private void setExecutablePermissions(File gradleHome) {
if (isWindows()) {
return;
}
File gradleCommand = new File(gradleHome, "bin/gradle");
String errorMessage = null;
try {
ProcessBuilder pb = new ProcessBuilder("chmod", "755", gradleCommand.getCanonicalPath());
Process p = pb.start();
if (p.waitFor() == 0) {
System.out.println("Set executable permissions for: " + gradleCommand.getAbsolutePath());
} else {
BufferedReader is = new BufferedReader(new InputStreamReader(p.getInputStream()));
Formatter stdout = new Formatter();
String line;
while ((line = is.readLine()) != null) {
stdout.format("%s%n", line);
}
errorMessage = stdout.toString();
}
} catch (IOException e) {
errorMessage = e.getMessage();
} catch (InterruptedException e) {
errorMessage = e.getMessage();
}
if (errorMessage != null) {
System.out.println(
"Could not set executable permissions for: " + gradleCommand.getAbsolutePath());
System.out.println("Please do this manually if you want to use the Gradle UI.");
}
}
/**
* This method will take in a string which will be a directory. It will make sure that the
* directory exists and return the absolute path
*
* @return the value of the absolute directory
*/
private String doesExistAndAbsolute(String dir) {
File tempDirFile = new File(dir);
try {
if (tempDirFile.exists()) {
if (tempDirFile.isAbsolute()) {
return dir;
} else {
tempDirFile = new File(System.getProperty("user.dir") + sep + dir);
if (tempDirFile.exists()) {
return tempDirFile.getAbsolutePath();
} else {
throw new NotDirectoryException(
ResourceHandler.getMessage("caption.reldirnotfound")
+ ": "
+ tempDirFile.getAbsolutePath());
}
}
} else {
throw new NotDirectoryException(
ResourceHandler.getMessage("caption.absdirnotfound")
+ ": "
+ tempDirFile.getAbsolutePath());
}
} catch (NotDirectoryException e) {
System.out.println(
ResourceHandler.getMessage("caption.absdirnotfound")
+ ": "
+ tempDirFile.getAbsolutePath());
return null; // this is just so it would compile
}
}
public void doSort(String ifile, String ofile, String tmpDirName, int maxRecords) {
System.out.println("Sorting " + ifile + " -> " + ofile);
File inputFile = new File(ifile);
File outputFile = new File(ofile);
Sorter sorter = Sorter.getSorter(inputFile, outputFile);
if (tmpDirName != null && tmpDirName.trim().length() > 0) {
File tmpDir = new File(tmpDirName);
if (!tmpDir.exists()) {
System.err.println(
"Error: tmp directory: " + tmpDir.getAbsolutePath() + " does not exist.");
throw new PreprocessingException(
"Error: tmp directory: " + tmpDir.getAbsolutePath() + " does not exist.");
}
sorter.setTmpDir(tmpDir);
}
sorter.setMaxRecords(maxRecords);
try {
sorter.run();
} catch (Exception e) {
e.printStackTrace();
// Delete output file as its probably corrupt
if (outputFile.exists()) {
outputFile.delete();
}
}
System.out.println("Done");
System.out.flush();
}
/** @param workTokDir Token directory (common for multiple nodes). */
private void cleanupResources(File workTokDir) {
RandomAccessFile lockFile = null;
FileLock lock = null;
try {
lockFile = new RandomAccessFile(new File(workTokDir, LOCK_FILE_NAME), "rw");
lock = lockFile.getChannel().lock();
if (lock != null) processTokenDirectory(workTokDir);
else if (log.isDebugEnabled())
log.debug(
"Token directory is being processed concurrently: " + workTokDir.getAbsolutePath());
} catch (OverlappingFileLockException ignored) {
if (log.isDebugEnabled())
log.debug(
"Token directory is being processed concurrently: " + workTokDir.getAbsolutePath());
} catch (FileLockInterruptionException ignored) {
Thread.currentThread().interrupt();
} catch (IOException e) {
