List of usage examples for java.lang String length
public int length()
From source file:HLA.java
public static void main(String[] args) throws IOException { if (!isVersionOrHigher()) { System.err.println("JRE of 1.8+ is required to run Kourami. Exiting."); System.exit(1);/* ww w.ja v a2s . c o m*/ } CommandLineParser parser = new DefaultParser(); Options options = HLA.createOption(); Options helponlyOpts = HLA.createHelpOption(); String[] bams = null; CommandLine line = null; boolean exitRun = false; try { CommandLine helpcheck = new DefaultParser().parse(helponlyOpts, args, true); if (helpcheck.getOptions().length > 0) HLA.help(options); else { line = parser.parse(options, args); if (line.hasOption("h"))//help")) HLA.help(options); else { if (line.hasOption("a")) HLA.TYPEADDITIONAL = true; HLA.OUTPREFIX = line.getOptionValue("o");//outfilePrefix"); String tmploc = line.getOptionValue("d");//msaDirectory"); HLA.MSAFILELOC = tmploc; if (tmploc.endsWith(File.separator)) HLA.MSAFILELOC = tmploc.substring(0, tmploc.length() - 1); if (!new File(HLA.MSAFILELOC).exists() || !new File(HLA.MSAFILELOC).isDirectory()) { System.err.println("Given msaDirectory: " + HLA.MSAFILELOC + "\t does NOT exist or is NOT a directory."); exitRun = true; } else if (!new File(HLA.MSAFILELOC + File.separator + "hla_nom_g.txt").exists()) { System.err.println("hla_nom_g.txt NOT FOUND in " + HLA.MSAFILELOC); System.err .println("Please download hla_nom_g.txt from the same IMGT Release as msa files."); exitRun = true; } } bams = line.getArgs(); if (bams.length < 1 || (bams.length == 1 && bams[bams.length - 1].equals("DEBUG1228"))) throw new ParseException("At least 1 bam file is required. See Usage:"); else { if (bams.length > 1 && bams[bams.length - 1].equals("DEBUG1228")) { String[] tmpbams = new String[bams.length - 1]; for (int i = 0; i < bams.length - 1; i++) tmpbams[i] = bams[i]; bams = tmpbams; HLA.DEBUG = true; } for (String b : bams) if (!new File(b).exists()) { System.err .println("Input bam : " + b + " DOES NOT exist. Please check the bam exists."); exitRun = true; } } } if (exitRun) throw new ParseException("Exitting . . ."); } catch (ParseException e) { System.err.println(e.getMessage()); //System.err.println("Failed to parse command line args. Check usage."); HLA.help(options); } String[] list = { "A", "B", "C", "DQA1", "DQB1", "DRB1" }; String[] extList = { "A", "B", "C", "DQA1", "DQB1", "DRB1", "DOA", "DMA", "DMB", "DPA1", "DPB1", "DRA", "DRB3", "DRB5", "F", "G", "H", "J", "L" }; //,"DPA1", "DPB1", "DRA", "DRB4", "F", "G" , "H", "J" ,"K", "L", "V"}; //,"DPA1", "DPB1", "DRA", "DRB3", "DRB4", "F", "G" , "H", "J" ,"K", "L", "V"}; if (HLA.TYPEADDITIONAL) list = extList; File[] bamfiles = new File[bams.length]; for (int i = 0; i < bams.length; i++) bamfiles[i] = new File(bams[i]); //check if <HLA.OUTPREFIX>.result is writable //if not exit. BufferedWriter resultWriter = null; try { resultWriter = new BufferedWriter(new FileWriter(HLA.OUTPREFIX + ".result")); } catch (IOException ioe) { ioe.printStackTrace(); System.err.println("\n\n>>> CANNOT open output file: " + HLA.OUTPREFIX + ".result <<<\n\n"); HLA.help(options); } HLA.log = new LogHandler(); for (int i = 0; i < args.length; i++) HLA.log.append(" " + args[i]); HLA.log.appendln(); try { System.err.println("----------------REF GRAPH CONSTRUCTION--------------"); HLA.log.appendln("----------------REF GRAPH CONSTRUCTION--------------"); HLA hla = new HLA(list, HLA.MSAFILELOC + File.separator + "hla_nom_g.txt"); //1. bubble counting before loading reads. //System.err.println("----------------BUBBLE COUNTING: REF GRAPH--------------"); //HLA.log.appendln("----------------BUBBLE COUNTING: REF GRAPH--------------"); //hla.countStems(); System.err.println("---------------- READ LOADING --------------"); HLA.log.appendln("---------------- READ LOADING --------------"); hla.loadReads(bamfiles); System.err.println("---------------- GRAPH CLEANING --------------"); HLA.log.appendln("---------------- GRAPH CLEANING --------------"); hla.flattenInsertionNodes(list); hla.removeUnused(list); hla.removeStems(list); /*updating error prob*/ hla.updateErrorProb(); hla.log.flush(); StringBuffer resultBuffer = new StringBuffer(); HLA.DEBUG3 = HLA.DEBUG; hla.countBubblesAndMerge(list, resultBuffer); hla.writeResults(resultBuffer, resultWriter); } catch (Exception e) { e.printStackTrace(); HLA.log.outToFile(); System.exit(-1); } /*printingWeights*/ //hla.printWeights(); HLA.log.outToFile(); HLA.log.appendln("NEW_NODE_ADDED:\t" + HLA.NEW_NODE_ADDED); HLA.log.appendln("HOPPPING:\t" + HLA.HOPPING); HLA.log.appendln("INSERTION_NODE_ADDED:\t" + HLA.INSERTION_NODE_ADDED); HLA.log.appendln("INSERTION_WITH_NO_NEW_NODE:\t" + HLA.INSERTION_WITH_NO_NEW_NODE); HLA.log.appendln("INSERTION_COUNTS:\t" + HLA.INSERTION); }
