + loadInline(pdbentry.getFile()); + } + else if (protocol.equals(AppletFormatAdapter.FILE) + || protocol.equals(AppletFormatAdapter.URL)) + { + viewer.openFile(pdbentry.getFile()); + } + else + { + // probably CLASSLOADER based datasource.. + // Try and get a reader on the datasource, and pass that to Jmol + try + { + java.io.Reader freader = null; + if (reader != null) + { + if (jalview.bin.JalviewLite.debug) + { + System.err + .println("AppletJmol:Trying to reuse existing PDBfile IO parser."); + } + // re-use the one we opened earlier + freader = reader.getReader(); + } + if (freader == null) + { + if (jalview.bin.JalviewLite.debug) + { + System.err + .println("AppletJmol:Creating new PDBfile IO parser."); + } + FileParse fp = new FileParse(pdbentry.getFile(), protocol); + fp.mark(); + // reader = new MCview.PDBfile(fp); + // could set ID, etc. + // if (!reader.isValid()) + // { + // throw new Exception("Invalid datasource. + // "+reader.getWarningMessage()); + // } + // fp.reset(); + freader = fp.getReader(); + } + if (freader == null) + { + throw new Exception( + "Invalid datasource. Could not obtain Reader."); + } + viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader); + } catch (Exception e) + { + // give up! + System.err.println("Couldn't access pdbentry id=" + + pdbentry.getId() + " and file=" + pdbentry.getFile() + + " using protocol=" + protocol); + e.printStackTrace(); + } + } + } + + jalview.bin.JalviewLite.addFrame(this, "Jmol", 400, 400); + } + + public void loadInline(String string) + { + loadedInline = true; + viewer.openStringInline(string); + } + + void setChainMenuItems(Vector chains) + { + chainMenu.removeAll(); + + MenuItem menuItem = new MenuItem("All"); + menuItem.addActionListener(this); + + chainMenu.add(menuItem); + + CheckboxMenuItem menuItemCB; + for (int c = 0; c < chains.size(); c++) + { + menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), + true); + menuItemCB.addItemListener(this); + chainMenu.add(menuItemCB); + } + } + + boolean allChainsSelected = false; + + void centerViewer() + { + StringBuffer cmd = new StringBuffer(); + for (int i = 0; i < chainMenu.getItemCount(); i++) + { + if (chainMenu.getItem(i) instanceof CheckboxMenuItem) + { + CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i); + if (item.getState()) + cmd.append(":" + item.getLabel() + " or "); + } + } + + if (cmd.length() > 0) + cmd.setLength(cmd.length() - 4); + + viewer + .evalString("select *;restrict " + cmd + ";cartoon;center " + + cmd); + } + + void closeViewer() + { + viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); + viewer.evalStringQuiet("zap"); + viewer.setJmolStatusListener(null); + viewer = null; + + // We'll need to find out what other + // listeners need to be shut down in Jmol + StructureSelectionManager.getStructureSelectionManager() + .removeStructureViewerListener(this, pdbentry.getId()); + + this.setVisible(false); + } + + public void actionPerformed(ActionEvent evt) + { + if (evt.getSource() == mappingMenuItem) + { + jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer( + false, null); + Frame frame = new Frame(); + frame.add(cap); + + jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", + 550, 600); + cap.setText(StructureSelectionManager.getStructureSelectionManager() + .printMapping(pdbentry.getFile())); + } + else if (evt.getSource() == charge) + { + colourBySequence = false; + seqColour.setState(false); + viewer + .evalStringQuiet("select *;color white;select ASP,GLU;color red;" + + "select LYS,ARG;color blue;select CYS;color yellow"); + } + + else if (evt.getSource() == chain) + { + colourBySequence = false; + seqColour.setState(false); + viewer.evalStringQuiet("select *;color chain"); + } + else if (evt.getSource() == zappo) + { + setJalviewColourScheme(new ZappoColourScheme()); + } + else if (evt.getSource() == taylor) + { + setJalviewColourScheme(new TaylorColourScheme()); + } + else if (evt.getSource() == hydro) + { + setJalviewColourScheme(new HydrophobicColourScheme()); + } + else if (evt.getSource() == helix) + { + setJalviewColourScheme(new HelixColourScheme()); + } + else if (evt.getSource() == strand) + { + setJalviewColourScheme(new StrandColourScheme()); + } + else if (evt.getSource() == turn) + { + setJalviewColourScheme(new TurnColourScheme()); + } + else if (evt.getSource() == buried) + { + setJalviewColourScheme(new BuriedColourScheme()); + } + else if (evt.getSource() == user) + { + new UserDefinedColours(this); + } + else if (evt.getSource() == jmolHelp) + { + try + { + ap.av.applet.getAppletContext().showDocument( + new java.net.URL( + "http://jmol.sourceforge.net/docs/JmolUserGuide/"), + "jmolHelp"); + } catch (java.net.MalformedURLException ex) + { + } + } + else + { + allChainsSelected = true; + for (int i = 0; i < chainMenu.getItemCount(); i++) + { + if (chainMenu.getItem(i) instanceof CheckboxMenuItem) + ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true); + } + centerViewer(); + allChainsSelected = false; + } + } + + public void setJalviewColourScheme(ColourSchemeI cs) + { + colourBySequence = false; + seqColour.setState(false); + + if (cs == null) + return; + + String res; + int index; + Color col; + + Enumeration en = ResidueProperties.aa3Hash.keys(); + StringBuffer command = new StringBuffer("select *;color white;"); + while (en.hasMoreElements()) + { + res = en.nextElement().toString(); + index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); + if (index > 20) + continue; + + col = cs.findColour(ResidueProperties.aa[index].charAt(0)); + + command.append("select " + res + ";color[" + col.getRed() + "," + + col.getGreen() + "," + col.getBlue() + "];"); + } + + viewer.evalStringQuiet(command.toString()); + } + + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == seqColour) + { + lastCommand = null; + colourBySequence = seqColour.getState(); + colourBySequence(ap); + } + else if (!allChainsSelected) + centerViewer(); + } + + public void keyPressed(KeyEvent evt) + { + if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible()) + { + viewer.evalString(inputLine.getText()); + history.append("\n$ " + inputLine.getText()); + inputLine.setText(""); + } + + } + + public void keyTyped(KeyEvent evt) + { + } + + public void keyReleased(KeyEvent evt) + { + } + + // //////////////////////////////// + // /StructureListener + public String getPdbFile() + { + return "???"; + } + + String lastMessage; + + public void mouseOverStructure(int atomIndex, String strInfo) + { + int pdbResNum; + + int chainSeparator = strInfo.indexOf(":"); + + if (chainSeparator == -1) + chainSeparator = strInfo.indexOf("."); + + pdbResNum = Integer.parseInt(strInfo.substring( + strInfo.indexOf("]") + 1, chainSeparator)); + + String chainId; + + if (strInfo.indexOf(":") > -1) + chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo + .indexOf(".")); + else + { + chainId = " "; + } + + if (lastMessage == null || !lastMessage.equals(strInfo)) + ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile()); + + lastMessage = strInfo; + } + + StringBuffer resetLastRes = new StringBuffer(); + + StringBuffer eval = new StringBuffer(); + + public void highlightAtom(int atomIndex, int pdbResNum, String chain, + String pdbfile) + { + if (!pdbfile.equals(pdbentry.getFile())) + return; + + if (resetLastRes.length() > 0) + { + viewer.evalStringQuiet(resetLastRes.toString()); + } + + eval.setLength(0); + eval.append("select " + pdbResNum); + + resetLastRes.setLength(0); + resetLastRes.append("select " + pdbResNum); + + eval.append(":"); + resetLastRes.append(":"); + if (!chain.equals(" ")) + { + eval.append(chain); + resetLastRes.append(chain); + } + + eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); + + resetLastRes.append(";wireframe 0;" + resetLastRes.toString() + + " and not hetero; spacefill 0;"); + + eval.append("spacefill 200;select