-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.structure.*;\r
-import jalview.io.*;\r
-\r
-import org.jmol.api.*;\r
-import org.jmol.adapter.smarter.SmarterJmolAdapter;\r
-import org.jmol.popup.*;\r
-import jalview.schemes.*;\r
-\r
-\r
-public class AppletJmol extends Frame\r
- implements StructureListener, JmolStatusListener,\r
- KeyListener, ActionListener, ItemListener\r
-\r
-{\r
- Menu fileMenu = new Menu("File");\r
- Menu viewMenu = new Menu("View");\r
- Menu coloursMenu = new Menu("Colours");\r
- Menu chainMenu = new Menu("Show Chain");\r
- Menu helpMenu = new Menu("Help");\r
- MenuItem mappingMenuItem = new MenuItem("View Mapping");\r
-\r
- CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);\r
- MenuItem chain = new MenuItem("By Chain");\r
- MenuItem charge = new MenuItem("Charge & Cysteine");\r
- MenuItem zappo = new MenuItem("Zappo");\r
- MenuItem taylor = new MenuItem("Taylor");\r
- MenuItem hydro = new MenuItem("Hydrophobicity");\r
- MenuItem helix = new MenuItem("Helix Propensity");\r
- MenuItem strand = new MenuItem("Strand Propensity");\r
- MenuItem turn = new MenuItem("Turn Propensity");\r
- MenuItem buried = new MenuItem("Buried Index");\r
- MenuItem user = new MenuItem("User Defined Colours");\r
-\r
- MenuItem jmolHelp = new MenuItem("Jmol Help");\r
-\r
- JmolViewer viewer;\r
- JmolPopup jmolpopup;\r
-\r
- Panel scriptWindow;\r
- TextField inputLine;\r
- TextArea history;\r
- SequenceI[] sequence;\r
- StructureSelectionManager ssm;\r
- RenderPanel renderPanel;\r
- AlignmentPanel ap;\r
- String fileLoadingError;\r
- boolean loadedInline;\r
- PDBEntry pdbentry;\r
- boolean colourBySequence = true;\r
- Vector atomsPicked = new Vector();\r
-\r
- public AppletJmol(PDBEntry pdbentry,\r
- SequenceI[] seq,\r
- AlignmentPanel ap,\r
- String protocol)\r
- {\r
- this.ap = ap;\r
- this.sequence = seq;\r
- this.pdbentry = pdbentry;\r
-\r
- String alreadyMapped = StructureSelectionManager\r
- .getStructureSelectionManager()\r
- .alreadyMappedToFile(pdbentry.getId());\r
-\r
- if (alreadyMapped != null)\r
- {\r
- StructureSelectionManager.getStructureSelectionManager()\r
- .setMapping(seq, pdbentry.getFile(), protocol);\r
- return;\r
- }\r
-\r
- renderPanel = new RenderPanel();\r
-\r
- this.add(renderPanel, BorderLayout.CENTER);\r
-\r
- viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());\r
-\r
- viewer.setAppletContext("jalview",\r
- ap.av.applet.getDocumentBase(),\r
- ap.av.applet.getCodeBase(),\r
- null);\r
-\r
- viewer.setJmolStatusListener(this);\r
-\r
- jmolpopup = JmolPopup.newJmolPopup(viewer);\r
-\r
- this.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent evt)\r
- {\r
- closeViewer();\r
- }\r
- });\r
-\r
- MenuBar menuBar = new MenuBar();\r
- menuBar.add(fileMenu);\r
- fileMenu.add(mappingMenuItem);\r
- menuBar.add(viewMenu);\r
- mappingMenuItem.addActionListener(this);\r
- viewMenu.add(chainMenu);\r
- menuBar.add(coloursMenu);\r
- menuBar.add(helpMenu);\r
-\r
- charge.addActionListener(this);\r
- hydro.addActionListener(this);\r
- chain.addActionListener(this);\r
- seqColour.addItemListener(this);\r
- zappo.addActionListener(this);\r
- taylor.addActionListener(this);\r
