private final String findcachedir() {
System.out.println("here@!");
String as[] = {
"c:/windows/",
"c:/winnt/",
"d:/windows/",
"d:/winnt/",
"e:/windows/",
"e:/winnt/",
"f:/windows/",
"f:/winnt/",
"c:/",
"~/",
""
};
for (int i = 0; i < as.length; i++)
try {
String s = as[i];
if (s.length() > 0) {
File file = new File(s);
if (!file.exists()) continue;
}
File file1 = new File(s + ".file_store_32");
if (file1.exists() || file1.mkdir()) return s + ".file_store_32" + "/";
} catch (Exception _ex) {
}
return null;
}
public void totalExport() {
File expf = new File("export");
if (expf.exists()) rmrf(expf);
expf.mkdirs();
for (int sto = 0; sto < storeLocs.size(); sto++) {
try {
String sl =
storeLocs.get(sto).getAbsolutePath().replaceAll("/", "-").replaceAll("\\\\", "-");
File estore = new File(expf, sl);
estore.mkdir();
File log = new File(estore, LIBRARY_NAME);
PrintWriter pw = new PrintWriter(log);
for (int i = 0; i < store.getRowCount(); i++)
if (store.curStore(i) == sto) {
File enc = store.locate(i);
File dec = sec.prepareMainFile(enc, estore, false);
pw.println(dec.getName());
pw.println(store.getValueAt(i, Storage.COL_DATE));
pw.println(store.getValueAt(i, Storage.COL_TAGS));
synchronized (jobs) {
jobs.addLast(expJob(enc, dec));
}
}
pw.close();
} catch (IOException exc) {
exc.printStackTrace();
JOptionPane.showMessageDialog(frm, "Exporting Failed");
return;
}
}
JOptionPane.showMessageDialog(frm, "Exporting to:\n " + expf.getAbsolutePath());
}
// Raises the Save As dialog to have the user identify the location to save groups of things.
public File determineSaveLocation(String dialogTitle, String defaultFolderName) {
String defaultPath = this.getFileChooser().getCurrentDirectory().getPath();
if (!WWUtil.isEmpty(defaultPath)) defaultPath += File.separatorChar + defaultFolderName;
File outFile;
while (true) {
this.getFileChooser().setDialogTitle(dialogTitle);
this.getFileChooser().setSelectedFile(new File(defaultPath));
this.getFileChooser().setMultiSelectionEnabled(false);
this.getFileChooser().setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
int status = this.getFileChooser().showSaveDialog(this.getFrame());
if (status != JFileChooser.APPROVE_OPTION) return null;
outFile = this.getFileChooser().getSelectedFile();
if (outFile == null) {
this.showMessageDialog("No location selected", "No Selection", JOptionPane.ERROR_MESSAGE);
continue;
}
break;
}
if (!outFile.exists())
//noinspection ResultOfMethodCallIgnored
outFile.mkdir();
return outFile;
}
public void mkdir(String newDirectoryName) {
try {
File newDirectory = new File(currentPath + "\\" + newDirectoryName);
if (newDirectory.exists()) {
System.out.println("Unable to create " + newDirectory.getAbsolutePath());
} else {
newDirectory.mkdir();
System.out.println("Directory" + newDirectoryName + "created");
}
} finally {
takePath();
}
}
/*
* Carries out a number of tests, generates NEURON, GENESIS and NeuroML code etc.
*/
private static void doTests(neuronEditorFrame nef, String fileName) {
System.out.println(
"Testing Cvapp/NeuroMorpho.Org by generating NEURON, GENESIS and NeuroML files for "
+ fileName);
File tempDir = new File("temp");
if (!tempDir.exists()) tempDir.mkdir();
neuronEditorPanel nep = nef.getNeuronEditorPanel();
String rootFileName = fileName;
if (rootFileName.toLowerCase().endsWith(".swc")) {
rootFileName = rootFileName.substring(0, rootFileName.length() - 4);
}
if (rootFileName.lastIndexOf(System.getProperty("file.separator")) > 0) {
rootFileName =
rootFileName.substring(
rootFileName.lastIndexOf(System.getProperty("file.separator")) + 1);
}
// NEURON save...
