/** Initialize the panel UI component values from the current site profile settings. */
public void updatePanel() {
{
File dir = pApp.getHomeDirectory();
if (dir == null) {
String home = System.getProperty("user.home");
if (home != null) {
File hdir = new File(home);
if ((hdir != null) && hdir.isDirectory()) dir = hdir.getParentFile();
}
}
if (dir == null) dir = new File("/home");
pHomeDirComp.setDir(dir);
}
{
File dir = pApp.getTemporaryDirectory();
if (dir == null) dir = new File("/var/tmp");
pTempDirComp.setDir(dir);
}
{
File dir = pApp.getUnixJavaHome();
if (dir == null) dir = new File(pApp.getJavaHome());
pJavaHomeDirComp.setDir(dir);
}
pJavadocDirComp.setDir(pApp.getUnixLocalJavadocDirectory());
pExtraJavaLibsComp.setJars(pApp.getUnixLocalJavaLibraries());
}
protected void fileNew() {
if (currentFile != null) {
if (!currentFile.isDirectory()) {
currentFile = currentFile.getParentFile();
}
}
graph.clear();
gp.update(gp.getGraphics());
}
/**
* The FileEvent listener.
*
* @param event the event.
*/
public void fileEventOccurred(FileEvent event) {
File file = event.getFile();
if (file != null) {
String dirPath;
if (file.isDirectory()) dirPath = file.getAbsolutePath();
else dirPath = file.getParentFile().getAbsolutePath();
properties.setProperty("directory", dirPath);
} else properties.remove("directory");
}
/**
* Delete the given files. Refuses to delete files outside the user plugin directory. This method
* throws no errors is the files don't exist or deletion failed.
*
* @param filenames An array of names of the files to be deleted.
*/
public static void deletePluginsOnStartup(String[] filenames) {
for (String s : filenames) {
File f = new File(s);
if (f.getParentFile().equals(PluginCore.userPluginDir)) {
// if (s.startsWith(PluginCore.userPluginDir.getPath())) {
boolean success = f.delete();
} else System.out.println("File outside of user plugin dir: " + s);
}
}
/** Returns false if Exception is thrown. */
private boolean setDirectory() {
String pathStr = dirTF.getText().trim();
if (pathStr.equals("")) pathStr = System.getProperty("user.dir");
try {
File dirPath = new File(pathStr);
if (!dirPath.isDirectory()) {
if (!dirPath.exists()) {
if (recursiveCheckBox.isSelected())
throw new NotDirectoryException(dirPath.getAbsolutePath());
else throw new NotFileException(dirPath.getAbsolutePath());
} else {
convertSet.setFile(dirPath);
convertSet.setDestinationPath(dirPath.getParentFile());
}
} else {
// Set the descriptors
setMatchingFileNames();
FlexFilter flexFilter = new FlexFilter();
flexFilter.addDescriptors(descriptors);
flexFilter.setFilesOnly(!recursiveCheckBox.isSelected());
convertSet.setSourcePath(dirPath, flexFilter);
convertSet.setDestinationPath(dirPath);
}
} catch (NotDirectoryException e1) {
final String caption = ResourceHandler.getMessage("notdirectory_dialog.caption1");
MessageFormat formatter;
String info_msg;
if (pathStr.equals("")) {
info_msg = ResourceHandler.getMessage("notdirectory_dialog.info5");
} else {
formatter = new MessageFormat(ResourceHandler.getMessage("notdirectory_dialog.info0"));
info_msg = formatter.format(new Object[] {pathStr});
}
final String info = info_msg;
JOptionPane.showMessageDialog(this, info, caption, JOptionPane.ERROR_MESSAGE);
return false;
} catch (NotFileException e2) {
final String caption = ResourceHandler.getMessage("notdirectory_dialog.caption0");
MessageFormat formatter =
new MessageFormat(ResourceHandler.getMessage("notdirectory_dialog.info1"));
final String info = formatter.format(new Object[] {pathStr});
JOptionPane.showMessageDialog(this, info, caption, JOptionPane.ERROR_MESSAGE);
return false;
}
return true; // no exception thrown
}
public GalaxyViewer(Settings settings, boolean animatorFrame) throws Exception {
super("Stars GalaxyViewer");
this.settings = settings;
this.animatorFrame = animatorFrame;
if (settings.gameName.equals("")) throw new Exception("GameName not defined in settings.");
setDefaultCloseOperation(EXIT_ON_CLOSE);
File dir = new File(settings.directory);