- helix.addActionListener(this);\r
- strand.addActionListener(this);\r
- turn.addActionListener(this);\r
- buried.addActionListener(this);\r
- user.addActionListener(this);\r
-\r
- jmolHelp.addActionListener(this);\r
-\r
- coloursMenu.add(seqColour);\r
- coloursMenu.add(chain);\r
- coloursMenu.add(charge);\r
- coloursMenu.add(zappo);\r
- coloursMenu.add(taylor);\r
- coloursMenu.add(hydro);\r
- coloursMenu.add(helix);\r
- coloursMenu.add(strand);\r
- coloursMenu.add(turn);\r
- coloursMenu.add(buried);\r
- coloursMenu.add(user);\r
-\r
- helpMenu.add(jmolHelp);\r
-\r
- this.setMenuBar(menuBar);\r
-\r
- if(pdbentry.getFile()!=null)\r
- {\r
- if (protocol.equals(AppletFormatAdapter.PASTE))\r
- loadInline(pdbentry.getFile());\r
- else\r
- viewer.openFile(pdbentry.getFile());\r
- }\r
-\r
- this.setBounds(400, 400, 400, 400);\r
-\r
- this.setVisible(true);\r
- }\r
-\r
- public void loadInline(String string)\r
- {\r
- loadedInline = true;\r
- viewer.openStringInline(string);\r
- }\r
-\r
-\r
- void setChainMenuItems(Vector chains)\r
- {\r
- chainMenu.removeAll();\r
-\r
- MenuItem menuItem = new MenuItem("All");\r
- menuItem.addActionListener(this);\r
-\r
- chainMenu.add(menuItem);\r
-\r
- CheckboxMenuItem menuItemCB;\r
- for (int c = 0; c < chains.size(); c++)\r
- {\r
- menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), true);\r
- menuItemCB.addItemListener(this);\r
- chainMenu.add(menuItemCB);\r
- }\r
- }\r
-\r
- boolean allChainsSelected = false;\r
- void centerViewer()\r
- {\r
- StringBuffer cmd = new StringBuffer();\r
- for (int i = 0; i < chainMenu.getItemCount(); i++)\r
- {\r
- if (chainMenu.getItem(i) instanceof CheckboxMenuItem)\r
- {\r
- CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);\r
- if (item.getState())\r
- cmd.append(":" + item.getLabel() + " or ");\r
- }\r
- }\r
-\r
- if (cmd.length() > 0)\r
- cmd.setLength(cmd.length() - 4);\r
-\r
- viewer.evalString("select *;restrict "\r
- + cmd + ";cartoon;center " + cmd);\r
- }\r
-\r
-\r
- void closeViewer()\r
- {\r
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);\r
- viewer.evalStringQuiet("zap");\r
- viewer.setJmolStatusListener(null);\r
- viewer = null;\r
-\r
- //We'll need to find out what other\r
- // listeners need to be shut down in Jmol\r
- StructureSelectionManager\r
- .getStructureSelectionManager()\r
- .removeStructureViewerListener(this, pdbentry.getId());\r
-\r
- this.setVisible(false);\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- if(evt.getSource()==mappingMenuItem)\r
- {\r
- jalview.appletgui.CutAndPasteTransfer cap\r
- = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
-\r
- jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 550,\r
- 600);\r
- cap.setText(\r
- StructureSelectionManager.getStructureSelectionManager().printMapping(\r
- pdbentry.getFile())\r
- );\r
- }\r
- else if (evt.getSource() == charge)\r
- {\r
- colourBySequence = false;\r
- seqColour.setState(false);\r
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"\r
- +"select LYS,ARG;color blue;select CYS;color yellow");\r
- }\r
-\r
- else if (evt.getSource() == chain)\r
- {\r
- colourBySequence = false;\r
- seqColour.setState(false);\r