none"); + + viewer.evalStringQuiet(eval.toString()); + + } + + public void updateColours(Object source) + { + colourBySequence((AlignmentPanel) source); + } + + // End StructureListener + // ////////////////////////// + + public Color getColour(int atomIndex, int pdbResNum, String chain, + String pdbfile) + { + if (!pdbfile.equals(pdbentry.getFile())) + return null; + + return new Color(viewer.getAtomArgb(atomIndex)); + } + + String lastCommand; + + FeatureRenderer fr = null; + + public void colourBySequence(AlignmentPanel sourceap) + { + this.ap = sourceap; + + if (!colourBySequence) + return; + + StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); + + if (mapping.length < 1) + return; + + SequenceRenderer sr = new SequenceRenderer(ap.av); + + boolean showFeatures = false; + + if (ap.av.showSequenceFeatures) + { + showFeatures = true; + if (fr == null) + { + fr = new jalview.appletgui.FeatureRenderer(ap.av); + } + + fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); + } + + StringBuffer command = new StringBuffer(); + + int lastPos = -1; + for (int s = 0; s < sequence.length; s++) + { + for (int sp, m = 0; m < mapping.length; m++) + { + if (mapping[m].getSequence() == sequence[s] + && (sp = ap.av.alignment.findIndex(sequence[s])) > -1) + { + SequenceI asp = ap.av.alignment.getSequenceAt(sp); + for (int r = 0; r < asp.getLength(); r++) + { + // no mapping to gaps in sequence + if (jalview.util.Comparison.isGap(asp.getCharAt(r))) + { + continue; + } + int pos = mapping[m].getPDBResNum(asp.findPosition(r)); + + if (pos < 1 || pos == lastPos) + continue; + + lastPos = pos; + + Color col = sr.getResidueBoxColour(sequence[s], r); + + if (showFeatures) + col = fr.findFeatureColour(col, sequence[s], r); + + if (command.toString().endsWith( + ":" + mapping[m].getChain() + ";color[" + col.getRed() + + "," + col.getGreen() + "," + col.getBlue() + + "]")) + { + command = condenseCommand(command.toString(), pos); + continue; + } + + command.append(";select " + pos); + + if (!mapping[m].getChain().equals(" ")) + { + command.append(":" + mapping[m].getChain()); + } + + command.append(";color[" + col.getRed() + "," + col.getGreen() + + "," + col.getBlue() + "]"); + } + break; + } + } + } + + if (lastCommand == null || !lastCommand.equals(command.toString())) + { + viewer.evalStringQuiet(command.toString()); + } + lastCommand = command.toString(); + } + + StringBuffer condenseCommand(String command, int pos) + { + + StringBuffer sb = new StringBuffer(command.substring(0, command + .lastIndexOf("select") + 7)); + + command = command.substring(sb.length()); + + String start; + + if (command.indexOf("-") > -1) + { + start = command.substring(0, command.indexOf("-")); + } + else + { + start = command.substring(0, command.indexOf(":")); + } + + sb.append(start + "-" + pos + command.substring(command.indexOf(":"))); + + return sb; + } + + // /////////////////////////////// + // JmolStatusListener + + public String eval(String strEval) + { + // System.out.println(strEval); + // "# 'eval' is implemented only for the applet."; + return null; + } + + public void createImage(String file, String type, int quality) + { + } + + public void setCallbackFunction(String callbackType, + String callbackFunction) + { + } + + public void notifyFileLoaded(String fullPathName, String fileName, + String modelName, Object clientFile, String errorMsg) + { + if (errorMsg != null) + { + fileLoadingError = errorMsg; + repaint(); + return; + } + + fileLoadingError = null; + + if (fileName != null) + { + // FILE LOADED OK + jmolpopup.updateComputedMenus(); + viewer + .