U.error(log, "Failed to process directory: " + workTokDir.getAbsolutePath(), e);
} finally {
U.releaseQuiet(lock);
U.closeQuiet(lockFile);
}
}
public static void createNgramsFromFolder(
File input_folder, File output_folder, int ngram_value) {
Stack<File> stack = new Stack<File>();
stack.push(input_folder);
while (!stack.isEmpty()) {
File child = stack.pop();
if (child.isDirectory()) {
for (File f : child.listFiles()) stack.push(f);
} else if (child.isFile()) {
try {
System.out.println("Processing: " + child.getAbsolutePath());
FileReader fr = new FileReader(child.getAbsolutePath());
FileWriter outputFile = new FileWriter(output_folder + "/file" + file_no);
BufferedReader br = new BufferedReader(fr);
String readline = "";
while ((readline = br.readLine()) != null) {
String[] words = readline.split("\\s+");
for (int i = 0; i < words.length - ngram_value + 1; i++) {
String ngram = "";
for (int j = 0; j < ngram_value; j++) ngram = ngram + " " + words[i + j];
outputFile.write(ngram + "\n");
}
}
file_no++;
outputFile.close();
br.close();
fr.close();
} catch (Exception e) {
System.out.println("File not found:" + e);
}
}
}
}
/**
* automatically generate non-existing help html files for existing commands in the CommandLoader
*
* @param cl the CommandLoader where you look for the existing commands
*/
public void createHelpText(CommandLoader cl) {
File dir = new File((getClass().getResource("..").getPath()));
dir = new File(dir, language);
if (!dir.exists() && !dir.mkdirs()) {
System.out.println("Failed to create " + dir.getAbsolutePath());
return;
}
for (String mnemo : cl.getMnemoList()) {
if (!exists(mnemo)) {
File file = new File(dir, mnemo + ".htm");
try {
file.createNewFile();
BufferedOutputStream os = new BufferedOutputStream(new FileOutputStream(file));
PrintStream ps = new PrintStream(os);
ps.println("<html>\n<head>\n<title>" + mnemo + "\n</title>\n</head>\n<body>");
ps.println("Command: " + mnemo.toUpperCase() + "<br>");
ps.println("arguments: <br>");
ps.println("effects: <br>");
ps.println("flags to be set: <br>");
ps.println("approx. clockcycles: <br>");
ps.println("misc: <br>");
ps.println("</body>\n</html>");
ps.flush();
ps.close();
} catch (IOException e) {
System.out.println("failed to create " + file.getAbsolutePath());
}
}
}
}
public void testGetAttributesForThisTestClass() throws IOException {
if (Os.isFamily(Os.FAMILY_WINDOWS)) {
System.out.println("WARNING: Unsupported OS, skipping test");
return;
}
URL resource =
Thread.currentThread()
.getContextClassLoader()
.getResource(getClass().getName().replace('.', '/') + ".class");
if (resource == null) {
throw new IllegalStateException(
"SOMETHING IS VERY WRONG. CANNOT FIND THIS TEST CLASS IN THE CLASSLOADER.");
}
File f = new File(resource.getPath().replaceAll("%20", " "));
Map attrs =
PlexusIoResourceAttributeUtils.getFileAttributesByPath(
f, new ConsoleLogger(Logger.LEVEL_INFO, "test"), Logger.LEVEL_DEBUG);
PlexusIoResourceAttributes fileAttrs =
(PlexusIoResourceAttributes) attrs.get(f.getAbsolutePath());
System.out.println("Got attributes for: " + f.getAbsolutePath() + fileAttrs);
assertNotNull(fileAttrs);
assertTrue(fileAttrs.isOwnerReadable());
assertEquals(System.getProperty("user.name"), fileAttrs.getUserName());
}
public static String createTempImageFile(String origFile, String prefix, String suffix)
throws Exception {
File outputFile = createTempFile(prefix, suffix);
outputFile.deleteOnExit();
copyFile(outputFile.getAbsolutePath(), origFile);
return outputFile.getAbsolutePath();
}
/* Scan the files in the new directory, and store them in the filelist.
