List of usage examples for java.lang String endsWith
public boolean endsWith(String suffix)
From source file:com.ilopez.jasperemail.JasperEmail.java
public static void main(String[] args) throws Exception { JasperEmail runJasperReports = new JasperEmail(); // Set up command line parser Options options = new Options(); Option reports = OptionBuilder.withArgName("reportlist").hasArg() .withDescription("Comma separated list of JasperReport XML input files").create("reports"); options.addOption(reports);//from ww w. j a v a 2 s. c o m Option emailTo = OptionBuilder.withArgName("emailaddress").hasArg() .withDescription("Email address to send generated reports to").create("emailto"); options.addOption(emailTo); Option emailFrom = OptionBuilder.withArgName("emailaddress").hasArg() .withDescription("Sender email address").create("emailfrom"); options.addOption(emailFrom); Option emailSubjectLine = OptionBuilder.withArgName("emailsubject").hasArg() .withDescription("Subject line of email").create("emailsubject"); options.addOption(emailSubjectLine); Option smtpHostOption = OptionBuilder.withArgName("smtphost").hasArg() .withDescription("Address of email server").create("smtphost"); options.addOption(smtpHostOption); Option smtpUserOption = OptionBuilder.withArgName("smtpuser").hasArg() .withDescription("Username if email server requires authentication").create("smtpuser"); options.addOption(smtpUserOption); Option smtpPassOption = OptionBuilder.withArgName("smtppass").hasArg() .withDescription("Password if email server requires authentication").create("smtppass"); options.addOption(smtpPassOption); Option smtpAuthOption = OptionBuilder.withArgName("smtpauth").hasArg() .withDescription("Set SMTP Authentication").create("smtpauth"); options.addOption(smtpAuthOption); Option smtpPortOption = OptionBuilder.withArgName("smtpport").hasArg() .withDescription("Port for the SMTP server 25/468/587/2525/2526").create("smtpport"); options.addOption(smtpPortOption); Option smtpTypeOption = OptionBuilder.withArgName("smtptype").hasArg() .withDescription("Define SMTP Type, one of: " + Arrays.asList(OptionValues.SMTPType.values())) .create("smtptype"); options.addOption(smtpTypeOption); Option outputFolder = OptionBuilder.withArgName("foldername").hasArg() .withDescription( "Folder to write generated reports to, with trailing separator (slash or backslash)") .create("folder"); options.addOption(outputFolder); Option dbJDBCClass = OptionBuilder.withArgName("jdbcclass").hasArg() .withDescription("Provide the JDBC Database Class ").create("jdbcclass"); options.addOption(dbJDBCClass); Option dbJDBCURL = OptionBuilder.withArgName("jdbcurl").hasArg() .withDescription("Provide the JDBC Database URL").create("jdbcurl"); options.addOption(dbJDBCURL); Option dbUserOption = OptionBuilder.withArgName("username").hasArg() .withDescription("Username to connect to databasewith").create("dbuser"); options.addOption(dbUserOption); Option dbPassOption = OptionBuilder.withArgName("password").hasArg().withDescription("Database password") .create("dbpass"); options.addOption(dbPassOption); Option outputTypeOption = OptionBuilder.withArgName("outputtype").hasArg() .withDescription("Output type, one of: " + Arrays.asList(OutputType.values())).create("output"); options.addOption(outputTypeOption); Option outputFilenameOption = OptionBuilder.withArgName("outputfilename").hasArg() .withDescription("Output filename (excluding filetype suffix)").create("filename"); options.addOption(outputFilenameOption); Option paramsOption = OptionBuilder.withArgName("parameters").hasArg().withDescription( "Parameters, e.g. param1=boolean:true,param2=string:ABC,param3=double:134.2,param4=integer:85") .create("params"); options.addOption(paramsOption); // Parse command line CommandLineParser parser = new GnuParser(); CommandLine commandLine = parser.parse(options, args); String reportsDefinitionFileNamesCvs = commandLine.getOptionValue("reports"); if (reportsDefinitionFileNamesCvs == null) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar JasperEmail.jar", options); System.out.println(); System.out.println("See http://github.com/ilopez/JasperEmail for further documentation"); System.out.println(); throw new IllegalArgumentException("No reports specified"); } String outputPath = commandLine.getOptionValue("folder"); List<String> reportDefinitionFileNames = Arrays.asList(reportsDefinitionFileNamesCvs.split(",")); List<String> outputFileNames = new ArrayList<String>(); String jdbcClass = commandLine.getOptionValue("jdbcclass"); String jdbcURL = commandLine.getOptionValue("jdbcurl"); String databaseUsername = commandLine.getOptionValue("dbuser"); String databasePassword = commandLine.getOptionValue("dbpass"); OutputType outputType = OutputType.PDF; String outputTypeString = commandLine.getOptionValue("output"); if (outputTypeString != null) { outputType = OutputType.valueOf(outputTypeString.toUpperCase()); } String parametersString = commandLine.getOptionValue("params"); Map parameters = runJasperReports.prepareParameters(parametersString); String outputFilenameSpecified = commandLine.getOptionValue("filename"); if (outputFilenameSpecified == null) { outputFilenameSpecified = ""; } // SMTP PORT Integer smtpport = Integer.parseInt(commandLine.getOptionValue("smtpport")); Boolean smtpauth = Boolean.parseBoolean(commandLine.getOptionValue("smtpauth")); OptionValues.SMTPType smtptype; String smtptypestring = commandLine.getOptionValue("smtpenc"); if (smtptypestring != null) { smtptype = OptionValues.SMTPType.valueOf(smtptypestring.toUpperCase()); } else { smtptype = OptionValues.SMTPType.PLAIN; } // SMTP TLS // SMTP // Iterate over reports, generating output for each for (String reportsDefinitionFileName : reportDefinitionFileNames) { String outputFilename = null; if ((reportDefinitionFileNames.size() == 1) && (!outputFilenameSpecified.equals(""))) { outputFilename = outputFilenameSpecified; } else { outputFilename = outputFilenameSpecified + reportsDefinitionFileName.replaceAll("\\..*$", ""); outputFilename = outputFilename.replaceAll("^.*\\/", ""); outputFilename = outputFilename.replaceAll("^.*\\\\", ""); } outputFilename = outputFilename.replaceAll("\\W", "").toLowerCase() + "." + outputType.toString().toLowerCase(); if (outputPath != null) { if (!outputPath.endsWith("\\") && !outputPath.endsWith("/")) { outputPath += java.io.File.separator; } outputFilename = outputPath + outputFilename; } System.out.println("Going to generate report " + outputFilename); runJasperReports.generateReport(reportsDefinitionFileName, jdbcClass, jdbcURL, databaseUsername, databasePassword, jdbcURL, parameters); outputFileNames.add(outputFilename); } String emailRecipientList = commandLine.getOptionValue("emailto"); if (emailRecipientList != null) { Set<String> emailRecipients = new HashSet<String>(Arrays.asList(emailRecipientList.split(","))); String emailSender = commandLine.getOptionValue("emailfrom"); String emailSubject = commandLine.getOptionValue("emailsubject"); if (emailSubject == null) { emailSubject = "Report attached"; } String emailHost = commandLine.getOptionValue("smtphost"); if (emailHost == null) { emailHost = "localhost"; } String emailUser = commandLine.getOptionValue("smtpuser"); String emailPass = commandLine.getOptionValue("smtppass"); System.out.println("Emailing reports to " + emailRecipients); runJasperReports.emailReport(emailHost, emailUser, emailPass, emailRecipients, emailSender, emailSubject, outputFileNames, smtpauth, smtptype, smtpport); } else { System.out.println("Email not generated (no recipients specified)"); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_ExtLibSearch.java
/** * @param args the command line arguments *///from www. ja va 2 s . c o m public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire targeted re-extraction analysis using external library (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_ExtLibSearch.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_extlibsearch.log"); } catch (Exception e) { } Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; float ExtProbThreshold = 0.99f; float RTWindow_Ext = -1f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Ext": { RTWindow_Ext = Float.parseFloat(value); break; } case "ExternalLibDecoyTag": { ExternalLibDecoyTag = value; if (ExternalLibDecoyTag.endsWith("_")) { ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1); } break; } } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); } for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "...."); //If the serialization file for ID file existed if (DiaFile.ReadSerializedLCMSID()) { DiaFile.IDsummary.ReduceMemoryUsage(); DiaFile.IDsummary.FastaPath = tandemPara.FastaPath; FileList.add(DiaFile); } } } //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search Logger.getRootLogger().info("Targeted extraction using external library"); //Read exteranl library FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, FilenameUtils.getBaseName(ExternalLibPath)); if (ExlibManager == null) { ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath)); //Import traML file ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag); //Check if there are decoy spectra ExlibManager.CheckDecoys(); //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath); ExlibManager.WriteFragmentLibSerialization(WorkFolder); } Logger.getRootLogger() .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size()); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } //Generate RT mapping RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter()); RTmap.GenerateModel(); RTmap.GenerateMappedPepIon(); diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.GenerateMassCalibrationRTMap(); //Perform targeted re-extraction diafile.TargetedExtractionQuant(false, ExlibManager, ExtProbThreshold, RTWindow_Ext); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); //Remove target IDs below the defined probability threshold diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold); diafile.ExportID(); diafile.ClearStructure(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); }