From source file:com.github.fritaly.graphml4j.samples.GradleDependenciesWithGroupsAndBuffering.java
public static void main(String[] args) throws Exception { if (args.length != 1) { System.out.println(String.format("%s <output-file>", GradleDependenciesWithGroupsAndBuffering.class.getSimpleName())); System.exit(1);/*from w w w .j av a2s . co m*/ } final File file = new File(args[0]); System.out.println("Writing GraphML file to " + file.getAbsolutePath() + " ..."); FileWriter fileWriter = null; Reader reader = null; LineNumberReader lineReader = null; try { fileWriter = new FileWriter(file); final com.github.fritaly.graphml4j.datastructure.Graph graph = new Graph(); // The dependency graph has been generated by Gradle with the // command "gradle dependencies". The output of this command has // been saved to a text file which will be parsed to rebuild the // dependency graph reader = new InputStreamReader( GradleDependenciesWithGroupsAndBuffering.class.getResourceAsStream("gradle-dependencies.txt")); lineReader = new LineNumberReader(reader); String line = null; // Stack containing the nodes per depth inside the dependency graph // (the topmost dependency is the first one in the stack) final Stack<Node> parentNodes = new Stack<Node>(); while ((line = lineReader.readLine()) != null) { // Determine the depth of the current dependency inside the // graph. The depth can be inferred from the indentation used by // Gradle. Each level of depth adds 5 more characters of // indentation final int initialLength = line.length(); // Remove the strings used by Gradle to indent dependencies line = StringUtils.replace(line, "+--- ", ""); line = StringUtils.replace(line, "| ", ""); line = StringUtils.replace(line, "\\--- ", ""); line = StringUtils.replace(line, " ", ""); // The depth can easily be inferred now final int depth = (initialLength - line.length()) / 5; // Remove unnecessary node ids while (depth <= parentNodes.size()) { parentNodes.pop(); } final Artifact artifact = createArtifact(line); Node node = graph.getNodeByData(artifact); // Has this dependency already been added to the graph ? if (node == null) { // No, add the node node = graph.addNode(artifact); } parentNodes.push(node); if (parentNodes.size() > 1) { // Generate an edge between the current node and its parent graph.addEdge("Depends on", parentNodes.get(parentNodes.size() - 2), node); } } // Create the groups after creating the nodes & edges for (Node node : graph.getNodes()) { final Artifact artifact = (Artifact) node.getData(); final String groupId = artifact.group; Node groupNode = graph.getNodeByData(groupId); if (groupNode == null) { groupNode = graph.addNode(groupId); } // add the node to the group node.setParent(groupNode); } graph.toGraphML(fileWriter, new Renderer() { @Override public String getNodeLabel(Node node) { return node.isGroup() ? node.getData().toString() : ((Artifact) node.getData()).getLabel(); } @Override public boolean isGroupOpen(Node node) { return true; } @Override public NodeStyle getNodeStyle(Node node) { // Customize the rendering of nodes final NodeStyle nodeStyle = new NodeStyle(); nodeStyle.setWidth(250.0f); return nodeStyle; } @Override public GroupStyles getGroupStyles(Node node) { return new GroupStyles(); } @Override public EdgeStyle getEdgeStyle(Edge edge) { return new EdgeStyle(); } }); System.out.println("Done"); } finally { // Calling GraphMLWriter.close() is necessary to dispose the underlying resources fileWriter.close(); lineReader.close(); reader.close(); } }
From source file:org.eclipse.swt.snippets.Snippet205.java