* Update the UI by refreshing the list adapter.
*/
private void loadDirectory(String newdirectory) {
if (newdirectory.equals("../")) {
try {
directory = new File(directory).getParent();
} catch (Exception e) {
}
} else {
directory = newdirectory;
}
SharedPreferences.Editor editor = getPreferences(0).edit();
editor.putString("lastBrowsedDirectory", directory);
editor.commit();
directoryView.setText(directory);
filelist = new ArrayList<FileUri>();
ArrayList<FileUri> sortedDirs = new ArrayList<FileUri>();
ArrayList<FileUri> sortedFiles = new ArrayList<FileUri>();
if (!newdirectory.equals(rootdir)) {
String parentDirectory = new File(directory).getParent() + "/";
Uri uri = Uri.parse("file://" + parentDirectory);
sortedDirs.add(new FileUri(uri, parentDirectory));
}
try {
File dir = new File(directory);
File[] files = dir.listFiles();
if (files != null) {
for (File file : files) {
if (file == null) {
continue;
}
String filename = file.getName();
if (file.isDirectory()) {
Uri uri = Uri.parse("file://" + file.getAbsolutePath() + "/");
FileUri fileuri = new FileUri(uri, uri.getPath());
sortedDirs.add(fileuri);
} else if (filename.endsWith(".mid")
|| filename.endsWith(".MID")
|| filename.endsWith(".midi")
|| filename.endsWith(".MIDI")) {
Uri uri = Uri.parse("file://" + file.getAbsolutePath());
FileUri fileuri = new FileUri(uri, uri.getLastPathSegment());
sortedFiles.add(fileuri);
}
}
}
} catch (Exception e) {
}
if (sortedDirs.size() > 0) {
Collections.sort(sortedDirs, sortedDirs.get(0));
}
if (sortedFiles.size() > 0) {
Collections.sort(sortedFiles, sortedFiles.get(0));
}
filelist.addAll(sortedDirs);
filelist.addAll(sortedFiles);
adapter = new IconArrayAdapter<FileUri>(this, android.R.layout.simple_list_item_1, filelist);
this.setListAdapter(adapter);
}
public Bundle(File dir) throws IOException {
if (!dir.exists()) {
throw new IllegalArgumentException(String.format("%s does not exist", dir.getAbsolutePath()));
}
if (!dir.canRead()) {
throw new IllegalArgumentException(String.format("%s cannot be read", dir.getAbsolutePath()));
}
if (!dir.isDirectory()) {
throw new IllegalArgumentException(
String.format("%s is not a directory", dir.getAbsolutePath()));
}
this.dir = dir;
config = new BundleConfig(new File(dir, "Config.pl"));
dataFiles = new ArrayList<File>();
dataFiles.addAll(
Arrays.asList(
dir.listFiles(
new FilenameFilter() {
public boolean accept(File dir, String name) {
String upper = name.toUpperCase();
return (upper.endsWith(".rdf")
|| upper.endsWith(".owl")
|| upper.endsWith(".n3")
|| upper.endsWith(".ttl"))
&& new File(dir, name).canRead();
}
})));
}
/** initialization. load all files. */
private void init() {
URL home = getClass().getResource("..");
File local;
if (home != null) {
System.out.println("looks like you are not starting from a jar-package");
local = new File(home.getPath() + "/" + helproot + "/" + language + "/");
System.out.println("local: " + local.getAbsolutePath());
initFile(local);
try {
local =
new File(
new File(home.getPath()).getParentFile().getParentFile(),
helproot + "/" + language);
System.out.println("local: " + local.getAbsolutePath());
initFile(local);
} catch (Exception e) {
System.out.println("but not loading from the developer workbench?!");
}
} else {
System.out.println("looks like you are starting from a jar-package");
local = CommandLoader.getLocation();
initJar(local);
}
List<String> l = getLanguages();