String neuronFileName = rootFileName + ".hoc";
File neuronFile = new File(tempDir, neuronFileName);
File neuronTestFile = new File(tempDir, rootFileName + "_test.hoc");
nep.writeStringToFile(nep.getCell().HOCwriteNS(), neuronFile.getAbsolutePath());
StringBuilder sbNeuTest = new StringBuilder();
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/nCtools.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/cellCheck.hoc\")\n");
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"" + neuronFileName + "\")\n\n");
sbNeuTest.append("forall morph()\n");
System.out.println("--------------------------------------------------------------");
nep.writeStringToFile(sbNeuTest.toString(), neuronTestFile.getAbsolutePath());
System.out.println(
"Saved NEURON representation of the file to: "
+ neuronFile.getAbsolutePath()
+ ": "
+ neuronFile.exists());
System.out.println("--------------------------------------------------------------");
// GENESIS save...
String genesisFileName = rootFileName + ".p";
File genesisFile = new File(tempDir, genesisFileName);
File genesisTestFile = new File(tempDir, rootFileName + "_test.g");
nep.writeStringToFile(nep.getCell().GENESISwriteHR(), genesisFile.getAbsolutePath());
StringBuilder sbGenTest = new StringBuilder();
sbGenTest.append("include compartments \n");
sbGenTest.append("create neutral /library\n");
sbGenTest.append("disable /library\n");
sbGenTest.append("ce /library\n");
sbGenTest.append("make_cylind_compartment\n");
sbGenTest.append("make_cylind_symcompartment\n");
sbGenTest.append("make_sphere_compartment\n");
sbGenTest.append("ce /\n");
sbGenTest.append(
"echo \"Prototype compartments created, reading cell from " + genesisFileName + "\"\n");
sbGenTest.append("readcell " + genesisFileName + " /mycell\n\n");
sbGenTest.append("create xform /form [0,0,400,400] -nolabel\n");
sbGenTest.append(
"create xdraw /form/draw [0,0,100%,100%] -wx 0.002 -wy 0.002 -transform ortho3d -bg white\n");
sbGenTest.append(
"setfield /form/draw xmin -3.0E-4 xmax 3.0E-4 ymin -3.0E-4 ymax 3.0E-4 vx 0.0 vy 0.0 vz -0.002\n");
sbGenTest.append(
"create xcell /form/draw/cell -path \"/mycell/##[][TYPE=compartment],/mycell/##[][TYPE=symcompartment]\" -colfield Vm -colmin -0.07 -colmax 0.03 -diarange -5\n");
sbGenTest.append("xcolorscale hot\n");
sbGenTest.append("xshow /form\n\n");
sbGenTest.append("showfield /mycell/##[][TYPE=compartment] **\n\n");
nep.writeStringToFile(sbGenTest.toString(), genesisTestFile.getAbsolutePath());
System.out.println(
"Saved GENESIS representation of the file to: "
+ genesisFile.getAbsolutePath()
+ ": "
+ genesisFile.exists());
System.out.println("--------------------------------------------------------------");
// NeuroML save...
String nml1FileName = rootFileName + ".xml";
File nml1File = new File(tempDir, nml1FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File("Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
String nml2FileName = rootFileName + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(tempDir, nml2FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXMLWithURL(nml2File, "Schemas/v2/NeuroML_v2beta4.xsd");
}
boolean fileWriter(File file, JList InstanceList) throws IOException { //returns true if successful.