public static void main(String[] args) { Display display = new Display(); final Shell shell = new Shell(display, SWT.SHELL_TRIM | SWT.DOUBLE_BUFFERED); shell.setText("Embedding objects in text"); final Image[] images = { new Image(display, 32, 32), new Image(display, 20, 40), new Image(display, 40, 20) }; int[] colors = { SWT.COLOR_BLUE, SWT.COLOR_MAGENTA, SWT.COLOR_GREEN }; for (int i = 0; i < images.length; i++) { GC gc = new GC(images[i]); gc.setBackground(display.getSystemColor(colors[i])); gc.fillRectangle(images[i].getBounds()); gc.dispose();// ww w. j a va 2s . c om } final Button button = new Button(shell, SWT.PUSH); button.setText("Button"); button.pack(); String text = "Here is some text with a blue image \uFFFC, a magenta image \uFFFC, a green image \uFFFC, and a button: \uFFFC."; final int[] imageOffsets = { 36, 55, 72 }; final TextLayout layout = new TextLayout(display); layout.setText(text); for (int i = 0; i < images.length; i++) { Rectangle bounds = images[i].getBounds(); TextStyle imageStyle = new TextStyle(null, null, null); imageStyle.metrics = new GlyphMetrics(bounds.height, 0, bounds.width); layout.setStyle(imageStyle, imageOffsets[i], imageOffsets[i]); } Rectangle bounds = button.getBounds(); TextStyle buttonStyle = new TextStyle(null, null, null); buttonStyle.metrics = new GlyphMetrics(bounds.height, 0, bounds.width); final int buttonOffset = text.length() - 2; layout.setStyle(buttonStyle, buttonOffset, buttonOffset); shell.addListener(SWT.Paint, event -> { GC gc = event.gc; Point margin = new Point(10, 10); layout.setWidth(shell.getClientArea().width - 2 * margin.x); layout.draw(event.gc, margin.x, margin.y); for (int i = 0; i < images.length; i++) { int offset = imageOffsets[i]; int lineIndex1 = layout.getLineIndex(offset); FontMetrics lineMetrics1 = layout.getLineMetrics(lineIndex1); Point point1 = layout.getLocation(offset, false); GlyphMetrics glyphMetrics1 = layout.getStyle(offset).metrics; gc.drawImage(images[i], point1.x + margin.x, point1.y + margin.y + lineMetrics1.getAscent() - glyphMetrics1.ascent); } int lineIndex2 = layout.getLineIndex(buttonOffset); FontMetrics lineMetrics2 = layout.getLineMetrics(lineIndex2); Point point2 = layout.getLocation(buttonOffset, false); GlyphMetrics glyphMetrics2 = layout.getStyle(buttonOffset).metrics; button.setLocation(point2.x + margin.x, point2.y + margin.y + lineMetrics2.getAscent() - glyphMetrics2.ascent); }); shell.open(); while (!shell.isDisposed()) { if (!display.readAndDispatch()) display.sleep(); } layout.dispose(); for (int i = 0; i < images.length; i++) { images[i].dispose(); } display.dispose(); }
From source file:TextLayoutImageControl.java
public static void main(String[] args) { Display display = new Display(); final Shell shell = new Shell(display, SWT.SHELL_TRIM | SWT.DOUBLE_BUFFERED); shell.setText("Embedding objects in text"); final Image[] images = { new Image(display, 32, 32), new Image(display, 20, 40), new Image(display, 40, 20) }; int[] colors = { SWT.COLOR_BLUE, SWT.COLOR_MAGENTA, SWT.COLOR_GREEN }; for (int i = 0; i < images.length; i++) { GC gc = new GC(images[i]); gc.setBackground(display.getSystemColor(colors[i])); gc.fillRectangle(images[i].getBounds()); gc.dispose();/*from w w w.ja v a2 s . c om*/ } final Button button = new Button(shell, SWT.PUSH); button.setText("Button"); button.pack(); String text = "Here is some text with a blue image \uFFFC, a magenta image \uFFFC, a green image \uFFFC, and a button: \uFFFC."; final int[] imageOffsets = { 36, 55, 72 }; final TextLayout layout = new TextLayout(display); layout.setText(text); for (int i = 0; i < images.length; i++) { Rectangle bounds = images[i].getBounds(); TextStyle imageStyle = new TextStyle(null, null, null); imageStyle.metrics = new GlyphMetrics(bounds.height, 0, bounds.width); layout.setStyle(imageStyle, imageOffsets[i], imageOffsets[i]); } Rectangle bounds = button.getBounds(); TextStyle buttonStyle = new TextStyle(null, null, null); buttonStyle.metrics = new GlyphMetrics(bounds.height, 0, bounds.width); final int buttonOffset = text.length() - 2; layout.setStyle(buttonStyle, buttonOffset, buttonOffset); shell.addListener(SWT.Paint, new Listener() { public void handleEvent(Event event) { GC gc = event.gc; Point margin = new Point(10, 10); layout.setWidth(shell.getClientArea().width - 2 * margin.x); layout.draw(event.gc, margin.x, margin.y); for (int i = 0; i < images.length; i++) { int offset = imageOffsets[i]; int lineIndex = layout.getLineIndex(offset); FontMetrics lineMetrics = layout.getLineMetrics(lineIndex); Point point = layout.getLocation(offset, false); GlyphMetrics glyphMetrics = layout.getStyle(offset).metrics; gc.drawImage(images[i], point.x + margin.x, point.y + margin.y + lineMetrics.getAscent() - glyphMetrics.ascent); } int lineIndex = layout.getLineIndex(buttonOffset); FontMetrics lineMetrics = layout.getLineMetrics(lineIndex); Point point = layout.getLocation(buttonOffset, false); GlyphMetrics glyphMetrics = layout.getStyle(buttonOffset).metrics; button.setLocation(point.x + margin.x, point.y + margin.y + lineMetrics.getAscent() - glyphMetrics.ascent); } }); shell.open(); while (!shell.isDisposed()) { if (!display.readAndDispatch()) display.sleep(); } layout.dispose(); for (int i = 0; i < images.length; i++) { images[i].dispose(); } display.dispose(); }
