List of usage examples for java.lang String toLowerCase
public String toLowerCase()
From source file:GGbot.pkg0.Mainclass.java
public static void main(String[] args) throws InterruptedException, TwitterException, DbxException, IOException, Exception { String input = ""; System.out.println("Welcomet to GGbot\nFor more information please take a look at the Read Me\n"); System.out.println("- Twitter: PlayerName (flex, returns the latest tweets from a player)\n" + "- Facebook: PlayerName (flex, returns all the information available about a player)\n" + "- Note to self: Input (notflex, create a new text document with your input, and put it in a drop box)\n" + "- Translate: Input (notflex, detects the language of your input and translate it to english)\n" + "- Wiki (flex, returns the definition of league of legends from wikipedia\n" + "- !Players: (returns the list of the players available in the library (only players from the teams: Cloud9, CLG, and TSM are available at the moment))\n" + "- !dropbox: (returns the link to the dropbox)\n\n" + "Start to chat now!\n"); while (!input.contains("bye")) { System.out.print("<User>"); Scanner scanner = new Scanner(System.in); input = scanner.nextLine();//from ww w . ja va 2s . c o m String output = bot.Bot(input.toLowerCase().trim()); System.out.println("<GGbot>" + WordUtils.wrap(output, 75)); } }
From source file:org.eclipse.swt.snippets.SnippetExplorer.java
/** * SnippetExplorer main method.//from w ww .j a v a2 s . c om * * @param args does not parse any arguments */ public static void main(String[] args) throws Exception { final String os = System.getProperty("os.name"); multiDisplaySupport = (os != null && os.toLowerCase().contains("windows")); if (canRunCommand("java")) { javaCommand = "java"; } else { final String javaHome = System.getProperty("java.home"); if (javaHome != null) { final Path java = Paths.get(javaHome, "bin", "java"); java.normalize(); if (canRunCommand(java.toString())) { javaCommand = java.toString(); } } } snippets = loadSnippets(); snippets.sort((a, b) -> { int cmp = Integer.compare(a.snippetNum, b.snippetNum); if (cmp == 0) { cmp = a.snippetName.compareTo(b.snippetName); } return cmp; }); new SnippetExplorer().open(); }
From source file:com.sforce.dataset.DatasetUtilMain.java
public static void main(String[] args) { printBanner();//w ww . ja v a 2 s .co m DatasetUtilParams params = new DatasetUtilParams(); if (args.length > 0) params.server = false; System.out.println(""); System.out.println("DatsetUtils called with {" + args.length + "} Params:"); for (int i = 0; i < args.length; i++) { if ((i & 1) == 0) { System.out.print("{" + args[i] + "}"); } else { if (i > 0 && args[i - 1].equalsIgnoreCase("--p")) System.out.println(":{*******}"); else System.out.println(":{" + args[i] + "}"); } if (i > 0 && args[i - 1].equalsIgnoreCase("--server")) { if (args[i] != null && args[i].trim().equalsIgnoreCase("false")) params.server = false; else if (args[i] != null && args[i].trim().equalsIgnoreCase("true")) params.server = true; } } System.out.println(""); if (!printlneula(params.server)) { System.out.println( "You do not have permission to use this software. Please delete it from this computer"); System.exit(-1); } String action = null; if (args.length >= 2) { for (int i = 1; i < args.length; i = i + 2) { if (args[i - 1].equalsIgnoreCase("--help") || args[i - 1].equalsIgnoreCase("-help") || args[i - 1].equalsIgnoreCase("help")) { printUsage(); } else if (args[i - 1].equalsIgnoreCase("--u")) { params.username = args[i]; } else if (args[i - 1].equalsIgnoreCase("--p")) { params.password = args[i]; } else if (args[i - 1].equalsIgnoreCase("--sessionId")) { params.sessionId = args[i]; } else if (args[i - 1].equalsIgnoreCase("--token")) { params.token = args[i]; } else if (args[i - 1].equalsIgnoreCase("--endpoint")) { params.endpoint = args[i]; } else if (args[i - 1].equalsIgnoreCase("--action")) { action = args[i]; } else if (args[i - 1].equalsIgnoreCase("--operation")) { if (args[i] != null) { if (args[i].equalsIgnoreCase("overwrite")) { params.Operation = args[i]; } else if (args[i].equalsIgnoreCase("upsert")) { params.Operation = args[i]; } else if (args[i].equalsIgnoreCase("append")) { params.Operation = args[i]; } else if (args[i].equalsIgnoreCase("delete")) { params.Operation = args[i]; } else { System.out.println("Invalid Operation {" + args[i] + "} Must be Overwrite or Upsert or Append or Delete"); System.exit(-1); } } } else if (args[i - 1].equalsIgnoreCase("--debug")) { params.debug = true; DatasetUtilConstants.debug = true; } else if (args[i - 1].equalsIgnoreCase("--ext")) { DatasetUtilConstants.ext = true; } else if (args[i - 1].equalsIgnoreCase("--inputFile")) { String tmp = args[i]; if (tmp != null) { File tempFile = new File(tmp); if (tempFile.exists()) { params.inputFile = tempFile.toString(); } else { System.out.println("File {" + args[i] + "} does not exist"); System.exit(-1); } } } else if (args[i - 1].equalsIgnoreCase("--dataset")) { params.dataset = args[i]; } else if (args[i - 1].equalsIgnoreCase("--datasetLabel")) { params.datasetLabel = args[i]; } else if (args[i - 1].equalsIgnoreCase("--app")) { params.app = args[i]; } else if (args[i - 1].equalsIgnoreCase("--useBulkAPI")) { if (args[i] != null && args[i].trim().equalsIgnoreCase("true")) params.useBulkAPI = true; } else if (args[i - 1].equalsIgnoreCase("--uploadFormat")) { if (args[i] != null && args[i].trim().equalsIgnoreCase("csv")) params.uploadFormat = "csv"; else if (args[i] != null && args[i].trim().equalsIgnoreCase("binary")) params.uploadFormat = "binary"; } else if (args[i - 1].equalsIgnoreCase("--rowLimit")) { if (args[i] != null && !args[i].trim().isEmpty()) params.rowLimit = (new BigDecimal(args[i].trim())).intValue(); } else if (args[i - 1].equalsIgnoreCase("--rootObject")) { params.rootObject = args[i]; } else if (args[i - 1].equalsIgnoreCase("--fileEncoding")) { params.fileEncoding = args[i]; } else if (args[i - 1].equalsIgnoreCase("--server")) { if (args[i] != null && args[i].trim().equalsIgnoreCase("true")) params.server = true; else if (args[i] != null && args[i].trim().equalsIgnoreCase("false")) params.server = false; } else if (args[i - 1].equalsIgnoreCase("--codingErrorAction")) { if (args[i] != null) { if (args[i].equalsIgnoreCase("IGNORE")) { params.codingErrorAction = CodingErrorAction.IGNORE; } else if (args[i].equalsIgnoreCase("REPORT")) { params.codingErrorAction = CodingErrorAction.REPORT; } else if (args[i].equalsIgnoreCase("REPLACE")) { params.codingErrorAction = CodingErrorAction.REPLACE; } } } else { printUsage(); System.out.println("\nERROR: Invalid argument: " + args[i - 1]); System.exit(-1); } } //end for if (params.username != null) { if (params.endpoint == null || params.endpoint.isEmpty()) { params.endpoint = DatasetUtilConstants.defaultEndpoint; } } } if (params.server) { System.out.println(); System.out.println("\n*******************************************************************************"); try { DatasetUtilServer datasetUtilServer = new DatasetUtilServer(); datasetUtilServer.init(args, true); } catch (Exception e) { e.printStackTrace(); } System.out.println("Server ended, exiting JVM....."); System.out.println("*******************************************************************************\n"); System.out.println("QUITAPP"); System.exit(0); } if (params.sessionId == null) { if (params.username == null || params.username.trim().isEmpty()) { params.username = getInputFromUser("Enter salesforce username: ", true, false); } if (params.username.equals("-1")) { params.sessionId = getInputFromUser("Enter salesforce sessionId: ", true, false); params.username = null; params.password = null; } else { if (params.password == null || params.password.trim().isEmpty()) { params.password = getInputFromUser("Enter salesforce password: ", true, true); } } } if (params.sessionId != null && !params.sessionId.isEmpty()) { while (params.endpoint == null || params.endpoint.trim().isEmpty()) { params.endpoint = getInputFromUser("Enter salesforce instance url: ", true, false); if (params.endpoint == null || params.endpoint.trim().isEmpty()) System.out.println("\nERROR: endpoint must be specified when sessionId is specified"); } while (params.endpoint.toLowerCase().contains("login.salesforce.com") || params.endpoint.toLowerCase().contains("test.salesforce.com") || params.endpoint.toLowerCase().contains("test") || params.endpoint.toLowerCase().contains("prod") || params.endpoint.toLowerCase().contains("sandbox")) { System.out.println("\nERROR: endpoint must be the actual serviceURL and not the login url"); params.endpoint = getInputFromUser("Enter salesforce instance url: ", true, false); } } else { if (params.endpoint == null || params.endpoint.isEmpty()) { params.endpoint = getInputFromUser("Enter salesforce instance url (default=prod): ", false, false); if (params.endpoint == null || params.endpoint.trim().isEmpty()) { params.endpoint = DatasetUtilConstants.defaultEndpoint; } } } try { if (params.endpoint.equalsIgnoreCase("PROD") || params.endpoint.equalsIgnoreCase("PRODUCTION")) { params.endpoint = DatasetUtilConstants.defaultEndpoint; } else if (params.endpoint.equalsIgnoreCase("TEST") || params.endpoint.equalsIgnoreCase("SANDBOX")) { params.endpoint = DatasetUtilConstants.defaultEndpoint.replace("login", "test"); } URL uri = new URL(params.endpoint); String protocol = uri.getProtocol(); String host = uri.getHost(); if (protocol == null || !protocol.equalsIgnoreCase("https")) { if (host == null || !