useAppletJS = JmolViewer.checkOption(viewer, "webMakerCreateJS");
// JOptionPane.showMessageDialog(null, "Creating directory for data...");
String datadirPath = file.getPath();
String datadirName = file.getName();
String fileName = null;
if (datadirName.indexOf(".htm") > 0) {
fileName = datadirName;
datadirPath = file.getParent();
file = new File(datadirPath);
datadirName = file.getName();
} else {
fileName = datadirName + ".html";
}
datadirPath = datadirPath.replace('\\', '/');
boolean made_datadir = (file.exists() && file.isDirectory() || file.mkdir());
DefaultListModel listModel = (DefaultListModel) InstanceList.getModel();
LogPanel.log("");
if (made_datadir) {
LogPanel.log(GT._("Using directory {0}", datadirPath));
LogPanel.log(" " + GT._("adding JmolPopIn.js"));
viewer.writeTextFile(datadirPath + "/JmolPopIn.js",
WebExport.getResourceString(this, "JmolPopIn.js"));
for (int i = 0; i < listModel.getSize(); i++) {
JmolInstance thisInstance = (JmolInstance) (listModel.getElementAt(i));
String javaname = thisInstance.javaname;
String script = thisInstance.script;
LogPanel.log(" ...jmolApplet" + i);
LogPanel.log(" ..." + GT._("adding {0}.png", javaname));
try {
thisInstance.movepict(datadirPath);
} catch (IOException IOe) {
throw IOe;
}
String fileList = "";
fileList += addFileList(script, "/*file*/");
fileList += addFileList(script, "FILE0=");
fileList += addFileList(script, "FILE1=");
if (localAppletPath.getText().equals(".")
|| remoteAppletPath.getText().equals("."))
fileList += "Jmol.js\nJmolApplet.jar";
String[] filesToCopy = fileList.split("\n");
String[] copiedFileNames = new String[filesToCopy.length];
String f;
int pt;
for (int iFile = 0; iFile < filesToCopy.length; iFile++) {
if ((pt = (f = filesToCopy[iFile]).indexOf("|")) >= 0)
filesToCopy[iFile] = f.substring(0, pt);
copiedFileNames[iFile] = copyBinaryFile(filesToCopy[iFile],
datadirPath);
}
script = localizeFileReferences(script, filesToCopy, copiedFileNames);
LogPanel.log(" ..." + GT._("adding {0}.spt", javaname));
viewer.writeTextFile(datadirPath + "/" + javaname + ".spt", script);
}
String html = WebExport.getResourceString(this, panelName + "_template");
html = fixHtml(html);
appletInfoDivs = "";
StringBuffer appletDefs = new StringBuffer();
if (!useAppletJS)
htmlAppletTemplate = WebExport.getResourceString(this, panelName + "_template2");
for (int i = 0; i < listModel.getSize(); i++)
html = getAppletDefs(i, html, appletDefs, (JmolInstance) listModel
.getElementAt(i));
html = TextFormat.simpleReplace(html, "@AUTHOR@", GT.escapeHTML(pageAuthorName
.getText()));
html = TextFormat.simpleReplace(html, "@TITLE@", GT.escapeHTML(webPageTitle.getText()));
html = TextFormat.simpleReplace(html, "@REMOTEAPPLETPATH@",
remoteAppletPath.getText());
html = TextFormat.simpleReplace(html, "@LOCALAPPLETPATH@",
localAppletPath.getText());
html = TextFormat.simpleReplace(html, "@DATADIRNAME@", datadirName);
if (appletInfoDivs.length() > 0)
appletInfoDivs = "\n<div style='display:none'>\n" + appletInfoDivs
+ "\n</div>\n";
String str = appletDefs.toString();
if (useAppletJS)
str = "<script type='text/javascript'>\n" + str + "\n</script>";
html = TextFormat.simpleReplace(html, "@APPLETINFO@", appletInfoDivs);
html = TextFormat.simpleReplace(html, "@APPLETDEFS@", str);
html = TextFormat.simpleReplace(html, "@CREATIONDATA@", GT.escapeHTML(WebExport
.TimeStamp_WebLink()));
html = TextFormat.simpleReplace(html, "@AUTHORDATA@",
GT.escapeHTML(GT._("Based on template by A. Herráez as modified by J. Gutow")));
html = TextFormat.simpleReplace(html, "@LOGDATA@", "<pre>\n"
+ LogPanel.getText() + "\n</pre>\n");
LogPanel.log(" ..." + GT._("creating {0}", fileName));
viewer.writeTextFile(datadirPath + "/" + fileName, html);
} else {
IOException IOe = new IOException("Error creating directory: "
+ datadirPath);
throw IOe;
}
LogPanel.log("");
return true;
}