List of usage examples for java.lang String equals
public boolean equals(Object anObject)
From source file:io.compgen.cgpipe.CGPipe.java
public static void main(String[] args) { String fname = null;/* ww w . ja va2 s . c o m*/ String logFilename = null; String outputFilename = null; PrintStream outputStream = null; int verbosity = 0; boolean silent = false; boolean dryrun = false; boolean silenceStdErr = false; boolean showHelp = false; List<String> targets = new ArrayList<String>(); Map<String, VarValue> confVals = new HashMap<String, VarValue>(); String k = null; for (int i = 0; i < args.length; i++) { String arg = args[i]; if (i == 0) { if (new File(arg).exists()) { fname = arg; silenceStdErr = true; continue; } } else if (args[i - 1].equals("-f")) { fname = arg; continue; } else if (args[i - 1].equals("-l")) { logFilename = arg; continue; } else if (args[i - 1].equals("-o")) { outputFilename = arg; continue; } if (arg.equals("-h") || arg.equals("-help") || arg.equals("--help")) { if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } confVals.put(k, VarBool.TRUE); } showHelp = true; } else if (arg.equals("-license")) { license(); System.exit(1); } else if (arg.equals("-s")) { if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } confVals.put(k, VarBool.TRUE); } silent = true; } else if (arg.equals("-nolog")) { if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } confVals.put(k, VarBool.TRUE); } silenceStdErr = true; } else if (arg.equals("-v")) { if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } confVals.put(k, VarBool.TRUE); } verbosity++; } else if (arg.equals("-vv")) { if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } confVals.put(k, VarBool.TRUE); } verbosity += 2; } else if (arg.equals("-vvv")) { if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } confVals.put(k, VarBool.TRUE); } verbosity += 3; } else if (arg.equals("-dr")) { if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } confVals.put(k, VarBool.TRUE); } dryrun = true; } else if (arg.startsWith("--")) { if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } confVals.put(k, VarBool.TRUE); } k = arg.substring(2); } else if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } if (confVals.containsKey(k)) { try { VarValue val = confVals.get(k); if (val.getClass().equals(VarList.class)) { ((VarList) val).add(VarValue.parseStringRaw(arg)); } else { VarList list = new VarList(); list.add(val); list.add(VarValue.parseStringRaw(arg)); confVals.put(k, list); } } catch (VarTypeException e) { System.err.println("Error setting variable: " + k + " => " + arg); System.exit(1); ; } } else { confVals.put(k, VarValue.parseStringRaw(arg)); } k = null; } else if (arg.charAt(0) != '-') { targets.add(arg); } } if (k != null) { if (k.contains("-")) { k = k.replaceAll("-", "_"); } confVals.put(k, VarBool.TRUE); } confVals.put("cgpipe.loglevel", new VarInt(verbosity)); if (fname == null) { usage(); System.exit(1); } if (!showHelp) { switch (verbosity) { case 0: SimpleFileLoggerImpl.setLevel(Level.INFO); break; case 1: SimpleFileLoggerImpl.setLevel(Level.DEBUG); break; case 2: SimpleFileLoggerImpl.setLevel(Level.TRACE); break; case 3: default: SimpleFileLoggerImpl.setLevel(Level.ALL); break; } } else { SimpleFileLoggerImpl.setLevel(Level.FATAL); } SimpleFileLoggerImpl.setSilent(silenceStdErr || showHelp); Log log = LogFactory.getLog(CGPipe.class); log.info("Starting new run: " + fname); if (logFilename != null) { confVals.put("cgpipe.log", new VarString(logFilename)); } if (System.getenv("CGPIPE_DRYRUN") != null && !System.getenv("CGPIPE_DRYRUN").equals("")) { dryrun = true; } JobRunner runner = null; try { // Load config values from global config. RootContext root = new RootContext(); loadInitFiles(root); // Load settings from environment