for (String aL : l) {
System.out.println("language found: " + aL);
}
}
/** @param args the command line arguments */
public static void main(String[] args) throws Exception {
// boolean Chinese = true;
// File f = new File("C:/Users/Xin/Documents/opt/allign-zh-trans");
// File out = new File("C:/Users/Xin/Documents/opt/out-zh");
boolean Chinese = false;
File f = new File("C:/Users/Xin/Documents/optest/allign-es-trans");
File out = new File("C:/Users/Xin/Documents/optest/out-es");
File seg = new File("C:/Users/Xin/Documents/optest/segmented-zh");
out.mkdirs();
seg.mkdirs();
for (String name : f.list()) {
String fullName = f.getAbsolutePath() + "/" + name;
String outName = out.getAbsolutePath() + "/" + name;
if (Chinese == true) {
String segName = seg.getAbsolutePath() + "/" + name;
ChineseSegment(fullName, segName);
BlEUClaculatorOnefile(segName, outName, Chinese);
} else {
BlEUClaculatorOnefile(fullName, outName, Chinese);
}
}
}
private void doGCTtoIGV(
String typeString,
String ifile,
File ofile,
String probefile,
int maxRecords,
String tmpDirName,
Genome genome)
throws IOException {
System.out.println("gct -> igv: " + ifile + " -> " + ofile.getAbsolutePath());
File tmpDir = null;
if (tmpDirName != null && tmpDirName.trim().length() > 0) {
tmpDir = new File(tmpDirName);
if (!tmpDir.exists()) {
System.err.println(
"Error: tmp directory: " + tmpDir.getAbsolutePath() + " does not exist.");
throw new PreprocessingException(
"Error: tmp directory: " + tmpDir.getAbsolutePath() + " does not exist.");
}
}
ResourceLocator locator = new ResourceLocator(ifile);
locator.setType(typeString);
GCTtoIGVConverter.convert(locator, ofile, probefile, maxRecords, tmpDir, genome);
}
public int runDirectorToInstall(
String message, File installFolder, String sourceRepo, String iuToInstall) {
String[] command =
new String[] { //
"-application",
"org.eclipse.equinox.p2.director", //
"-repository",
sourceRepo,
"-installIU",
iuToInstall, //
"-destination",
installFolder.getAbsolutePath(), //
"-bundlepool",
installFolder.getAbsolutePath(), //
"-roaming",
"-profile",
"PlatformProfile",
"-profileProperties",
"org.eclipse.update.install.features=true", //
"-p2.os",
Platform.getOS(),
"-p2.ws",
Platform.getWS(),
"-p2.arch",
Platform.getOSArch()
};
return runEclipse(message, command);
}
/**
* Shuts down the test harness, and makes the best attempt possible to delete dataDir, unless the
* system property "solr.test.leavedatadir" is set.
*/
@Override
public void tearDown() throws Exception {
log.info("####TEARDOWN_START " + getTestName());
if (factoryProp == null) {
System.clearProperty("solr.directoryFactory");
}
if (h != null) {
h.close();
}
String skip = System.getProperty("solr.test.leavedatadir");
if (null != skip && 0 != skip.trim().length()) {
System.err.println(
"NOTE: per solr.test.leavedatadir, dataDir will not be removed: "
+ dataDir.getAbsolutePath());
} else {
if (!recurseDelete(dataDir)) {
System.err.println(
"!!!! WARNING: best effort to remove " + dataDir.getAbsolutePath() + " FAILED !!!!!");
}
}
resetExceptionIgnores();
super.tearDown();
}
/*
* Set up the platform binary download and get it ready to run the tests.
* This method is not intended to be called by clients, it will be called
* automatically when the clients use a ReconcilerTestSuite. If the executable isn't
* found on the file-system after the call, then we fail.