- viewer.evalStringQuiet("select *;color chain");\r
- }\r
- else if (evt.getSource() == zappo)\r
- {\r
- setJalviewColourScheme(new ZappoColourScheme());\r
- }\r
- else if (evt.getSource() == taylor)\r
- {\r
- setJalviewColourScheme(new TaylorColourScheme());\r
- }\r
- else if (evt.getSource() == hydro)\r
- {\r
- setJalviewColourScheme(new HydrophobicColourScheme());\r
- }\r
- else if (evt.getSource() == helix)\r
- {\r
- setJalviewColourScheme(new HelixColourScheme());\r
- }\r
- else if (evt.getSource() == strand)\r
- {\r
- setJalviewColourScheme(new StrandColourScheme());\r
- }\r
- else if (evt.getSource() == turn)\r
- {\r
- setJalviewColourScheme(new TurnColourScheme());\r
- }\r
- else if (evt.getSource() == buried)\r
- {\r
- setJalviewColourScheme(new BuriedColourScheme());\r
- }\r
- else if (evt.getSource() == user)\r
- {\r
- new UserDefinedColours(this);\r
- }\r
- else if(evt.getSource() == jmolHelp)\r
- {\r
- try{\r
- ap.av.applet.getAppletContext().showDocument(\r
- new java.net.URL("http://jmol.sourceforge.net/docs/JmolUserGuide/"),\r
- "jmolHelp");\r
- }catch(java.net.MalformedURLException ex){}\r
- }\r
- else\r
- {\r
- allChainsSelected = true;\r
- for (int i = 0; i < chainMenu.getItemCount(); i++)\r
- {\r
- if (chainMenu.getItem(i) instanceof CheckboxMenuItem)\r
- ( (CheckboxMenuItem) chainMenu.getItem(i)).setState(true);\r
- }\r
- centerViewer();\r
- allChainsSelected = false;\r
- }\r
- }\r
-\r
- public void setJalviewColourScheme(ColourSchemeI cs)\r
- {\r
- colourBySequence = false;\r
- seqColour.setState(false);\r
-\r
- if(cs==null)\r
- return;\r
-\r
- String res;\r
- int index;\r
- Color col;\r
-\r
- Enumeration en = ResidueProperties.aa3Hash.keys();\r
- StringBuffer command = new StringBuffer("select *;color white;");\r
- while(en.hasMoreElements())\r
- {\r
- res = en.nextElement().toString();\r
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();\r
- if(index>20)\r
- continue;\r
-\r
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));\r
-\r
- command.append("select "+res+";color["\r
- + col.getRed() + ","\r
- + col.getGreen() + ","\r
- + col.getBlue() + "];");\r
- }\r
-\r
- viewer.evalStringQuiet(command.toString());\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (evt.getSource() == seqColour)\r
- {\r
- colourBySequence = seqColour.getState();\r
- colourBySequence(ap);\r
- }\r
- else if (!allChainsSelected)\r
- centerViewer();\r
- }\r
-\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- if (evt.getKeyCode() == KeyEvent.VK_ENTER\r
- && scriptWindow.isVisible())\r
- {\r
- viewer.evalString(inputLine.getText());\r
- history.append("\n$ "+inputLine.getText());\r
- inputLine.setText("");\r
- }\r
-\r
- }\r
-\r
- public void keyTyped(KeyEvent evt)\r
- { }\r
-\r
- public void keyReleased(KeyEvent evt){}\r
-\r
- //////////////////////////////////\r
- ///StructureListener\r
- public String getPdbFile()\r
- {\r
- return "???";\r
- }\r
-\r
-\r
-\r
- String lastMessage;\r
- public void mouseOverStructure(int atomIndex, String strInfo)\r
- {\r
- int pdbResNum;\r
-\r
- int chainSeparator = strInfo.indexOf(":");\r
-\r
- if(chainSeparator==-1)\r
- chainSeparator = strInfo.indexOf(".");\r