variables. root.loadEnvironment(); // Set cmd-line arguments if (silent) { root.setOutputStream(null); } if (outputFilename != null) { outputStream = new PrintStream(new FileOutputStream(outputFilename)); root.setOutputStream(outputStream); } for (String k1 : confVals.keySet()) { log.info("config: " + k1 + " => " + confVals.get(k1).toString()); } root.update(confVals); root.set("cgpipe.procs", new VarInt(Runtime.getRuntime().availableProcessors())); // update the URL Source loader configs SourceLoader.updateRemoteHandlers(root.cloneString("cgpipe.remote")); // Now check for help, only after we've setup the remote handlers... if (showHelp) { try { Parser.showHelp(fname); System.exit(0); } catch (IOException e) { System.err.println("Unable to find pipeline: " + fname); System.exit(1); } } // Set the global config values // globalConfig.putAll(root.cloneValues()); // Parse the AST and run it Parser.exec(fname, root); // Load the job runner *after* we execute the script to capture any config changes runner = JobRunner.load(root, dryrun); // find a build-target, and submit the job(s) to a runner if (targets.size() > 0) { for (String target : targets) { log.debug("building: " + target); BuildTarget initTarget = root.build(target); if (initTarget != null) { runner.submitAll(initTarget, root); } else { System.out.println("CGPIPE ERROR: Unable to find target: " + target); } } } else { BuildTarget initTarget = root.build(); if (initTarget != null) { runner.submitAll(initTarget, root); // Leave this commented out - it should be allowed to run cgpipe scripts w/o a target defined (testing) // } else { // System.out.println("CGPIPE ERROR: Unable to find default target"); } } runner.done(); if (outputStream != null) { outputStream.close(); } } catch (ASTParseException | ASTExecException | RunnerException | FileNotFoundException e) { if (outputStream != null) { outputStream.close(); } if (runner != null) { runner.abort(); } if (e.getClass().equals(ExitException.class)) { System.exit(((ExitException) e).getReturnCode()); } System.out.println("CGPIPE ERROR " + e.getMessage()); if (verbosity > 0) { e.printStackTrace(); } System.exit(1); } }
From source file:io.s4.comm.util.JSONUtil.java
public static void main(String[] args) { Map<String, Object> outerMap = new HashMap<String, Object>(); outerMap.put("doubleValue", 0.3456d); outerMap.put("integerValue", 175647); outerMap.put("longValue", 0x0000005000067000l); outerMap.put("stringValue", "Hello there"); Map<String, Object> innerMap = null; List<Map<String, Object>> innerList1 = new ArrayList<Map<String, Object>>(); innerMap = new HashMap<String, Object>(); innerMap.put("name", "kishore"); innerMap.put("count", 1787265); innerList1.add(innerMap);/*from ww w .ja v a 2 s . c om*/ innerMap = new HashMap<String, Object>(); innerMap.put("name", "fred"); innerMap.put("count", 11); innerList1.add(innerMap); outerMap.put("innerList1", innerList1); List<Integer> innerList2 = new ArrayList<Integer>(); innerList2.add(65); innerList2.add(2387894); innerList2.add(456); outerMap.put("innerList2", innerList2); JSONObject jsonObject = toJSONObject(outerMap); String flatJSONString = null; try { System.out.println(jsonObject.toString(3)); flatJSONString = jsonObject.toString(); Object o = jsonObject.get("innerList1"); if (!(o instanceof JSONArray)) { System.out.println("Unexpected type of list " + o.getClass().getName()); } else { JSONArray jsonArray = (JSONArray) o; o = jsonArray.get(0); if (!(o instanceof JSONObject)) { System.out.println("Unexpected type of map " + o.getClass().getName()); } else { JSONObject innerJSONObject = (JSONObject) o; System.out.println(innerJSONObject.get("name")); } } } catch (JSONException je) { je.printStackTrace(); } if (!flatJSONString.equals(toJsonString(outerMap))) { System.out.println("JSON strings don't match!!"); } Map<String, Object> map = getMapFromJson(flatJSONString); Object o = map.get("doubleValue"); if (!