File map = new File(dir, settings.getGameName() + ".MAP");
if (map.exists() == false) {
File f = new File(dir.getParentFile(), settings.getGameName() + ".MAP");
if (f.exists()) map = f;
else {
String error = "Could not find " + map.getAbsolutePath() + "\n";
error += "Export this file from Stars! (Only needs to be done one time pr game)";
throw new Exception(error);
}
}
Vector<File> mFiles = new Vector<File>();
Vector<File> hFiles = new Vector<File>();
for (File f : dir.listFiles()) {
if (f.getName().toUpperCase().endsWith("MAP")) continue;
if (f.getName().toUpperCase().endsWith("HST")) continue;
if (f.getName().toUpperCase().startsWith(settings.getGameName() + ".M")) mFiles.addElement(f);
else if (f.getName().toUpperCase().startsWith(settings.getGameName() + ".H"))
hFiles.addElement(f);
}
if (mFiles.size() == 0) throw new Exception("No M-files found matching game name.");
if (hFiles.size() == 0) throw new Exception("No H-files found matching game name.");
parseMapFile(map);
Vector<File> files = new Vector<File>();
files.addAll(mFiles);
files.addAll(hFiles);
p = new Parser(files);
calculateColors();
// UI:
JPanel cp = (JPanel) getContentPane();
cp.setLayout(new BorderLayout());
cp.add(universe, BorderLayout.CENTER);
JPanel south = createPanel(0, hw, new JLabel("Search: "), search, names, zoom, colorize);
search.setPreferredSize(new Dimension(100, -1));
cp.add(south, BorderLayout.SOUTH);
hw.addActionListener(this);
names.addActionListener(this);
zoom.addChangeListener(this);
search.addKeyListener(this);
colorize.addActionListener(this);
setSize(800, 600);
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
setLocation((screen.width - getWidth()) / 2, (screen.height - getHeight()) / 2);
setVisible(animatorFrame == false);
if (animatorFrame) names.setSelected(false);
}
@Nullable
private static File findOldConfigDir(
@NotNull File configDir, @Nullable String customPathSelector) {
final File selectorDir = CONFIG_RELATED_PATH.isEmpty() ? configDir : configDir.getParentFile();
final File parent = selectorDir.getParentFile();
if (parent == null || !parent.exists()) {
return null;
}
File maxFile = null;
long lastModified = 0;
final String selector =
PathManager.getPathsSelector() != null
? PathManager.getPathsSelector()
: selectorDir.getName();
final String prefix = getPrefixFromSelector(selector);
final String customPrefix =
customPathSelector != null ? getPrefixFromSelector(customPathSelector) : null;
for (File file :
parent.listFiles(
new FilenameFilter() {
@Override
public boolean accept(@NotNull File file, @NotNull String name) {
return StringUtil.startsWithIgnoreCase(name, prefix)
|| customPrefix != null && StringUtil.startsWithIgnoreCase(name, customPrefix);
}
})) {
File options = new File(file, CONFIG_RELATED_PATH + OPTIONS_XML);
if (!options.exists()) {
continue;
}
long modified = options.lastModified();
if (modified > lastModified) {
lastModified = modified;
maxFile = file;
}
}
return maxFile != null ? new File(maxFile, CONFIG_RELATED_PATH) : null;
}
private void updateLinuxServiceInstaller() {
try {
File dir = new File(directory, "CTP");
if (suppressFirstPathElement) dir = dir.getParentFile();
Properties props = new Properties();
String ctpHome = dir.getAbsolutePath();
cp.appendln(Color.black, "...CTP_HOME: " + ctpHome);
ctpHome = ctpHome.replaceAll("\\\\", "\\\\\\\\");
props.put("CTP_HOME", ctpHome);
File javaHome = new File(System.getProperty("java.home"));
String javaBin = (new File(javaHome, "bin")).getAbsolutePath();
cp.appendln(Color.black, "...JAVA_BIN: " + javaBin);
javaBin = javaBin.replaceAll("\\\\", "\\\\\\\\");
props.put("JAVA_BIN", javaBin);
File linux = new File(dir, "linux");
File install = new File(linux, "ctpService-ubuntu.sh");
cp.appendln(Color.black, "Linux service installer:");
cp.appendln(Color.black, "...file: " + install.getAbsolutePath());
String bat = getFileText(install);
bat = replace(bat, props); // do the substitutions
bat = bat.replace("\r", "");
setFileText(install, bat);
// If this is an ISN installation, put the script in the correct place.