From source file:kilim.tools.Weaver.java
/** * <pre>//from w w w . j a v a 2 s. c o m * Usage: java kilim.tools.Weaver -d <output directory> {source classe, jar, directory ...} * </pre> * * If directory names or jar files are given, all classes in that container are processed. It is * perfectly fine to specify the same directory for source and output like this: * <pre> * java kilim.tools.Weaver -d ./classes ./classes * </pre> * Ensure that all classes to be woven are in the classpath. The output directory does not have to be * in the classpath during weaving. * * @see #weave(List) for run-time weaving. */ public static void main(String[] args) throws IOException { // System.out.println(System.getProperty("java.class.path")); Detector detector = Detector.DEFAULT; String currentName = null; for (String name : parseArgs(args)) { try { if (name.endsWith(".class")) { if (exclude(name)) continue; currentName = name; weaveFile(name, new BufferedInputStream(new FileInputStream(name)), detector); } else if (name.endsWith(".jar")) { for (FileLister.Entry fe : new FileLister(name)) { currentName = fe.getFileName(); if (currentName.endsWith(".class")) { currentName = currentName.substring(0, currentName.length() - 6).replace('/', '.'); if (exclude(currentName)) continue; weaveFile(currentName, fe.getInputStream(), detector); } } } else if (new File(name).isDirectory()) { for (FileLister.Entry fe : new FileLister(name)) { currentName = fe.getFileName(); if (currentName.endsWith(".class")) { if (exclude(currentName)) continue; weaveFile(currentName, fe.getInputStream(), detector); } } } else { weaveClass(name, detector); } } catch (KilimException ke) { log.error("Error weaving " + currentName + ". " + ke.getMessage()); // ke.printStackTrace(); System.exit(1); } catch (IOException ioe) { log.error("Unable to find/process '" + currentName + "'"); System.exit(1); } catch (Throwable t) { log.error("Error weaving " + currentName); t.printStackTrace(); System.exit(1); } } System.exit(err); }
From source file:Main.java
public static void main(String[] args) { String url = "jdbc:mySubprotocol:myDataSource"; Connection con;/*from ww w .ja v a 2s .com*/ Statement stmt; try { Class.forName("myDriver.ClassName"); } catch (java.lang.ClassNotFoundException e) { System.err.print("ClassNotFoundException: "); System.err.println(e.getMessage()); } try { con = DriverManager.getConnection(url, "myLogin", "myPassword"); stmt = con.createStatement(); Vector dataTypes = getDataTypes(con); String tableName; String columnName; String sqlType; String prompt = "Enter the new table name and hit Return: "; tableName = getInput(prompt); String createTableString = "create table " + tableName + " ("; String commaAndSpace = ", "; boolean firstTime = true; while (true) { System.out.println(""); prompt = "Enter a column name " + "(or nothing when finished) \nand hit Return: "; columnName = getInput(prompt); if (firstTime) { if (columnName.length() == 0) { System.out.print("Need at least one column;"); System.out.println(" please try again"); continue; } else { createTableString += columnName + " "; firstTime = false; } } else if (columnName.length() == 0) { break; } else { createTableString += commaAndSpace + columnName + " "; } String localTypeName = null; String paramString = ""; while (true) { System.out.println(""); System.out.println("LIST OF TYPES YOU MAY USE: "); boolean firstPrinted = true; int length = 0; for (int i = 0; i < dataTypes.size(); i++) { DataType dataType = (DataType) dataTypes.get(i); if (!dataType.needsToBeSet()) { if (!firstPrinted) System.out.print(commaAndSpace); else firstPrinted = false; System.out.print(dataType.getSQLType()); length += dataType.getSQLType().length(); if (length > 50) { System.out.println(""); length = 0; firstPrinted = true; } } } System.out.println(""); int index; prompt = "Enter a column type " + "from the list and hit Return: "; sqlType = getInput(prompt); for (index = 0; index < dataTypes.size(); index++) { DataType