(o instanceof Double)) { System.out.println("Expected type Double, got " + o.getClass().getName()); Double doubleValue = (Double) o; if (doubleValue != 0.3456d) { System.out.println("Expected 0.3456, got " + doubleValue); } } o = map.get("innerList1"); if (!(o instanceof List)) { System.out.println("Expected implementation of List, got " + o.getClass().getName()); } else { List innerList = (List) o; o = innerList.get(0); if (!(o instanceof Map)) { System.out.println("Expected implementation of Map, got " + o.getClass().getName()); } else { innerMap = (Map) o; System.out.println(innerMap.get("name")); } } System.out.println(map); }
From source file:DIA_Umpire_Quant.DIA_Umpire_ExtLibSearch.java
/** * @param args the command line arguments *//*from w w w . j a v a 2 s . co 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:it.cnr.icar.eric.client.xml.registry.jaas.LoginModuleManager.java
/** * @param args the command line arguments *///from w ww . ja v a2 s. c o m public static void main(String[] args) { for (int i = 0; i < args.length; i++) { try { String argFlag = args[i]; if (argFlag.equals("-d")) { createDefaultLoginFile = true; } else if (argFlag.equals("-l")) { createLoginFile = true; } else if (argFlag.equals("-c")) { getCallbackHandler = true; } else { // if no flags execute all methods createDefaultLoginFile = true; createLoginFile = true; getCallbackHandler = true; } } catch (RuntimeException ex) { // use defaults continue; } } if (args.length == 0) { createLoginFile = true; } LoginModuleManager loginModuleMgr = new LoginModuleManager(); try { if (createDefaultLoginFile) { log.info( JAXRResourceBundle.getInstance().getString("message.startingCreateDefaultLoginConfigFile")); loginModuleMgr.createDefaultLoginConfigFile(); } if (createLoginFile) { log.info(JAXRResourceBundle.getInstance().getString("message.startingCreateLoginConfigFile")); loginModuleMgr.createLoginConfigFile(); } if (getCallbackHandler) { log.info(JAXRResourceBundle.getInstance().getString("message.startingGetCallbackHandler")); loginModuleMgr.getCallbackHandler(); } } catch (Throwable t) { t.printStackTrace(); } }
From source file:com.zimbra.common.mime.MimeDetect.java
public static void main(String[] args) { int limit = -1; MimeDetect md = new MimeDetect(); Options opts = new Options(); CommandLineParser parser = new GnuParser(); int ret = 1;//w ww .j a va 2 s .co m opts.addOption("d", "data", false, "data only"); opts.addOption("g", "globs", true, "globs file"); opts.addOption("l", "limit", true, "size limit"); opts.addOption("m", "magic", true, "magic file"); opts.addOption("n", "name", false, "name only"); opts.addOption("v", "validate", false, "validate extension and data"); try { CommandLine cl = parser.parse(opts, args); String file; String globs = LC.shared_mime_info_globs.value(); String magic = LC.shared_mime_info_magic.value(); String type; if (cl.hasOption('g')) globs = cl.getOptionValue('g'); if (cl.hasOption('l')) limit = Integer.parseInt(cl.getOptionValue('l')); if (cl.hasOption('m')) magic = cl.getOptionValue('m'); if (cl.getArgs().length != 1) usage(opts); file = cl.getArgs()[0]; md.parse(globs, magic); if (cl.hasOption('n')) { type = md.detect(file); } else if (file.equals("-")) { type = md.detect(System.in, limit); } else if (cl.hasOption('d')) { type = md.detect(new FileInputStream(file), limit); } else if (cl.hasOption('v')) { type = md.validate(new File(file), limit); } else { type = md.detect(new File(file), limit); } if (type == null) { System.out.println("unknown"); } else { System.out.println(type); ret = 0; } } catch (Exception e) { e.printStackTrace(System.out); if (e instanceof UnrecognizedOptionException) usage(opts); } System.exit(ret); }
