// 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 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());
}
PageSmoother(String pdf) throws IOException {
File file = new File(pdf);
ndone = 0;
RandomAccessFile raf = new RandomAccessFile(file, "r");
FileChannel channel = raf.getChannel();
ByteBuffer buf = channel.map(FileChannel.MapMode.READ_ONLY, 0, channel.size());
pdffile = new PDFFile(buf);
page1 = new CountDownLatch(1);
raf.close();
tmpdir = File.createTempFile("pagesmoother", "");
tmpdir.delete();
tmpdir.mkdir();
}
private void setupLock() {
if (dataDir == null) {
lockDir = null;
} else {
File dir = new File(dataDir, LOCK_FILE);
if (!dir.mkdir()) {
dir.delete();
if (!dir.mkdir()) {
dir = null;
if (getBoolean("application.showLocalStorageDialogs", true)) {
Resources.showMessageDialog(
null,
JOptionPane.ERROR_MESSAGE,
messageBundle,
"fontManager.properties.title",
"manager.properties.session.nolock",
LOCK_FILE);
}
}
}
lockDir = dir;
}
}
/**
* Create/Replace a Directory
*
* @param Direct the Directory in which the new Directory is made
*/
public void createDirectory(String Direct) {
File dir = new File(Direct + File_Direct + "\\");
if (dir.isDirectory()) { // Check if this directory already exists
if (JOptionPane.showConfirmDialog(
null, "This directory already exists, do you wish to replace it?", "Replace", 0)
!= 0) {
return;
}
// Delete directory
DeleteDirect(Direct + File_Direct + "\\");
}
// Replace/Create directory
dir.mkdir();
Msgs.Type("Directory created", Display);
}
public SeatInfo() {
File file = new File(".", "data");
file.mkdir();
File f = new File(file, "SeatInfo.txt");
try {
raf = new RandomAccessFile(f, "rw");
if (raf.length() == 0) {
raf.setLength(31 * 4 * FLIGHT_PER_DAY);
for (int i = 0; i < 31 * FLIGHT_PER_DAY; i++) raf.writeInt(0);
}
} catch (Exception e) {
e.printStackTrace();
}
}
/** Get the default folder */
public File getDefaultFolder() {
final File recentFolder = _folderTracker.getMostRecentFile();
if (recentFolder != null && recentFolder.exists()) {
if (_subfolderName != null) {
final File defaultFolder = new File(recentFolder, _subfolderName);
if (!defaultFolder.exists()) {
defaultFolder.mkdir();
}
return defaultFolder;
} else {
return recentFolder;
}
}
return null;
}
public String getJLMPropertiesDir() {
String jlmPropertiesDir = null;
String value = Game.getProperty("jlm.configuration.file.path");
if (value != null) {
String paths[] = value.split(",");
for (String localPath : paths) {
localPath = localPath.replace("$HOME$", System.getProperty("user.home"));
File localPropertiesFileParentDirectory = new File(localPath);
File localPropertiesFileDirectory =
new File(localPath, Game.getLocalPropertiesSubdirectory());
if (!localPropertiesFileParentDirectory.exists()) {
continue;
} else if (localPropertiesFileDirectory.exists() || localPropertiesFileDirectory.mkdir()) {
jlmPropertiesDir = localPropertiesFileParentDirectory.getPath();
break;
} else {
Logger.log(
"Game:storeProperties",
"cannot create local properties store directory ("
+ localPropertiesFileDirectory
+ ")");
}
}
} else {
JOptionPane.showConfirmDialog(
null,
"No path provided in the property file (or property file not found)\n"
+ "You may want to export your session with the menu 'Session/Export session'\n"
+ "to save your work manually.\n\n"
+ "Quit without saving?",
"Cannot save your changes. Quit without saving?",
JOptionPane.YES_NO_OPTION,
JOptionPane.ERROR_MESSAGE);
return null;
}
return jlmPropertiesDir;
}
public static void copyFolder(File src, File dest, JLabel updatelbl, JLabel updatelbl2)
throws IOException {
if (src.isDirectory()) {
if (!dest.exists()) {
dest.mkdir();
updatelbl.setText("Directory copied from " + src + " to " + dest);
}
String files[] = src.list();
for (String file : files) {
File srcFile = new File(src, file);
File destFile = new File(dest, file);
// recursive copy
copyFolder(srcFile, destFile, updatelbl, updatelbl2);
}
} else {
InputStream in = new FileInputStream(src);
OutputStream out = new FileOutputStream(dest);
byte[] buffer = new byte[1024];
int length;
while ((length = in.read(buffer)) > 0) {
out.write(buffer, 0, length);
}
in.close();
out.close();
updatelbl.setText("File copied from " + src);
updatelbl2.setText(" to " + dest);
}
}
/*
* 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");
}
@Override
public void run() {
this.cardIndex = 0;
File base = new File(Constants.IO.imageBaseDir);
if (!base.exists()) {
base.mkdir();
}
Connection.ProxyType configProxyType =
Connection.ProxyType.valueByText(
PreferencesDialog.getCachedValue(PreferencesDialog.KEY_PROXY_TYPE, "None"));
Proxy.Type type = Proxy.Type.DIRECT;
switch (configProxyType) {
case HTTP:
type = Proxy.Type.HTTP;
break;
case SOCKS:
type = Proxy.Type.SOCKS;
break;
case NONE:
default:
p = Proxy.NO_PROXY;
break;
}
if (type != Proxy.Type.DIRECT) {
try {
String address = PreferencesDialog.getCachedValue(PreferencesDialog.KEY_PROXY_ADDRESS, "");
Integer port =
Integer.parseInt(
PreferencesDialog.getCachedValue(PreferencesDialog.KEY_PROXY_PORT, "80"));
p = new Proxy(type, new InetSocketAddress(address, port));
} catch (Exception ex) {
throw new RuntimeException("Gui_DownloadPictures : error 1 - " + ex);
}
}
if (p != null) {
HashSet<String> ignoreUrls = SettingsManager.getIntance().getIgnoreUrls();
ArrayList<CardDownloadData> cardsToDownload = this.checkBox.isSelected() ? type2cards : cards;
update(0, cardsToDownload.size());
for (int i = 0; i < cardsToDownload.size() && !cancel; i++) {
try {
CardDownloadData card = cardsToDownload.get(i);
log.info("Downloading card: " + card.getName() + " (" + card.getSet() + ")");
String url;
if (ignoreUrls.contains(card.getSet()) || card.isToken()) {
if (card.getCollectorId() != 0) {
continue;
}
url = cardImageSource.generateTokenUrl(card);
} else {
url = cardImageSource.generateURL(card);
}
if (url != null) {
Logger.getLogger(this.getClass()).info(url);
Runnable task = new DownloadTask(card, new URL(url), cardsToDownload.size());
executor.execute(task);
} else {
synchronized (sync) {
update(cardIndex + 1, cardsToDownload.size());
}
}
} catch (Exception ex) {
log.error(ex, ex);
}
}
executor.shutdown();
while (!executor.isTerminated()) {
try {
Thread.sleep(1000);
} catch (InterruptedException ie) {
}
}
}
try {
TVFS.umount();
} catch (FsSyncException e) {
e.printStackTrace();
JOptionPane.showMessageDialog(
null, "Couldn't unmount zip files", "Error", JOptionPane.ERROR_MESSAGE);
} finally {
System.gc();
}
closeButton.setText("Close");
}
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;
}