String osName = System.getProperty("os.name").toLowerCase();
if (programName.equals("ISN") && !osName.contains("windows")) {
install = new File(linux, "ctpService-red.sh");
cp.appendln(Color.black, "ISN service installer:");
cp.appendln(Color.black, "...file: " + install.getAbsolutePath());
bat = getFileText(install);
bat = replace(bat, props); // do the substitutions
bat = bat.replace("\r", "");
File initDir = new File("/etc/init.d");
File initFile = new File(initDir, "ctpService");
if (initDir.exists()) {
setOwnership(initDir, "edge", "edge");
setFileText(initFile, bat);
initFile.setReadable(true, false); // everybody can read //Java 1.6
initFile.setWritable(true); // only the owner can write //Java 1.6
initFile.setExecutable(true, false); // everybody can execute //Java 1.6
}
}
} catch (Exception ex) {
ex.printStackTrace();
System.err.println("Unable to update the Linux service ctpService.sh file");
}
}
public static byte[] recvFile(Socket sock, File out)
throws IOException, NoSuchAlgorithmException {
FileOutputStream mainOut = new FileOutputStream(out);
byte[] ret = null;
boolean reading = true;
MessageDigest major = MessageDigest.getInstance(SecureUtils.STD_HASH);
int block = 0;
while (reading) { // while there is data to be read
long readln = readInteger(sock.getInputStream()); // read the length of the next block
if (readln == TRANS_FINISH) { // if there are no more block
mainOut.close();
ret = major.digest();
sock.getOutputStream().write(ret); // send my major hash
long finishReply = readInteger(sock.getInputStream()); // read the reply
if (finishReply == TRANS_FINISH) { // if the major hash was correct
reading = false; // complete the transaction
} else { // else the major has was incorrect
out.delete(); // delete the file
mainOut = new FileOutputStream(out); // reset the output streams
// start again
block = 0;
major = MessageDigest.getInstance(SecureUtils.STD_HASH);
ret = null;
}
} else { // else there are more blocks
File tempOut = new File(out.getParentFile(), out.getName() + ".part" + block);
FileOutputStream partStream = new FileOutputStream(tempOut); // spawn a temporary file
byte[] hash =
hashpipe(sock.getInputStream(), partStream, readln); // read the block to temp file
partStream.close();
sock.getOutputStream().write(hash); // send my minor hash
long minorReply = readInteger(sock.getInputStream()); // read the reply
if (minorReply == TRANS_SUCCESS) { // if the transfer was correct
FileInputStream partIn = new FileInputStream(tempOut);
hashpipe(partIn, mainOut, readln, major); // send the temp file to the main file
block++;
} else { // if the transfer was wrong
// do nothing
}
tempOut.delete(); // delete the temp file
}
}
return ret;
}
private static boolean deleteWithSubordinates(File file) {
final String baseName = file.getName();
final File[] files =
file.getParentFile()
.listFiles(
new FileFilter() {
@Override
public boolean accept(final File pathname) {
return pathname.getName().startsWith(baseName);
}
});
boolean ok = true;
if (files != null) {
for (File f : files) {
ok &= FileUtil.delete(f);
}
}
return ok;
}
// If this is a new installation, ask the user for a
// port for the server; otherwise, return the negative
// of the configured port. If the user selects an illegal
// port, return zero.
private int getPort() {
// Note: directory points to the parent of the CTP directory.
File ctp = new File(directory, "CTP");
if (suppressFirstPathElement) ctp = ctp.getParentFile();
File config = new File(ctp, "config.xml");
if (!config.exists()) {
// No config file - must be a new installation.
// Figure out whether this is Windows or something else.