From source file:DIA_Umpire_Quant.DIA_Umpire_IntLibSearch.java
/** * @param args the command line arguments *//*from www .j ava 2 s . com*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire targeted re-extraction analysis using internal 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_IntLibSearch.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_intlibsearch.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 InternalLibID = ""; float ProbThreshold = 0.99f; float RTWindow_Int = -1f; float Freq = 0f; int TopNFrag = 6; 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 "InternalLibID": { InternalLibID = value; break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "Fasta": { tandemPara.FastaPath = value; 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<>(); try { 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="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (FileList.size() > 1) { Logger.getRootLogger().info("Targeted re-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, ProbThreshold, 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> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:edu.umn.cs.spatialHadoop.operations.DistributedJoin.java
public static void main(String[] args) throws IOException, InterruptedException { OperationsParams params = new OperationsParams(new GenericOptionsParser(args)); Path[] allFiles = params.getPaths(); if (allFiles.length < 2) { System.err.println("This operation requires at least two input files"); printUsage();//from w w w. j a v a 2 s . com System.exit(1); } if (allFiles.length == 2 && !params.checkInput()) { // One of the input files does not exist printUsage(); System.exit(1); } if (allFiles.length > 2 && !params.checkInputOutput()) { printUsage(); System.exit(1); } Path[] inputPaths = allFiles.length == 2 ? allFiles : params.getInputPaths(); Path outputPath = allFiles.length == 2 ? null : params.getOutputPath(); if (params.get("heuristic-repartition", "yes").equals("no")) { isGeneralRepartitionMode = false; System.out.println("heuristic-repartition is false"); } if (params.get("all-inmemory-load", "yes").equals("no")) { isOneShotReadMode = false; System.out.println("all-inmemory-load is false"); } if (params.get("direct-join", "no").equals("yes")) { System.out.println("Reparition the smaller dataset then join the two datasets directly"); } if (params.get("repartition-only", "no").equals("yes")) { System.out.println("Repartition-only is true"); isReduceInactive = true; } if (params.get("joining-per-once") != null) { System.out.println("joining-per-once is set to: " + params.get("joining-per-once")); joiningThresholdPerOnce = Integer.parseInt(params.get("joining-per-once")); } if (params.get("filter-only") != null) { System.out.println("filer-only mode is set to: " + params.get("filter-only")); if (params.get("filter-only").equals("yes")) { isFilterOnly = true; } else { isFilterOnly = false; } } long result_size; if (inputPaths[0].equals(inputPaths[1])) { // Special case for self join selfJoinLocal(inputPaths[0], outputPath, params); } String repartition = params.get("repartition", "no"); if (repartition.equals("auto")) { result_size = distributedJoinSmart(inputPaths, outputPath, params); } else if (repartition.equals("yes")) { int file_to_repartition = selectRepartition(inputPaths, params); if (params.get("direct-join").equals("yes")) { result_size = repartitionJoinStep(inputPaths, file_to_repartition, outputPath, params); } else { repartitionStep(inputPaths, file_to_repartition, params); result_size = joinStep(inputPaths, outputPath, params); } } else if (repartition.equals("no")) { result_size = joinStep(inputPaths, outputPath, params); } else { throw new RuntimeException("Illegal parameter repartition:" + repartition); } System.out.println("Result size: " + result_size); }