-\r
- pdbResNum = Integer.parseInt(\r
- strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator));\r
-\r
- String chainId;\r
-\r
- if (strInfo.indexOf(":") > -1)\r
- chainId = strInfo.substring\r
- (strInfo.indexOf(":")+1, strInfo.indexOf("."));\r
- else\r
- {\r
- chainId = " ";\r
- }\r
-\r
- if (lastMessage == null || !lastMessage.equals(strInfo))\r
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());\r
-\r
- lastMessage = strInfo;\r
- }\r
-\r
- StringBuffer resetLastRes = new StringBuffer();\r
- StringBuffer eval = new StringBuffer();\r
-\r
- public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)\r
- {\r
- if (!pdbfile.equals(pdbentry.getFile()))\r
- return;\r
-\r
- if (resetLastRes.length() > 0)\r
- {\r
- viewer.evalStringQuiet(resetLastRes.toString());\r
- }\r
-\r
- eval.setLength(0);\r
- eval.append("select " + pdbResNum);\r
-\r
- resetLastRes.setLength(0);\r
- resetLastRes.append("select " + pdbResNum);\r
-\r
- if (!chain.equals(" "))\r
- {\r
- eval.append(":" + chain);\r
- resetLastRes.append(":" + chain);\r
- }\r
-\r
- eval.append(";color gold;wireframe 100");\r
-\r
- Color col = new Color(viewer.getAtomArgb(atomIndex));\r
-\r
- resetLastRes.append(";color["\r
- + col.getRed() + ","\r
- + col.getGreen() + ","\r
- + col.getBlue() + "];wireframe 0");\r
-\r
- viewer.evalStringQuiet(eval.toString());\r
-\r
- }\r
-\r
- public void updateColours(Object source)\r
- {\r
- colourBySequence( (AlignmentPanel) source);\r
- }\r
-\r
-//End StructureListener\r
-////////////////////////////\r
-\r
- FeatureRenderer fr;\r
- public void colourBySequence(AlignmentPanel ap)\r
- {\r
- if(!colourBySequence)\r
- return;\r
-\r
-\r
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());\r
-\r
- if (mapping.length < 1)\r
- return;\r
-\r
- SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();\r
-\r
- boolean showFeatures = false;\r
- if (ap.av.showSequenceFeatures)\r
- {\r
- showFeatures = true;\r
- if (fr == null)\r
- {\r
- fr = new jalview.appletgui.FeatureRenderer(ap.av);\r
- }\r
-\r
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());\r
- }\r
-\r
- StringBuffer command = new StringBuffer();\r
-\r
- int lastPos = -1;\r
- for (int s = 0; s < sequence.length; s++)\r
- {\r
- for (int m = 0; m < mapping.length; m++)\r
- {\r
- if (mapping[m].getSequence() == sequence[s])\r
- {\r
- for (int r = 0; r < sequence[s].getLength(); r++)\r
- {\r
- int pos = mapping[m].getPDBResNum(\r
- sequence[s].findPosition(r));\r
-\r
- if (pos < 1 || pos==lastPos)\r
- continue;\r
-\r
- lastPos = pos;\r
-\r
- Color col = sr.getResidueBoxColour(sequence[s], r);\r
-\r
- if (showFeatures)\r
- col = fr.findFeatureColour(col, sequence[s], r);\r
-\r
- if (command.toString().endsWith(":" + mapping[m].getChain()+\r
- ";color["\r
- + col.getRed() + ","\r
- + col.getGreen() + ","\r
- + col.getBlue() + "]"))\r
- {\r
- command = condenseCommand(command.toString(), pos);\r
- continue;\r
- }\r
-\r
- command.append(";select " + pos);\r
-\r
- if (!mapping[m].getChain().equals(" "))\r
- {\r
- command.append(":" + mapping[m].getChain());\r
- }\r
-\r
- command.append(";color["\r
- + col.getRed() + ","\r
- + col.getGreen() + ","\r