String os = System.getProperty("os.name").toLowerCase();
int defPort = ((os.contains("windows") && !programName.equals("ISN")) ? 80 : 1080);
int userPort = 0;
while (userPort == 0) {
String port =
JOptionPane.showInputDialog(
null,
"This is a new "
+ programName
+ " installation.\n\n"
+ "Select a port number for the web server.\n\n",
Integer.toString(defPort));
try {
userPort = Integer.parseInt(port.trim());
} catch (Exception ex) {
userPort = -1;
}
if ((userPort < 80) || (userPort > 32767)) userPort = 0;
}
return userPort;
} else {
try {
Document doc = getDocument(config);
Element root = doc.getDocumentElement();
Element server = getFirstNamedChild(root, "Server");
String port = server.getAttribute("port");
return -Integer.parseInt(port);
} catch (Exception ex) {
}
}
return 0;
}
private void updateWindowsServiceInstaller() {
try {
File dir = new File(directory, "CTP");
if (suppressFirstPathElement) dir = dir.getParentFile();
File windows = new File(dir, "windows");
File install = new File(windows, "install.bat");
cp.appendln(Color.black, "Windows service installer:");
cp.appendln(Color.black, "...file: " + install.getAbsolutePath());
String bat = getFileText(install);
Properties props = new Properties();
String home = dir.getAbsolutePath();
cp.appendln(Color.black, "...home: " + home);
home = home.replaceAll("\\\\", "\\\\\\\\");
props.put("home", home);
bat = replace(bat, props);
setFileText(install, bat);
} catch (Exception ex) {
ex.printStackTrace();
System.err.println("Unable to update the windows service install.barfile.");
}
}
private void installConfigFile(int port) {
if (port > 0) {
System.out.println("Looking for /config/config.xml");
InputStream is = getClass().getResourceAsStream("/config/config.xml");
if (is != null) {
try {
File ctp = new File(directory, "CTP");
if (suppressFirstPathElement) ctp = ctp.getParentFile();
File config = new File(ctp, "config.xml");
Document doc = getDocument(is);
Element root = doc.getDocumentElement();
Element server = getFirstNamedChild(root, "Server");
System.out.println("...setting the port to " + port);
server.setAttribute("port", Integer.toString(port));
adjustConfiguration(root, ctp);
setFileText(config, toString(doc));
} catch (Exception ex) {
System.err.println("...Error: unable to install the config.xml file");
}
} else System.err.println("...could not find it.");
}
}
/**
* Class constructor; creates a new Installer object, displays a JFrame introducing the program,
* allows the user to select an install directory, and copies files from the jar into the
* directory.
*/
public Installer(String args[]) {
// Inputs are --install-dir INSTALL_DIR
for (int k = 0; k < args.length; k = k + 2) {
switch (args[k]) {
case "--install-dir":
directory = new File(args[k + 1]);
System.out.println(directory);
break;
case "--port":
port = Integer.parseInt(args[k + 1]);
break;
}
}
cp = new Stream();
// Find the installer program so we can get to the files.
installer = getInstallerProgramFile();
String name = installer.getName();
programName = (name.substring(0, name.indexOf("-"))).toUpperCase();
// Get the installation information
thisJava = System.getProperty("java.version");
thisJavaBits = System.getProperty("sun.arch.data.model") + " bits";
// Find the ImageIO Tools and get the version
String javaHome = System.getProperty("java.home");
File extDir = new File(javaHome);
extDir = new File(extDir, "lib");
extDir = new File(extDir, "ext");
File clib = getFile(extDir, "clibwrapper_jiio", ".jar");
File jai = getFile(extDir, "jai_imageio", ".jar");
imageIOTools = (clib != null) && clib.exists() && (jai != null) && jai.exists();
if (imageIOTools) {
Hashtable<String, String> jaiManifest = getManifestAttributes(jai);
imageIOVersion = jaiManifest.get("Implementation-Version");
}
// Get the CTP.jar parameters
Hashtable<String, String> manifest = getJarManifestAttributes("/CTP/libraries/CTP.jar");
programDate = manifest.get("Date");
buildJava = manifest.get("Java-Version");
// Get the util.jar parameters
Hashtable<String, String> utilManifest = getJarManifestAttributes("/CTP/libraries/util.jar");
utilJava = utilManifest.get("Java-Version");
// Get the MIRC.jar parameters (if the plugin is present)
Hashtable<String, String> mircManifest = getJarManifestAttributes("/CTP/libraries/MIRC.jar");
if (mircManifest != null) {
mircJava = mircManifest.get("Java-Version");
mircDate = mircManifest.get("Date");
mircVersion = mircManifest.get("Version");
}
// Set up the installation information for display
if (imageIOVersion.equals("")) {
imageIOVersion = "<b><font color=\"red\">not installed</font></b>";
} else if (imageIOVersion.startsWith("1.0")) {
imageIOVersion = "<b><font color=\"red\">" + imageIOVersion + "</font></b>";
}
if (thisJavaBits.startsWith("64")) {
thisJavaBits = "<b><font color=\"red\">" + thisJavaBits + "</font></b>";
}
boolean javaOK = (thisJava.compareTo(buildJava) >= 0);
javaOK &= (thisJava.compareTo(utilJava) >= 0);
javaOK &= (thisJava.compareTo(mircJava) >= 0);
if (!javaOK) {
thisJava = "<b><font color=\"red\">" + thisJava + "</font></b>";
}
if (directory == null) exit();
// Point to the parent of the directory in which to install the program.