From source file:com.swdouglass.winter.Winter.java
/** * @param args the command line arguments *//* w w w. j a v a 2 s.c o m*/ public static void main(String[] args) { String packageName = "com.swdouglass"; String idColumnName = "id"; String action = "class"; String tableName = ""; Getopt g = new Getopt("Winter", args, "cp:i:t:"); // int c; while ((c = g.getopt()) != -1) { switch (c) { case 'p': packageName = g.getOptarg(); break; case 'c': action = "class"; //default anyway break; case 'i': idColumnName = g.getOptarg(); break; case 't': tableName = g.getOptarg(); break; case '?': default: System.out.print("Usage: java -jar Winter.jar -t table_name -p package_name [ -i index ]"); System.exit(-1); } } Winter w = new Winter(); if (action.equals("class")) { w.generateClassFromTable(tableName, idColumnName, packageName);// table name, package name } }
From source file:Gen.java
public static void main(String[] args) throws Exception { try {// w w w .ja v a 2s .c om File[] files = null; if (System.getProperty("dir") != null && !System.getProperty("dir").equals("")) { files = new File(System.getProperty("dir")).listFiles(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toUpperCase().endsWith(".XML"); }; }); } else { String fileName = System.getProperty("file") != null && !System.getProperty("file").equals("") ? System.getProperty("file") : "rjmap.xml"; files = new File[] { new File(fileName) }; } log.info("files : " + Arrays.toString(files)); if (files == null || files.length == 0) { log.info("no files to parse"); System.exit(0); } boolean formatsource = true; if (System.getProperty("formatsource") != null && !System.getProperty("formatsource").equals("") && System.getProperty("formatsource").equalsIgnoreCase("false")) { formatsource = false; } GEN_ROOT = System.getProperty("outputdir"); if (GEN_ROOT == null || GEN_ROOT.equals("")) { GEN_ROOT = new File(files[0].getAbsolutePath()).getParent() + FILE_SEPARATOR + "distrib"; } GEN_ROOT = new File(GEN_ROOT).getAbsolutePath().replace('\\', '/'); if (GEN_ROOT.endsWith("/")) GEN_ROOT = GEN_ROOT.substring(0, GEN_ROOT.length() - 1); System.out.println("GEN ROOT:" + GEN_ROOT); MAPPING_JAR_NAME = System.getProperty("mappingjar") != null && !System.getProperty("mappingjar").equals("") ? System.getProperty("mappingjar") : "mapping.jar"; if (!MAPPING_JAR_NAME.endsWith(".jar")) MAPPING_JAR_NAME += ".jar"; GEN_ROOT_SRC = GEN_ROOT + FILE_SEPARATOR + "src"; GEN_ROOT_LIB = GEN_ROOT + FILE_SEPARATOR + ""; DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance(); domFactory.setNamespaceAware(true); domFactory.setValidating(false); DocumentBuilder documentBuilder = domFactory.newDocumentBuilder(); for (int f = 0; f < files.length; ++f) { log.info("parsing file : " + files[f]); Document document = documentBuilder.parse(files[f]); Vector<Node> initNodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "scripts"), "initScript", initNodes); for (int i = 0; i < initNodes.size(); ++i) { NamedNodeMap attrs = initNodes.elementAt(i).getAttributes(); boolean embed = attrs.getNamedItem("embed") != null && attrs.getNamedItem("embed").getNodeValue().equalsIgnoreCase("true"); StringBuffer vbuffer = new StringBuffer(); if (attrs.getNamedItem("inline") != null) { vbuffer.append(attrs.getNamedItem("inline").getNodeValue()); vbuffer.append('\n'); } else { String fname = attrs.getNamedItem("name").getNodeValue(); if (!fname.startsWith("\\") && !fname.startsWith("/") && fname.toCharArray()[1] != ':') { String path = files[f].getAbsolutePath(); path = path.substring(0, path.lastIndexOf(FILE_SEPARATOR)); fname = new File(path + FILE_SEPARATOR + fname).getCanonicalPath(); } vbuffer.append(Utils.getFileAsStringBuffer(fname)); } initScriptBuffer.append(vbuffer); if (embed) embedScriptBuffer.append(vbuffer); } Vector<Node> packageInitNodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "scripts"), "packageScript", packageInitNodes); for (int i = 0; i < packageInitNodes.size(); ++i) { NamedNodeMap attrs = packageInitNodes.elementAt(i).getAttributes(); String packageName = attrs.getNamedItem("package").getNodeValue(); if (packageName.equals("")) packageName = "rGlobalEnv"; if (!packageName.endsWith("Function")) packageName += "Function"; if (packageEmbedScriptHashMap.get(packageName) == null) { packageEmbedScriptHashMap.put(packageName, new StringBuffer()); } StringBuffer vbuffer = packageEmbedScriptHashMap.get(packageName); // if (!packageName.equals("rGlobalEnvFunction")) { // vbuffer.append("library("+packageName.substring(0,packageName.lastIndexOf("Function"))+")\n"); // } if (attrs.getNamedItem("inline") != null) { vbuffer.append(attrs.getNamedItem("inline").getNodeValue() + "\n"); initScriptBuffer.append(attrs.getNamedItem("inline").getNodeValue() + "\n"); } else { String fname = attrs.getNamedItem("name").getNodeValue(); if (!fname.startsWith("\\") && !fname.startsWith("/") && fname.toCharArray()[1] != ':') { String path = files[f].getAbsolutePath(); path = path.substring(0, path.lastIndexOf(FILE_SEPARATOR)); fname = new File(path + FILE_SEPARATOR + fname).getCanonicalPath(); } StringBuffer fileBuffer = Utils.getFileAsStringBuffer(fname); vbuffer.append(fileBuffer); initScriptBuffer.append(fileBuffer); } } Vector<Node> functionsNodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "functions"), "function", functionsNodes); for (int i = 0; i < functionsNodes.size(); ++i) { NamedNodeMap attrs = functionsNodes.elementAt(i).getAttributes(); String functionName = attrs.getNamedItem("name").getNodeValue(); boolean forWeb = attrs.getNamedItem("forWeb") != null && attrs.getNamedItem("forWeb").getNodeValue().equalsIgnoreCase("true"); String signature = (attrs.getNamedItem("signature") == null ? "" : attrs.getNamedItem("signature").getNodeValue() + ","); String renameTo = (attrs.getNamedItem("renameTo") == null ? null : attrs.getNamedItem("renameTo").getNodeValue()); HashMap<String, FAttributes> sigMap = Globals._functionsToPublish.get(functionName); if (sigMap == null) { sigMap = new HashMap<String, FAttributes>(); Globals._functionsToPublish.put(functionName, sigMap); if (attrs.getNamedItem("returnType") == null) { _functionsVector.add(new String[] { functionName }); } else { _functionsVector.add( new String[] { functionName, attrs.getNamedItem("returnType").getNodeValue() }); } } sigMap.put(signature, new FAttributes(renameTo, forWeb)); if (forWeb) _webPublishingEnabled = true; } if (System.getProperty("targetjdk") != null && !System.getProperty("targetjdk").equals("") && System.getProperty("targetjdk").compareTo("1.5") < 0) { if (_webPublishingEnabled || (System.getProperty("ws.r.api") != null && System.getProperty("ws.r.api").equalsIgnoreCase("true"))) { log.info("be careful, web publishing disabled beacuse target JDK<1.5"); } _webPublishingEnabled = false; } else { if (System.getProperty("ws.r.api") == null || System.getProperty("ws.r.api").equals("") || !System.getProperty("ws.r.api").equalsIgnoreCase("false")) { _webPublishingEnabled = true; } if (_webPublishingEnabled && System.getProperty("java.version").compareTo("1.5") < 0) { log.info("be careful, web publishing disabled beacuse a JDK<1.5 is in use"); _webPublishingEnabled = false; } } Vector<Node> s4Nodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "s4classes"), "class", s4Nodes); if (s4Nodes.size() > 0) { String formalArgs = ""; String signature = ""; for (int i = 0; i < s4Nodes.size(); ++i) { NamedNodeMap