*/
public void initialize() throws Exception {
initialized = false;
File file = getPlatformZip();
output = getUniqueFolder();
toRemove.add(output);
// for now we will exec to un-tar archives to keep the executable bits
if (file.getName().toLowerCase().endsWith(".zip")) {
try {
FileUtils.unzipFile(file, output);
} catch (IOException e) {
fail("0.99", e);
}
} else {
untar("1.0", file);
}
File exe = new File(output, getExeFolder() + "eclipse.exe");
if (!exe.exists()) {
exe = new File(output, getExeFolder() + "eclipse");
if (!exe.exists())
fail(
"Executable file: "
+ exe.getAbsolutePath()
+ "(or .exe) not found after extracting: "
+ file.getAbsolutePath()
+ " to: "
+ output);
}
initialized = true;
}
protected int runEclipse(String message, File location, String[] args, File extensions) {
File root = new File(Activator.getBundleContext().getProperty("java.home"));
root = new File(root, "bin");
File exe = new File(root, "javaw.exe");
if (!exe.exists()) exe = new File(root, "java");
assertTrue("Java executable not found in: " + exe.getAbsolutePath(), exe.exists());
List<String> command = new ArrayList<String>();
Collections.addAll(
command,
new String[] {
(new File(location == null ? output : location, getExeFolder() + "eclipse"))
.getAbsolutePath(),
"--launcher.suppressErrors",
"-nosplash",
"-vm",
exe.getAbsolutePath()
});
Collections.addAll(command, args);
Collections.addAll(command, new String[] {"-vmArgs", "-Dosgi.checkConfiguration=true"});
// command-line if you want to run and allow a remote debugger to connect
if (debug)
Collections.addAll(
command,
new String[] {
"-Xdebug", "-Xnoagent", "-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8787"
});
int result = run(message, command.toArray(new String[command.size()]));
// 13 means that we wrote something out in the log file.
// so try and parse it and fail via that message if we can.
if (result == 13) parseExitdata(message);
return result;
}
private static String getArtifactResolverJar(boolean isMaven3) throws IOException {
Class marker =
isMaven3 ? MavenArtifactResolvedM3RtMarker.class : MavenArtifactResolvedM2RtMarker.class;
File classDirOrJar = new File(PathUtil.getJarPathForClass(marker));
if (!classDirOrJar.isDirectory()) {
return classDirOrJar.getAbsolutePath(); // it's a jar in IDEA installation.
}
// it's a classes directory, we are in development mode.
File tempFile = FileUtil.createTempFile("idea-", "-artifactResolver.jar");
tempFile.deleteOnExit();
ZipOutputStream zipOutput = new ZipOutputStream(new FileOutputStream(tempFile));
try {
ZipUtil.addDirToZipRecursively(zipOutput, null, classDirOrJar, "", null, null);
if (isMaven3) {
File m2Module = new File(PathUtil.getJarPathForClass(MavenModuleMap.class));
String commonClassesPath = MavenModuleMap.class.getPackage().getName().replace('.', '/');
ZipUtil.addDirToZipRecursively(
zipOutput, null, new File(m2Module, commonClassesPath), commonClassesPath, null, null);
}
} finally {
zipOutput.close();
}
return tempFile.getAbsolutePath();
}
/**
* Load classes from given file. File could be either directory or JAR file.
*
* @param clsLdr Class loader to load files.
* @param file Either directory or JAR file which contains classes or references to them.
* @return Set of found and loaded classes or empty set if file does not exist.
* @throws GridSpiException Thrown if given JAR file references to none existed class or
* IOException occurred during processing.