// so the copy process works correctly for directory trees.
//
// If the user has selected a directory named "CTP",
// then assume that this is the directory in which
// to install the program.
//
// If the directory is not CTP, see if it is called "RSNA" and contains
// the Launcher program, in which case we can assume that it is an
// installation that was done with Bill Weadock's all-in-one installer for Windows.
//
// If neither of those cases is true, then this is already the parent of the
// directory in which to install the program
if (directory.getName().equals("CTP")) {
directory = directory.getParentFile();
} else if (directory.getName().equals("RSNA")
&& (new File(directory, "Launcher.jar")).exists()) {
suppressFirstPathElement = true;
}
// Cleanup old releases
cleanup(directory);
// Get a port for the server.
if (port < 0) {
if (checkServer(-port, false)) {
System.err.println(
"CTP appears to be running.\nPlease stop CTP and run the installer again.");
System.exit(0);
}
}
// Now install the files and report the results.
int count =
unpackZipFile(installer, "CTP", directory.getAbsolutePath(), suppressFirstPathElement);
if (count > 0) {
// Create the service installer batch files.
updateWindowsServiceInstaller();
updateLinuxServiceInstaller();
// If this was a new installation, set up the config file and set the port
installConfigFile(port);
// Make any necessary changes in the config file to reflect schema evolution
fixConfigSchema();
System.out.println("Installation complete.");
System.out.println(programName + " has been installed successfully.");
System.out.println(count + " files were installed.");
} else {
System.err.println("Installation failed.");
System.err.println(programName + " could not be fully installed.");
}
if (!programName.equals("ISN") && startRunner(new File(directory, "CTP"))) System.exit(0);
}
@Override
public void run() {
try {
StringBuilder filePath = new StringBuilder();
filePath.append(Constants.IO.imageBaseDir).append(File.separator);
filePath
.append(card.hashCode())
.append(".")
.append(card.getName().replace(":", "").replace("//", "-"))
.append(".jpg");
File temporaryFile = new File(filePath.toString());
String imagePath = CardImageUtils.generateImagePath(card);
TFile outputFile = new TFile(imagePath);
if (!outputFile.exists()) {
outputFile.getParentFile().mkdirs();
}
File existingFile = new File(imagePath.replaceFirst("\\w{3}.zip", ""));
if (existingFile.exists()) {
new TFile(existingFile).cp_rp(outputFile);
synchronized (sync) {
update(cardIndex + 1, count);
}
existingFile.delete();
File parent = existingFile.getParentFile();
if (parent != null && parent.isDirectory() && parent.list().length == 0) {
parent.delete();
}
return;
}
BufferedOutputStream out;
// Logger.getLogger(this.getClass()).info(url.toString());
URLConnection httpConn = url.openConnection(p);
httpConn.connect();
if (((HttpURLConnection) httpConn).getResponseCode() == 200) {
try (BufferedInputStream in =
new BufferedInputStream(((HttpURLConnection) httpConn).getInputStream())) {
// try (BufferedInputStream in = new
// BufferedInputStream(url.openConnection(p).getInputStream())) {
out = new BufferedOutputStream(new TFileOutputStream(temporaryFile));
byte[] buf = new byte[1024];
int len;
while ((len = in.read(buf)) != -1) {
// user cancelled
if (cancel) {
in.close();
out.flush();
out.close();
temporaryFile.delete();
return;
}
out.write(buf, 0, len);
}
}
out.flush();
out.close();
if (card.isTwoFacedCard()) {
BufferedImage image = ImageIO.read(temporaryFile);
if (image.getHeight() == 470) {
BufferedImage renderedImage = new BufferedImage(265, 370, BufferedImage.TYPE_INT_RGB);
renderedImage.getGraphics();
Graphics2D graphics2D = renderedImage.createGraphics();
if (card.isTwoFacedCard() && card.isSecondSide()) {
graphics2D.drawImage(image, 0, 0, 265, 370, 313, 62, 578, 432, null);
} else {
graphics2D.drawImage(image, 0, 0, 265, 370, 41, 62, 306, 432, null);
}
graphics2D.dispose();
writeImageToFile(renderedImage, outputFile);
} else {
new TFile(temporaryFile).cp_rp(outputFile);
}
temporaryFile.delete();
} else {
new TFile(temporaryFile).cp_rp(outputFile);
temporaryFile.delete();
}
} else {
Logger.getLogger(this.getClass())
.error(convertStreamToString(((HttpURLConnection) httpConn).getErrorStream()));
}
} catch (Exception e) {
log.error(e, e);
}
synchronized (sync) {
update(cardIndex + 1, count);
}
}
public void actionPerformed(ActionEvent e) {
if (isDirectorySelected()) {
File dir = getDirectory();
if (dir != null) {
try {
// Strip trailing ".."