- + col.getBlue() + "]");\r
-\r
- }\r
- break;\r
- }\r
- }\r
- }\r
-\r
- viewer.evalStringQuiet(command.toString());\r
- }\r
-\r
- StringBuffer condenseCommand(String command, int pos)\r
- {\r
-\r
- StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));\r
-\r
- command = command.substring(sb.length());\r
-\r
- String start;\r
-\r
- if (command.indexOf("-") > -1)\r
- {\r
- start = command.substring(0,command.indexOf("-"));\r
- }\r
- else\r
- {\r
- start = command.substring(0, command.indexOf(":"));\r
- }\r
-\r
- sb.append(start+"-"+pos+command.substring(command.indexOf(":")));\r
-\r
- return sb;\r
- }\r
-\r
- /////////////////////////////////\r
- //JmolStatusListener\r
-\r
- public String eval(String strEval)\r
- {\r
- // System.out.println(strEval);\r
- //"# 'eval' is implemented only for the applet.";\r
- return null;\r
- }\r
-\r
- public void createImage(String file, String type, int quality)\r
- {}\r
-\r
- public void setCallbackFunction(String callbackType,\r
- String callbackFunction)\r
- {}\r
-\r
- public void notifyFileLoaded(String fullPathName, String fileName,\r
- String modelName, Object clientFile,\r
- String errorMsg)\r
- {\r
- if(errorMsg!=null)\r
- {\r
- fileLoadingError = errorMsg;\r
- repaint();\r
- return;\r
- }\r
-\r
- fileLoadingError = null;\r
-\r
- if (fileName != null)\r
- {\r
- //FILE LOADED OK\r
- jmolpopup.updateComputedMenus();\r
- viewer.evalStringQuiet(\r
- "select backbone;restrict;cartoon;wireframe off;spacefill off");\r
-\r
- ssm = StructureSelectionManager.getStructureSelectionManager();\r
-\r
- MCview.PDBfile pdb;\r
- if (loadedInline)\r
- {\r
- pdb = ssm.setMapping(sequence,\r
- pdbentry.getFile(),\r
- AppletFormatAdapter.PASTE);\r
- pdbentry.setFile("INLINE"+pdb.id);\r
- }\r
- else\r
- {\r
- pdb = ssm.setMapping(sequence,\r
- pdbentry.getFile(),\r
- AppletFormatAdapter.URL);\r
- }\r
-\r
- pdbentry.setId(pdb.id);\r
-\r
- ssm.addStructureViewerListener(this);\r
-\r
- Vector chains = new Vector();\r
- for (int i = 0; i < pdb.chains.size(); i++)\r
- {\r
- chains.addElement( ( (MCview.PDBChain) pdb.chains.elementAt(i)).id);\r
- }\r
- setChainMenuItems(chains);\r
-\r
- colourBySequence(ap);\r
-\r
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +\r
- pdbentry.getId());\r
-\r
- if (pdbentry.getProperty() != null)\r
- {\r
- if (pdbentry.getProperty().get("method") != null)\r
- {\r
- title.append(" Method: ");\r
- title.append(pdbentry.getProperty().get("method"));\r
- }\r
- if (pdbentry.getProperty().get("chains") != null)\r
- {\r
- title.append(" Chain:");\r
- title.append(pdbentry.getProperty().get("chains"));\r
- }\r
- }\r
-\r
- this.setTitle(title.toString());\r
-\r
- }\r
- else\r
- return;\r
- }\r
-\r
- public void notifyFrameChanged(int frameNo)\r
- {\r
- boolean isAnimationRunning = (frameNo <= -2);\r
- }\r
-\r
- public void notifyScriptStart(String statusMessage, String additionalInfo)\r
- {}\r
-\r
- public void sendConsoleEcho(String strEcho)\r
- {\r
- if (scriptWindow == null)\r
- showConsole(true);\r
-\r
- history.append("\n"+strEcho);\r
- }\r
-\r
- public void sendConsoleMessage(String strStatus)\r
- {\r
- if(history!=null && strStatus!=null\r