dataType = (DataType) dataTypes.get(index); if (dataType.getSQLType().equalsIgnoreCase(sqlType) && !dataType.needsToBeSet()) { break; } } localTypeName = null; paramString = ""; if (index < dataTypes.size()) { // there was a match String params; DataType dataType = (DataType) dataTypes.get(index); params = dataType.getParams(); localTypeName = dataType.getLocalType(); if (params != null) { prompt = "Enter " + params + ": "; paramString = "(" + getInput(prompt) + ")"; } break; } else { // use the name as given prompt = "Are you sure? " + "Enter 'y' or 'n' and hit Return: "; String check = getInput(prompt) + " "; check = check.toLowerCase().substring(0, 1); if (check.equals("n")) continue; else { localTypeName = sqlType; break; } } } createTableString += localTypeName + paramString; } createTableString += ")"; System.out.println(""); System.out.print("Your CREATE TABLE statement as "); System.out.println("sent to your DBMS: "); System.out.println(createTableString); System.out.println(""); stmt.executeUpdate(createTableString); stmt.close(); con.close(); } catch (SQLException ex) { System.err.println("SQLException: " + ex.getMessage()); } }
From source file:edu.uthscsa.ric.papaya.builder.Builder.java
public static void main(final String[] args) { final Builder builder = new Builder(); // process command line final CommandLine cli = builder.createCLI(args); builder.setUseSample(cli.hasOption(ARG_SAMPLE)); builder.setUseAtlas(cli.hasOption(ARG_ATLAS)); builder.setLocal(cli.hasOption(ARG_LOCAL)); builder.setPrintHelp(cli.hasOption(ARG_HELP)); builder.setUseImages(cli.hasOption(ARG_IMAGE)); builder.setSingleFile(cli.hasOption(ARG_SINGLE)); builder.setUseParamFile(cli.hasOption(ARG_PARAM_FILE)); builder.setUseTitle(cli.hasOption(ARG_TITLE)); // print help, if necessary if (builder.isPrintHelp()) { builder.printHelp();//from ww w . j ava 2s . co m return; } // find project root directory if (cli.hasOption(ARG_ROOT)) { try { builder.projectDir = (new File(cli.getOptionValue(ARG_ROOT))).getCanonicalFile(); } catch (final IOException ex) { System.err.println("Problem finding root directory. Reason: " + ex.getMessage()); } } if (builder.projectDir == null) { builder.projectDir = new File(System.getProperty("user.dir")); } // clean output dir final File outputDir = new File(builder.projectDir + "/" + OUTPUT_DIR); System.out.println("Cleaning output directory..."); try { builder.cleanOutputDir(outputDir); } catch (final IOException ex) { System.err.println("Problem cleaning build directory. Reason: " + ex.getMessage()); } if (builder.isLocal()) { System.out.println("Building for local usage..."); } // write JS final File compressedFileJs = new File(outputDir, OUTPUT_JS_FILENAME); // build properties try { final File buildFile = new File(builder.projectDir + "/" + BUILD_PROP_FILE); builder.readBuildProperties(buildFile); builder.buildNumber++; // increment build number builder.writeBuildProperties(compressedFileJs, true); builder.writeBuildProperties(buildFile, false); } catch (final IOException ex) { System.err.println("Problem handling build properties. Reason: " + ex.getMessage()); } String htmlParameters = null; if (builder.isUseParamFile()) { final String paramFileArg = cli.getOptionValue(ARG_PARAM_FILE); if (paramFileArg != null) { try { System.out.println("Including parameters..."); final String parameters = FileUtils.readFileToString(new File(paramFileArg), "UTF-8"); htmlParameters = "var params = " + parameters + ";"; } catch (final IOException ex) { System.err.println("Problem reading parameters file! " + ex.getMessage()); } } } String title = null; if (builder.isUseTitle()) { String str = cli.getOptionValue(ARG_TITLE); if (str != null) { str = str.trim(); str = str.replace("\"", ""); str = str.replace("'", ""); if (str.length() > 0) { title = str; System.out.println("Using title: " + title); } } } try { final JSONArray loadableImages = new JSONArray(); // sample image if (builder.isUseSample()) { System.out.println("Including sample image..."); final File sampleFile = new File(builder.projectDir + "/" + SAMPLE_IMAGE_NII_FILE); final String filename = Utilities .replaceNonAlphanumericCharacters(Utilities.removeNiftiExtensions(sampleFile.getName())); if (builder.isLocal()) { loadableImages.put(new JSONObject("{\"nicename\":\"Sample Image\",\"name\":\"" + filename + "\",\"encode\":\"" + filename + "\"}")); final String sampleEncoded = Utilities.encodeImageFile(sampleFile); FileUtils.writeStringToFile(compressedFileJs, "var " + filename + "= \"" + sampleEncoded + "\";\n", "UTF-8", true); } else { loadableImages.put(new JSONObject("{\"nicename\":\"Sample Image\",\"name\":\"" + filename + "\",\"url\":\"" + SAMPLE_IMAGE_NII_FILE + "\"}")); FileUtils.copyFile(sampleFile, new File(outputDir + "/" + SAMPLE_IMAGE_NII_FILE)); } } // atlas if (builder.isUseAtlas()) { Atlas atlas = null; try { String atlasArg = cli.getOptionValue(ARG_ATLAS); if (atlasArg == null) { atlasArg = (builder.projectDir + "/" + SAMPLE_DEFAULT_ATLAS_FILE); } final File atlasXmlFile = new File(atlasArg); System.out.println("Including atlas " + atlasXmlFile); atlas = new Atlas(atlasXmlFile); final File atlasJavaScriptFile = atlas.createAtlas(builder.isLocal()); System.out.println("Using atlas image file " + atlas.getImageFile()); if (builder.isLocal()) { loadableImages.put( new JSONObject("{\"nicename\":\"Atlas\",\"name\":\"" + atlas.getImageFileNewName() + "\",\"encode\":\"" + atlas.getImageFileNewName() + "\",\"hide\":true}")); } else { final File atlasImageFile = atlas.getImageFile(); final String atlasPath = "data/" + atlasImageFile.getName(); loadableImages.put(new JSONObject("{\"nicename\":\"Atlas\",\"name\":\"" + atlas.getImageFileNewName() + "\",\"url\":\"" + atlasPath + "\",\"hide\":true}")); FileUtils.copyFile(atlasImageFile, new File(outputDir + "/" + atlasPath)); } builder.writeFile(atlasJavaScriptFile, compressedFileJs); } catch (final IOException ex) { System.err.println("Problem finding atlas file. Reason: " + ex.getMessage()); } } // additional images if (builder.isUseImages()) { final String[] imageArgs = cli.getOptionValues(ARG_IMAGE); if (imageArgs != null) { for (final String imageArg : imageArgs) { final File file = new File(imageArg); System.out.println("Including image " + file); final String filename = Utilities .replaceNonAlphanumericCharacters(Utilities.removeNiftiExtensions(file.getName())); if (builder.isLocal()) { loadableImages.put(new JSONObject( "{\"nicename\":\"" + Utilities.removeNiftiExtensions(file.getName()) + "\",\"name\":\"" + filename + "\",\"encode\":\"" + filename + "\"}")); final String sampleEncoded = Utilities.encodeImageFile(file); FileUtils.writeStringToFile(compressedFileJs, "var " + filename + "= \"" + sampleEncoded + "\";\n", "UTF-8", true); } else { final String filePath = "data/" + file.getName(); loadableImages.put(new JSONObject( "{\"nicename\":\"" + Utilities.removeNiftiExtensions(file.getName()) + "\",\"name\":\"" + filename + "\",\"url\":\"" + filePath + "\"}")); FileUtils.copyFile(file, new File(outputDir + "/" + filePath)); } } } } File tempFileJs = null; try { tempFileJs = builder.createTempFile(); } catch (final IOException ex) { System.err.println("Problem creating temp write file. Reason: " + ex.getMessage()); } // write image refs FileUtils.writeStringToFile(tempFileJs, "var " + PAPAYA_LOADABLE_IMAGES + " = " + loadableImages.toString() + ";\n", "UTF-8", true); // compress JS tempFileJs = builder.concatenateFiles(JS_FILES, "js", tempFileJs); System.out.println("Compressing JavaScript... "); FileUtils.writeStringToFile(compressedFileJs, "\n", "UTF-8", true); builder.compressJavaScript(tempFileJs, compressedFileJs, new YuiCompressorOptions()); //tempFileJs.deleteOnExit(); } catch (final IOException ex) { System.err.println("Problem concatenating JavaScript. Reason: " + ex.getMessage()); } // compress CSS final File compressedFileCss = new File(outputDir, OUTPUT_CSS_FILENAME); try { final File concatFile = builder.concatenateFiles(CSS_FILES, "css", null); System.out.println("Compressing CSS... "); builder.compressCSS(concatFile, compressedFileCss, new YuiCompressorOptions()); concatFile.deleteOnExit(); } catch (final IOException ex) { System.err.println("Problem concatenating CSS. Reason: " + ex.getMessage()); } // write HTML try { System.out.println("Writing HTML... "); if (builder.singleFile) { builder.writeHtml(outputDir, compressedFileJs, compressedFileCss, htmlParameters, title); } else { builder.writeHtml(outputDir, htmlParameters, title); } } catch (final IOException ex) { System.err.println("Problem writing HTML. Reason: " + ex.getMessage()); } System.out.println("Done! Output files located at " + outputDir); }
From source file:com.genentech.chemistry.openEye.apps.SDFEStateCalculator.java