From source file:com.github.wshackle.java4cpp.J4CppMain.java
public static void main(String[] args) throws IOException, ClassNotFoundException { main_completed = false;//w ww. j a va 2 s. co m Options options = new Options(); options.addOption(Option.builder("?").desc("Print this message").longOpt("help").build()); options.addOption(Option.builder("n").hasArg().desc("C++ namespace for newly generated classes.") .longOpt("namespace").build()); options.addOption( Option.builder("c").hasArgs().desc("Single Java class to extract.").longOpt("classes").build()); options.addOption( Option.builder("p").hasArgs().desc("Java Package prefix to extract").longOpt("packages").build()); options.addOption(Option.builder("o").hasArg().desc("Output C++ source file.").longOpt("output").build()); options.addOption(Option.builder("j").hasArg().desc("Input jar file").longOpt("jar").build()); options.addOption(Option.builder("h").hasArg().desc("Output C++ header file.").longOpt("header").build()); options.addOption(Option.builder("l").hasArg() .desc("Maximum limit on classes to extract from jars.[default=200]").longOpt("limit").build()); options.addOption(Option.builder("v").desc("enable verbose output").longOpt("verbose").build()); options.addOption(Option.builder().hasArg().desc("Classes per output file.[default=10]") .longOpt(CLASSESPEROUTPUT).build()); options.addOption(Option.builder().hasArgs().desc( "Comma seperated list of nativeclass=javaclass native where nativeclass will be generated as an extension/implementation of the java class.") .longOpt("natives").build()); options.addOption(Option.builder().hasArg() .desc("library name for System.loadLibrary(...) for native extension classes") .longOpt("loadlibname").build()); String output = null; String header = null; String jar = null; Set<String> classnamesToFind = null; Set<String> packageprefixes = null; String loadlibname = null; Map<String, String> nativesNameMap = null; Map<String, Class> nativesClassMap = null; int limit = DEFAULT_LIMIT; int classes_per_file = 10; List<Class> classes = new ArrayList<>(); String limitstring = Integer.toString(limit); try { // parse the command line arguments System.out.println("args = " + Arrays.toString(args)); CommandLine line = new DefaultParser().parse(options, args); loadlibname = line.getOptionValue("loadlibname"); verbose = line.hasOption("verbose"); if (line.hasOption(CLASSESPEROUTPUT)) { String cpoStr = line.getOptionValue(CLASSESPEROUTPUT); try { int cpoI = Integer.valueOf(cpoStr); classes_per_file = cpoI; } catch (Exception e) { System.err.println("Option for " + CLASSESPEROUTPUT + "=\"" + cpoStr + "\""); printHelpAndExit(options, args); } } if (line.hasOption("natives")) { String natives[] = line.getOptionValues("natives"); if (verbose) { System.out.println("natives = " + Arrays.toString(natives)); } nativesNameMap = new HashMap<>(); nativesClassMap = new HashMap<>(); for (int i = 0; i < natives.length; i++) { int eq_index = natives[i].indexOf('='); String nativeClassName = natives[i].substring(0, eq_index).trim(); String javaClassName = natives[i].substring(eq_index + 1).trim(); Class javaClass = null; try { javaClass = Class.forName(javaClassName); } catch (ClassNotFoundException e) { //e.printStackTrace(); System.err.println("Class for " + javaClassName + " not found. (It may be found later in jar if specified.)"); } nativesNameMap.put(javaClassName, nativeClassName); if (javaClass != null) { nativesClassMap.put(nativeClassName, javaClass); if (!classes.contains(javaClass)) { classes.add(javaClass); } } } } // // validate that block-size has been set // if (line.hasOption("block-size")) { // // print the value of block-size // if(verbose) System.out.println(line.getOptionValue("block-size")); // } jar = line.getOptionValue("jar", jar); if (verbose) { System.out.println("jar = " + jar); } if (null != jar) { if (jar.startsWith("~/")) { jar = new File(new File(getHomeDir()), jar.substring(2)).getCanonicalPath(); } if (jar.startsWith("./")) { jar = new File(new File(getCurrentDir()), jar.substring(2)).getCanonicalPath(); } if (jar.startsWith("../")) { jar = new File(new File(getCurrentDir()).getParentFile(), jar.substring(3)).getCanonicalPath(); } } if (line.hasOption("classes")) { classnamesToFind = new HashSet<String>(); String classStrings[] = line.getOptionValues("classes"); if (verbose) { System.out.println("classStrings = " + Arrays.toString(classStrings)); } classnamesToFind.addAll(Arrays.asList(classStrings)); if (verbose) { System.out.println("classnamesToFind = " + classnamesToFind); } } // if (!line.hasOption("namespace")) { // if (classname != null && classname.length() > 0) { // namespace = classname.toLowerCase().replace(".", "_"); // } else if (jar != null && jar.length() > 0) { // int lastSep = jar.lastIndexOf(File.separator); // int start = Math.max(0, lastSep + 1); // int period = jar.indexOf('.', start + 1); // int end = Math.max(start + 1, period); // namespace = jar.substring(start, end).toLowerCase(); // namespace = namespace.replace(" ", "_"); // if (namespace.indexOf("-") > 0) { // namespace = namespace.substring(0, namespace.indexOf("-")); // } // } // } namespace = line.getOptionValue("namespace", namespace); if (verbose) { System.out.println("namespace = " + namespace); } if (null != namespace) { output = namespace + ".cpp"; } output = line.getOptionValue("output", output); if (verbose) { System.out.println("output = " + output); } if (null != output) { if (output.startsWith("~/")) { output = System.getProperty("user.home") + output.substring(1); } header = output.substring(0, output.lastIndexOf('.')) + ".h"; } else { output = "out.cpp"; } header = line.getOptionValue("header", header); if (verbose) { System.out.println("header = " + header); } if (null != header) { if (header.startsWith("~/")) { header = System.getProperty("user.home") + header.substring(1); } } else { header = "out.h"; } if (line.hasOption("packages")) { packageprefixes = new HashSet<String>(); packageprefixes.addAll(Arrays.asList(line.getOptionValues("packages"))); } if (line.hasOption("limit")) { limitstring = line.getOptionValue("limit", Integer.toString(DEFAULT_LIMIT)); limit = Integer.valueOf(limitstring); } if (line.hasOption("help")) { printHelpAndExit(options, args); } } catch (ParseException exp) { if (verbose) { System.out.println("Unexpected exception:" + exp.getMessage()); } printHelpAndExit(options, args); } Set<Class> excludedClasses = new HashSet<>(); Set<String> foundClassNames = new HashSet<>(); excludedClasses.add(Object.class); excludedClasses.add(String.class); excludedClasses.add(void.class); excludedClasses.add(Void.class); excludedClasses.add(Class.class); excludedClasses.add(Enum.class); Set<String> packagesSet = new TreeSet<>(); List<URL> urlsList = new ArrayList<>(); String cp = System.getProperty("java.class.path"); if (verbose) { System.out.println("System.getProperty(\"java.class.path\") = " + cp); } if (null != cp) { for (String cpe : cp.split(File.pathSeparator)) { if (verbose) { System.out.println("class path element = " + cpe); } File f = new File(cpe); if (f.isDirectory()) { urlsList.add(new URL("file:" + f.getCanonicalPath() + File.separator)); } else if (cpe.endsWith(".jar")) { urlsList.add(new URL("jar:file:" + f.getCanonicalPath() + "!/")); } } } cp = System.getenv("CLASSPATH"); if (verbose) { System.out.println("System.getenv(\"CLASSPATH\") = " + cp); } if (null != cp) { for (String cpe : cp.split(File.pathSeparator)) { if (verbose) { System.out.println("class path element = " + cpe); } File f = new File(cpe); if (f.isDirectory()) { urlsList.add(new URL("file:" + f.getCanonicalPath() + File.separator)); } else if (cpe.endsWith(".jar")) { urlsList.add(new URL("jar:file:" + f.getCanonicalPath() + "!