/*
* 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
") > -1 || data.indexOf("") > -1)) { out.println(data); } } out.close(); } catch (Exception ex) { ex.printStackTrace(); } } } public void viewMapping_actionPerformed(ActionEvent actionEvent) { jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600); cap.setText(StructureSelectionManager.getStructureSelectionManager() .printMapping(pdbentry.getFile())); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void eps_actionPerformed(ActionEvent e) { makePDBImage(jalview.util.ImageMaker.EPS); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void png_actionPerformed(ActionEvent e) { makePDBImage(jalview.util.ImageMaker.PNG); } void makePDBImage(int type) { int width = getWidth(); int height = getHeight(); jalview.util.ImageMaker im; if (type == jalview.util.ImageMaker.PNG) { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, "Make PNG image from view", width, height, null, null); } else { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, "Make EPS file from view", width, height, null, this .getTitle()); } if (im.getGraphics() != null) { Rectangle rect = new Rectangle(width, height); viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect); im.writeImage(); } } public void seqColour_actionPerformed(ActionEvent actionEvent) { lastCommand = null; colourBySequence = seqColour.isSelected(); colourBySequence(ap.alignFrame.alignPanel); } public void chainColour_actionPerformed(ActionEvent actionEvent) { colourBySequence = false; seqColour.setSelected(false); viewer.evalStringQuiet("select *;color chain"); } public void chargeColour_actionPerformed(ActionEvent actionEvent) { colourBySequence = false; seqColour.setSelected(false); viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;" + "select LYS,ARG;color blue;select CYS;color yellow"); } public void zappoColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new ZappoColourScheme()); } public void taylorColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new TaylorColourScheme()); } public void hydroColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new HydrophobicColourScheme()); } public void helixColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new HelixColourScheme()); } public void strandColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new StrandColourScheme()); } public void turnColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new TurnColourScheme()); } public void buriedColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new BuriedColourScheme()); } public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; seqColour.setSelected(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 userColour_actionPerformed(ActionEvent actionEvent) { new UserDefinedColours(this, null); } public void backGround_actionPerformed(ActionEvent actionEvent) { java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour", null); if (col != null) { viewer.evalStringQuiet("background [" + col.getRed() + "," + col.getGreen() + "," + col.getBlue() + "];"); } } public void jmolHelp_actionPerformed(ActionEvent actionEvent) { try { jalview.util.BrowserLauncher .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/"); } catch (Exception ex) { } } // //////////////////////////////// // /StructureListener public String getPdbFile() { return pdbentry.getFile(); } Pattern pattern = Pattern .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"); String lastMessage; public void mouseOverStructure(int atomIndex, String strInfo) { Matcher matcher = pattern.matcher(strInfo); matcher.find(); matcher.group(1); int pdbResNum = Integer.parseInt(matcher.group(2)); String chainId = matcher.group(3); if (chainId != null) chainId = chainId.substring(1, chainId.length()); 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) { // TODO: rna: remove CA dependency in select string 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() // + ".*;spacefill 0;"); + " and not hetero;spacefill 0;"); eval.append("spacefill 200;select none"); // System.out.println("jmol:\n"+eval+"\n"); viewer.evalStringQuiet(eval.toString()); } public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile) { if (!pdbfile.equals(pdbentry.getFile())) return null; return new Color(viewer.getAtomArgb(atomIndex)); } public void updateColours(Object source) { colourBySequence((AlignmentPanel) source); } // End StructureListener // ////////////////////////// String lastCommand; FeatureRenderer fr = null; public void colourBySequence(AlignmentPanel sourceap) { this.ap = sourceap; if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av) 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.gui.FeatureRenderer(ap); } fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); } StringBuffer command = new StringBuffer(); int lastPos = -1; for (int sp, s = 0; s < sequence.length; s++) { for (int 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(asp, r); if (showFeatures) col = fr.findFeatureColour(col, asp, r); if (command.toString().endsWith( ":" + mapping[m].getChain() + ";color[" + col.getRed() + "," + col.getGreen() + "," + col.getBlue() + "]")) { command = condenseCommand(command, 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(StringBuffer command, int pos) { StringBuffer sb = new StringBuffer(command.substring(0, command .lastIndexOf("select") + 7)); command.delete(0, 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) { System.out.println("JMOL CREATE IMAGE"); } public void notifyFileLoaded(String fullPathName, String fileName, String modelName, String errorMsg, int modelParts) { if (errorMsg != null) { fileLoadingError = errorMsg; repaint(); return; } fileLoadingError = null; if (fileName != null) { // TODO: do some checking using the modelPts number of parts against our own estimate of the number of chains // FILE LOADED OK ssm = StructureSelectionManager.getStructureSelectionManager(); MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry .getFile(), AppletFormatAdapter.FILE); ssm.addStructureViewerListener(this); Vector chains = new Vector(); for (int i = 0; i < pdbFile.chains.size(); i++) { chains .