*/
static Set<Class<? extends GridTask<?, ?>>> getClasses(ClassLoader clsLdr, File file)
throws GridSpiException {
Set<Class<? extends GridTask<?, ?>>> rsrcs = new HashSet<Class<? extends GridTask<?, ?>>>();
if (file.exists() == false) {
return rsrcs;
}
GridUriDeploymentFileResourceLoader fileRsrcLdr =
new GridUriDeploymentFileResourceLoader(clsLdr, file);
if (file.isDirectory()) {
findResourcesInDirectory(fileRsrcLdr, file, rsrcs);
} else {
try {
for (JarEntry entry : U.asIterable(new JarFile(file.getAbsolutePath()).entries())) {
Class<? extends GridTask<?, ?>> rsrc = fileRsrcLdr.createResource(entry.getName(), false);
if (rsrc != null) {
rsrcs.add(rsrc);
}
}
} catch (IOException e) {
throw new GridSpiException(
"Failed to discover classes in file: " + file.getAbsolutePath(), e);
}
}
return rsrcs;
}
public int compare(Object o1, Object o2) {
File f1 = (File) o1;
File f2 = (File) o2;
if (f1.isDirectory()) {
if (f2.isDirectory()) {
switch (mode) {
// Filename or Type
case 1:
case 4:
return sign
* f1.getAbsolutePath()
.toUpperCase()
.compareTo(f2.getAbsolutePath().toUpperCase());
// Filesize
case 2:
return sign * (new Long(f1.length()).compareTo(new Long(f2.length())));
// Date
case 3:
return sign * (new Long(f1.lastModified()).compareTo(new Long(f2.lastModified())));
default:
return 1;
}
} else return -1;
} else if (f2.isDirectory()) return 1;
else {
switch (mode) {
case 1:
return sign
* f1.getAbsolutePath().toUpperCase().compareTo(f2.getAbsolutePath().toUpperCase());
case 2:
return sign * (new Long(f1.length()).compareTo(new Long(f2.length())));
case 3:
return sign * (new Long(f1.lastModified()).compareTo(new Long(f2.lastModified())));
case 4:
{ // Sort by extension
int tempIndexf1 = f1.getAbsolutePath().lastIndexOf('.');
int tempIndexf2 = f2.getAbsolutePath().lastIndexOf('.');
if ((tempIndexf1 == -1) && (tempIndexf2 == -1)) { // Neither have an extension
return sign
* f1.getAbsolutePath()
.toUpperCase()
.compareTo(f2.getAbsolutePath().toUpperCase());
}
// f1 has no extension
else if (tempIndexf1 == -1) return -sign;
// f2 has no extension
else if (tempIndexf2 == -1) return sign;
// Both have an extension
else {
String tempEndf1 = f1.getAbsolutePath().toUpperCase().substring(tempIndexf1);
String tempEndf2 = f2.getAbsolutePath().toUpperCase().substring(tempIndexf2);
return sign * tempEndf1.compareTo(tempEndf2);
}
}
default:
return 1;
}
}
}
/*
* Untar the given file in the output directory.
*/
private void untar(String message, File file) {
String name = file.getName();
File gzFile = new File(output, name);
output.mkdirs();
run(message, new String[] {"cp", file.getAbsolutePath(), gzFile.getAbsolutePath()});
run(message, new String[] {"tar", "-zpxf", gzFile.getAbsolutePath()});
gzFile.delete();
}
void clearPath(File f) {
String root = dir.getAbsolutePath();
String dir = f.getAbsolutePath();
if (dir.startsWith(root)) {
String[] dirNames = dir.substring(root.length()).split(File.separator + "subdir");
if (clearPath(f, dirNames, 1)) return;
}
clearPath(f, null, -1);
}
/**
* Builds an object graph representing an MDMI map.
*
* @param filePath XMI file containing the map definition.
* @return
*/
public static List<MessageGroup> build(File file, ModelValidationResults valResults) {
try {
return buildFromRawModel(XMIParser.parse(file), valResults);
} catch (FileNotFoundException exc) {
throw new MdmiException(exc, "MapBuilder: file {0} not found!", file.getAbsolutePath());
} catch (XMLStreamException exc) {
throw new MdmiException(
exc, "MapBuilder: file {0} is not a valid XML file!", file.getAbsolutePath());
}
}
/** Display a dialog which allows the user to export a scene to an OBJ file. */
public static void exportFile(BFrame parent, Scene theScene) {
// Display a dialog box with options on how to export the scene.