attrs = s4Nodes.elementAt(i).getAttributes(); String s4Name = attrs.getNamedItem("name").getNodeValue(); formalArgs += "p" + i + (i == s4Nodes.size() - 1 ? "" : ","); signature += "'" + s4Name + "'" + (i == s4Nodes.size() - 1 ? "" : ","); } String genBeansScriptlet = "setGeneric('" + PUBLISH_S4_HEADER + "', function(" + formalArgs + ") standardGeneric('" + PUBLISH_S4_HEADER + "'));" + "setMethod('" + PUBLISH_S4_HEADER + "', signature(" + signature + ") , function(" + formalArgs + ") { })"; initScriptBuffer.append(genBeansScriptlet); _functionsVector.add(new String[] { PUBLISH_S4_HEADER, "numeric" }); } } if (!new File(GEN_ROOT_LIB).exists()) regenerateDir(GEN_ROOT_LIB); else { clean(GEN_ROOT_LIB, true); } for (int i = 0; i < rwebservicesScripts.length; ++i) DirectJNI.getInstance().getRServices().sourceFromResource(rwebservicesScripts[i]); String lastStatus = DirectJNI.getInstance().runR(new ExecutionUnit() { public void run(Rengine e) { DirectJNI.getInstance().toggleMarker(); DirectJNI.getInstance().sourceFromBuffer(initScriptBuffer.toString()); log.info(" init script status : " + DirectJNI.getInstance().cutStatusSinceMarker()); for (int i = 0; i < _functionsVector.size(); ++i) { String[] functionPair = _functionsVector.elementAt(i); log.info("dealing with : " + functionPair[0]); regenerateDir(GEN_ROOT_SRC); String createMapStr = "createMap("; boolean isGeneric = e.rniGetBoolArrayI( e.rniEval(e.rniParse("isGeneric(\"" + functionPair[0] + "\")", 1), 0))[0] == 1; log.info("is Generic : " + isGeneric); if (isGeneric) { createMapStr += functionPair[0]; } else { createMapStr += "\"" + functionPair[0] + "\""; } createMapStr += ", outputDirectory=\"" + GEN_ROOT_SRC .substring(0, GEN_ROOT_SRC.length() - "/src".length()).replace('\\', '/') + "\""; createMapStr += ", typeMode=\"robject\""; createMapStr += (functionPair.length == 1 || functionPair[1] == null || functionPair[1].trim().equals("") ? "" : ", S4DefaultTypedSig=TypedSignature(returnType=\"" + functionPair[1] + "\")"); createMapStr += ")"; log.info("------------------------------------------"); log.info("-- createMapStr=" + createMapStr); DirectJNI.getInstance().toggleMarker(); e.rniEval(e.rniParse(createMapStr, 1), 0); String createMapStatus = DirectJNI.getInstance().cutStatusSinceMarker(); log.info(" createMap status : " + createMapStatus); log.info("------------------------------------------"); deleteDir(GEN_ROOT_SRC + "/org/kchine/r/rserviceJms"); compile(GEN_ROOT_SRC); jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar", null); URL url = null; try { url = new URL( "jar:file:" + (GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar") .replace('\\', '/') + "!/"); } catch (Exception ex) { ex.printStackTrace(); } DirectJNI.generateMaps(url, true); } } }); log.info(lastStatus); log.info(DirectJNI._rPackageInterfacesHash); regenerateDir(GEN_ROOT_SRC); for (int i = 0; i < _functionsVector.size(); ++i) { unjar(GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar", GEN_ROOT_SRC); } regenerateRPackageClass(true); generateS4BeanRef(); if (formatsource) applyJalopy(GEN_ROOT_SRC); compile(GEN_ROOT_SRC); for (String k : DirectJNI._rPackageInterfacesHash.keySet()) { Rmic rmicTask = new Rmic(); rmicTask.setProject(_project); rmicTask.setTaskName("rmic_packages"); rmicTask.setClasspath(new Path(_project, GEN_ROOT_SRC)); rmicTask.setBase(new File(GEN_ROOT_SRC)); rmicTask.setClassname(k + "ImplRemote"); rmicTask.init(); rmicTask.execute(); } // DirectJNI._rPackageInterfacesHash=new HashMap<String, // Vector<Class<?>>>(); // DirectJNI._rPackageInterfacesHash.put("org.bioconductor.packages.rGlobalEnv.rGlobalEnvFunction",new // Vector<Class<?>>()); if (_webPublishingEnabled) { jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar", null); URL url = new URL( "jar:file:" + (GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar").replace('\\', '/') + "!