dir = ShellFolder.getNormalizedFile(dir);
} catch (IOException ex) {
// Ok, use f as is
}
changeDirectory(dir);
return;
}
}
JFileChooser chooser = getFileChooser();
String filename = getFileName();
FileSystemView fs = chooser.getFileSystemView();
File dir = chooser.getCurrentDirectory();
if (filename != null) {
// Remove whitespaces from end of filename
int i = filename.length() - 1;
while (i >= 0 && filename.charAt(i) <= ' ') {
i--;
}
filename = filename.substring(0, i + 1);
}
if (filename == null || filename.length() == 0) {
// no file selected, multiple selection off, therefore cancel the approve action
resetGlobFilter();
return;
}
File selectedFile = null;
File[] selectedFiles = null;
// Unix: Resolve '~' to user's home directory
if (File.separatorChar == '/') {
if (filename.startsWith("~/")) {
filename = System.getProperty("user.home") + filename.substring(1);
} else if (filename.equals("~")) {
filename = System.getProperty("user.home");
}
}
if (chooser.isMultiSelectionEnabled()
&& filename.length() > 1
&& filename.charAt(0) == '"'
&& filename.charAt(filename.length() - 1) == '"') {
List<File> fList = new ArrayList<File>();
String[] files = filename.substring(1, filename.length() - 1).split("\" \"");
// Optimize searching files by names in "children" array
Arrays.sort(files);
File[] children = null;
int childIndex = 0;
for (String str : files) {
File file = fs.createFileObject(str);
if (!file.isAbsolute()) {
if (children == null) {
children = fs.getFiles(dir, false);
Arrays.sort(children);
}
for (int k = 0; k < children.length; k++) {
int l = (childIndex + k) % children.length;
if (children[l].getName().equals(str)) {
file = children[l];
childIndex = l + 1;
break;
}
}
}
fList.add(file);
}
if (!fList.isEmpty()) {
selectedFiles = fList.toArray(new File[fList.size()]);
}
resetGlobFilter();
} else {
selectedFile = fs.createFileObject(filename);
if (!selectedFile.isAbsolute()) {
selectedFile = fs.getChild(dir, filename);
}
// check for wildcard pattern
FileFilter currentFilter = chooser.getFileFilter();
if (!selectedFile.exists() && isGlobPattern(filename)) {
changeDirectory(selectedFile.getParentFile());
if (globFilter == null) {
globFilter = new GlobFilter();
}
try {
globFilter.setPattern(selectedFile.getName());
if (!(currentFilter instanceof GlobFilter)) {
actualFileFilter = currentFilter;
}
chooser.setFileFilter(null);
chooser.setFileFilter(globFilter);
return;
} catch (PatternSyntaxException pse) {
// Not a valid glob pattern. Abandon filter.
}
}
resetGlobFilter();
// Check for directory change action
boolean isDir = (selectedFile != null && selectedFile.isDirectory());
boolean isTrav = (selectedFile != null && chooser.isTraversable(selectedFile));
boolean isDirSelEnabled = chooser.isDirectorySelectionEnabled();
boolean isFileSelEnabled = chooser.isFileSelectionEnabled();
boolean isCtrl =
(e != null
&& (e.getModifiers() & Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()) != 0);
if (isDir && isTrav && (isCtrl || !isDirSelEnabled)) {
changeDirectory(selectedFile);
return;
} else if ((isDir || !isFileSelEnabled)
&& (!isDir || !isDirSelEnabled)
&& (!isDirSelEnabled || selectedFile.exists())) {
selectedFile = null;
}
}
if (selectedFiles != null || selectedFile != null) {
if (selectedFiles != null || chooser.isMultiSelectionEnabled()) {
if (selectedFiles == null) {
selectedFiles = new File[] {selectedFile};
}
chooser.setSelectedFiles(selectedFiles);
// Do it again. This is a fix for bug 4949273 to force the
// selected value in case the ListSelectionModel clears it
// for non-existing file names.