// ValueField errorField = new ValueField(0.05, ValueField.POSITIVE);
// final ValueField widthField = new ValueField(200.0, ValueField.INTEGER+ValueField.POSITIVE);
// final ValueField heightField = new ValueField(200.0, ValueField.INTEGER+ValueField.POSITIVE);
// final ValueSlider qualitySlider = new ValueSlider(0.0, 1.0, 100, 0.5);
// final BCheckBox smoothBox = new BCheckBox(Translate.text("subdivideSmoothMeshes"), true);
final BCheckBox injectChoice = new BCheckBox(Translate.text("Inject"), true);
// final BCheckBox UVChoice = new BCheckBox(Translate.text("Export UV"), true);
/*BComboBox exportChoice = new BComboBox(new String [] {
Translate.text("exportWholeScene"),
Translate.text("selectedObjectsOnly")
});*/
ComponentsDialog dlg;
if (theScene.getSelection().length > 0)
dlg =
new ComponentsDialog(
parent,
Translate.text("InjectToM2"),
new Widget[] {injectChoice},
new String[] {null, null, null, null, null});
else
dlg =
new ComponentsDialog(
parent,
Translate.text("exportToM2"),
new Widget[] {injectChoice},
new String[] {null, null, null, null});
if (!dlg.clickedOk()) return;
// Ask the user to select the output file.
BFileChooser fc = new BFileChooser(BFileChooser.SAVE_FILE, Translate.text("exportToWMO"));
fc.setSelectedFile(new File("Untitled.m2"));
if (ArtOfIllusion.getCurrentDirectory() != null)
fc.setDirectory(new File(ArtOfIllusion.getCurrentDirectory()));
if (!fc.showDialog(parent)) return;
File dir = fc.getDirectory();
f = fc.getSelectedFile();
String name = f.getName();
String baseName = (name.endsWith(".m2") ? name.substring(0, name.length() - 3) : name);
ArtOfIllusion.setCurrentDirectory(dir.getAbsolutePath());
m2 obj = null;
try {
obj = new m2(fileLoader.openBuffer(f.getAbsolutePath()));
} catch (InvalidClassException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
writeScene(theScene, obj, false, 0.05, false, injectChoice.getState());
}
public Graph(WeightedBVGraph graph, String[] names) {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
if (names.length != graph.numNodes())
throw new Error("Problem with the list of names for the nodes in the graph.");
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
this.graph = graph;
WeightedArcSet list = new WeightedArcSet();
ArcLabelledNodeIterator it = graph.nodeIterator();
while (it.hasNext()) {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
Integer aux1 = it.nextInt();
Integer aux2 = null;
ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
WeightedArc arc = (WeightedArc) cons[0].newInstance(aux2, aux1, suc.label().getFloat());
list.add(arc);
this.nodes.put(aux1, names[aux1]);
this.nodes.put(aux2, names[aux2]);
this.nodesReverse.put(names[aux1], aux1);
this.nodesReverse.put(names[aux2], aux2);
} catch (Exception ex) {
throw new Error(ex);
}
}
reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
protected static DefaultFontMapper getMapper() {
if (mapper == null) {
// long t = System.currentTimeMillis();
mapper = new DefaultFontMapper();
if (PApplet.platform == PApplet.MACOSX) {
try {
String homeLibraryFonts = System.getProperty("user.home") + "/Library/Fonts";
mapper.insertDirectory(homeLibraryFonts);
} catch (Exception e) {
// might be a security issue with getProperty() and user.home
// if this sketch is running from the web
}
// add the system font paths
mapper.insertDirectory("/System/Library/Fonts");
mapper.insertDirectory("/Library/Fonts");
} else if (PApplet.platform == PApplet.WINDOWS) {
// how to get the windows fonts directory?
// could be c:\winnt\fonts or c:\windows\fonts or not even c:
// maybe do a Runtime.exec() on echo %WINDIR% ?
// Runtime.exec solution might be a mess on systems where the
// the backslash/colon characters not really used (i.e. JP)
// find the windows fonts folder
File roots[] = File.listRoots();
for (int i = 0; i < roots.length; i++) {
if (roots[i].toString().startsWith("A:")) {
// Seems to be a problem with some machines that the A:
// drive is returned as an actual root, even if not available.