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id); } setChainMenuItems(chains); jmolpopup.updateComputedMenus(); if (!loadingFromArchive) { viewer .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off"); colourBySequence(ap); } if (fr != null) fr.featuresAdded(); loadingFromArchive = false; } else return; } public void sendConsoleEcho(String strEcho) { if (scriptWindow != null) scriptWindow.sendConsoleEcho(strEcho); } public void sendConsoleMessage(String strStatus) { if (scriptWindow != null) scriptWindow.sendConsoleMessage(strStatus); } public void notifyScriptTermination(String strStatus, int msWalltime) { if (scriptWindow != null) scriptWindow.notifyScriptTermination(strStatus, msWalltime); } public void handlePopupMenu(int x, int y) { jmolpopup.show(x, y); } public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) { notifyAtomPicked(iatom, strMeasure, null); } public void notifyAtomPicked(int atomIndex, String strInfo, String strData) { if (strData!=null) { Cache.log.info("Non null pick data string: "+strData+" (other info: '"+strInfo+"' pos "+atomIndex+")"); } Matcher matcher = pattern.matcher(strInfo); matcher.find(); matcher.group(1); String resnum = new String(matcher.group(2)); String chainId = matcher.group(3); String picked = resnum; if (chainId != null) picked += (":" + chainId.substring(1, chainId.length())); picked = "(("+picked+".CA" + ")|("+picked+".P"+"))"; if (!atomsPicked.contains(picked)) { if (chainId != null) viewer.evalString("select " + picked + ";label %n %r:%c"); else viewer.evalString("select " + picked + ";label %n %r"); atomsPicked.addElement(picked); } else { viewer.evalString("select " + picked + ";label off"); atomsPicked.removeElement(picked); } if (scriptWindow != null) { scriptWindow.sendConsoleMessage(strInfo); scriptWindow.sendConsoleMessage("\n"); } } public void notifyAtomHovered(int atomIndex, String strInfo, String data) { if (data!=null) { Cache.log.info("Non null hover data string: "+data+" (other info: '"+strInfo+"' pos "+atomIndex+")"); } mouseOverStructure(atomIndex, strInfo); } @Override public void showUrl(String url) { try { jalview.util.BrowserLauncher.openURL(url); } catch (IOException e) { Cache.log.error("Failed to launch Jmol-associated url "+url,e); // TODO: 2.6 : warn user if browser was not configured. } } public void showConsole(boolean showConsole) { if (scriptWindow == null) scriptWindow = new ScriptWindow(this); if (showConsole) { if (splitPane == null) { splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT); splitPane.setTopComponent(renderPanel); splitPane.setBottomComponent(scriptWindow); this.getContentPane().add(splitPane, BorderLayout.CENTER); } splitPane.setDividerLocation(getHeight() - 200); splitPane.validate(); } else { if (splitPane != null) splitPane.setVisible(false); splitPane = null; this.getContentPane().add(renderPanel, BorderLayout.CENTER); } validate(); } public float[][] functionXY(String functionName, int x, int y) { return null; } // /End JmolStatusListener // ///////////////////////////// class RenderPanel extends JPanel { final Dimension currentSize = new Dimension(); final Rectangle rectClip = new Rectangle(); public void paintComponent(Graphics g) { getSize(currentSize); g.getClipBounds(rectClip); 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 if (fileLoadingError != 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("Error loading file..." + pdbentry.getId(), 20, currentSize.height / 2); } else { viewer.renderScreenImage(g, currentSize, rectClip); } } } String viewId = null; public String getViewId() { if (viewId == null) { viewId = System.currentTimeMillis() + "." + this.hashCode(); } return viewId; } @Override public String createImage(String fileName, String type, Object textOrBytes, int quality) { // TODO Auto-generated method stub return null; } @Override public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) { // TODO Auto-generated method stub return null; } @Override public Hashtable getRegistryInfo() { // TODO Auto-generated method stub return null; } @Override public void notifyCallback(int type, Object[] data) { try { switch (type) { case JmolConstants.CALLBACK_LOADSTRUCT: notifyFileLoaded((String) data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer) data[5]).intValue()); break; case JmolConstants.CALLBACK_PICK: notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); // also highlight in alignment case JmolConstants.CALLBACK_HOVER: notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); break; case JmolConstants.CALLBACK_SCRIPT: notifyScriptTermination((String)data[2], ((Integer)data[3]).intValue()); break; case JmolConstants.CALLBACK_ECHO: sendConsoleEcho((String)data[1]); break; case JmolConstants.CALLBACK_MESSAGE: sendConsoleMessage((data==null) ? ((String) null) : (String)data[1]); break; case JmolConstants.CALLBACK_MEASURE: case JmolConstants.CALLBACK_CLICK: default: System.err.println("Unhandled callback "+type+" "+data); break; } } catch (Exception e) { Cache.log.warn("Squashed Jmol callback handler error: ",e); } } @Override public boolean notifyEnabled(int callbackPick) { switch (callbackPick) { case JmolConstants.CALLBACK_ECHO: case JmolConstants.CALLBACK_LOADSTRUCT: case JmolConstants.CALLBACK_MEASURE: case JmolConstants.CALLBACK_MESSAGE: case JmolConstants.CALLBACK_PICK: case JmolConstants.CALLBACK_SCRIPT: case JmolConstants.CALLBACK_HOVER: case JmolConstants.CALLBACK_ERROR: return true; case JmolConstants.CALLBACK_CLICK: case JmolConstants.CALLBACK_ANIMFRAME: case JmolConstants.CALLBACK_MINIMIZATION: case JmolConstants.CALLBACK_RESIZE: case JmolConstants.CALLBACK_SYNC: } return false; } @Override public void setCallbackFunction(String callbackType, String callbackFunction) { Cache.log.debug("Ignoring set-callback request to associate "+callbackType+" with function "+callbackFunction); } }