chooser.setSelectedFiles(selectedFiles);
} else {
chooser.setSelectedFile(selectedFile);
}
chooser.approveSelection();
} else {
if (chooser.isMultiSelectionEnabled()) {
chooser.setSelectedFiles(null);
} else {
chooser.setSelectedFile(null);
}
chooser.cancelSelection();
}
}
public void run() {
// String a =
// "http://neuromorpho.org/neuroMorpho/dableFiles/borst/CNG%20version/dCH-cobalt.CNG.swc"; //
// For developer use
if (myArgs.length == 0) {
String usage =
"\nError, missing SWC file containing morphology!\n\nUsage: \n java -cp build cvapp.main swc_file [-test]"
+ "\n or:\n ./run.sh swc_file ["
+ TEST_FLAG
+ "|"
+ TEST_NOGUI_FLAG
+ "|"
+ NEUROML1_EXPORT_FLAG
+ "|"
+ NEUROML2_EXPORT_FLAG
+ "]\n\n"
+ "where swc_file is the file name or URL of the SWC morphology file\n";
System.out.println(usage);
System.exit(0);
}
String a = myArgs[0];
File baseDir = new File(".");
if ((new File(a)).exists()) {
baseDir = (new File(a)).getParentFile();
}
try {
File root =
new File(main.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
.getParentFile();
if (!a.startsWith("http://") && !a.startsWith("file://")) {
a = "file://" + (new File(a)).getCanonicalPath();
}
boolean supressGui = false;
if (myArgs.length == 2
&& (myArgs[1].equals(TEST_NOGUI_FLAG)
|| myArgs[1].equals(NEUROML1_EXPORT_FLAG)
|| myArgs[1].equals(NEUROML2_EXPORT_FLAG))) {
supressGui = true;
}
neuronEditorFrame nef = null;
nef = new neuronEditorFrame(700, 600, supressGui);
// nef.validate();
nef.pack();
centerWindow(nef);
nef.setVisible(!supressGui);
nef.setReadWrite(true, true);
int indexof = a.lastIndexOf('/') + 1;
String directory = a.substring(0, indexof);
String fileName = a.substring(indexof, a.length());
URL u = new URL(a);
String sdata[] = readStringArrayFromURL(u);
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + fileName);
nef.loadFile(sdata, directory, fileName);
System.out.println("Loaded: " + fileName);
if (myArgs.length == 2 && myArgs[1].equals(TEST_ONE_FLAG)) {
// Thread.sleep(1000);
doTests(nef, fileName);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML1_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml1FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".xml"
: rootFile.getName() + ".xml";
File nml1File = new File(rootFile.getParentFile(), nml1FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
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(root, "Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
System.exit(0);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML2_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml2FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".cell.nml"
: rootFile.getName() + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(rootFile.getParentFile(), nml2FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved the NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXML(nml2File, new File(root, "Schemas/v2/NeuroML_v2beta4.xsd"));
System.exit(0);
} else if (myArgs.length == 2
&& (myArgs[1].equals(TEST_FLAG) || (myArgs[1].equals(TEST_NOGUI_FLAG)))) {
// Thread.sleep(1000);
doTests(nef, fileName);
File exampleDir = new File("twoCylSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("spherSomaSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("caseExamples");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
if (supressGui) System.exit(0);
}
} catch (Exception exception) {
System.err.println("Error while handling SWC file (" + a + ")");
exception.printStackTrace();
}
}
private void process() {
int width = Integer.parseInt(xres.getText());
int height = Integer.parseInt(yres.getText());
boolean preserveAspect = aspect.isSelected();
Color bg = new Color(red.getValue(), green.getValue(), blue.getValue());
String outDir = output.getText();
String suffix = ((String) format.getSelectedItem()).toLowerCase();
String preText = prepend.getText();
String appText = append.getText();
int scaleType = -1;
String alg = (String) algorithm.getSelectedItem();
if (alg.equals("Smooth")) scaleType = Image.SCALE_SMOOTH;
else if (alg.equals("Standard")) scaleType = Image.SCALE_DEFAULT;