/")); } } } if (verbose) { System.out.println("urlsList = " + urlsList); } if (null != jar && jar.length() > 0) { Path jarPath = FileSystems.getDefault().getPath(jar); ZipInputStream zip = new ZipInputStream(Files.newInputStream(jarPath, StandardOpenOption.READ)); URL jarUrl = new URL("jar:file:" + jarPath.toFile().getCanonicalPath() + "!/"); urlsList.add(jarUrl); URL[] urls = urlsList.toArray(new URL[urlsList.size()]); if (verbose) { System.out.println("urls = " + Arrays.toString(urls)); } URLClassLoader cl = URLClassLoader.newInstance(urls); for (ZipEntry entry = zip.getNextEntry(); entry != null; entry = zip.getNextEntry()) { // This ZipEntry represents a class. Now, what class does it represent? String entryName = entry.getName(); if (verbose) { System.out.println("entryName = " + entryName); } if (!entry.isDirectory() && entryName.endsWith(".class")) { if (entryName.indexOf('$') >= 0) { continue; } String classFileName = entry.getName().replace('/', '.'); String className = classFileName.substring(0, classFileName.length() - ".class".length()); if (classnamesToFind != null && classnamesToFind.size() > 0 && !classnamesToFind.contains(className)) { if (verbose) { System.out.println("skipping className=" + className + " because it does not found in=" + classnamesToFind); } continue; } try { Class clss = cl.loadClass(className); if (null != nativesClassMap && null != nativesNameMap && nativesNameMap.containsKey(className)) { nativesClassMap.put(nativesNameMap.get(className), clss); if (!classes.contains(clss)) { classes.add(clss); } } if (packageprefixes != null && packageprefixes.size() > 0) { if (null == clss.getPackage()) { continue; } final String pkgName = clss.getPackage().getName(); boolean matchFound = false; for (String prefix : packageprefixes) { if (pkgName.startsWith(prefix)) { matchFound = true; break; } } if (!matchFound) { continue; } } Package p = clss.getPackage(); if (null != p) { packagesSet.add(clss.getPackage().getName()); } if (!classes.contains(clss) && isAddableClass(clss, excludedClasses)) { if (null != classnamesToFind && classnamesToFind.contains(className) && !foundClassNames.contains(className)) { foundClassNames.add(className); if (verbose) { System.out.println("foundClassNames = " + foundClassNames); } } // if(verbose) System.out.println("clss = " + clss); classes.add(clss); // Class superClass = clss.getSuperclass(); // while (null != superClass // && !classes.contains(superClass) // && isAddableClass(superClass, excludedClasses)) { // classes.add(superClass); // superClass = superClass.getSuperclass(); // } } } catch (ClassNotFoundException | NoClassDefFoundError ex) { System.err.println( "Caught " + ex.getClass().getName() + ":" + ex.getMessage() + " for className=" + className + ", entryName=" + entryName + ", jarPath=" + jarPath); } } } } if (null != classnamesToFind) { if (verbose) { System.out.println("Checking classnames arguments"); } for (String classname : classnamesToFind) { if (verbose) { System.out.println("classname = " + classname); } if (foundClassNames.contains(classname)) { if (verbose) { System.out.println("foundClassNames.contains(" + classname + ")"); } continue; } try { if (classes.contains(Class.forName(classname))) { if (verbose) { System.out.println("Classes list already contains: " + classname); } continue; } } catch (Exception e) { } if (null != classname && classname.length() > 0) { urlsList.add(new URL("file://" + System.getProperty("user.dir") + "/")); URL[] urls = urlsList.toArray(new URL[urlsList.size()]); if (verbose) { System.out.println("urls = " + Arrays.toString(urls)); } URLClassLoader cl = URLClassLoader.newInstance(urls); Class c = null; try { c = cl.loadClass(classname); } catch (ClassNotFoundException e) { System.err.println("Class " + classname + " not found "); } if (verbose) { System.out.println("c = " + c); } if (null == c) { try { c = ClassLoader.getSystemClassLoader().loadClass(classname); } catch (ClassNotFoundException e) { if (verbose) { System.out.println("System ClassLoader failed to find " + classname); } } } if (null != c) { classes.add(c); } else { System.err.println("Class " + classname + " not found"); } } } if (verbose) { System.out.println("Finished checking classnames arguments"); } } if (classes == null || classes.size() < 1) { if (null == nativesClassMap || nativesClassMap.keySet().size() < 1) { System.err.println("No Classes specified or found."); System.exit(1); } } if (verbose) { System.out.println("Classes found = " + classes.size()); } if (classes.size() > limit) { System.err.println("limit=" + limit); System.err.println( "Too many classes please use -c or -p options to limit classes or -l to increase limit."); if (verbose) { System.out.println("packagesSet = " + packagesSet); } System.exit(1); } List<Class> newClasses = new ArrayList<Class>(); for (Class clss : classes) { Class superClass = clss.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && isAddableClass(superClass, excludedClasses)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } try { Field fa[] = clss.getDeclaredFields(); for (Field f : fa) { if (Modifier.isPublic(f.getModifiers())) { Class fClass = f.getType(); if (!classes.contains(fClass) && !newClasses.contains(fClass) && isAddableClass(fClass, excludedClasses)) { newClasses.add(fClass); } } } } catch (NoClassDefFoundError e) { e.printStackTrace(); } for (Method m : clss.getDeclaredMethods()) { if (m.isSynthetic()) { continue; } if (!Modifier.isPublic(m.getModifiers()) || Modifier.isAbstract(m.getModifiers())) { continue; } Class retType = m.getReturnType(); if (verbose) { System.out.println("Checking dependancies for Method = " + m); } if (!classes.contains(retType) && !newClasses.contains(retType) && isAddableClass(retType, excludedClasses)) { newClasses.add(retType); superClass = retType.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && isAddableClass(superClass, excludedClasses)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } } for (Class paramType : m.getParameterTypes()) { if (!classes.contains(paramType) && !newClasses.contains(paramType) && isAddableClass(paramType, excludedClasses)) { newClasses.add(paramType); superClass = paramType.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && !excludedClasses.contains(superClass)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } } } } } if (null != nativesClassMap) { for (Class clss : nativesClassMap.values()) { if (null != clss) { Class superClass = clss.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && !excludedClasses.contains(superClass)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } } } } if (verbose) { System.out.println("Dependency classes needed = " + newClasses.size()); } classes.addAll(newClasses); List<Class> newOrderClasses = new ArrayList<>(); for (Class clss : classes) { if (newOrderClasses.contains(clss)) { continue; } Class superClass = clss.getSuperclass(); Stack<Class> stack = new Stack<>(); while (null != superClass && !newOrderClasses.contains(superClass) && !superClass.equals(java.lang.Object.class)) { stack.push(superClass); superClass = superClass.getSuperclass(); } while (!stack.empty()) { newOrderClasses.add(stack.pop()); } newOrderClasses.add(clss); } classes = newOrderClasses; if (verbose) { System.out.println("Total number of classes = " + classes.size()); System.out.println("classes = " + classes); } String forward_header = header.substring(0, header.lastIndexOf('.')) + "_fwd.h"; Map<String, String> map = new HashMap<>(); map.put(JAR, jar != null ? jar : ""); map.put("%CLASSPATH_PREFIX%", getCurrentDir() + ((jar != null) ? (File.pathSeparator + ((new File(jar).getCanonicalPath()).replace("\\", "\\\\"))) : "")); map.put("%FORWARD_HEADER%", forward_header); map.put("%HEADER%", header); map.put("%PATH_SEPERATOR%", File.pathSeparator); String tabs = ""; String headerDefine = forward_header.substring(Math.max(0, forward_header.indexOf(File.separator))) .replace(".", "_"); map.put(HEADER_DEFINE, headerDefine); map.put(NAMESPACE, namespace); if (null != nativesClassMap) { for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); try (PrintWriter pw = new PrintWriter(new FileWriter(nativeClassName + ".java"))) { if (javaClass.isInterface()) { pw.println("public class " + nativeClassName + " implements " + javaClass.getCanonicalName() + ", AutoCloseable{"); } else { pw.println("public class " + nativeClassName + " extends " + javaClass.getCanonicalName() + " implements AutoCloseable{"); } if (null != loadlibname && loadlibname.length() > 0) { pw.println(TAB_STRING + "static {"); pw.println(TAB_STRING + TAB_STRING + "System.loadLibrary(\"" + loadlibname + "\");"); pw.println(TAB_STRING + "}"); pw.println(); } pw.println(TAB_STRING + "public " + nativeClassName + "() {"); pw.println(TAB_STRING + "}"); pw.println(); pw.println(TAB_STRING + "private long nativeAddress=0;"); pw.println(TAB_STRING + "private boolean nativeDeleteOnClose=false;"); pw.println(); pw.println(TAB_STRING + "protected " + nativeClassName + "(final long nativeAddress) {"); pw.println(TAB_STRING + TAB_STRING + "this.nativeAddress = nativeAddress;"); pw.println(TAB_STRING + "}"); pw.println(TAB_STRING + "private native void nativeDelete();"); pw.println(); pw.println(TAB_STRING + "@Override"); pw.println(TAB_STRING + "public synchronized void close() {"); // pw.println(TAB_STRING + TAB_STRING + "if(nativeAddress != 0 && nativeDeleteOnClose) {"); pw.println(TAB_STRING + TAB_STRING + "nativeDelete();"); // pw.println(TAB_STRING + TAB_STRING + "}"); // pw.println(TAB_STRING + TAB_STRING + "nativeAddress=0;"); // pw.println(TAB_STRING + TAB_STRING + "nativeDeleteOnClose=false;"); pw.println(TAB_STRING + "}"); pw.println(); pw.println(TAB_STRING + "protected void finalizer() {"); pw.println(TAB_STRING + TAB_STRING + "close();"); pw.println(TAB_STRING + "}"); pw.println(); Method ma[] = javaClass.getDeclaredMethods(); for (Method m : ma) { int modifiers = m.getModifiers(); if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !m.isDefault() && !m.isSynthetic()) { pw.println(); pw.println(TAB_STRING + "@Override"); String params = ""; for (int i = 0; i < m.getParameterTypes().length; i++) { params += m.getParameterTypes()[i].getCanonicalName() + " param" + i; if (i < m.getParameterTypes().length - 1) { params += ","; } } pw.println(TAB_STRING + "native public " + m.getReturnType().getCanonicalName() + " " + m.getName() + "(" + params + ");"); // + IntStream.range(0, m.getParameterTypes().length) // .mapToObj(i -> m.getParameterTypes()[i].getCanonicalName() + " param" + i) // .collect(Collectors.joining(",")) + ");"); } } pw.println("}"); } } } try (PrintWriter pw = new PrintWriter(new FileWriter(forward_header))) { tabs = ""; processTemplate(pw, map, "header_fwd_template_start.h", tabs); Class lastClass = null; for (int class_index = 0; class_index < classes.size(); class_index++) { Class clss = classes.get(class_index); String clssOnlyName = getCppClassName(clss); tabs = openClassNamespace(clss, pw, tabs, lastClass); tabs += TAB_STRING; pw.println(tabs + "class " + clssOnlyName + ";"); tabs = tabs.substring(0, tabs.length() - 1); Class nextClass = (class_index < (classes.size() - 1)) ? classes.get(class_index + 1) : null; tabs = closeClassNamespace(clss, pw, tabs, nextClass); lastClass = clss; } processTemplate(pw, map, "header_fwd_template_end.h", tabs); } headerDefine = header.substring(Math.max(0, header.indexOf(File.separator))).replace(".", "_"); map.put(HEADER_DEFINE, headerDefine); map.put(NAMESPACE, namespace); if (classes_per_file < 1) { classes_per_file = classes.size(); } final int num_class_segments = (classes.size() > 1) ? ((classes.size() + classes_per_file - 1) / classes_per_file) : 1; String fmt = "%d"; if (num_class_segments > 10) { fmt = "%02d"; } if (num_class_segments > 100) { fmt = "%03d"; } String header_file_base = header; if (header_file_base.endsWith(".h")) { header_file_base = header_file_base.substring(0, header_file_base.length() - 2); } else if (header_file_base.endsWith(".hh")) { header_file_base = header_file_base.substring(0, header_file_base.length() - 3); } else if (header_file_base.endsWith(".hpp")) { header_file_base = header_file_base.substring(0, header_file_base.length() - 4); } try (PrintWriter pw = new PrintWriter(new FileWriter(header))) { tabs = ""; processTemplate(pw, map, HEADER_TEMPLATE_STARTH, tabs); for (int segment_index = 0; segment_index < num_class_segments; segment_index++) { String header_segment_file = header_file_base + String.format(fmt, segment_index) + ".h"; pw.println("#include \"" + header_segment_file + "\""); } if (null != nativesClassMap) { tabs = TAB_STRING; for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); pw.println(); pw.println(tabs + "class " + nativeClassName + "Context;"); pw.println(); map.put(CLASS_NAME, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); processTemplate(pw, map, HEADER_CLASS_STARTH, tabs); tabs += TAB_STRING; pw.println(tabs + nativeClassName + "Context *context;"); pw.println(tabs + nativeClassName + "();"); pw.println(tabs + "~" + nativeClassName + "();"); Method methods[] = javaClass.getDeclaredMethods(); for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { pw.println(tabs + getNativeMethodCppDeclaration(method, javaClass)); } } pw.println(tabs + "void initContext(" + nativeClassName + "Context *ctx,bool isref);"); pw.println(tabs + "void deleteContext();"); tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}; // end class " + nativeClassName); } } tabs = ""; processTemplate(pw, map, HEADER_TEMPLATE_ENDH, tabs); } for (int segment_index = 0; segment_index < num_class_segments; segment_index++) { String header_segment_file = header_file_base + String.format(fmt, segment_index) + ".h"; try (PrintWriter pw = new PrintWriter(new FileWriter(header_segment_file))) { tabs = ""; //processTemplate(pw, map, HEADER_TEMPLATE_STARTH, tabs); pw.println("// Never include this file (" + header_segment_file + ") directly. include " + header + " instead."); pw.println(); Class lastClass = null; final int start_segment_index = segment_index * classes_per_file; final int end_segment_index = Math.min(segment_index * classes_per_file + classes_per_file, classes.size()); List<Class> classesSegList = classes.subList(start_segment_index, end_segment_index); pw.println(); pw.println(tabs + "// start_segment_index = " + start_segment_index); pw.println(tabs + "// start_segment_index = " + end_segment_index); pw.println(tabs + "// segment_index = " + segment_index); pw.println(tabs + "// classesSegList=" + classesSegList); pw.println(); for (int class_index = 0; class_index < classesSegList.size(); class_index++) { Class clss = classesSegList.get(class_index); pw.println(); pw.println(tabs + "// class_index = " + class_index + " clss=" + clss); pw.println(); String clssName = clss.getCanonicalName(); tabs = openClassNamespace(clss, pw, tabs, lastClass); String clssOnlyName = getCppClassName(clss); map.put(CLASS_NAME, clssOnlyName); map.put("%BASE_CLASS_FULL_NAME%", classToCppBase(clss)); map.put(OBJECT_CLASS_FULL_NAME, getCppRelativeName(Object.class, clss)); tabs += TAB_STRING; processTemplate(pw, map, HEADER_CLASS_STARTH, tabs); tabs += TAB_STRING; Constructor constructors[] = clss.getDeclaredConstructors(); if (!hasNoArgConstructor(constructors)) { if (Modifier.isAbstract(clss.getModifiers()) || clss.isInterface()) { pw.println(tabs + "protected:"); pw.println(tabs + clssOnlyName + "() {};"); pw.println(tabs + "public:"); } else { if (constructors.length > 0) { pw.println(tabs + "protected:"); } pw.println(tabs + clssOnlyName + "();"); if (constructors.length > 0) { pw.println(tabs + "public:"); } } } for (Constructor c : constructors) { if (c.getParameterTypes().length == 0 && Modifier.isProtected(c.getModifiers())) { pw.println(tabs + "protected:"); pw.println(tabs + clssOnlyName + "();"); pw.println(tabs + "public:"); } if (checkConstructor(c, clss, classes)) { continue; } if (c.getParameterTypes().length == 1 && clss.isAssignableFrom(c.getParameterTypes()[0])) { continue; } if (!Modifier.isPublic(c.getModifiers())) { continue; } if (c.getParameterTypes().length == 1) { if (c.getParameterTypes()[0].getName().equals(clss.getName())) { // if(verbose) System.out.println("skipping constructor."); continue; } } if (!checkParameters(c.getParameterTypes(), classes)) { continue; } pw.println( tabs + clssOnlyName + getCppParamDeclarations(c.getParameterTypes(), clss) + ";"); if (isConstructorToMakeEasy(c, clss)) { pw.println(tabs + clssOnlyName + getEasyCallCppParamDeclarations(c.getParameterTypes(), clss) + ";"); } } pw.println(tabs + "~" + clssOnlyName + "();"); Field fa[] = clss.getDeclaredFields(); for (int findex = 0; findex < fa.length; findex++) { Field field = fa[findex]; if (addGetterMethod(field, clss, classes)) { pw.println(tabs + getCppFieldGetterDeclaration(field, clss)); } if (addSetterMethod(field, clss, classes)) { pw.println(tabs + getCppFieldSetterDeclaration(field, clss)); } } Method methods[] = clss.getDeclaredMethods(); for (int j = 0; j < methods.length; j++) { Method method = methods[j]; if (!checkMethod(method, classes)) { continue; } if ((method.getModifiers() & Modifier.PUBLIC) == Modifier.PUBLIC) { pw.println(tabs + getCppDeclaration(method, clss)); } if (isArrayStringMethod(method)) { pw.println(tabs + getCppModifiers(method.getModifiers()) + getCppType(method.getReturnType(), clss) + " " + fixMethodName(method) + "(int argc,const char **argv);"); } if (isMethodToMakeEasy(method)) { pw.println(tabs + getEasyCallCppDeclaration(method, clss)); } } tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}; // end class " + clssOnlyName); tabs = tabs.substring(0, tabs.length() - 1); Class nextClass = (class_index < (classesSegList.size() - 1)) ? classesSegList.get(class_index + 1) : null; tabs = closeClassNamespace(clss, pw, tabs, nextClass); pw.println(); lastClass = clss; } //processTemplate(pw, map, HEADER_TEMPLATE_ENDH, tabs); } } for (int segment_index = 0; segment_index < num_class_segments; segment_index++) { String output_segment_file = output; if (output_segment_file.endsWith(".cpp")) { output_segment_file = output_segment_file.substring(0, output_segment_file.length() - 4); } else if (output_segment_file.endsWith(".cc")) { output_segment_file = output_segment_file.substring(0, output_segment_file.length() - 3); } output_segment_file += "" + String.format(fmt, segment_index) + ".cpp"; try (PrintWriter pw = new PrintWriter(new FileWriter(output_segment_file))) { tabs = ""; if (segment_index < 1) { processTemplate(pw, map, "cpp_template_start_first.cpp", tabs); } else { processTemplate(pw, map, CPP_TEMPLATE_STARTCPP, tabs); } final int start_segment_index = segment_index * classes_per_file; final int end_segment_index = Math.min(segment_index * classes_per_file + classes_per_file, classes.size()); List<Class> classesSegList = classes.subList(start_segment_index, end_segment_index); pw.println(); pw.println(tabs + "// start_segment_index = " + start_segment_index); pw.println(tabs + "// start_segment_index = " + end_segment_index); pw.println(tabs + "// segment_index = " + segment_index); pw.println(tabs + "// classesSegList=" + classesSegList); pw.println(); Class lastClass = null; for (int class_index = 0; class_index < classesSegList.size(); class_index++) { Class clss = classesSegList.get(class_index); pw.println(); pw.println(tabs + "// class_index = " + class_index + " clss=" + clss); pw.println(); String clssName = clss.getCanonicalName(); tabs = openClassNamespace(clss, pw, tabs, lastClass); String clssOnlyName = getCppClassName(clss); map.put(CLASS_NAME, clssOnlyName); map.put("%BASE_CLASS_FULL_NAME%", classToCppBase(clss)); map.put(FULL_CLASS_NAME, clssName); String fcjs = classToJNISignature(clss); fcjs = fcjs.substring(1, fcjs.length() - 1); map.put(FULL_CLASS_JNI_SIGNATURE, fcjs); if (verbose) { System.out.println("fcjs = " + fcjs); } map.put(OBJECT_CLASS_FULL_NAME, getCppRelativeName(Object.class, clss)); map.put("%INITIALIZE_CONTEXT%", ""); map.put("%INITIALIZE_CONTEXT_REF%", ""); processTemplate(pw, map, CPP_START_CLASSCPP, tabs); Constructor constructors[] = clss.getDeclaredConstructors(); if (!hasNoArgConstructor(constructors)) { if (!Modifier.isAbstract(clss.getModifiers()) && !clss.isInterface()) { pw.println(tabs + clssOnlyName + "::" + clssOnlyName + "() : " + classToCppBase(clss) + "((jobject)NULL,false) {"); map.put(JNI_SIGNATURE, "()V"); map.put(CONSTRUCTOR_ARGS, ""); processTemplate(pw, map, CPP_NEWCPP, tabs); pw.println(tabs + "}"); pw.println(); } } for (Constructor c : constructors) { if (checkConstructor(c, clss, classes)) { continue; } Class[] paramClasses = c.getParameterTypes(); pw.println(tabs + clssOnlyName + "::" + clssOnlyName + getCppParamDeclarations(paramClasses, clss) + " : " + classToCppBase(clss) + "((jobject)NULL,false) {"); tabs = tabs + TAB_STRING; map.put(JNI_SIGNATURE, "(" + getJNIParamSignature(paramClasses) + ")V"); map.put(CONSTRUCTOR_ARGS, (paramClasses.length > 0 ? "," : "") + getCppParamNames(paramClasses)); processTemplate(pw, map, CPP_NEWCPP, tabs); tabs = tabs.substring(0, tabs.length() - 1); pw.println(tabs + "}"); pw.println(); if (isConstructorToMakeEasy(c, clss)) { pw.println(tabs + clssOnlyName + "::" + clssOnlyName + getEasyCallCppParamDeclarations(c.getParameterTypes(), clss) + " : " + classToCppBase(clss) + "((jobject)NULL,false) {"); processTemplate(pw, map, "cpp_start_easy_constructor.cpp", tabs); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jstring " + parmName + " = env->NewStringUTF(easyArg_" + paramIndex + ");"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + getCppArrayType(paramClasse.getComponentType()) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= env->New" + callString + "Array(easyArg_" + paramIndex + "_length);"); pw.println(tabs + "env->Set" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); } else { pw.println(tabs + getCppType(paramClasse, clss) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= easyArg_" + paramIndex + ";"); } } processTemplate(pw, map, "cpp_new_easy_internals.cpp", tabs); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + "env->Get" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else { } } processTemplate(pw, map, "cpp_end_easy_constructor.cpp", tabs); pw.println(tabs + "}"); } } pw.println(); pw.println(tabs + "// Destructor for " + clssName); pw.println(tabs + clssOnlyName + "::~" + clssOnlyName + "() {"); pw.println(tabs + "\t// Place-holder for later extensibility."); pw.println(tabs + "}"); pw.println(); Field fa[] = clss.getDeclaredFields(); for (int findex = 0; findex < fa.length; findex++) { Field field = fa[findex]; if (addGetterMethod(field, clss, classes)) { pw.println(); pw.println(tabs + "// Field getter for " + field.getName()); pw.println(getCppFieldGetterDefinitionStart(tabs, clssOnlyName, field, clss)); map.put("%FIELD_NAME%", field.getName()); map.put(JNI_SIGNATURE, classToJNISignature(field.getType())); Class returnClass = field.getType(); map.put(METHOD_ONFAIL, getOnFailString(returnClass, clss)); map.put(METHOD_ARGS, ""); map.put("%METHOD_RETURN%", isVoid(returnClass) ? "" : "return"); map.put("%METHOD_CALL_TYPE%", getMethodCallString(returnClass)); map.put("%METHOD_RETURN_TYPE%", getCppType(returnClass, clss)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, clss)); if (Modifier.isStatic(field.getModifiers())) { processTemplate(pw, map, "cpp_static_getfield.cpp", tabs); } else { processTemplate(pw, map, "cpp_getfield.cpp", tabs); } pw.println(tabs + "}"); } if (addSetterMethod(field, clss, classes)) { pw.println(); pw.println(tabs + "// Field setter for " + field.getName()); pw.println(getCppFieldSetterDefinitionStart(tabs, clssOnlyName, field, clss)); map.put("%FIELD_NAME%", field.getName()); map.put(JNI_SIGNATURE, classToJNISignature(field.getType())); Class returnClass = void.class; map.put(METHOD_ONFAIL, getOnFailString(returnClass, clss)); Class[] paramClasses = new Class[] { field.getType() }; String methodArgs = getCppParamNames(paramClasses); map.put(METHOD_ARGS, (paramClasses.length > 0 ? "," : "") + methodArgs); map.put("%METHOD_RETURN%", isVoid(returnClass) ? "" : "return"); map.put("%METHOD_CALL_TYPE%", getMethodCallString(field.getType())); map.put("%METHOD_RETURN_TYPE%", getCppType(returnClass, clss)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, clss)); if (Modifier.isStatic(field.getModifiers())) { processTemplate(pw, map, "cpp_static_setfield.cpp", tabs); } else { processTemplate(pw, map, "cpp_setfield.cpp", tabs); } pw.println(tabs + "}"); } } Method methods[] = clss.getDeclaredMethods(); for (int j = 0; j < methods.length; j++) { Method method = methods[j]; if (checkMethod(method, classes)) { pw.println(); pw.println(getCppMethodDefinitionStart(tabs, clssOnlyName, method, clss)); map.put(METHOD_NAME, method.getName()); if (fixMethodName(method).contains("equals2")) { if (verbose) { System.out.println("debug me"); } } map.put("%JAVA_METHOD_NAME%", method.getName()); Class[] paramClasses = method.getParameterTypes(); String methodArgs = getCppParamNames(paramClasses); map.put(METHOD_ARGS, (paramClasses.length > 0 ? "," : "") + methodArgs); Class returnClass = method.getReturnType(); map.put(JNI_SIGNATURE, "(" + getJNIParamSignature(paramClasses) + ")" + classToJNISignature(returnClass)); map.put(METHOD_ONFAIL, getOnFailString(returnClass, clss)); map.put("%METHOD_RETURN%", isVoid(returnClass) ? "" : "return"); map.put("%METHOD_CALL_TYPE%", getMethodCallString(returnClass)); map.put("%METHOD_RETURN_TYPE%", getCppType(returnClass, clss)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, clss)); tabs += TAB_STRING; if (!Modifier.isStatic(method.getModifiers())) { processTemplate(pw, map, CPP_METHODCPP, tabs); } else { processTemplate(pw, map, CPP_STATIC_METHODCPP, tabs); } tabs = tabs.substring(0, tabs.length() - TAB_STRING.length()); pw.println(tabs + "}"); if (isArrayStringMethod(method)) { map.put(METHOD_RETURN_STORE, isVoid(returnClass) ? "" : getCppType(returnClass, clss) + " returnVal="); map.put(METHOD_RETURN_GET, isVoid(returnClass) ? "return ;" : "return returnVal;"); processTemplate(pw, map, CPP_EASY_STRING_ARRAY_METHODCPP, tabs); } else if (isMethodToMakeEasy(method)) { pw.println(); pw.println(tabs + "// Easy call alternative for " + method.getName()); pw.println(getEasyCallCppMethodDefinitionStart(tabs, clssOnlyName, method, clss)); tabs += TAB_STRING; map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclareOut(returnClass, clss)); processTemplate(pw, map, "cpp_start_easy_method.cpp", tabs); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jstring " + parmName + " = env->NewStringUTF(easyArg_" + paramIndex + ");"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + getCppArrayType(paramClasse.getComponentType()) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= env->New" + callString + "Array(easyArg_" + paramIndex + "_length);"); pw.println(tabs + "env->Set" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); } else { pw.println(tabs + getCppType(paramClasse, clss) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= easyArg_" + paramIndex + ";"); } } String methodArgsIn = getCppParamNamesIn(paramClasses); String retStoreOut = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnOutVarType(returnClass, clss) + ") "; pw.println(tabs + retStoreOut + fixMethodName(method) + "(" + methodArgsIn + ");"); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + "env->Get" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else { } } processTemplate(pw, map, "cpp_end_easy_method.cpp", tabs); if (!isVoid(returnClass)) { pw.println(tabs + "return retVal;"); } tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}"); pw.println(); } } } processTemplate(pw, map, CPP_END_CLASSCPP, tabs); tabs = tabs.substring(0, tabs.length() - 1); Class nextClass = (class_index < (classesSegList.size() - 1)) ? classesSegList.get(class_index + 1) : null; tabs = closeClassNamespace(clss, pw, tabs, nextClass); lastClass = clss; } if (segment_index < 1) { if (null != nativesClassMap) { for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); map.put(CLASS_NAME, nativeClassName); map.put(FULL_CLASS_NAME, nativeClassName); map.put(FULL_CLASS_JNI_SIGNATURE, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); map.put("%INITIALIZE_CONTEXT%", "context=NULL; initContext(NULL,false);"); map.put("%INITIALIZE_CONTEXT_REF%", "context=NULL; initContext(objref.context,true);"); tabs += TAB_STRING; processTemplate(pw, map, CPP_START_CLASSCPP, tabs); pw.println(); pw.println(tabs + nativeClassName + "::" + nativeClassName + "() : " + getModifiedClassName(javaClass).replace(".", "::") + "((jobject)NULL,false) {"); tabs += TAB_STRING; pw.println(tabs + "context=NULL;"); pw.println(tabs + "initContext(NULL,false);"); map.put(JNI_SIGNATURE, "()V"); map.put(CONSTRUCTOR_ARGS, ""); processTemplate(pw, map, "cpp_new_native.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}"); pw.println(); pw.println(tabs + "// Destructor for " + nativeClassName); pw.println(tabs + nativeClassName + "::~" + nativeClassName + "() {"); pw.println(tabs + TAB_STRING + "if(NULL != context) {"); pw.println(tabs + TAB_STRING + TAB_STRING + "deleteContext();"); pw.println(tabs + TAB_STRING + "}"); pw.println(tabs + TAB_STRING + "context=NULL;"); pw.println(tabs + "}"); pw.println(); // pw.println(tabs + "public:"); // pw.println(tabs + nativeClassName + "();"); // pw.println(tabs + "~" + nativeClassName + "();"); tabs = tabs.substring(TAB_STRING.length()); // Method methods[] = javaClass.getDeclaredMethods(); // for (int j = 0; j < methods.length; j++) { // Method method = methods[j]; // int modifiers = method.getModifiers(); // if (!Modifier.isPublic(modifiers)) { // continue; // } // pw.println(tabs + getCppDeclaration(method, javaClass)); // } // pw.println(tabs + "}; // end class " + nativeClassName); processTemplate(pw, map, CPP_END_CLASSCPP, tabs); } } processTemplate(pw, map, "cpp_template_end_first.cpp", tabs); tabs = ""; if (null != nativesClassMap) { pw.println("using namespace " + namespace + ";"); pw.println("#ifdef __cplusplus"); pw.println("extern \"C\" {"); pw.println("#endif"); int max_method_count = 0; tabs = ""; for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); map.put(CLASS_NAME, nativeClassName); map.put(FULL_CLASS_NAME, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); map.put(FULL_CLASS_JNI_SIGNATURE, nativeClassName); map.put(METHOD_ONFAIL, "return;"); Method methods[] = javaClass.getDeclaredMethods(); if (max_method_count < methods.length) { max_method_count = methods.length; } for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { Class[] paramClasses = method.getParameterTypes(); String methodArgs = getCppParamNames(paramClasses); map.put(METHOD_ARGS, methodArgs); map.put(METHOD_NAME, method.getName()); Class returnClass = method.getReturnType(); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put(METHOD_ONFAIL, getOnFailString(returnClass, javaClass)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, javaClass)); pw.println(); String paramDecls = getCppParamDeclarations(paramClasses, javaClass); String argsToAdd = method.getParameterTypes().length > 0 ? "," + paramDecls.substring(1, paramDecls.length() - 1) : ""; pw.println("JNIEXPORT " + getCppType(returnClass, javaClass) + " JNICALL Java_" + nativeClassName + "_" + method.getName() + "(JNIEnv *env, jobject jthis" + argsToAdd + ") {"); tabs = TAB_STRING; processTemplate(pw, map, "cpp_native_wrap.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); pw.println("}"); pw.println(); } } pw.println("JNIEXPORT void JNICALL Java_" + nativeClassName + "_nativeDelete(JNIEnv *env, jobject jthis) {"); tabs += TAB_STRING; map.put(METHOD_ONFAIL, getOnFailString(void.class, javaClass)); processTemplate(pw, map, "cpp_native_delete.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}"); pw.println(); } pw.println("#ifdef __cplusplus"); pw.println("} // end extern \"C\""); pw.println("#endif"); map.put("%MAX_METHOD_COUNT%", Integer.toString(max_method_count + 1)); processTemplate(pw, map, "cpp_start_register_native.cpp", tabs); for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); map.put(CLASS_NAME, nativeClassName); map.put(FULL_CLASS_NAME, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); processTemplate(pw, map, "cpp_start_register_native_class.cpp", tabs); tabs += TAB_STRING; Method methods[] = javaClass.getDeclaredMethods(); int method_number = 0; for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { map.put("%METHOD_NUMBER%", Integer.toString(method_number)); map.put(METHOD_NAME, method.getName()); map.put(JNI_SIGNATURE, "(" + getJNIParamSignature(method.getParameterTypes()) + ")" + classToJNISignature(method.getReturnType())); processTemplate(pw, map, "cpp_register_native_item.cpp", tabs); method_number++; } } map.put("%METHOD_NUMBER%", Integer.toString(method_number)); map.put(METHOD_NAME, "nativeDelete"); map.put(JNI_SIGNATURE, "()V"); processTemplate(pw, map, "cpp_register_native_item.cpp", tabs); map.put("%NUM_NATIVE_METHODS%", Integer.toString(method_number)); processTemplate(pw, map, "cpp_end_register_native_class.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); } processTemplate(pw, map, "cpp_end_register_native.cpp", tabs); } else { pw.println("// No Native classes : registerNativMethods not needed."); pw.println("static void registerNativeMethods(JNIEnv *env) {}"); } } else { processTemplate(pw, map, CPP_TEMPLATE_ENDCPP, tabs); } } if (null != nativesClassMap) { tabs = ""; for (Entry<String, Class> e : nativesClassMap.entrySet()) { String nativeClassName = e.getKey(); File nativeClassHeaderFile = new File( namespace.toLowerCase() + "_" + nativeClassName.toLowerCase() + ".h"); map.put("%NATIVE_CLASS_HEADER%", nativeClassHeaderFile.getName()); map.put(CLASS_NAME, nativeClassName); if (nativeClassHeaderFile.exists()) { if (verbose) { System.out.println("skipping " + nativeClassHeaderFile.getCanonicalPath() + " since it already exists."); } } else { try (PrintWriter pw = new PrintWriter(new FileWriter(nativeClassHeaderFile))) { processTemplate(pw, map, "header_native_imp.h", tabs); } } File nativeClassCppFile = new File( namespace.toLowerCase() + "_" + nativeClassName.toLowerCase() + ".cpp"); if (nativeClassCppFile.exists()) { if (verbose) { System.out.println("skipping " + nativeClassCppFile.getCanonicalPath() + " since it already exists."); } } else { try (PrintWriter pw = new PrintWriter(new FileWriter(nativeClassCppFile))) { processTemplate(pw, map, "cpp_native_imp_start.cpp", tabs); Class javaClass = e.getValue(); Method methods[] = javaClass.getDeclaredMethods(); int method_number = 0; for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { Class[] paramClasses = method.getParameterTypes(); // String methodArgs = getCppParamNames(paramClasses); String paramDecls = getCppParamDeclarations(paramClasses, javaClass); String methodArgs = method.getParameterTypes().length > 0 ? paramDecls.substring(1, paramDecls.length() - 1) : ""; map.put(METHOD_ARGS, methodArgs); map.put(METHOD_NAME, method.getName()); Class returnClass = method.getReturnType(); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put(METHOD_ONFAIL, getOnFailString(returnClass, javaClass)); map.put("%RETURN_TYPE%", getCppType(returnClass, javaClass)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, javaClass)); processTemplate(pw, map, "cpp_native_imp_stub.cpp", tabs); } } processTemplate(pw, map, "cpp_native_imp_end.cpp", tabs); } } } } } main_completed = true; }
From source file:CTmousetrack.java