(host.toLowerCase().endsWith("internal.salesforce.com") || host.toLowerCase().endsWith("localhost"))) { System.out.println("\nERROR: Invalid endpoint. UNSUPPORTED_CLIENT: HTTPS Required in endpoint"); System.exit(-1); } } if (uri.getPath() == null || uri.getPath().isEmpty() || uri.getPath().equals("/")) { uri = new URL(uri.getProtocol(), uri.getHost(), uri.getPort(), DatasetUtilConstants.defaultSoapEndPointPath); } params.endpoint = uri.toString(); } catch (MalformedURLException e) { e.printStackTrace(); System.out.println("\nERROR: endpoint is not a valid URL"); System.exit(-1); } PartnerConnection partnerConnection = null; if (params.username != null || params.sessionId != null) { try { partnerConnection = DatasetUtils.login(0, params.username, params.password, params.token, params.endpoint, params.sessionId, params.debug); } catch (ConnectionException e) { e.printStackTrace(); System.exit(-1); } catch (MalformedURLException e) { e.printStackTrace(); System.exit(-1); } } if (args.length == 0 || action == null) { // System.out.println("\n*******************************************************************************"); //// FileListenerUtil.startAllListener(partnerConnection); // try { // Thread.sleep(1000); // } catch (InterruptedException e) { // } // System.out.println("*******************************************************************************\n"); // System.out.println(); // System.out.println("\n*******************************************************************************"); // try { // DatasetUtilServer datasetUtilServer = new DatasetUtilServer(); // datasetUtilServer.init(args, false); // } catch (Exception e) { // e.printStackTrace(); // } // System.out.println("*******************************************************************************\n"); // System.out.println(); while (true) { action = getActionFromUser(); if (action == null || action.isEmpty()) { System.exit(-1); } params = new DatasetUtilParams(); getRequiredParams(action, partnerConnection, params); @SuppressWarnings("unused") boolean status = doAction(action, partnerConnection, params); // if(status) // { // if(action.equalsIgnoreCase("load") && params.debug) // createListener(partnerConnection, params); // } } } else { doAction(action, partnerConnection, params); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_Quant.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) 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:jetbrains.exodus.env.Reflect.java
public static void main(@NotNull final String[] args) throws Exception { if (args.length == 0) { printUsage();/*from w ww.jav a 2 s .c om*/ return; } String envPath = null; String envPath2 = null; boolean hasOptions = false; boolean gatherLogStats = false; boolean validateRoots = false; boolean traverse = false; boolean copy = false; boolean traverseAll = false; boolean utilizationInfo = false; final Set<String> files2Clean = new LinkedHashSet<>(); for (final String arg : args) { if (arg.startsWith("-")) { hasOptions = true; if ("-ls".equalsIgnoreCase(arg)) { gatherLogStats = true; } else if ("-r".equalsIgnoreCase(arg)) { validateRoots = true; } else if ("-t".equalsIgnoreCase(arg)) { traverse = true; } else if ("-c".equalsIgnoreCase(arg)) { copy = true; } else if ("-ta".equalsIgnoreCase(arg)) { traverseAll = true; } else if ("-u".equalsIgnoreCase(arg)) { utilizationInfo = true; } else if (arg.toLowerCase().startsWith("-cl")) { files2Clean.add(arg.substring(2)); } else { printUsage(); return; } } else { if (envPath == null) { envPath = arg; } else { envPath2 = arg; break; } } } if (envPath == null || (copy && envPath2 == null)) { printUsage(); return; } System.out.println("Started investigation of " + envPath); final Reflect reflect = new Reflect(new File(envPath)); if (files2Clean.size() > 0) { for (final String file : files2Clean) { reflect.cleanFile(file); } } if (!hasOptions) { reflect.gatherLogStats(); reflect.traverse(); } else { List<DatabaseRoot> roots = null; if (validateRoots || traverseAll) { roots = reflect.roots(); } if (gatherLogStats) { reflect.gatherLogStats(); } if (traverse) { reflect.traverse(); } if (copy) { reflect.copy(new File(envPath2)); } if (utilizationInfo) { reflect.spaceInfoFromUtilization(); } if (traverseAll) { reflect.traverseAll(roots); } } }