/** * @param args/*from www.j a va 2 s. com*/ */ public static void main(String... args) throws IOException { // create command line Options object Options options = new Options(); Option opt = new Option(OPT_INFILE, true, "input file oe-supported Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_ESTATE_COUNT, false, "Output the the counts (occurrence) for each E-state atom group." + " E-state counts will be output if no output option is specified"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_ESTATE_SUM, false, "Output the sum of the E-state indices for each E-state atom group" + " in addition to the output of the" + " E-state atom groups."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_ESTATE_SYMBOL, false, "Output the E-state atom group symbol"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_UNASSIGNED_ATOMS, false, "Output atoms in the given molecules that" + " could not be assigned to an E-state atom group"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_UNASSIGNED_COUNT, false, "Output the number of atoms in the given molecules that" + " could not be assigned to an E-state atom group"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_ESTATE_INDICE, false, "Output the E-state indice of all atoms in the given molecule" + " in one field."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_SMARTS, true, "Description of the group of interest. If specified, the" + " E-state indice of atoms matching the SMARTS are output" + " in separated fields."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_PRINT_DETAILS, false, "Output the details of the calculation to stderr"); opt.setRequired(false); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String inFile = cmd.getOptionValue(OPT_INFILE); String outFile = cmd.getOptionValue(OPT_OUTFILE); String smarts = cmd.getOptionValue(OPT_SMARTS); boolean outputESIndex = cmd.hasOption(OPT_ESTATE_INDICE); boolean outputESCount = cmd.hasOption(OPT_ESTATE_COUNT); boolean outputESSum = cmd.hasOption(OPT_ESTATE_SUM); boolean outputESSymbol = cmd.hasOption(OPT_ESTATE_SYMBOL); boolean outputUnkCount = cmd.hasOption(OPT_UNASSIGNED_COUNT); boolean outputUnkAtoms = cmd.hasOption(OPT_UNASSIGNED_ATOMS); boolean printDetails = cmd.hasOption(OPT_PRINT_DETAILS); SDFEStateCalculator calculator = new SDFEStateCalculator(outFile); if (!outputESCount && !outputESSum && !outputUnkCount && !outputESSymbol && !outputESIndex && (smarts == null || smarts.length() == 0)) outputESCount = true; try { calculator.prepare(outputESCount, outputESSum, outputESSymbol, outputUnkCount, outputUnkAtoms, outputESIndex, smarts, printDetails); calculator.run(inFile); } finally { calculator.close(); } }
From source file:com.cisco.dvbu.ps.deploytool.DeployManagerUtil.java
@SuppressWarnings("rawtypes") public static void main(String[] args) { if (logger.isDebugEnabled()) { logger.debug("Entering Main method"); }//from www .j a v a 2 s . c o m if (args == null || args.length <= 1) { throw new ValidationException("Invalid Arguments"); } initSpring(); logger.info("--------------------------------------------------------"); logger.info("------------------ DEPLOYMENT MANAGER ------------------"); logger.info("--------------------------------------------------------"); try { boolean validMethod = false; initAdapter(); DeployManager deployManager = getDeployManager(); Class deployManagerClass = deployManager.getClass(); Method[] methods = deployManagerClass.getMethods(); // Number of method arguments int numInputArgs = args.length - 1; for (int i = 0; i < methods.length; i++) { String method = methods[i].getName(); int numMethodArgs = methods[i].getParameterTypes().length; if (methods[i].getName().equals(args[0]) && numMethodArgs == numInputArgs) { validMethod = true; try { if (logger.isInfoEnabled()) { logger.info("Calling Action " + args[0]); } // Determine which parameter is the password parameter when invoking methods. // The list and parameter number are contained in DeployManager.methodList. int maskParamNum = CommonUtils.getMaskParamNum(args[0], numInputArgs, DeployManager.methodList); String[] methodArgs = new String[args.length - 1]; for (int j = 0; j < args.length; j++) { //Skip arg[0] - method name if (j > 0) { methodArgs[j - 1] = args[j]; String arg = ""; if (args[j] != null) { arg = args[j].trim(); } if (logger.isDebugEnabled()) { // This is a special case. If a method in the DeployManager.methodList is being invoked then it has the potential of // containing a password. If it