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off"); + + ssm = StructureSelectionManager.getStructureSelectionManager(); + MCview.PDBfile pdb; + if (loadedInline) + { + pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(), + AppletFormatAdapter.PASTE); + pdbentry.setFile("INLINE" + pdb.id); + } + else + { + // TODO: Jmol can in principle retrieve from CLASSLOADER but this needs + // to be tested. See mantis bug + // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 + + pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(), + AppletFormatAdapter.URL); + + } + + pdbentry.setId(pdb.id); + + ssm.addStructureViewerListener(this); + + Vector chains = new Vector(); + for (int i = 0; i < pdb.chains.size(); i++) + { + chains.addElement(((MCview.PDBChain) pdb.chains.elementAt(i)).id); + } + setChainMenuItems(chains); + + colourBySequence(ap); + + StringBuffer title = new StringBuffer(sequence[0].getName() + ":" + + pdbentry.getId()); + + if (pdbentry.getProperty() != null) + { + if (pdbentry.getProperty().get("method") != null) + { + title.append(" Method: "); + title.append(pdbentry.getProperty().get("method")); + } + if (pdbentry.getProperty().get("chains") != null) + { + title.append(" Chain:"); + title.append(pdbentry.getProperty().get("chains")); + } + } + + this.setTitle(title.toString()); + + } + else + return; + } + + public void notifyFrameChanged(int frameNo) + { + boolean isAnimationRunning = (frameNo <= -2); + } + + public void notifyScriptStart(String statusMessage, String additionalInfo) + { + } + + public void sendConsoleEcho(String strEcho) + { + if (scriptWindow == null) + showConsole(true); + + history.append("\n" + strEcho); + } + + public void sendConsoleMessage(String strStatus) + { + if (history != null && strStatus != null + && !strStatus.equals("Script completed")) + { + history.append("\n" + strStatus); + } + } + + public void notifyScriptTermination(String strStatus, int msWalltime) + { + } + + public void handlePopupMenu(int x, int y) + { + jmolpopup.show(x, y); + } + + public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) + { + notifyAtomPicked(iatom, strMeasure); + } + + public void notifyNewDefaultModeMeasurement(int count, String strInfo) + { + } + + public void notifyAtomPicked(int atomIndex, String strInfo) + { + + int chainSeparator = strInfo.indexOf(":"); + + if (chainSeparator == -1) + chainSeparator = strInfo.indexOf("."); + + String picked = strInfo.substring(strInfo.indexOf("]") + 1, + chainSeparator); + + if (strInfo.indexOf(":") > -1) + picked += strInfo.substring(strInfo.indexOf(":") + 1, strInfo + .indexOf(".")); + + picked += ".CA"; + + if (!atomsPicked.contains(picked)) + { + viewer.evalString("select " + picked + ";label %n %r:%c"); + atomsPicked.addElement(picked); + } + else + { + viewer.evalString("select " + picked + ";label off"); + atomsPicked.removeElement(picked); + } + } + + public void notifyAtomHovered(int atomIndex, String strInfo) + { + mouseOverStructure(atomIndex, strInfo); + } + + public void sendSyncScript(String script, String appletName) + { + } + + public void showUrl(String url) + { + try + { + ap.av.applet.getAppletContext().showDocument(new java.net.URL(url), + "jmolOutput"); + } catch (java.net.MalformedURLException ex) + { + } + } + + 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); + scriptWindow.setVisible(false); + history.setEditable(false); + inputLine.addKeyListener(this); + } + + scriptWindow.setVisible(!scriptWindow.isVisible()); + validate(); + } + + public float functionXY(String functionName, int x, int y) + { + return 0; + } + + // /End JmolStatusListener + // ///////////////////////////// + + class RenderPanel extends Panel + { + Dimension currentSize = new Dimension(); + + Rectangle rectClip = new Rectangle(); + + public void update(Graphics g) + { + paint(g); + } + + public void paint(Graphics g) + { + currentSize = this.getSize(); + rectClip = g.getClipBounds(); + + if (viewer == null) + { + g.setColor(Color.black); + g.fillRect(0, 0, currentSize.width, currentSize.height); + g.setColor(Color.white); + g.setFont(new Font("Verdana", Font.BOLD, 14)); + g.drawString("Retrieving PDB data....", 20, currentSize.height / 2); + } + else + { + viewer.renderScreenImage(g, currentSize, rectClip); + } + } + } + +}