// This won't fix the issue if the same thing happens with
// other removable drive devices, but should fix the
// initial/problem as cited by the bug report:
// http://dev.processing.org/bugs/show_bug.cgi?id=478
// If not, will need to use the other fileExists() code below.
continue;
}
File folder = new File(roots[i], "WINDOWS/Fonts");
if (folder.exists()) {
mapper.insertDirectory(folder.getAbsolutePath());
break;
}
folder = new File(roots[i], "WINNT/Fonts");
if (folder.exists()) {
mapper.insertDirectory(folder.getAbsolutePath());
break;
}
}
}
// System.out.println("mapping " + (System.currentTimeMillis() - t));
}
return mapper;
}
public static void main(String[] args) {
BackgroundEstimation estimation = new BolstadEMBackgroundEstimation();
// BackgroundEstimation estimation = new UniformBackgroundEstimation();
String key = args[0];
WorkflowProperties props = new WorkflowProperties();
File fplus = new File(props.getDirectory(), String.format("%s_plus.raw", key));
File fminus = new File(props.getDirectory(), String.format("%s_negative.raw", key));
// LogTransform transform = LogTransform.NONE;
LogTransform transform = LogTransform.LOG_TO_EXP;
BackgroundRemoval norm = new BackgroundRemoval(estimation, transform);
try {
System.out.println(String.format("Loading: %s", fplus.getName()));
norm.load(new WorkflowDataLoader(fplus));
System.out.println(String.format("Loading: %s", fminus.getName()));
norm.load(new WorkflowDataLoader(fminus));
WorkflowIndexing indexing = props.getIndexing(key);
System.out.println(String.format("Removing background..."));
norm.removeBackground();
Filter<ProbeLine, ProbeLine> plus =
new Filter<ProbeLine, ProbeLine>() {
public ProbeLine execute(ProbeLine p) {
return p.strand.equals("+") ? p : null;
}
};
Filter<ProbeLine, ProbeLine> minus =
new Filter<ProbeLine, ProbeLine>() {
public ProbeLine execute(ProbeLine p) {
return p.strand.equals("-") ? p : null;
}
};
System.out.println(String.format("Outputting background-removed results..."));
File plusOut = new File(props.getDirectory(), String.format("%s_plus.corrected", key));
File minusOut = new File(props.getDirectory(), String.format("%s_negative.corrected", key));
outputProbes(new FilterIterator<ProbeLine, ProbeLine>(plus, norm.iterator()), plusOut);
System.out.println(String.format("\t%s", plusOut.getAbsolutePath()));
outputProbes(new FilterIterator<ProbeLine, ProbeLine>(minus, norm.iterator()), minusOut);
System.out.println(String.format("\t%s", minusOut.getAbsolutePath()));
} catch (IOException e) {
e.printStackTrace();
}
}
public void addResource(File object) {
ResourceModel rm = new ResourceModel();
rm.setName(object.getName());
rm.setFilePath(object.getAbsolutePath());
String filePath = rm.getFilePath();
if (filePath.endsWith(".jpeg") || filePath.endsWith(".gif")) rm.setDataType("Image");
else if (filePath.endsWith(".au")) rm.setDataType("AudioStream");
if (rm.getDataType().equals("Image")) rm.setImage(loadImage(object.getAbsolutePath()));
else if (rm.getDataType().equals("AudioStream"))
rm.setAudioStream(loadAudio(object.getAbsolutePath()));
resources.put(rm.getName(), rm);
}
/** 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
}
String askForReadFilename() {
int returnVal = sqlLoadChooser.showOpenDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION) {
File file = sqlLoadChooser.getSelectedFile();
System.out.println("Selected read file " + file.getAbsolutePath());
// return file.getName();
return file.getAbsolutePath();
} else {
System.out.println("Open command cancelled by user.");
}
return null;
}