public static void main(String[] args) { String outLoc = new String("." + File.separator + "CTdata"); // Location of the base output data folder; only used when writing out CT data to a local folder String srcName = "CTmousetrack"; // name of the output CT source long blockPts = 10; // points per block flush long sampInterval = 10; // time between sampling updates, msec double trimTime = 0.0; // amount of data to keep (trim time), sec boolean debug = false; // turn on debug? // Specify the CT output connection CTWriteMode writeMode = CTWriteMode.LOCAL; // The selected mode for writing out CT data String serverHost = ""; // Server (FTP or HTTP/S) host:port String serverUser = ""; // Server (FTP or HTTPS) username String serverPassword = ""; // Server (FTP or HTTPS) password // For UDP output mode DatagramSocket udpServerSocket = null; InetAddress udpServerAddress = null; String udpHost = ""; int udpPort = -1; // Concatenate all of the CTWriteMode types String possibleWriteModes = ""; for (CTWriteMode wm : CTWriteMode.values()) { possibleWriteModes = possibleWriteModes + ", " + wm.name(); }//from w ww.ja v a 2 s.co m // Remove ", " from start of string possibleWriteModes = possibleWriteModes.substring(2); // // Argument processing using Apache Commons CLI // // 1. Setup command line options Options options = new Options(); options.addOption("h", "help", false, "Print this message."); options.addOption(Option.builder("o").argName("base output dir").hasArg().desc( "Base output directory when writing data to local folder (i.e., this is the location of CTdata folder); default = \"" + outLoc + "\".") .build()); options.addOption(Option.builder("s").argName("source name").hasArg() .desc("Name of source to write data to; default = \"" + srcName + "\".").build()); options.addOption(Option.builder("b").argName("points per block").hasArg() .desc("Number of points per block; UDP output mode will use 1 point/block; default = " + Long.toString(blockPts) + ".") .build()); options.addOption(Option.builder("dt").argName("samp interval msec").hasArg() .desc("Sampling period in msec; default = " + Long.toString(sampInterval) + ".").build()); options.addOption(Option.builder("t").argName("trim time sec").hasArg().desc( "Trim (ring-buffer loop) time (sec); this is only used when writing data to local folder; specify 0 for indefinite; default = " + Double.toString(trimTime) + ".") .build()); options.addOption( Option.builder("w").argName("write mode").hasArg() .desc("Type of write connection; one of " + possibleWriteModes + "; all but UDP mode write out to CT; default = " + writeMode.name() + ".") .build()); options.addOption(Option.builder("host").argName("host[:port]").hasArg() .desc("Host:port when writing via FTP, HTTP, HTTPS, UDP.").build()); options.addOption(Option.builder("u").argName("username,password").hasArg() .desc("Comma-delimited username and password when writing to CT via FTP or HTTPS.").build()); options.addOption("x", "debug", false, "Enable CloudTurbine debug output."); // 2. Parse command line options CommandLineParser parser = new DefaultParser(); CommandLine line = null; try { line = parser.parse(options, args); } catch (ParseException exp) { // oops, something went wrong System.err.println("Command line argument parsing failed: " + exp.getMessage()); return; } // 3. Retrieve the command line values if (line.hasOption("help")) { // Display help message and quit HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(120); formatter.printHelp("CTmousetrack", "", options, "NOTE: UDP output is a special non-CT output mode where single x,y points are sent via UDP to the specified host:port."); return; } outLoc = line.getOptionValue("o", outLoc); if (!outLoc.endsWith("\\") && !outLoc.endsWith("/")) { outLoc = outLoc + File.separator; } // Make sure the base output folder location ends in "CTdata" if (!outLoc.endsWith("CTdata\\") && !outLoc.endsWith("CTdata/")) { outLoc = outLoc + "CTdata" + File.separator; } srcName = line.getOptionValue("s", srcName); blockPts = Long.parseLong(line.getOptionValue("b", Long.toString(blockPts))); sampInterval = Long.parseLong(line.getOptionValue("dt", Long.toString(sampInterval))); trimTime = Double.parseDouble(line.getOptionValue("t", Double.toString(trimTime))); // Type of output connection String writeModeStr = line.getOptionValue("w", writeMode.name()); boolean bMatch = false; for (CTWriteMode wm : CTWriteMode.values()) { if (wm.name().toLowerCase().equals(writeModeStr.toLowerCase())) { writeMode = wm; bMatch = true; } } if (!bMatch) { System.err.println("Unrecognized write mode, \"" + writeModeStr + "\"; write mode must be one of " + possibleWriteModes); System.exit(0); } if (writeMode != CTWriteMode.LOCAL) { // User must have specified the host // If FTP or HTTPS, they may also specify username/password serverHost = line.getOptionValue("host", serverHost); if (serverHost.isEmpty()) { System.err.println( "When using write mode \"" + writeModeStr + "\", you must specify the server host."); System.exit(0); } if (writeMode == CTWriteMode.UDP) { // Force blockPts to be 1 blockPts = 1; // User must have specified both host and port int colonIdx = serverHost.indexOf(':'); if ((colonIdx == -1) || (colonIdx >= serverHost.length() - 1)) { System.err.println( "For UDP output mode, both the host and port (<host>:<port>)) must be specified."); System.exit(0); } udpHost = serverHost.substring(0, colonIdx); String udpPortStr = serverHost.substring(colonIdx + 1); try { udpPort = Integer.parseInt(udpPortStr); } catch (NumberFormatException nfe) { System.err.println("The UDP port must be a positive integer."); System.exit(0); } } if ((writeMode == CTWriteMode.FTP) || (writeMode == CTWriteMode.HTTPS)) { String userpassStr = line.getOptionValue("u", ""); if (!userpassStr.isEmpty()) { // This string should be comma-delimited username and password String[] userpassCSV = userpassStr.split(","); if (userpassCSV.length != 2) { System.err.println("When specifying a username and password for write mode \"" + writeModeStr + "\", separate the username and password by a comma."); System.exit(0); } serverUser = userpassCSV[0]; serverPassword = userpassCSV[1]; } } } debug = line.hasOption("debug"); System.err.println("CTmousetrack parameters:"); System.err.println("\toutput mode = " + writeMode.name()); if (writeMode == CTWriteMode.UDP) { System.err.println("\twrite to " + udpHost + ":" + udpPort); } else { System.err.println("\tsource = " + srcName); System.err.println("\ttrim time = " + trimTime + " sec"); } System.err.println("\tpoints per block = " + blockPts); System.err.println("\tsample interval = " + sampInterval + " msec"); try { // // Setup CTwriter or UDP output // CTwriter ctw = null; CTinfo.setDebug(debug); if (writeMode == CTWriteMode.LOCAL) { ctw = new CTwriter(outLoc + srcName, trimTime); System.err.println("\tdata will be written to local folder \"" + outLoc + "\""); } else if (writeMode == CTWriteMode.FTP) { CTftp ctftp = new CTftp(srcName); try { ctftp.login(serverHost, serverUser, serverPassword); } catch (Exception e) { throw new IOException( new String("Error logging into FTP server \"" + serverHost + "\":\n" + e.getMessage())); } ctw = ctftp; // upcast to CTWriter System.err.println("\tdata will be written to FTP server at " + serverHost); } else if (writeMode == CTWriteMode.HTTP) { // Don't send username/pw in HTTP mode since they will be unencrypted CThttp cthttp = new CThttp(srcName, "http://" + serverHost); ctw = cthttp; // upcast to CTWriter System.err.println("\tdata will be written to HTTP server at " + serverHost); } else if (writeMode == CTWriteMode.HTTPS) { CThttp cthttp = new CThttp(srcName, "https://" + serverHost); // Username/pw are optional for HTTPS mode; only use them if username is not empty if (!serverUser.isEmpty()) { try { cthttp.login(serverUser, serverPassword); } catch (Exception e) { throw new IOException(new String( "Error logging into HTTP server \"" + serverHost + "\":\n" + e.getMessage())); } } ctw = cthttp; // upcast to CTWriter System.err.println("\tdata will be written to HTTPS server at " + serverHost); } else if (writeMode == CTWriteMode.UDP) { try { udpServerSocket = new DatagramSocket(); } catch (SocketException se) { System.err.println("Error creating socket for UDP:\n" + se); System.exit(0); } try { udpServerAddress = InetAddress.getByName(udpHost); } catch (UnknownHostException uhe) { System.err.println("Error getting UDP server host address:\n" + uhe); System.exit(0); } } if (writeMode != CTWriteMode.UDP) { ctw.setBlockMode(blockPts > 1, blockPts > 1); ctw.autoFlush(0); // no autoflush ctw.autoSegment(1000); } // screen dims Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); double width = screenSize.getWidth(); double height = screenSize.getHeight(); // use Map for consolidated putData Map<String, Object> cmap = new LinkedHashMap<String, Object>(); // loop and write some output for (int i = 0; i < 1000000; i++) { // go until killed long currentTime = System.currentTimeMillis(); Point mousePos = MouseInfo.getPointerInfo().getLocation(); float x_pt = (float) (mousePos.getX() / width); // normalize float y_pt = (float) ((height - mousePos.getY()) / height); // flip Y (so bottom=0) if (writeMode != CTWriteMode.UDP) { // CT output mode ctw.setTime(currentTime); cmap.clear(); cmap.put("x", x_pt); cmap.put("y", y_pt); ctw.putData(cmap); if (((i + 1) % blockPts) == 0) { ctw.flush(); System.err.print("."); } } else { // UDP output mode // We force blockPts to be 1 for UDP output mode, i.e. we "flush" the data every time // Write the following data (21 bytes total): // header = "MOUSE", 5 bytes // current time, long, 8 bytes // 2 floats (x,y) 4 bytes each, 8 bytes int len = 21; ByteBuffer bb = ByteBuffer.allocate(len); String headerStr = "MOUSE"; bb.put(headerStr.getBytes("UTF-8")); bb.putLong(currentTime); bb.putFloat(x_pt); bb.putFloat(y_pt); // Might be able to use the following, but not sure: // byte[] sendData = bb.array(); byte[] sendData = new byte[len]; bb.position(0); bb.get(sendData, 0, len); DatagramPacket sendPacket = new DatagramPacket(sendData, sendData.length, udpServerAddress, udpPort); try { udpServerSocket.send(sendPacket); } catch (IOException e) { System.err.println("Test server caught exception trying to send data to UDP client:\n" + e); } System.err.print("."); } try { Thread.sleep(sampInterval); } catch (Exception e) { } ; } if (writeMode != CTWriteMode.UDP) { ctw.flush(); // wrap up } } catch (Exception e) { System.err.println("CTmousetrack exception: " + e); e.printStackTrace(); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_Quant.java
/** * @param args the command line arguments *//*from www .j a va2 s .com*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire quantitation with targeted re-extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire_quant.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_quant.log"); } catch (Exception e) { } try { Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String UserMod = ""; String Combined_Prot = ""; String InternalLibID = ""; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; boolean DefaultProtFiltering = true; boolean DataSetLevelPepFDR = false; float ProbThreshold = 0.99f; float ExtProbThreshold = 0.99f; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; float MinFragMz = 200f; String FilterWeight = "GW"; float MinWeight = 0.9f; float RTWindow_Int = -1f; float RTWindow_Ext = -1f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean InternalLibSearch = false; boolean ExternalLibSearch = false; boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "TargetedExtraction": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "InternalLibSearch": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "ExternalLibSearch": { ExternalLibSearch = Boolean.parseBoolean(value); break; } case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "UserMod": { UserMod = value; break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } case "DataSetLevelPepFDR": { DataSetLevelPepFDR = Boolean.parseBoolean(value); break; } case "InternalLibID": { InternalLibID = value; break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "RTWindow_Ext": { RTWindow_Ext = Float.parseFloat(value); break; } case "ExternalLibDecoyTag": { ExternalLibDecoyTag = value; if (ExternalLibDecoyTag.endsWith("_")) { ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1); } break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "ReSearchProb": { //ReSearchProb = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "MinFragMz": { MinFragMz = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); if (!UserMod.equals("")) { PTMManager.GetInstance().ImportUserMod(UserMod); } //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } } } LCMSID combinePepID = null; if (DataSetLevelPepFDR) { combinePepID = LCMSID.ReadLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); if (combinePepID == null) { FDR_DataSetLevel fdr = new FDR_DataSetLevel(); fdr.GeneratePepIonList(FileList, tandemPara, WorkFolder + "combinePepID.SerFS"); combinePepID = fdr.combineID; combinePepID.WriteLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); } } //process each DIA file for quantification based on untargeted identifications for (DIAPack DiaFile : FileList) { long time = System.currentTimeMillis(); Logger.getRootLogger().info("Loading identification results " + DiaFile.Filename + "...."); //If the LCMSID serialization is found if (!DiaFile.ReadSerializedLCMSID()) { DiaFile.ParsePepXML(tandemPara, combinePepID); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); } DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(DiaFile.Filename + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (InternalLibSearch && FileList.size() > 1) { Logger.getRootLogger().info("Module C: Targeted extraction using internal library"); FragmentLibManager libManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, InternalLibID); if (libManager == null) { Logger.getRootLogger().info("Building internal spectral library"); libManager = new FragmentLibManager(InternalLibID); ArrayList<LCMSID> LCMSIDList = new ArrayList<>(); for (DIAPack dia : FileList) { LCMSIDList.add(dia.IDsummary); } libManager.ImportFragLibTopFrag(LCMSIDList, Freq, TopNFrag); libManager.WriteFragmentLibSerialization(WorkFolder); } libManager.ReduceMemoryUsage(); Logger.getRootLogger() .info("Building retention time prediction model and generate candidate peptide list"); for (int i = 0; i < FileList.size(); i++) { FileList.get(i).IDsummary.ClearMappedPep(); } for (int i = 0; i < FileList.size(); i++) { for (int j = i + 1; j < FileList.size(); j++) { RTAlignedPepIonMapping alignment = new RTAlignedPepIonMapping(WorkFolder, FileList.get(i).GetParameter(), FileList.get(i).IDsummary, FileList.get(j).IDsummary); alignment.GenerateModel(); alignment.GenerateMappedPepIon(); } FileList.get(i).ExportID(); FileList.get(i).IDsummary = null; } Logger.getRootLogger().info("Targeted matching........"); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } if (!diafile.IDsummary.GetMappedPepIonList().isEmpty()) { diafile.UseMappedIon = true; diafile.FilterMappedIonByProb = false; diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); diafile.GenerateMassCalibrationRTMap(); diafile.TargetedExtractionQuant(false, libManager, 1.1f, RTWindow_Int); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); diafile.IDsummary.RemoveLowProbMappedIon(ProbThreshold); diafile.ExportID(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); diafile.ClearStructure(); } diafile.IDsummary = null; System.gc(); } Logger.getRootLogger().info( "================================================================================================="); } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search if (ExternalLibSearch) { Logger.getRootLogger().info("Module C: Targeted extraction using external library"); //Read exteranl library FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, FilenameUtils.getBaseName(ExternalLibPath)); if (ExlibManager == null) { ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath)); //Import traML file ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag); //Check if there are decoy spectra ExlibManager.CheckDecoys(); //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath); ExlibManager.WriteFragmentLibSerialization(WorkFolder); } Logger.getRootLogger() .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size()); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } //Generate RT mapping RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter()); RTmap.GenerateModel(); RTmap.GenerateMappedPepIon(); diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.GenerateMassCalibrationRTMap(); //Perform targeted re-extraction diafile.TargetedExtractionQuant(false, ExlibManager, ProbThreshold, RTWindow_Ext); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); //Remove target IDs below the defined probability threshold diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold); diafile.ExportID(); diafile.ClearStructure(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); } } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); diafile.IDsummary.ClearAssignPeakCluster(); //diafile.IDsummary.ClearPSMs(); } if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.MinFragMZ = MinFragMz; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:Main.java
public static boolean isGif(String path) { return path.endsWith("gif") || path.endsWith("Gif"); }
From source file:Main.java
private static String cutEnds(String s) { if (s.endsWith("/")) { return s.substring(0, s.length() - 1); } else {/* w w w . j av a2 s . co m*/ return s; } }
From source file:Main.java
public static boolean isImage(String fileName) { return fileName.endsWith(".jpg") || fileName.endsWith(".jpeg") || fileName.endsWith(".png"); }
From source file:Main.java
public static boolean checksIfExpressionEndsCorrectly(String expression) { return expression.endsWith(")"); }
From source file:Main.java
private static boolean isClass(String fileName) { return fileName.endsWith(CLASS_EXT); }