- 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)
- {
- 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(";wireframe 100;"+eval.toString()+".CA;");
-
- resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
-
- eval.append("spacefill 200;select none");
-
- 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 s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[s]
- && ap.av.alignment.findIndex(sequence[s])>-1)
- {
- 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, 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 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
- 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 notifyFrameChanged(int frameNo)
- {
- boolean isAnimationRunning = (frameNo <= -2);
- }
-
- public void notifyScriptStart(String statusMessage, String additionalInfo)
- {}
-
- 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);
- }
-
- public void notifyNewDefaultModeMeasurement(int count, String strInfo)
- {}
-
- public void notifyAtomPicked(int atomIndex, String strInfo)
- {
- 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+=".CA";
-
-
- 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