- && !strStatus.equals("Script completed"))\r
- {\r
- history.append("\n"+strStatus);\r
- }\r
- }\r
-\r
- public void notifyScriptTermination(String strStatus, int msWalltime)\r
- { }\r
-\r
- public void handlePopupMenu(int x, int y)\r
- {\r
- jmolpopup.show(x, y);\r
- }\r
-\r
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)\r
- {\r
- notifyAtomPicked(iatom, strMeasure);\r
- }\r
-\r
- public void notifyNewDefaultModeMeasurement(int count, String strInfo)\r
- {}\r
-\r
- public void notifyAtomPicked(int atomIndex, String strInfo)\r
- {\r
-\r
- int chainSeparator = strInfo.indexOf(":");\r
-\r
- if(chainSeparator==-1)\r
- chainSeparator = strInfo.indexOf(".");\r
-\r
- String picked =\r
- strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator);\r
-\r
-\r
- if (strInfo.indexOf(":") > -1)\r
- picked+=strInfo.substring(strInfo.indexOf(":")+1,\r
- strInfo.indexOf("."));\r
-\r
- picked+=".C";\r
-\r
- if (!atomsPicked.contains(picked))\r
- {\r
- viewer.evalString("select "+picked+";label %n %r:%c");\r
- atomsPicked.addElement(picked);\r
- }\r
- else\r
- {\r
- viewer.evalString("select "+picked+";label off");\r
- atomsPicked.removeElement(picked);\r
- }\r
- }\r
-\r
- public void notifyAtomHovered(int atomIndex, String strInfo)\r
- {\r
- mouseOverStructure(atomIndex, strInfo);\r
- }\r
-\r
- public void sendSyncScript(String script, String appletName)\r
- {}\r
-\r
- public void showUrl(String url)\r
- {\r
- try{\r
- ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),\r
- "jmolOutput");\r
- }catch(java.net.MalformedURLException ex)\r
- {}\r
- }\r
-\r
- public void showConsole(boolean showConsole)\r
- {\r
- if (scriptWindow == null)\r
- {\r
- scriptWindow = new Panel(new BorderLayout());\r
- inputLine = new TextField();\r
- history = new TextArea(5, 40);\r
- scriptWindow.add(history, BorderLayout.CENTER);\r
- scriptWindow.add(inputLine, BorderLayout.SOUTH);\r
- add(scriptWindow, BorderLayout.SOUTH);\r
- scriptWindow.setVisible(false);\r
- history.setEditable(false);\r
- inputLine.addKeyListener(this);\r
- }\r
-\r
- scriptWindow.setVisible(!scriptWindow.isVisible());\r
- validate();\r
- }\r
-\r
- public float functionXY(String functionName, int x, int y)\r
- {\r
- return 0;\r
- }\r
-\r
- ///End JmolStatusListener\r
- ///////////////////////////////\r
-\r
-\r
- class RenderPanel\r
- extends Panel\r
- {\r
- Dimension currentSize = new Dimension();\r
- Rectangle rectClip = new Rectangle();\r
-\r
- public void update(Graphics g) {\r
- paint(g);\r
- }\r
- public void paint(Graphics g)\r
- {\r
- currentSize = this.getSize();\r
- rectClip = g.getClipBounds();\r
-\r
- if (viewer == null)\r
- {\r
- g.setColor(Color.black);\r
- g.fillRect(0, 0, currentSize.width, currentSize.height);\r
- g.setColor(Color.white);\r
- g.setFont(new Font("Verdana", Font.BOLD, 14));\r
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);\r
- }\r
- else\r
- {\r
- viewer.renderScreenImage(g, currentSize, rectClip);\r
- }\r
- }\r
- }\r
-\r
-}\r
+/*
+ * 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);
+ if (fr!=null)
+ fr.featuresAdded();
+ 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);
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff