List of usage examples for java.util Collections sort
@SuppressWarnings("unchecked") public static <T extends Comparable<? super T>> void sort(List<T> list)
From source file:edu.ucla.cs.scai.swim.qa.ontology.dbpedia.tipicality.Test.java
public static void main(String[] args) throws IOException, ClassNotFoundException { String path = DBpediaOntology.DBPEDIA_CSV_FOLDER; if (args != null && args.length > 0) { path = args[0];/*from ww w .j ava 2 s . c o m*/ if (!path.endsWith("/")) { path = path + "/"; } } stopAttributes.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"); stopAttributes.add("http://www.w3.org/2002/07/owl#sameAs"); stopAttributes.add("http://dbpedia.org/ontology/wikiPageRevisionID"); stopAttributes.add("http://dbpedia.org/ontology/wikiPageID"); stopAttributes.add("http://purl.org/dc/elements/1.1/description"); stopAttributes.add("http://dbpedia.org/ontology/thumbnail"); stopAttributes.add("http://dbpedia.org/ontology/type"); try (ObjectInputStream ois = new ObjectInputStream(new FileInputStream(path + "counts.bin"))) { categories = (HashSet<String>) ois.readObject(); attributes = (HashSet<String>) ois.readObject(); categoryCount = (HashMap<String, Integer>) ois.readObject(); attributeCount = (HashMap<String, Integer>) ois.readObject(); categoryAttributeCount = (HashMap<String, HashMap<String, Integer>>) ois.readObject(); attributeCategoryCount = (HashMap<String, HashMap<String, Integer>>) ois.readObject(); } System.out.println(categories.size() + " categories found"); System.out.println(attributes.size() + " attributes found"); n = 0; for (Map.Entry<String, Integer> e : categoryCount.entrySet()) { n += e.getValue(); } System.out.println(n); HashMap<String, ArrayList<Pair>> sortedCategoryAttributes = new HashMap<>(); for (String category : categories) { //System.out.println(category); //System.out.println("-----------"); ArrayList<Pair> attributesRank = new ArrayList<Pair>(); Integer c = categoryCount.get(category); if (c == null || c == 0) { continue; } HashMap<String, Integer> thisCategoryAttributeCount = categoryAttributeCount.get(category); for (Map.Entry<String, Integer> e : thisCategoryAttributeCount.entrySet()) { attributesRank.add(new Pair(e.getKey(), 1.0 * e.getValue() / c)); } Collections.sort(attributesRank); for (Pair p : attributesRank) { //System.out.println("A:" + p.getS() + "\t" + p.getP()); } //System.out.println("==============================="); sortedCategoryAttributes.put(category, attributesRank); } for (String attribute : attributes) { //System.out.println(attribute); //System.out.println("-----------"); ArrayList<Pair> categoriesRank = new ArrayList<>(); Integer a = attributeCount.get(attribute); if (a == null || a == 0) { continue; } HashMap<String, Integer> thisAttributeCategoryCount = attributeCategoryCount.get(attribute); for (Map.Entry<String, Integer> e : thisAttributeCategoryCount.entrySet()) { categoriesRank.add(new Pair(e.getKey(), 1.0 * e.getValue() / a)); } Collections.sort(categoriesRank); for (Pair p : categoriesRank) { //System.out.println("C:" + p.getS() + "\t" + p.getP()); } //System.out.println("==============================="); } HashMap<Integer, Integer> histogram = new HashMap<>(); histogram.put(0, 0); histogram.put(1, 0); histogram.put(2, 0); histogram.put(Integer.MAX_VALUE, 0); int nTest = 0; if (args != null && args.length > 0) { path = args[0]; if (!path.endsWith("/")) { path = path + "/"; } } for (File f : new File(path).listFiles()) { if (f.isFile() && f.getName().endsWith(".csv")) { String category = f.getName().replaceFirst("\\.csv", ""); System.out.println("Category: " + category); ArrayList<HashSet<String>> entities = extractEntities(f, 2); for (HashSet<String> attributesOfThisEntity : entities) { nTest++; ArrayList<String> rankedCategories = rankedCategories(attributesOfThisEntity); boolean found = false; for (int i = 0; i < rankedCategories.size() && !found; i++) { if (rankedCategories.get(i).equals(category)) { Integer count = histogram.get(i); if (count == null) { histogram.put(i, 1); } else { histogram.put(i, count + 1); } found = true; } } if (!found) { histogram.put(Integer.MAX_VALUE, histogram.get(Integer.MAX_VALUE) + 1); } } System.out.println("Tested entities: " + nTest); System.out.println("1: " + histogram.get(0)); System.out.println("2: " + histogram.get(1)); System.out.println("3: " + histogram.get(2)); System.out.println("+3: " + (nTest - histogram.get(2) - histogram.get(1) - histogram.get(0) - histogram.get(Integer.MAX_VALUE))); System.out.println("NF: " + histogram.get(Integer.MAX_VALUE)); } } }
From source file:com.turn.ttorrent.cli.TorrentMain.java
/** * Torrent reader and creator./*from w w w . ja va2s .c om*/ * * <p> * You can use the {@code main()} function of this class to read or create * torrent files. See usage for details. * </p> * */ public static void main(String[] args) { BasicConfigurator.configure(new ConsoleAppender(new PatternLayout("%-5p: %m%n"))); CmdLineParser parser = new CmdLineParser(); CmdLineParser.Option help = parser.addBooleanOption('h', "help"); CmdLineParser.Option filename = parser.addStringOption('t', "torrent"); CmdLineParser.Option create = parser.addBooleanOption('c', "create"); CmdLineParser.Option pieceLength = parser.addIntegerOption('l', "length"); CmdLineParser.Option announce = parser.addStringOption('a', "announce"); try { parser.parse(args); } catch (CmdLineParser.OptionException oe) { System.err.println(oe.getMessage()); usage(System.err); System.exit(1); } // Display help and exit if requested if (Boolean.TRUE.equals((Boolean) parser.getOptionValue(help))) { usage(System.out); System.exit(0); } String filenameValue = (String) parser.getOptionValue(filename); if (filenameValue == null) { usage(System.err, "Torrent file must be provided!"); System.exit(1); } Integer pieceLengthVal = (Integer) parser.getOptionValue(pieceLength); if (pieceLengthVal == null) { pieceLengthVal = Torrent.DEFAULT_PIECE_LENGTH; } else { pieceLengthVal = pieceLengthVal * 1024; } logger.info("Using piece length of {} bytes.", pieceLengthVal); Boolean createFlag = (Boolean) parser.getOptionValue(create); //For repeated announce urls @SuppressWarnings("unchecked") Vector<String> announceURLs = (Vector<String>) parser.getOptionValues(announce); String[] otherArgs = parser.getRemainingArgs(); if (Boolean.TRUE.equals(createFlag) && (otherArgs.length != 1 || announceURLs.isEmpty())) { usage(System.err, "Announce URL and a file or directory must be " + "provided to create a torrent file!"); System.exit(1); } OutputStream fos = null; try { if (Boolean.TRUE.equals(createFlag)) { if (filenameValue != null) { fos = new FileOutputStream(filenameValue); } else { fos = System.out; } //Process the announce URLs into URIs List<URI> announceURIs = new ArrayList<URI>(); for (String url : announceURLs) { announceURIs.add(new URI(url)); } //Create the announce-list as a list of lists of URIs //Assume all the URI's are first tier trackers List<List<URI>> announceList = new ArrayList<List<URI>>(); announceList.add(announceURIs); File source = new File(otherArgs[0]); if (!source.exists() || !source.canRead()) { throw new IllegalArgumentException( "Cannot access source file or directory " + source.getName()); } String creator = String.format("%s (ttorrent)", System.getProperty("user.name")); Torrent torrent = null; if (source.isDirectory()) { List<File> files = new ArrayList<File>( FileUtils.listFiles(source, TrueFileFilter.TRUE, TrueFileFilter.TRUE)); Collections.sort(files); torrent = Torrent.create(source, files, pieceLengthVal, announceList, creator); } else { torrent = Torrent.create(source, pieceLengthVal, announceList, creator); } torrent.save(fos); } else { Torrent.load(new File(filenameValue), true); } } catch (Exception e) { logger.error("{}", e.getMessage(), e); System.exit(2); } finally { if (fos != System.out) { IOUtils.closeQuietly(fos); } } }
From source file:at.tuwien.ifs.somtoolbox.apps.VisualisationImageSaver.java
public static void main(String[] args) { JSAPResult res = OptionFactory.parseResults(args, OPTIONS); String uFile = res.getString("unitDescriptionFile"); String wFile = res.getString("weightVectorFile"); String dwmFile = res.getString("dataWinnerMappingFile"); String cFile = res.getString("classInformationFile"); String vFile = res.getString("inputVectorFile"); String tFile = res.getString("templateVectorFile"); String ftype = res.getString("filetype"); boolean unitGrid = res.getBoolean("unitGrid"); String basename = res.getString("basename"); if (basename == null) { basename = FileUtils.extractSOMLibInputPrefix(uFile); }/*w ww.j a va2s . co m*/ basename = new File(basename).getAbsolutePath(); int unitW = res.getInt("width"); int unitH = res.getInt("height", unitW); String[] vizs = res.getStringArray("vis"); GrowingSOM gsom = null; CommonSOMViewerStateData state = CommonSOMViewerStateData.getInstance(); try { SOMLibFormatInputReader inputReader = new SOMLibFormatInputReader(wFile, uFile, null); gsom = new GrowingSOM(inputReader); SharedSOMVisualisationData d = new SharedSOMVisualisationData(cFile, null, null, dwmFile, vFile, tFile, null); d.readAvailableData(); state.inputDataObjects = d; gsom.setSharedInputObjects(d); Visualizations.initVisualizations(d, inputReader, 0, Palettes.getDefaultPalette(), Palettes.getAvailablePalettes()); } catch (FileNotFoundException e) { // TODO Auto-generated catch block e.printStackTrace(); System.exit(1); } catch (SOMLibFileFormatException e) { // TODO Auto-generated catch block e.printStackTrace(); System.exit(1); } if (ArrayUtils.isEmpty(vizs)) { System.out.println("No specific visualisation specified - saving all available visualisations."); vizs = Visualizations.getReadyVisualizationNames(); System.out.println("Found " + vizs.length + ": " + Arrays.toString(vizs)); } for (String viz : vizs) { BackgroundImageVisualizerInstance v = Visualizations.getVisualizationByName(viz); if (v == null) { System.out.println("Visualization '" + viz + "' not found!"); continue; } BackgroundImageVisualizer i = v.getVis(); GrowingLayer layer = gsom.getLayer(); try { int height = unitH * layer.getYSize(); int width = unitW * layer.getXSize(); HashMap<String, BufferedImage> visualizationFlavours = i.getVisualizationFlavours(v.getVariant(), gsom, width, height); ArrayList<String> keys = new ArrayList<String>(visualizationFlavours.keySet()); Collections.sort(keys); // if the visualisation has more than 5 flavours, we create a sub-dir for it String subDirName = ""; String oldBasename = basename; // save original base name for later if (keys.size() > 5) { String parentDir = new File(basename).getParentFile().getPath(); // get the parent path String filePrefix = basename.substring(parentDir.length()); // end the file name prefix subDirName = parentDir + File.separator + filePrefix + "_" + viz + File.separator; // compose a new // subdir name new File(subDirName).mkdir(); // create the dir basename = subDirName + filePrefix; // and extend the base name by the subdir } for (String key : keys) { File out = new File(basename + "_" + viz + key + "." + ftype); System.out.println("Generating visualisation '" + viz + "' as '" + out.getPath() + "'."); BufferedImage image = visualizationFlavours.get(key); if (unitGrid) { VisualisationUtils.drawUnitGrid(image, gsom, width, height); } ImageIO.write(image, ftype, out); } basename = oldBasename; // reset base name } catch (SOMToolboxException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } System.exit(0); }
From source file:net.dontdrinkandroot.lastfm.api.CheckImplementationStatus.java
public static void main(final String[] args) throws DocumentException, IOException { CheckImplementationStatus.xmlReader = new Parser(); CheckImplementationStatus.saxReader = new SAXReader(CheckImplementationStatus.xmlReader); final String packagePrefix = "net.dontdrinkandroot.lastfm.api.model."; final Map<String, Map<String, URL>> packages = CheckImplementationStatus.parseOverview(); final StringBuffer html = new StringBuffer(); html.append("<html>\n"); html.append("<head>\n"); html.append("<title>Implementation Status</title>\n"); html.append("</head>\n"); html.append("<body>\n"); html.append("<h1>Implementation Status</h1>\n"); final StringBuffer wiki = new StringBuffer(); int numImplemented = 0; int numTested = 0; int numMethods = 0; final List<String> packageList = new ArrayList<String>(packages.keySet()); Collections.sort(packageList); for (final String pkg : packageList) { System.out.println("Parsing " + pkg); html.append("<h2>" + pkg + "</h2>\n"); wiki.append("\n===== " + pkg + " =====\n\n"); Class<?> modelClass = null; final String className = packagePrefix + pkg; try {/* w ww.jav a2 s . c o m*/ modelClass = Class.forName(className); System.out.println("\tClass " + modelClass.getName() + " exists"); } catch (final ClassNotFoundException e) { // e.printStackTrace(); System.out.println("\t" + className + ": DOES NOT exist"); } Class<?> testClass = null; final String testClassName = packagePrefix + pkg + "Test"; try { testClass = Class.forName(testClassName); System.out.println("\tTestClass " + testClass.getName() + " exists"); } catch (final ClassNotFoundException e) { // e.printStackTrace(); System.out.println("\t" + testClassName + ": TestClass for DOES NOT exist"); } final List<String> methods = new ArrayList<String>(packages.get(pkg).keySet()); Collections.sort(methods); final Method[] classMethods = modelClass.getMethods(); final Method[] testMethods = testClass.getMethods(); html.append("<table>\n"); html.append("<tr><th>Method</th><th>Implemented</th><th>Tested</th></tr>\n"); wiki.append("^ Method ^ Implemented ^ Tested ^\n"); numMethods += methods.size(); for (final String method : methods) { System.out.println("\t\t parsing " + method); html.append("<tr>\n"); html.append("<td>" + method + "</td>\n"); wiki.append("| " + method + " "); boolean classMethodFound = false; for (final Method classMethod : classMethods) { if (classMethod.getName().equals(method)) { classMethodFound = true; break; } } if (classMethodFound) { System.out.println("\t\t\tMethod " + method + " found"); html.append("<td style=\"background-color: green\">true</td>\n"); wiki.append("| yes "); numImplemented++; } else { System.out.println("\t\t\t" + method + " NOT found"); html.append("<td style=\"background-color: red\">false</td>\n"); wiki.append("| **no** "); } boolean testMethodFound = false; final String testMethodName = "test" + StringUtils.capitalize(method); for (final Method testMethod : testMethods) { if (testMethod.getName().equals(testMethodName)) { testMethodFound = true; break; } } if (testMethodFound) { System.out.println("\t\t\tTestMethod " + method + " found"); html.append("<td style=\"background-color: green\">true</td>\n"); wiki.append("| yes |\n"); numTested++; } else { System.out.println("\t\t\t" + testMethodName + " NOT found"); html.append("<td style=\"background-color: red\">false</td>\n"); wiki.append("| **no** |\n"); } html.append("</tr>\n"); } html.append("</table>\n"); // for (String methodName : methods) { // URL url = pkg.getValue().get(methodName); // System.out.println("PARSING: " + pkg.getKey() + "." + methodName + ": " + url); // String html = loadIntoString(url); // String description = null; // Matcher descMatcher = descriptionPattern.matcher(html); // if (descMatcher.find()) { // description = descMatcher.group(1).trim(); // } // boolean post = false; // Matcher postMatcher = postPattern.matcher(html); // if (postMatcher.find()) { // post = true; // } // Matcher paramsMatcher = paramsPattern.matcher(html); // List<String[]> params = new ArrayList<String[]>(); // boolean authenticated = false; // if (paramsMatcher.find()) { // String paramsString = paramsMatcher.group(1); // Matcher paramMatcher = paramPattern.matcher(paramsString); // while (paramMatcher.find()) { // String[] param = new String[3]; // param[0] = paramMatcher.group(1); // param[1] = paramMatcher.group(3); // param[2] = paramMatcher.group(5); // // System.out.println(paramMatcher.group(1) + "|" + paramMatcher.group(3) + "|" + // paramMatcher.group(5)); // if (param[0].equals("")) { // /* DO NOTHING */ // } else if (param[0].equals("api_key")) { // /* DO NOTHING */ // } else if (param[0].equals("api_sig")) { // authenticated = true; // } else { // params.add(param); // } // } // } // } // count++; // } html.append("<hr />"); html.append("<p>" + numImplemented + "/" + numMethods + " implemented (" + numImplemented * 100 / numMethods + "%)</p>"); html.append("<p>" + numTested + "/" + numMethods + " tested (" + numTested * 100 / numMethods + "%)</p>"); html.append("</body>\n"); html.append("</html>\n"); FileOutputStream out = new FileOutputStream(new File(FileUtils.getTempDirectory(), "apistatus.html")); IOUtils.write(html, out); IOUtils.closeQuietly(out); out = new FileOutputStream(new File(FileUtils.getTempDirectory(), "apistatus.wiki.txt")); IOUtils.write(wiki, out); IOUtils.closeQuietly(out); }
From source file:ClassFileUtilities.java
/** * Program that computes the dependencies between the Batik jars. * <p>//from ww w . jav a 2s. com * Run this from the main Batik distribution directory, after building * the jars. For every jar file in the batik-xxx/ build directory, * it will determine which other jar files it directly depends on. * The output is lines of the form: * </p> * <pre> <i>number</i>,<i>from</i>,<i>to</i></pre> * <p> * where mean that the <i>from</i> jar has <i>number</i> class files * that depend on class files in the <i>to</i> jar. * </p> */ public static void main(String[] args) { boolean showFiles = false; if (args.length == 1 && args[0].equals("-f")) { showFiles = true; } else if (args.length != 0) { System.err.println("usage: ClassFileUtilities [-f]"); System.err.println(); System.err.println(" -f list files that cause each jar file dependency"); System.exit(1); } File cwd = new File("."); File buildDir = null; String[] cwdFiles = cwd.list(); for (int i = 0; i < cwdFiles.length; i++) { if (cwdFiles[i].startsWith("batik-")) { buildDir = new File(cwdFiles[i]); if (!buildDir.isDirectory()) { buildDir = null; } else { break; } } } if (buildDir == null || !buildDir.isDirectory()) { System.out.println("Directory 'batik-xxx' not found in current directory!"); return; } try { Map cs = new HashMap(); Map js = new HashMap(); collectJars(buildDir, js, cs); Set classpath = new HashSet(); Iterator i = js.values().iterator(); while (i.hasNext()) { classpath.add(((Jar) i.next()).jarFile); } i = cs.values().iterator(); while (i.hasNext()) { ClassFile fromFile = (ClassFile) i.next(); // System.out.println(fromFile.name); Set result = getClassDependencies(fromFile.getInputStream(), classpath, false); Iterator j = result.iterator(); while (j.hasNext()) { ClassFile toFile = (ClassFile) cs.get(j.next()); if (fromFile != toFile && toFile != null) { fromFile.deps.add(toFile); } } } i = cs.values().iterator(); while (i.hasNext()) { ClassFile fromFile = (ClassFile) i.next(); Iterator j = fromFile.deps.iterator(); while (j.hasNext()) { ClassFile toFile = (ClassFile) j.next(); Jar fromJar = fromFile.jar; Jar toJar = toFile.jar; if (fromFile.name.equals(toFile.name) || toJar == fromJar || fromJar.files.contains(toFile.name)) { continue; } Integer n = (Integer) fromJar.deps.get(toJar); if (n == null) { fromJar.deps.put(toJar, new Integer(1)); } else { fromJar.deps.put(toJar, new Integer(n.intValue() + 1)); } } } List triples = new ArrayList(10); i = js.values().iterator(); while (i.hasNext()) { Jar fromJar = (Jar) i.next(); Iterator j = fromJar.deps.keySet().iterator(); while (j.hasNext()) { Jar toJar = (Jar) j.next(); Triple t = new Triple(); t.from = fromJar; t.to = toJar; t.count = ((Integer) fromJar.deps.get(toJar)).intValue(); triples.add(t); } } Collections.sort(triples); i = triples.iterator(); while (i.hasNext()) { Triple t = (Triple) i.next(); System.out.println(t.count + "," + t.from.name + "," + t.to.name); if (showFiles) { Iterator j = t.from.files.iterator(); while (j.hasNext()) { ClassFile fromFile = (ClassFile) j.next(); Iterator k = fromFile.deps.iterator(); while (k.hasNext()) { ClassFile toFile = (ClassFile) k.next(); if (toFile.jar == t.to && !t.from.files.contains(toFile.name)) { System.out.println("\t" + fromFile.name + " --> " + toFile.name); } } } } } } catch (IOException e) { e.printStackTrace(); } }
From source file:net.wedjaa.elasticparser.tester.ESSearchTester.java
public static void main(String[] args) { System.out.println("ES Search Testing started."); System.out.println("Starting local node..."); Settings nodeSettings = ImmutableSettings.settingsBuilder().put("transport.tcp.port", "9600-9700") .put("http.port", "9500").put("http.max_content_length", "104857600").build(); Node node = NodeBuilder.nodeBuilder().settings(nodeSettings).clusterName("elasticparser.unittest").node(); node.start();/*from w w w .j a v a 2 s .c om*/ // Populate our test index System.out.println("Preparing Unit Test Index - this may take a while..."); populateTest(); try { System.out.println("...OK - Executing query!"); // Try our searches ESSearch search = new ESSearch(null, null, ESSearch.ES_MODE_AGGS, "localhost", 9600, "elasticparser.unittest"); search.search(getQuery("test-aggs.json")); Map<String, Object> hit = null; while ((hit = search.next()) != null) { System.out.println("Hit: {"); for (String key : hit.keySet()) { System.out.println(" " + key + ": " + hit.get(key)); } System.out.println("};"); } search.close(); Map<String, Class<?>> fields = search.getFields(getQuery("test-aggs.json")); List<String> sortedKeys = new ArrayList<String>(fields.keySet()); Collections.sort(sortedKeys); Iterator<String> sortedKeyIter = sortedKeys.iterator(); while (sortedKeyIter.hasNext()) { String fieldname = sortedKeyIter.next(); System.out.println(" --> " + fieldname + "[" + fields.get(fieldname).getCanonicalName() + "]"); } } catch (Exception ex) { System.out.println("Exception: " + ex); } finally { System.out.println("Stopping Test Node"); node.stop(); } }
From source file:de.unisb.cs.st.javaslicer.slicing.DirectSlicer.java
public static void main(String[] args) { Options options = createOptions();/*from w w w.j a v a 2 s. c o m*/ CommandLineParser parser = new GnuParser(); CommandLine cmdLine; try { cmdLine = parser.parse(options, args, true); } catch (ParseException e) { System.err.println("Error parsing the command line arguments: " + e.getMessage()); return; } if (cmdLine.hasOption('h')) { printHelp(options, System.out); System.exit(0); } String[] additionalArgs = cmdLine.getArgs(); if (additionalArgs.length != 2) { printHelp(options, System.err); System.exit(-1); } File traceFile = new File(additionalArgs[0]); String slicingCriterionString = additionalArgs[1]; Long threadId = null; if (cmdLine.hasOption('t')) { try { threadId = Long.parseLong(cmdLine.getOptionValue('t')); } catch (NumberFormatException e) { System.err.println("Illegal thread id: " + cmdLine.getOptionValue('t')); System.exit(-1); } } TraceResult trace; try { trace = TraceResult.readFrom(traceFile); } catch (IOException e) { System.err.format("Could not read the trace file \"%s\": %s%n", traceFile, e); System.exit(-1); return; } List<SlicingCriterion> sc = null; try { sc = StaticSlicingCriterion.parseAll(slicingCriterionString, trace.getReadClasses()); } catch (IllegalArgumentException e) { System.err.println("Error parsing slicing criterion: " + e.getMessage()); System.exit(-1); return; } List<ThreadId> threads = trace.getThreads(); if (threads.size() == 0) { System.err.println("The trace file contains no tracing information."); System.exit(-1); } ThreadId tracing = null; for (ThreadId t : threads) { if (threadId == null) { if ("main".equals(t.getThreadName()) && (tracing == null || t.getJavaThreadId() < tracing.getJavaThreadId())) tracing = t; } else if (t.getJavaThreadId() == threadId.longValue()) { tracing = t; } } if (tracing == null) { System.err.println(threadId == null ? "Couldn't find the main thread." : "The thread you specified was not found."); System.exit(-1); return; } long startTime = System.nanoTime(); DirectSlicer slicer = new DirectSlicer(trace); if (cmdLine.hasOption("--progress")) slicer.addProgressMonitor(new ConsoleProgressMonitor()); Set<Instruction> slice = slicer.getDynamicSlice(tracing, sc); long endTime = System.nanoTime(); List<Instruction> sliceList = new ArrayList<Instruction>(slice); Collections.sort(sliceList); System.out.println("The dynamic slice for criterion " + sc + ":"); for (Instruction insn : sliceList) { System.out.format((Locale) null, "%s.%s:%d %s%n", insn.getMethod().getReadClass().getName(), insn.getMethod().getName(), insn.getLineNumber(), insn.toString()); } System.out.format((Locale) null, "%nSlice consists of %d bytecode instructions.%n", sliceList.size()); System.out.format((Locale) null, "Computation took %.2f seconds.%n", 1e-9 * (endTime - startTime)); }
From source file:graticules2wld.Main.java
/** * @param args/*from w w w.j a v a 2 s .c o m*/ * @throws Exception */ public static void main(String[] args) throws Exception { /* parse the command line arguments */ // create the command line parser CommandLineParser parser = new PosixParser(); // create the Options Options options = new Options(); options.addOption("x", "originx", true, "x component of projected coordinates of upper left pixel"); options.addOption("y", "originy", true, "y component of projected coordinates of upper left pixel"); options.addOption("u", "tometers", true, "multiplication factor to get source units into meters"); options.addOption("h", "help", false, "prints this usage page"); options.addOption("d", "debug", false, "prints debugging information to stdout"); double originNorthing = 0; double originEasting = 0; String inputFileName = null; String outputFileName = null; try { // parse the command line arguments CommandLine line = parser.parse(options, args); if (line.hasOption("help")) printUsage(0); // print usage then exit using a non error exit status if (line.hasOption("debug")) debug = true; // these arguments are required if (!line.hasOption("originy") || !line.hasOption("originx")) printUsage(1); originNorthing = Double.parseDouble(line.getOptionValue("originy")); originEasting = Double.parseDouble(line.getOptionValue("originx")); if (line.hasOption("tometers")) unitsToMeters = Double.parseDouble(line.getOptionValue("tometers")); // two args should be left. the input csv file name and the output wld file name. String[] iofiles = line.getArgs(); if (iofiles.length < 2) { printUsage(1); } inputFileName = iofiles[0]; outputFileName = iofiles[1]; } catch (ParseException exp) { System.err.println("Unexpected exception:" + exp.getMessage()); System.exit(1); } // try to open the input file for reading and the output file for writing File graticulesCsvFile; BufferedReader csvReader = null; File wldFile; BufferedWriter wldWriter = null; try { graticulesCsvFile = new File(inputFileName); csvReader = new BufferedReader(new FileReader(graticulesCsvFile)); } catch (IOException exp) { System.err.println("Could not open input file for reading: " + inputFileName); System.exit(1); } try { wldFile = new File(outputFileName); wldWriter = new BufferedWriter(new FileWriter(wldFile)); } catch (IOException exp) { System.err.println("Could not open output file for writing: " + outputFileName); System.exit(1); } // list of lon graticules and lat graticules ArrayList<Graticule> lonGrats = new ArrayList<Graticule>(); ArrayList<Graticule> latGrats = new ArrayList<Graticule>(); // read the source CSV and convert its information into the two ArrayList<Graticule> data structures readCSV(csvReader, lonGrats, latGrats); // we now need to start finding the world file paramaters DescriptiveStatistics stats = new DescriptiveStatistics(); // find theta and phi for (Graticule g : latGrats) { stats.addValue(g.angle()); } double theta = stats.getMean(); // we use the mean of the lat angles as theta if (debug) System.out.println("theta range = " + Math.toDegrees(stats.getMax() - stats.getMin())); stats.clear(); for (Graticule g : lonGrats) { stats.addValue(g.angle()); } double phi = stats.getMean(); // ... and the mean of the lon angles for phi if (debug) System.out.println("phi range = " + Math.toDegrees(stats.getMax() - stats.getMin())); stats.clear(); // print these if in debug mode if (debug) { System.out.println("theta = " + Math.toDegrees(theta) + "deg"); System.out.println("phi = " + Math.toDegrees(phi) + "deg"); } // find x and y (distance beteen pixels in map units) Collections.sort(latGrats); Collections.sort(lonGrats); int prevMapValue = 0; //fixme: how to stop warning about not being initilised? Line2D prevGratPixelSys = new Line2D.Double(); boolean first = true; for (Graticule g : latGrats) { if (!first) { int deltaMapValue = Math.abs(g.realValue() - prevMapValue); double deltaPixelValue = (g.l.ptLineDist(prevGratPixelSys.getP1()) + (g.l.ptLineDist(prevGratPixelSys.getP2()))) / 2; double delta = deltaMapValue / deltaPixelValue; stats.addValue(delta); } else { first = false; prevMapValue = g.realValue(); prevGratPixelSys = (Line2D) g.l.clone(); } } double y = stats.getMean(); if (debug) System.out.println("y range = " + (stats.getMax() - stats.getMin())); stats.clear(); first = true; for (Graticule g : lonGrats) { if (!first) { int deltaMapValue = g.realValue() - prevMapValue; double deltaPixelValue = (g.l.ptLineDist(prevGratPixelSys.getP1()) + (g.l.ptLineDist(prevGratPixelSys.getP2()))) / 2; double delta = deltaMapValue / deltaPixelValue; stats.addValue(delta); } else { first = false; prevMapValue = g.realValue(); prevGratPixelSys = (Line2D) g.l.clone(); } } double x = stats.getMean(); if (debug) System.out.println("x range = " + (stats.getMax() - stats.getMin())); stats.clear(); if (debug) { System.out.println("x = " + x); System.out.println("y = " + y); } SimpleRegression regression = new SimpleRegression(); // C, F are translation terms: x, y map coordinates of the center of the upper-left pixel for (Graticule g : latGrats) { // find perp dist to pixel space 0,0 Double perpPixelDist = g.l.ptLineDist(new Point2D.Double(0, 0)); // find the map space distance from this graticule to the center of the 0,0 pixel Double perpMapDist = perpPixelDist * y; // perpMapDist / perpPixelDist = y regression.addData(perpMapDist, g.realValue()); } double F = regression.getIntercept(); regression.clear(); for (Graticule g : lonGrats) { // find perp dist to pixel space 0,0 Double perpPixelDist = g.l.ptLineDist(new Point2D.Double(0, 0)); // find the map space distance from this graticule to the center of the 0,0 pixel Double perpMapDist = perpPixelDist * x; // perpMapDist / perpPixelDist = x regression.addData(perpMapDist, g.realValue()); } double C = regression.getIntercept(); regression.clear(); if (debug) { System.out.println("Upper Left pixel has coordinates " + C + ", " + F); } // convert to meters C *= unitsToMeters; F *= unitsToMeters; // C,F store the projected (in map units) coordinates of the upper left pixel. // originNorthing,originEasting is the offset we need to apply to 0,0 to push the offsets into our global coordinate system C = originEasting + C; F = originNorthing + F; // calculate the affine transformation matrix elements double D = -1 * x * unitsToMeters * Math.sin(theta); double A = x * unitsToMeters * Math.cos(theta); double B = y * unitsToMeters * Math.sin(phi); // if should be negative, it'll formed by negative sin double E = -1 * y * unitsToMeters * Math.cos(phi); /* * Line 1: A: pixel size in the x-direction in map units/pixel * Line 2: D: rotation about y-axis * Line 3: B: rotation about x-axis * Line 4: E: pixel size in the y-direction in map units, almost always negative[3] * Line 5: C: x-coordinate of the center of the upper left pixel * Line 6: F: y-coordinate of the center of the upper left pixel */ if (debug) { System.out.println("A = " + A); System.out.println("D = " + D); System.out.println("B = " + B); System.out.println("E = " + E); System.out.println("C = " + C); System.out.println("F = " + F); // write the world file System.out.println(); System.out.println("World File:"); System.out.println(A); System.out.println(D); System.out.println(B); System.out.println(E); System.out.println(C); System.out.println(F); } // write to the .wld file wldWriter.write(A + "\n"); wldWriter.write(D + "\n"); wldWriter.write(B + "\n"); wldWriter.write(E + "\n"); wldWriter.write(C + "\n"); wldWriter.write(F + "\n"); wldWriter.close(); }
From source file:com.act.lcms.v2.MZCollisionCounter.java
public static void main(String[] args) throws Exception { CLIUtil cliUtil = new CLIUtil(MassChargeCalculator.class, HELP_MESSAGE, OPTION_BUILDERS); CommandLine cl = cliUtil.parseCommandLine(args); File inputFile = new File(cl.getOptionValue(OPTION_INPUT_INCHI_LIST)); if (!inputFile.exists()) { cliUtil.failWithMessage("Input file at does not exist at %s", inputFile.getAbsolutePath()); }//from w w w .ja va 2s . c o m List<MassChargeCalculator.MZSource> sources = new ArrayList<>(); try (BufferedReader reader = new BufferedReader(new FileReader(inputFile))) { String line; while ((line = reader.readLine()) != null) { line = line.trim(); sources.add(new MassChargeCalculator.MZSource(line)); if (sources.size() % 1000 == 0) { LOGGER.info("Loaded %d sources from input file", sources.size()); } } } Set<String> considerIons = Collections.emptySet(); if (cl.hasOption(OPTION_ONLY_CONSIDER_IONS)) { List<String> ions = Arrays.asList(cl.getOptionValues(OPTION_ONLY_CONSIDER_IONS)); LOGGER.info("Only considering ions for m/z calculation: %s", StringUtils.join(ions, ", ")); considerIons = new HashSet<>(ions); } TSVWriter<String, Long> tsvWriter = new TSVWriter<>(Arrays.asList("collisions", "count")); tsvWriter.open(new File(cl.getOptionValue(OPTION_OUTPUT_FILE))); try { LOGGER.info("Loaded %d sources in total from input file", sources.size()); MassChargeCalculator.MassChargeMap mzMap = MassChargeCalculator.makeMassChargeMap(sources, considerIons); if (!cl.hasOption(OPTION_COUNT_WINDOW_INTERSECTIONS)) { // Do an exact analysis of the m/z collisions if windowing is not specified. LOGGER.info("Computing precise collision histogram."); Iterable<Double> mzs = mzMap.ionMZIter(); Map<Integer, Long> collisionHistogram = histogram( StreamSupport.stream(mzs.spliterator(), false).map(mz -> { // See comment about Iterable below. try { return mzMap.ionMZToMZSources(mz).size(); } catch (NoSuchElementException e) { LOGGER.error("Caught no such element exception for mz %f: %s", mz, e.getMessage()); throw e; } })); List<Integer> sortedCollisions = new ArrayList<>(collisionHistogram.keySet()); Collections.sort(sortedCollisions); for (Integer collision : sortedCollisions) { tsvWriter.append(new HashMap<String, Long>() { { put("collisions", collision.longValue()); put("count", collisionHistogram.get(collision)); } }); } } else { /* After some deliberation (thanks Gil!), the windowed variant of this calculation counts the number of * structures whose 0.01 Da m/z windows (for some set of ions) overlap with each other. * * For example, let's assume we have five total input structures, and are only searching for one ion. Let's * also assume that three of those structures have m/z A and the remaining two have m/z B. The windows might * look like this in the m/z domain: * |----A----| * |----B----| * Because A represents three structures and overlaps with B, which represents two, we assign A a count of 5-- * this is the number of structures we believe could fall into the range of A given our current peak calling * approach. Similarly, B is assigned a count of 5, as the possibility for collision/confusion is symmetric. * * Note that this is an over-approximation of collisions, as we could more precisely only consider intersections * when the exact m/z of B falls within the window around A and vice versa. However, because we have observed * cases where the MS sensor doesn't report structures at exactly the m/z we predict, we employ this weaker * definition of intersection to give a slightly pessimistic view of what confusions might be possible. */ // Compute windows for every m/z. We don't care about the original mz values since we just want the count. List<Double> mzs = mzMap.ionMZsSorted(); final Double windowHalfWidth; if (cl.hasOption(OPTION_WINDOW_HALFWIDTH)) { // Don't use get with default for this option, as we want the exact FP value of the default tolerance. windowHalfWidth = Double.valueOf(cl.getOptionValue(OPTION_WINDOW_HALFWIDTH)); } else { windowHalfWidth = DEFAULT_WINDOW_TOLERANCE; } /* Window = (lower bound, upper bound), counter of represented m/z's that collide with this window, and number * of representative structures (which will be used in counting collisions). */ LinkedList<CollisionWindow> allWindows = new LinkedList<CollisionWindow>() { { for (Double mz : mzs) { // CPU for memory trade-off: don't re-compute the window bounds over and over and over and over and over. try { add(new CollisionWindow(mz, windowHalfWidth, mzMap.ionMZToMZSources(mz).size())); } catch (NoSuchElementException e) { LOGGER.error("Caught no such element exception for mz %f: %s", mz, e.getMessage()); throw e; } } } }; // Sweep line time! The window ranges are the interesting points. We just accumulate overlap counts as we go. LinkedList<CollisionWindow> workingSet = new LinkedList<>(); List<CollisionWindow> finished = new LinkedList<>(); while (allWindows.size() > 0) { CollisionWindow thisWindow = allWindows.pop(); // Remove any windows from the working set that don't overlap with the next window. while (workingSet.size() > 0 && workingSet.peekFirst().getMaxMZ() < thisWindow.getMinMZ()) { finished.add(workingSet.pop()); } for (CollisionWindow w : workingSet) { /* Add the size of the new overlapping window's structure count to each of the windows in the working set, * which represents the number of possible confused structures that fall within the overlapping region. * We exclude the window itself as it should already have counted the colliding structures it represents. */ w.getAccumulator().add(thisWindow.getStructureCount()); /* Reciprocally, add the structure counts of all windows with which the current window overlaps to it. */ thisWindow.getAccumulator().add(w.getStructureCount()); } // Now that accumulation is complete, we can safely add the current window. workingSet.add(thisWindow); } // All the interesting events are done, so drop the remaining windows into the finished set. finished.addAll(workingSet); Map<Long, Long> collisionHistogram = histogram( finished.stream().map(w -> w.getAccumulator().longValue())); List<Long> sortedCollisions = new ArrayList<>(collisionHistogram.keySet()); Collections.sort(sortedCollisions); for (Long collision : sortedCollisions) { tsvWriter.append(new HashMap<String, Long>() { { put("collisions", collision); put("count", collisionHistogram.get(collision)); } }); } } } finally { if (tsvWriter != null) { tsvWriter.close(); } } }
From source file:de.citec.csra.elancsv.parser.SimpleParser.java
public static void main(String[] args) throws IOException, ParseException { Options opts = new Options(); opts.addOption("file", true, "Tab-separated ELAN export file to load."); opts.addOption("tier", true, "Tier to analyze. Optional: Append ::num to interpret annotations numerically."); opts.addOption("format", true, "How to read information from the file name. %V -> participant, %A -> annoatator, %C -> condition, e.g. \"%V - %A\""); opts.addOption("help", false, "Print this help and exit"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(opts, args); if (cmd.hasOption("help")) { helpExit(opts, "where OPTION includes:"); }/*w w w.ja v a2 s.c o m*/ String infile = cmd.getOptionValue("file"); if (infile == null) { helpExit(opts, "Error: no file given."); } String format = cmd.getOptionValue("format"); if (format == null) { helpExit(opts, "Error: no format given."); } String tier = cmd.getOptionValue("tier"); if (tier == null) { helpExit(opts, "Error: no tier given."); } // TODO count values in annotations (e.g. search all robot occurrences) String[] tn = tier.split("::"); boolean numeric = false; if (tn.length == 2 && tn[1].equals("num")) { numeric = true; tier = tn[0]; } format = "^" + format + "$"; format = format.replaceFirst("%V", "(?<V>.*?)"); format = format.replaceFirst("%A", "(?<A>.*?)"); format = format.replaceFirst("%C", "(?<C>.*?)"); Pattern pa = Pattern.compile(format); Map<String, Participant> participants = new HashMap<>(); BufferedReader br = new BufferedReader(new FileReader(infile)); String line; int lineno = 0; while ((line = br.readLine()) != null) { String[] parts = line.split("\t"); lineno++; if (parts.length < 5) { System.err.println("WARNING: line '" + lineno + "' too short '" + line + "'"); continue; } Annotation a = new Annotation(Long.valueOf(parts[ElanFormat.START.field]), Long.valueOf(parts[ElanFormat.STOP.field]), Long.valueOf(parts[ElanFormat.DURATION.field]), parts[ElanFormat.VALUE.field]); String tname = parts[ElanFormat.TIER.field]; String file = parts[ElanFormat.FILE.field].replaceAll(".eaf", ""); Matcher m = pa.matcher(file); String vp = file; String condition = "?"; String annotator = "?"; String participantID = vp; if (m.find()) { vp = m.group("V"); if (format.indexOf("<A>") > 0) { annotator = m.group("A"); } if (format.indexOf("<C>") > 0) { condition = m.group("C"); } } participantID = vp + ";" + annotator; if (!participants.containsKey(participantID)) { participants.put(participantID, new Participant(vp, condition, annotator)); } Participant p = participants.get(participantID); if (!p.tiers.containsKey(tname)) { p.tiers.put(tname, new Tier(tname)); } p.tiers.get(tname).annotations.add(a); } Map<String, Map<String, Number>> values = new HashMap<>(); Set<String> rownames = new HashSet<>(); String allCountKey = "c: all values"; String allDurationKey = "d: all values"; String allMeanKey = "m: all values"; for (Map.Entry<String, Participant> e : participants.entrySet()) { // System.out.println(e); Tier t = e.getValue().tiers.get(tier); String participantID = e.getKey(); if (!values.containsKey(participantID)) { values.put(participantID, new HashMap<String, Number>()); } Map<String, Number> row = values.get(participantID); //participant id if (t != null) { row.put(allCountKey, 0l); row.put(allDurationKey, 0l); row.put(allMeanKey, 0l); for (Annotation a : t.annotations) { long countAll = (long) row.get(allCountKey) + 1; long durationAll = (long) row.get(allDurationKey) + a.duration; long meanAll = durationAll / countAll; row.put(allCountKey, countAll); row.put(allDurationKey, durationAll); row.put(allMeanKey, meanAll); if (!numeric) { String countKey = "c: " + a.value; String durationKey = "d: " + a.value; String meanKey = "m: " + a.value; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(durationKey)) { row.put(durationKey, 0l); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } long count = (long) row.get(countKey) + 1; long duration = (long) row.get(durationKey) + a.duration; double mean = duration * 1.0 / count; row.put(countKey, count); row.put(durationKey, duration); row.put(meanKey, mean); rownames.add(countKey); rownames.add(durationKey); rownames.add(meanKey); } else { String countKey = "c: " + t.name; String sumKey = "s: " + t.name; String meanKey = "m: " + t.name; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(sumKey)) { row.put(sumKey, 0d); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } double d = 0; try { d = Double.valueOf(a.value); } catch (NumberFormatException ex) { } long count = (long) row.get(countKey) + 1; double sum = (double) row.get(sumKey) + d; double mean = sum / count; row.put(countKey, count); row.put(sumKey, sum); row.put(meanKey, mean); rownames.add(countKey); rownames.add(sumKey); rownames.add(meanKey); } } } } ArrayList<String> list = new ArrayList(rownames); Collections.sort(list); StringBuilder header = new StringBuilder("ID;Annotator;"); header.append(allCountKey); header.append(";"); header.append(allDurationKey); header.append(";"); header.append(allMeanKey); header.append(";"); for (String l : list) { header.append(l); header.append(";"); } System.out.println(header); for (Map.Entry<String, Map<String, Number>> e : values.entrySet()) { StringBuilder row = new StringBuilder(e.getKey()); row.append(";"); if (e.getValue().containsKey(allCountKey)) { row.append(e.getValue().get(allCountKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allDurationKey)) { row.append(e.getValue().get(allDurationKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allMeanKey)) { row.append(e.getValue().get(allMeanKey)); } else { row.append("0"); } row.append(";"); for (String l : list) { if (e.getValue().containsKey(l)) { row.append(e.getValue().get(l)); } else { row.append("0"); } row.append(";"); } System.out.println(row); } }