- String[] modelFileNames = null;
-
- // ////////////////////////////////
- // /StructureListener
- public String[] getPdbFile()
- {
- if (modelFileNames == null)
- {
- String mset[] = new String[viewer.getModelCount()];
- for (int i = 0; i < mset.length; i++)
- {
- try {
- String mname = viewer.getModelFileName(i);
- if (mname==null)
- {
- System.err.println("Model "+i+" has no filename!");
- continue;
- }
- File fpath = new File(mname);
- mset[i] = fpath.toString();
- } catch (Exception e)
- {
- System.err.println("Couldn't parse "+viewer.getModelFileName(i)+" as a file!");
- }
- }
- modelFileNames = mset;
- }
- return modelFileNames;
- }
-
- Pattern pattern = Pattern
- .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+).*(/[0-9]*)?");
-
- String lastMessage;
-
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- // copied from AppJmol - will be refactored to binding eventually
- int pdbResNum;
- int mdlSep = strInfo.indexOf("/");
- int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
-
- if (chainSeparator == -1)
- {
- chainSeparator = strInfo.indexOf(".");
- if (mdlSep > -1 && mdlSep < chainSeparator)
- {
- chainSeparator1 = chainSeparator;
- chainSeparator = mdlSep;
- }
- }
- 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 = " ";
- }
-
- String pdbfilename = pdbentry.getFile();
- if (mdlSep > -1)
- {
- if (chainSeparator1 == -1)
- {
- chainSeparator1 = strInfo.indexOf(".", mdlSep);
- }
- String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
- chainSeparator1) : strInfo.substring(mdlSep + 1);
- try
- {
- // recover PDB filename for the model hovered over.
- pdbfilename = viewer
- .getModelFileName(new Integer(mdlId).intValue() - 1);
- } catch (Exception e)
- {
- }
- ;
- }
- if (lastMessage == null || !lastMessage.equals(strInfo))
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
-
- lastMessage = strInfo;
-/*
- * Old Implementation based on Pattern regex.
- 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 = " ";
- }
- String mdlId = matcher.group(4);
- String pdbfilename = pdbentry.getFile();
-
- if (mdlId!=null && mdlId.length()>0)
- {
- try {
- // recover PDB filename for the model hovered over.
- pdbfilename = viewer.getModelFileName(new Integer(mdlId).intValue()-1);
- } catch (Exception e) {};
- }
- if (lastMessage == null || !lastMessage.equals(strInfo))
- {
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
- }
- lastMessage = strInfo; */
- }
-
- StringBuffer resetLastRes = new StringBuffer();
-
- StringBuffer eval = new StringBuffer();
-
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- int mdlNum = 1+getModelNum(pdbfile);
- if (mdlNum==0)
- {
- return;
- }
-
- jmolHistory(false);
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return;
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum); // +modelNum
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum); // +modelNum
-
- if (!chain.equals(" "))
- {
- eval.append(":");
- resetLastRes.append(":");
- eval.append(chain);
- resetLastRes.append(chain);
- }
- // if (mdlNum != 0)
- {
- eval.append(" /" + (mdlNum));
- resetLastRes.append(" /" + (mdlNum));
- }
- 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());
- jmolHistory(true);
- }
-
- 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;
-
- String[] files = getPdbFile();
-
- 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();
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
-
-
- 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);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
- + col.getBlue() + "]";
- if (command.toString().endsWith(newSelcom))
- {
- command = condenseCommand(command, pos);
- continue;
- }
-
- command.append(";select " + pos);
- command.append(newSelcom);
- }
- break;
- }
- }
- }
- }
- jmolHistory(false);
-
- if (lastCommand == null || !lastCommand.equals(command.toString()))
- {
- viewer.evalStringQuiet(command.toString());
- }
- jmolHistory(true);
- 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 fileName2,
- String modelName, String errorMsg, int modelParts)
- {
- if (errorMsg != null)
- {
- fileLoadingError = errorMsg;
- repaint();
- return;
- }
-
- fileLoadingError = null;
- modelFileNames = null;
-
- String[] modelfilenames = getPdbFile();
- ssm = StructureSelectionManager.getStructureSelectionManager();
- boolean modelsloaded=false;
- for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
- {
- String fileName = modelfilenames[modelnum];
-
- if (fileName != null)
- {
- modelsloaded=true;
- // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename
- if (pdbentry.getFile().equals(fileName))
- {
- // TODO: do some checking using the modelPts number of parts against our
- // own estimate of the number of chains
- // FILE LOADED OK
- MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
- .getFile(), AppletFormatAdapter.FILE);
- Vector chains = new Vector();
- for (int i = 0; i < pdbFile.chains.size(); i++)
- {
- chains
- .addElement(new String(pdbFile.id+":"+((MCview.PDBChain) pdbFile.chains.elementAt(i)).id));
- }
- setChainMenuItems(chains);
-
- if (!loadingFromArchive)
- {
- viewer
- .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- colourBySequence(ap);
- }
- if (fr != null)
- fr.featuresAdded();
-
- loadingFromArchive = false;
- }
- else {
- // this is a foreign pdb file that jalview doesn't know about - add it to the dataset
- // and try to find a home - either on a matching sequence or as a new sequence.
- String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
- "PDB");
- // parse pdb file into a chain, etc.
- // locate best match for pdb in associated views and add mapping to
- // ssm
- modelsloaded=true;
- }
- }
- }
- if (modelsloaded)
- {
- ssm.addStructureViewerListener(this);
- jmolpopup.updateComputedMenus();
- }
- }
-
- 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()));
-*/
- int chainSeparator = strInfo.indexOf(":");
- int p=0;
- if (chainSeparator == -1)
- chainSeparator = strInfo.indexOf(".");
-
- String picked = strInfo.substring(strInfo.indexOf("]") + 1,
- chainSeparator);
- String mdlString="";
- if ((p=strInfo.indexOf(":")) > -1)
- picked += strInfo.substring(p + 1, strInfo
- .indexOf("."));
-
- if ((p=strInfo.indexOf("/"))> -1)
- {
- mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
- }
- picked = "((" + picked + ".CA" + mdlString+")|(" + picked + ".P" + mdlString+"))";
- jmolHistory(false);
- if (!atomsPicked.contains(picked))
- {
- // TODO: re-instate chain ID separator dependent labelling for both applet and application
-// 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);
- }
- jmolHistory(true);
- 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.
- }
- }