/"); ClassLoader cl = new URLClassLoader(new URL[] { url }, Globals.class.getClassLoader()); for (String className : DirectJNI._rPackageInterfacesHash.keySet()) { if (cl.loadClass(className + "Web").getDeclaredMethods().length == 0) continue; log.info("######## " + className); WsGen wsgenTask = new WsGen(); wsgenTask.setProject(_project); wsgenTask.setTaskName("wsgen"); FileSet rjb_fileSet = new FileSet(); rjb_fileSet.setProject(_project); rjb_fileSet.setDir(new File(".")); rjb_fileSet.setIncludes("RJB.jar"); DirSet src_dirSet = new DirSet(); src_dirSet.setDir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/")); Path classPath = new Path(_project); classPath.addFileset(rjb_fileSet); classPath.addDirset(src_dirSet); wsgenTask.setClasspath(classPath); wsgenTask.setKeep(true); wsgenTask.setDestdir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/")); wsgenTask.setResourcedestdir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/")); wsgenTask.setSei(className + "Web"); wsgenTask.init(); wsgenTask.execute(); } new File(GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar").delete(); } embedRScripts(); HashMap<String, String> marker = new HashMap<String, String>(); marker.put("RJBMAPPINGJAR", "TRUE"); Properties props = new Properties(); props.put("PACKAGE_NAMES", PoolUtils.objectToHex(DirectJNI._packageNames)); props.put("S4BEANS_MAP", PoolUtils.objectToHex(DirectJNI._s4BeansMapping)); props.put("S4BEANS_REVERT_MAP", PoolUtils.objectToHex(DirectJNI._s4BeansMappingRevert)); props.put("FACTORIES_MAPPING", PoolUtils.objectToHex(DirectJNI._factoriesMapping)); props.put("S4BEANS_HASH", PoolUtils.objectToHex(DirectJNI._s4BeansHash)); props.put("R_PACKAGE_INTERFACES_HASH", PoolUtils.objectToHex(DirectJNI._rPackageInterfacesHash)); props.put("ABSTRACT_FACTORIES", PoolUtils.objectToHex(DirectJNI._abstractFactories)); new File(GEN_ROOT_SRC + "/" + "maps").mkdirs(); FileOutputStream fos = new FileOutputStream(GEN_ROOT_SRC + "/" + "maps/rjbmaps.xml"); props.storeToXML(fos, null); fos.close(); jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + MAPPING_JAR_NAME, marker); if (_webPublishingEnabled) genWeb(); DirectJNI._mappingClassLoader = null; } finally { System.exit(0); } }
From source file:com.enjoyxstudy.selenium.autoexec.AutoExecServer.java
/** * @param args/* w w w . j av a2 s. co m*/ * @throws Exception */ public static void main(String[] args) throws Exception { String command = null; if (args.length == 0) { command = COMMAND_STARTUP; } else if (args[0].equals(COMMAND_STARTUP)) { command = COMMAND_STARTUP; } else if (args[0].equals(COMMAND_SHUTDOWN)) { command = COMMAND_SHUTDOWN; } if (command == null) { throw new IllegalArgumentException(); } String propertyFile = DEFAULT_PROPERTY_FILE_NAME; // default if (args.length == 2) { propertyFile = args[1]; } final Properties properties = new Properties(); FileInputStream inputStream = new FileInputStream(propertyFile); try { properties.load(inputStream); } finally { inputStream.close(); } if (command.equals(COMMAND_STARTUP)) { new Thread(new Runnable() { public void run() { try { AutoExecServer autoExecServer = new AutoExecServer(); autoExecServer.startup(properties); autoExecServer.runningLoop(); autoExecServer.destroy(); } catch (Exception e) { log.error("Error", e); e.printStackTrace(); } finally { System.exit(0); } } }).start(); } else { StringBuilder commandURL = new StringBuilder("http://localhost:"); commandURL.append( PropertiesUtils.getInt(properties, "port", RemoteControlConfiguration.getDefaultPort())); commandURL.append(CONTEXT_PATH_COMMAND); RemoteControlClient client = new RemoteControlClient(commandURL.toString()); client.stopServer(); } }