does that password is blanked out on display with "********". if (maskParamNum != j) { logger.debug("arg[" + j + "]=" + arg); } else { if (arg.length() == 0) { logger.debug("arg[" + j + "]=" + arg); } else { logger.debug("arg[" + j + "]=********"); } } } } } // Invoke the action Object returnValue = methods[i].invoke(deployManager, (Object[]) methodArgs); if (logger.isDebugEnabled()) { logger.debug(" Result from invoking method " + args[0] + " " + returnValue); } } catch (IllegalArgumentException e) { logger.error("Error while invoking method " + args[0], e); throw new ValidationException(e.getMessage(), e); } catch (IllegalAccessException e) { logger.error("Error while invoking method " + args[0], e); throw new ValidationException(e.getMessage(), e); } catch (InvocationTargetException e) { logger.error("Error while invoking method " + args[0], e); throw new ValidationException(e.getMessage(), e); } catch (Throwable e) { throw new ValidationException(e.getMessage(), e); } } } if (!validMethod) { logger.error("Passed in method " + args[0] + " does not exist or does not match the number of required arguments."); throw new ValidationException("Passed in method " + args[0] + " does not exist or does not match the number of required arguments."); } } catch (CompositeException e) { logger.error("Error occured while executing ", e); throw e; } if (logger.isDebugEnabled()) { logger.debug("Leaving Main method"); } }
From source file:com.github.fritaly.graphml4j.samples.GradleDependencies.java
public static void main(String[] args) throws Exception { if (args.length != 1) { System.out.println(String.format("%s <output-file>", GradleDependencies.class.getSimpleName())); System.exit(1);/*w w w.j a v a 2 s. com*/ } final File file = new File(args[0]); System.out.println("Writing GraphML file to " + file.getAbsolutePath() + " ..."); FileWriter fileWriter = null; GraphMLWriter graphWriter = null; Reader reader = null; LineNumberReader lineReader = null; try { fileWriter = new FileWriter(file); graphWriter = new GraphMLWriter(fileWriter); // Customize the rendering of nodes final NodeStyle nodeStyle = graphWriter.getNodeStyle(); nodeStyle.setWidth(250.0f); graphWriter.setNodeStyle(nodeStyle); // The dependency graph has been generated by Gradle with the // command "gradle dependencies". The output of this command has // been saved to a text file which will be parsed to rebuild the // dependency graph reader = new InputStreamReader(GradleDependencies.class.getResourceAsStream("gradle-dependencies.txt")); lineReader = new LineNumberReader(reader); String line = null; // Stack containing the node identifiers per depth inside the // dependency graph (the topmost dependency is the first one in the // stack) final Stack<String> parentIds = new Stack<String>(); // Open the graph graphWriter.graph(); // Map storing the node identifiers per label final Map<String, String> nodeIdsByLabel = new TreeMap<String, String>(); while ((line = lineReader.readLine()) != null) { // Determine the depth of the current dependency inside the // graph. The depth can be inferred from the indentation used by // Gradle. Each level of depth adds 5 more characters of // indentation final int initialLength = line.length(); // Remove the strings used by Gradle to indent dependencies line = StringUtils.replace(line, "+--- ", ""); line = StringUtils.replace(line, "| ", ""); line = StringUtils.replace(line, "\\--- ", ""); line = StringUtils.replace(line, " ", ""); // The depth can easily be inferred now final int depth = (initialLength - line.length()) / 5; // Remove unnecessary node ids while (depth <= parentIds.size()) { parentIds.pop(); } // Compute a nice label from the dependency (group, artifact, // version) tuple final String label = computeLabel(line); // Has this dependency already been added to the graph ? if (!nodeIdsByLabel.containsKey(label)) { // No, add the node nodeIdsByLabel.put(label, graphWriter.node(label)); } final String nodeId = nodeIdsByLabel.get(label); parentIds.push(nodeId); if (parentIds.size() > 1) { // Generate an edge between the current node and its parent graphWriter.edge(parentIds.get(parentIds.size() - 2), nodeId); } } // Close the graph graphWriter.closeGraph(); System.out.println("Done"); } finally { // Calling GraphMLWriter.close() is necessary to dispose the underlying resources graphWriter.close(); fileWriter.close(); lineReader.close(); reader.close(); } }