From source file:de.mendelson.comm.as2.AS2.java
/**Method to start the server on from the command line*/ public static void main(String args[]) { // TODO remove cleanup();/* w ww . j ava 2 s. c o m*/ String language = null; boolean startHTTP = true; boolean allowAllClients = false; int optind; for (optind = 0; optind < args.length; optind++) { if (args[optind].toLowerCase().equals("-lang")) { language = args[++optind]; } else if (args[optind].toLowerCase().equals("-nohttpserver")) { startHTTP = false; } else if (args[optind].toLowerCase().equals("-allowallclients")) { allowAllClients = true; } else if (args[optind].toLowerCase().equals("-?")) { AS2.printUsage(); System.exit(1); } else if (args[optind].toLowerCase().equals("-h")) { AS2.printUsage(); System.exit(1); } else if (args[optind].toLowerCase().equals("-help")) { AS2.printUsage(); System.exit(1); } } //load language from preferences if (language == null) { PreferencesAS2 preferences = new PreferencesAS2(); language = preferences.get(PreferencesAS2.LANGUAGE); } if (language != null) { if (language.toLowerCase().equals("en")) { Locale.setDefault(Locale.ENGLISH); } else if (language.toLowerCase().equals("de")) { Locale.setDefault(Locale.GERMAN); } else if (language.toLowerCase().equals("fr")) { Locale.setDefault(Locale.FRENCH); } else { AS2.printUsage(); System.out.println(); System.out.println("Language " + language + " is not supported."); System.exit(1); } } Splash splash = new Splash("/de/mendelson/comm/as2/client/Splash.jpg"); AffineTransform transform = new AffineTransform(); splash.setTextAntiAliasing(false); transform.setToScale(1.0, 1.0); splash.addDisplayString(new Font("Verdana", Font.BOLD, 11), 7, 262, AS2ServerVersion.getFullProductName(), new Color(0x65, 0xB1, 0x80), transform); splash.setVisible(true); splash.toFront(); //start server try { //register the database drivers for the VM Class.forName("org.hsqldb.jdbcDriver"); //initialize the security provider BCCryptoHelper helper = new BCCryptoHelper(); helper.initialize(); AS2Server as2Server = new AS2Server(startHTTP, allowAllClients); AS2Agent agent = new AS2Agent(as2Server); } catch (UpgradeRequiredException e) { //an upgrade to HSQLDB 2.x is required, delete the lock file Logger.getLogger(AS2Server.SERVER_LOGGER_NAME).warning(e.getMessage()); JOptionPane.showMessageDialog(null, e.getClass().getName() + ": " + e.getMessage()); AS2Server.deleteLockFile(); System.exit(1); } catch (Throwable e) { if (splash != null) { splash.destroy(); } JOptionPane.showMessageDialog(null, e.getMessage()); System.exit(1); } //start client AS2Gui gui = new AS2Gui(splash, "localhost"); gui.setVisible(true); splash.destroy(); splash.dispose(); }
From source file:com.github.braully.graph.UtilResultCompare.java
public static void main(String... args) throws Exception { Options options = new Options(); Option input = new Option("i", "input", true, "input file path"); input.setRequired(false);/*ww w .java2 s . c om*/ options.addOption(input); Option output = new Option("o", "output", true, "output file"); output.setRequired(false); options.addOption(output); CommandLineParser parser = new DefaultParser(); HelpFormatter formatter = new HelpFormatter(); CommandLine cmd; try { cmd = parser.parse(options, args); } catch (ParseException e) { System.out.println(e.getMessage()); formatter.printHelp("UtilResult", options); System.exit(1); return; } String inputFilePath = cmd.getOptionValue("input"); if (inputFilePath == null) { inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-quartic-ht.txt"; // inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-mft-parcial-ht.txt"; // inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-highlyirregular-ht.txt"; // inputFilePath = "/home/strike/Documentos/grafos-processados/mtf/resultado-ht.txt"; // inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-hypo-parcial-ht.txt"; // inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-eul-ht.txt"; // inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-almhypo-ht.txt"; // inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-Almost_hypohamiltonian_graphs_cubic-parcial-ht.txt"; } if (inputFilePath != null) { if (inputFilePath.toLowerCase().endsWith(".txt")) { processFileTxt(inputFilePath); } else if (inputFilePath.toLowerCase().endsWith(".json")) { processFileJson(inputFilePath); } } }