else if (alg.equals("Fast")) scaleType = Image.SCALE_FAST;
else if (alg.equals("Replicate")) scaleType = Image.SCALE_REPLICATE;
else if (alg.equals("Area averaging")) {
scaleType = Image.SCALE_AREA_AVERAGING;
}
DefaultListModel model = (DefaultListModel) list.getModel();
int size = model.size();
progress.setValue(0);
progress.setMaximum(4 * size);
for (int i = 0; i < size; i++) {
ThumbFile tf = (ThumbFile) model.elementAt(i);
list.setSelectedValue(tf, true);
String tail = " (" + (i + 1) + " of " + size + ")";
progress.setValue(4 * i);
progress.setString("Reading" + tail);
// construct input and output filenames
String inFile = tf.getPath();
String outFile = outDir + SLASH + tf.getName();
int ndx = outFile.lastIndexOf(SLASH);
String s1 = outFile.substring(0, ndx + SLASH.length());
String s2 = outFile.substring(ndx + SLASH.length());
int dot_ndx = s2.lastIndexOf(".");
if (dot_ndx >= 0) s2 = s2.substring(0, dot_ndx);
// make the thumbnail file name
outFile = s1 + preText + s2 + appText + "." + suffix;
// read in the file to an image
BufferedImage image = null;
try {
image = ImageIO.read(new File(inFile));
} catch (IOException exc) {
exc.printStackTrace();
}
progress.setValue(4 * i + 1);
progress.setString("Resizing" + tail);
// resize image
int w, h;
if (preserveAspect) {
int ow = image.getWidth();
int oh = image.getHeight();
double oasp = (double) ow / oh;
double tasp = (double) width / height;
if (oasp > tasp) {
w = width;
h = (int) (w / oasp);
} else {
h = height;
w = (int) (oasp * h);
}
} else {
w = width;
h = height;
}
Image resized = image.getScaledInstance(w, h, scaleType);
progress.setValue(4 * i + 2);
progress.setString("Painting" + tail);
// create thumbnail
BufferedImage thumb = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
Graphics2D g2d = thumb.createGraphics();
g2d.setColor(bg);
g2d.fillRect(0, 0, width, height);
g2d.drawImage(resized, (width - w) / 2, (height - h) / 2, this);
g2d.dispose();
progress.setValue(4 * i + 3);
progress.setString("Writing" + tail);
// save thumbnail to disk
File out = new File(outFile);
File parent = out.getParentFile();
if (parent != null && !parent.exists()) parent.mkdirs();
try {
ImageIO.write(thumb, suffix, out);
} catch (IOException exc) {
exc.printStackTrace();
}
}
list.setSelectedIndices(new int[0]);
progress.setValue(4 * size);
progress.setString("Complete");
}
public void run() {
going = true;
while (going) {
String chose = null;
synchronized (jobs) {
chose = jobs.poll();
}
if (chose != null) {
cur = chose;
updateStatus();
long time = System.currentTimeMillis();
String op = "export";
String targ = null;
boolean success = false;
if (chose.charAt(0) == IMPORT_FLAG) {
String[] brk = chose.split(",", 4); // 4 parts to an import string
File imp = new File(brk[1]);
targ = imp.getName();
if (edtImport(imp, brk[2], brk[3])) {
// import successful
success = true;
if (checkImports) op = "import & check";
else op = "import (fast)";
store.fireTableDataChanged();
} else {
// no import
}
} else {
String[] brk = chose.split(",", 3); // 3 parts to an export string
File pla = new File(brk[2]);
targ = pla.getName();
if (edtExport(new File(brk[1]), pla)) {
// export succeeded
success = true;
// System.out.println(pla.getParentFile().getAbsolutePath() + ", " +
// tempLoc.getAbsolutePath() + ", " + pla.getParentFile().equals(tempLoc));
try {
if (pla.getParentFile().getCanonicalPath().equals(tempLoc.getCanonicalPath()))
secureUse(pla);
} catch (IOException exc) {
System.err.println("Failed to retrieve canonical path?");
}
} else {
// export failed
}
}
if (success)
System.out.println(
"Completed " + op + " in " + (System.currentTimeMillis() - time) + "ms - " + targ);
cur = null;
updateStatus();
} else {
if (needsSave && idx == 0) {
boolean alldone = true;
for (int i = 0; i < numThreads; i++) {
if (encryptDecryptThreads[i].getCur() != null) {
alldone = false;
break;
}
}
if (alldone) {
System.out.println("Automatically saving");
try {
store.saveAll(tempLoc);
} catch (IOException e) {
System.err.println("Automatic save failed");
}
needsSave = false;
}
}
try {
Thread.sleep(500);
} catch (InterruptedException e) {
// do nothing
}
}
}
}