From source file:com.github.vatbub.tictactoe.view.Main.java
public static void main(String[] args) { Common.getInstance().setAppName("tictactoev2"); FOKLogger.enableLoggingOfUncaughtExceptions(); try {//from w w w . j a v a 2 s . c o m applicationConfiguration = new Config(new URL( "https://raw.githubusercontent.com/vatbub/tictactoe/master/remoteconfig/client.properties"), Main.class.getResource("fallbackConfig.properties"), true, "tictactoeClientConfigCache.properties", true); } catch (IOException e) { FOKLogger.log(Main.class.getName(), Level.SEVERE, "Could not read the remote config", e); } for (String arg : args) { if (arg.toLowerCase().matches("mockappversion=.*")) { // Set the mock version String version = arg.substring(arg.toLowerCase().indexOf('=') + 1); Common.getInstance().setMockAppVersion(version); } else if (arg.toLowerCase().matches("mockbuildnumber=.*")) { // Set the mock build number String buildnumber = arg.substring(arg.toLowerCase().indexOf('=') + 1); Common.getInstance().setMockBuildNumber(buildnumber); } else if (arg.toLowerCase().matches("mockpackaging=.*")) { // Set the mock packaging String packaging = arg.substring(arg.toLowerCase().indexOf('=') + 1); Common.getInstance().setMockPackaging(packaging); } else if (arg.toLowerCase().matches("locale=.*")) { // set the gui language String guiLanguageCode = arg.substring(arg.toLowerCase().indexOf('=') + 1); FOKLogger.info(Main.class.getName(), "Setting language: " + guiLanguageCode); Locale.setDefault(new Locale(guiLanguageCode)); } } launch(args); }
From source file:hyperheuristics.main.comparisons.ComputeIndicators.java
public static void main(String[] args) throws IOException, InterruptedException { int[] numberOfObjectivesArray = new int[] { 2, 4 }; String[] problems = new String[] { "OO_MyBatis", "OA_AJHsqldb", "OA_AJHotDraw", "OO_BCEL", "OO_JHotDraw", "OA_HealthWatcher", // "OA_TollSystems", "OO_JBoss" }; String[] heuristicFunctions = new String[] { LowLevelHeuristic.CHOICE_FUNCTION, LowLevelHeuristic.MULTI_ARMED_BANDIT, LowLevelHeuristic.RANDOM }; String[] algorithms = new String[] { "NSGA-II", // "SPEA2" };/*ww w. ja v a2 s . c o m*/ MetricsUtil metricsUtil = new MetricsUtil(); DecimalFormat decimalFormatter = new DecimalFormat("0.00E0"); Mean mean = new Mean(); StandardDeviation standardDeviation = new StandardDeviation(); InvertedGenerationalDistance igd = new InvertedGenerationalDistance(); GenerationalDistance gd = new GenerationalDistance(); Spread spread = new Spread(); Coverage coverage = new Coverage(); for (int objectives : numberOfObjectivesArray) { try (FileWriter IGDWriter = new FileWriter("experiment/IGD_" + objectives + ".tex"); FileWriter spreadWriter = new FileWriter("experiment/SPREAD_" + objectives + ".tex"); FileWriter GDWriter = new FileWriter("experiment/GD_" + objectives + ".tex"); FileWriter coverageWriter = new FileWriter("experiment/COVERAGE_" + objectives + ".tex")) { StringBuilder latexTableBuilder = new StringBuilder(); latexTableBuilder.append("\\documentclass{paper}\n").append("\n") .append("\\usepackage[T1]{fontenc}\n").append("\\usepackage[latin1]{inputenc}\n") .append("\\usepackage[hidelinks]{hyperref}\n").append("\\usepackage{tabulary}\n") .append("\\usepackage{booktabs}\n").append("\\usepackage{multirow}\n") .append("\\usepackage{amsmath}\n").append("\\usepackage{mathtools}\n") .append("\\usepackage{graphicx}\n").append("\\usepackage{array}\n") .append("\\usepackage[linesnumbered,ruled,inoutnumbered]{algorithm2e}\n") .append("\\usepackage{subfigure}\n").append("\\usepackage[hypcap]{caption}\n") .append("\\usepackage{pdflscape}\n").append("\n").append("\\begin{document}\n").append("\n") .append("\\begin{landscape}\n").append("\n"); pfKnown: { latexTableBuilder.append("\\begin{table}[!htb]\n").append("\t\\centering\n") .append("\t\\def\\arraystretch{1.5}\n") // .append("\t\\setlength{\\tabcolsep}{10pt}\n") // .append("\t\\fontsize{8pt}{10pt}\\selectfont\n") .append("\t\\caption{INDICATOR found for $PF_{known}$ for ").append(objectives) .append(" objectives}\n").append("\t\\label{tab:INDICATOR ").append(objectives) .append(" objectives}\n").append("\t\\begin{tabulary}{\\linewidth}{c"); for (String algorithm : algorithms) { latexTableBuilder.append("c"); for (String heuristicFunction : heuristicFunctions) { latexTableBuilder.append("c"); } } latexTableBuilder.append("}\n").append("\t\t\\toprule\n").append("\t\t\\textbf{System}"); for (String algorithm : algorithms) { latexTableBuilder.append(" & \\textbf{").append(algorithm).append("}"); for (String heuristicFunction : heuristicFunctions) { latexTableBuilder.append(" & \\textbf{").append(algorithm).append("-") .append(heuristicFunction).append("}"); } } latexTableBuilder.append("\\\\\n").append("\t\t\\midrule\n"); for (String problem : problems) { NonDominatedSolutionList trueFront = new NonDominatedSolutionList(); pfTrueComposing: { for (String algorithm : algorithms) { SolutionSet mecbaFront = metricsUtil.readNonDominatedSolutionSet( "resultado/" + algorithm.toLowerCase().replaceAll("-", "") + "/" + problem + "_Comb_" + objectives + "obj/All_FUN_" + algorithm.toLowerCase().replaceAll("-", "") + "-" + problem); trueFront.addAll(mecbaFront); for (String hyperHeuristic : heuristicFunctions) { SolutionSet front = metricsUtil.readNonDominatedSolutionSet( "experiment/" + algorithm + "/" + objectives + "objectives/" + hyperHeuristic + "/" + problem + "/FUN.txt"); trueFront.addAll(front); } } } double[][] trueFrontMatrix = trueFront.writeObjectivesToMatrix(); HashMap<String, Double> igdMap = new HashMap<>(); HashMap<String, Double> gdMap = new HashMap<>(); HashMap<String, Double> spreadMap = new HashMap<>(); HashMap<String, Double> coverageMap = new HashMap<>(); for (String algorithm : algorithms) { double[][] mecbaFront = metricsUtil .readFront("resultado/" + algorithm.toLowerCase().replaceAll("-", "") + "/" + problem + "_Comb_" + objectives + "obj/All_FUN_" + algorithm.toLowerCase().replaceAll("-", "") + "-" + problem); igdMap.put(algorithm, igd.invertedGenerationalDistance(mecbaFront, trueFrontMatrix, objectives)); gdMap.put(algorithm, gd.generationalDistance(mecbaFront, trueFrontMatrix, objectives)); spreadMap.put(algorithm, spread.spread(mecbaFront, trueFrontMatrix, objectives)); coverageMap.put(algorithm, coverage.coverage(mecbaFront, trueFrontMatrix)); for (String heuristic : heuristicFunctions) { double[][] heuristicFront = metricsUtil.readFront("experiment/" + algorithm + "/" + objectives + "objectives/" + heuristic + "/" + problem + "/FUN.txt"); igdMap.put(algorithm + "-" + heuristic, igd .invertedGenerationalDistance(heuristicFront, trueFrontMatrix, objectives)); gdMap.put(algorithm + "-" + heuristic, gd.generationalDistance(heuristicFront, trueFrontMatrix, objectives)); spreadMap.put(algorithm + "-" + heuristic, spread.spread(heuristicFront, trueFrontMatrix, objectives)); coverageMap.put(algorithm + "-" + heuristic, coverage.coverage(heuristicFront, trueFrontMatrix)); } } latexTableBuilder.append("\t\t").append(problem); String latexTable = latexTableBuilder.toString(); latexTableBuilder = new StringBuilder(); latexTable = latexTable.replaceAll("O[OA]\\_", "").replaceAll("ChoiceFunction", "CF") .replaceAll("MultiArmedBandit", "MAB"); IGDWriter.write(latexTable.replaceAll("INDICATOR", "IGD")); spreadWriter.write(latexTable.replaceAll("INDICATOR", "Spread")); GDWriter.write(latexTable.replaceAll("INDICATOR", "GD")); coverageWriter.write(latexTable.replaceAll("INDICATOR", "Coverage")); String bestHeuristicIGD = "NULL"; String bestHeuristicGD = "NULL"; String bestHeuristicSpread = "NULL"; String bestHeuristicCoverage = "NULL"; getBest: { double bestMeanIGD = Double.POSITIVE_INFINITY; double bestMeanGD = Double.POSITIVE_INFINITY; double bestMeanSpread = Double.NEGATIVE_INFINITY; double bestMeanCoverage = Double.NEGATIVE_INFINITY; for (String heuristic : igdMap.keySet()) { double heuristicIGD = igdMap.get(heuristic); double heuristicGD = gdMap.get(heuristic); double heuristicSpread = spreadMap.get(heuristic); double heuristicCoverage = coverageMap.get(heuristic); if (heuristicIGD < bestMeanIGD) { bestMeanIGD = heuristicIGD; bestHeuristicIGD = heuristic; } if (heuristicGD < bestMeanGD) { bestMeanGD = heuristicGD; bestHeuristicGD = heuristic; } if (heuristicSpread > bestMeanSpread) { bestMeanSpread = heuristicSpread; bestHeuristicSpread = heuristic; } if (heuristicCoverage > bestMeanCoverage) { bestMeanCoverage = heuristicCoverage; bestHeuristicCoverage = heuristic; } } } StringBuilder igdBuilder = new StringBuilder(); StringBuilder gdBuilder = new StringBuilder(); StringBuilder spreadBuilder = new StringBuilder(); StringBuilder coverageBuilder = new StringBuilder(); String[] newHeuristicFunctions = new String[heuristicFunctions.length * algorithms.length + algorithms.length]; fulfillNewHeuristics: { int i = 0; for (String algorithm : algorithms) { newHeuristicFunctions[i++] = algorithm; for (String heuristicFunction : heuristicFunctions) { newHeuristicFunctions[i++] = algorithm + "-" + heuristicFunction; } } } for (String heuristic : newHeuristicFunctions) { igdBuilder.append(" & "); boolean bold = heuristic.equals(bestHeuristicIGD) || igdMap.get(heuristic).equals(igdMap.get(bestHeuristicIGD)); if (bold) { igdBuilder.append("\\textbf{"); } igdBuilder.append(decimalFormatter.format(igdMap.get(heuristic))); if (bold) { igdBuilder.append("}"); } gdBuilder.append(" & "); bold = heuristic.equals(bestHeuristicGD) || gdMap.get(heuristic).equals(gdMap.get(bestHeuristicGD)); if (bold) { gdBuilder.append("\\textbf{"); } gdBuilder.append(decimalFormatter.format(gdMap.get(heuristic))); if (bold) { gdBuilder.append("}"); } spreadBuilder.append(" & "); bold = heuristic.equals(bestHeuristicSpread) || spreadMap.get(heuristic).equals(spreadMap.get(bestHeuristicSpread)); if (bold) { spreadBuilder.append("\\textbf{"); } spreadBuilder.append(decimalFormatter.format(spreadMap.get(heuristic))); if (bold) { spreadBuilder.append("}"); } coverageBuilder.append(" & "); bold = heuristic.equals(bestHeuristicCoverage) || coverageMap.get(heuristic).equals(coverageMap.get(bestHeuristicCoverage)); if (bold) { coverageBuilder.append("\\textbf{"); } coverageBuilder.append(decimalFormatter.format(coverageMap.get(heuristic))); if (bold) { coverageBuilder.append("}"); } } IGDWriter.write(igdBuilder + "\\\\\n"); spreadWriter.write(spreadBuilder + "\\\\\n"); GDWriter.write(gdBuilder + "\\\\\n"); coverageWriter.write(coverageBuilder + "\\\\\n"); } latexTableBuilder = new StringBuilder(); latexTableBuilder.append("\t\t\\bottomrule\n").append("\t\\end{tabulary}\n") .append("\\end{table}\n\n"); } averages: { latexTableBuilder.append("\\begin{table}[!htb]\n").append("\t\\centering\n") .append("\t\\def\\arraystretch{1.5}\n") // .append("\t\\setlength{\\tabcolsep}{10pt}\n") // .append("\t\\fontsize{8pt}{10pt}\\selectfont\n") .append("\t\\caption{INDICATOR averages found for ").append(objectives) .append(" objectives}\n").append("\t\\label{tab:INDICATOR ").append(objectives) .append(" objectives}\n").append("\t\\begin{tabulary}{\\linewidth}{c"); for (String algorithm : algorithms) { latexTableBuilder.append("c"); for (String heuristicFunction : heuristicFunctions) { latexTableBuilder.append("c"); } } latexTableBuilder.append("}\n").append("\t\t\\toprule\n").append("\t\t\\textbf{System}"); for (String algorithm : algorithms) { latexTableBuilder.append(" & \\textbf{").append(algorithm).append("}"); for (String heuristicFunction : heuristicFunctions) { latexTableBuilder.append(" & \\textbf{").append(algorithm).append("-") .append(heuristicFunction).append("}"); } } latexTableBuilder.append("\\\\\n").append("\t\t\\midrule\n"); for (String problem : problems) { NonDominatedSolutionList trueFront = new NonDominatedSolutionList(); pfTrueComposing: { for (String algorithm : algorithms) { SolutionSet mecbaFront = metricsUtil.readNonDominatedSolutionSet( "resultado/" + algorithm.toLowerCase().replaceAll("-", "") + "/" + problem + "_Comb_" + objectives + "obj/All_FUN_" + algorithm.toLowerCase().replaceAll("-", "") + "-" + problem); trueFront.addAll(mecbaFront); for (String hyperHeuristic : heuristicFunctions) { SolutionSet front = metricsUtil.readNonDominatedSolutionSet( "experiment/" + algorithm + "/" + objectives + "objectives/" + hyperHeuristic + "/" + problem + "/FUN.txt"); trueFront.addAll(front); } } } double[][] trueFrontMatrix = trueFront.writeObjectivesToMatrix(); HashMap<String, double[]> igdMap = new HashMap<>(); HashMap<String, double[]> gdMap = new HashMap<>(); HashMap<String, double[]> spreadMap = new HashMap<>(); HashMap<String, double[]> coverageMap = new HashMap<>(); mocaito: { for (String algorithm : algorithms) { double[] mecbaIGDs = new double[EXECUTIONS]; double[] mecbaGDs = new double[EXECUTIONS]; double[] mecbaSpreads = new double[EXECUTIONS]; double[] mecbaCoverages = new double[EXECUTIONS]; for (int i = 0; i < EXECUTIONS; i++) { double[][] mecbaFront = metricsUtil.readFront("resultado/" + algorithm.toLowerCase().replaceAll("-", "") + "/" + problem + "_Comb_" + objectives + "obj/FUN_" + algorithm.toLowerCase().replaceAll("-", "") + "-" + problem + "-" + i + ".NaoDominadas"); mecbaIGDs[i] = igd.invertedGenerationalDistance(mecbaFront, trueFrontMatrix, objectives); mecbaGDs[i] = gd.generationalDistance(mecbaFront, trueFrontMatrix, objectives); mecbaSpreads[i] = spread.spread(mecbaFront, trueFrontMatrix, objectives); mecbaCoverages[i] = coverage.coverage(mecbaFront, trueFrontMatrix); } igdMap.put(algorithm, mecbaIGDs); gdMap.put(algorithm, mecbaGDs); spreadMap.put(algorithm, mecbaSpreads); coverageMap.put(algorithm, mecbaCoverages); } } for (String algorithm : algorithms) { for (String heuristic : heuristicFunctions) { double[] hhIGDs = new double[EXECUTIONS]; double[] hhGDs = new double[EXECUTIONS]; double[] hhSpreads = new double[EXECUTIONS]; double[] hhCoverages = new double[EXECUTIONS]; for (int i = 0; i < EXECUTIONS; i++) { double[][] hhFront = metricsUtil .readFront("experiment/" + algorithm + "/" + objectives + "objectives/" + heuristic + "/" + problem + "/EXECUTION_" + i + "/FUN.txt"); hhIGDs[i] = igd.invertedGenerationalDistance(hhFront, trueFrontMatrix, objectives); hhGDs[i] = gd.generationalDistance(hhFront, trueFrontMatrix, objectives); hhSpreads[i] = spread.spread(hhFront, trueFrontMatrix, objectives); hhCoverages[i] = coverage.coverage(hhFront, trueFrontMatrix); } igdMap.put(algorithm + "-" + heuristic, hhIGDs); gdMap.put(algorithm + "-" + heuristic, hhGDs); spreadMap.put(algorithm + "-" + heuristic, hhSpreads); coverageMap.put(algorithm + "-" + heuristic, hhCoverages); } } HashMap<String, HashMap<String, Boolean>> igdResult = KruskalWallisTest.test(igdMap); HashMap<String, HashMap<String, Boolean>> gdResult = KruskalWallisTest.test(gdMap); HashMap<String, HashMap<String, Boolean>> spreadResult = KruskalWallisTest.test(spreadMap); HashMap<String, HashMap<String, Boolean>> coverageResult = KruskalWallisTest .test(coverageMap); latexTableBuilder.append("\t\t").append(problem); String latexTable = latexTableBuilder.toString(); latexTable = latexTable.replaceAll("O[OA]\\_", "").replaceAll("ChoiceFunction", "CF") .replaceAll("MultiArmedBandit", "MAB"); IGDWriter.write(latexTable.replaceAll("INDICATOR", "IGD")); spreadWriter.write(latexTable.replaceAll("INDICATOR", "Spread")); GDWriter.write(latexTable.replaceAll("INDICATOR", "GD")); coverageWriter.write(latexTable.replaceAll("INDICATOR", "Coverage")); latexTableBuilder = new StringBuilder(); String bestHeuristicIGD = "NULL"; String bestHeuristicGD = "NULL"; String bestHeuristicSpread = "NULL"; String bestHeuristicCoverage = "NULL"; getBest: { double bestMeanIGD = Double.POSITIVE_INFINITY; double bestMeanGD = Double.POSITIVE_INFINITY; double bestMeanSpread = Double.NEGATIVE_INFINITY; double bestMeanCoverage = Double.NEGATIVE_INFINITY; for (String heuristic : igdMap.keySet()) { double heuristicMeanIGD = mean.evaluate(igdMap.get(heuristic)); double heuristicMeanGD = mean.evaluate(gdMap.get(heuristic)); double heuristicMeanSpread = mean.evaluate(spreadMap.get(heuristic)); double heuristicMeanCoverage = mean.evaluate(coverageMap.get(heuristic)); if (heuristicMeanIGD < bestMeanIGD) { bestMeanIGD = heuristicMeanIGD; bestHeuristicIGD = heuristic; } if (heuristicMeanGD < bestMeanGD) { bestMeanGD = heuristicMeanGD; bestHeuristicGD = heuristic; } if (heuristicMeanSpread > bestMeanSpread) { bestMeanSpread = heuristicMeanSpread; bestHeuristicSpread = heuristic; } if (heuristicMeanCoverage > bestMeanCoverage) { bestMeanCoverage = heuristicMeanCoverage; bestHeuristicCoverage = heuristic; } } } StringBuilder igdBuilder = new StringBuilder(); StringBuilder gdBuilder = new StringBuilder(); StringBuilder spreadBuilder = new StringBuilder(); StringBuilder coverageBuilder = new StringBuilder(); String[] newHeuristicFunctions = new String[heuristicFunctions.length * algorithms.length + algorithms.length]; fulfillNewHeuristics: { int i = 0; for (String algorithm : algorithms) { newHeuristicFunctions[i++] = algorithm; for (String heuristicFunction : heuristicFunctions) { newHeuristicFunctions[i++] = algorithm + "-" + heuristicFunction; } } } for (String heuristic : newHeuristicFunctions) { igdBuilder.append(" & "); boolean bold = heuristic.equals(bestHeuristicIGD) || !igdResult.get(heuristic).get(bestHeuristicIGD); if (bold) { igdBuilder.append("\\textbf{"); } igdBuilder.append(decimalFormatter.format(mean.evaluate(igdMap.get(heuristic))) + " (" + decimalFormatter.format(standardDeviation.evaluate(igdMap.get(heuristic))) + ")"); if (bold) { igdBuilder.append("}"); } gdBuilder.append(" & "); bold = heuristic.equals(bestHeuristicGD) || !gdResult.get(heuristic).get(bestHeuristicGD); if (bold) { gdBuilder.append("\\textbf{"); } gdBuilder.append(decimalFormatter.format(mean.evaluate(gdMap.get(heuristic))) + " (" + decimalFormatter.format(standardDeviation.evaluate(gdMap.get(heuristic))) + ")"); if (bold) { gdBuilder.append("}"); } spreadBuilder.append(" & "); bold = heuristic.equals(bestHeuristicSpread) || !spreadResult.get(heuristic).get(bestHeuristicSpread); if (bold) { spreadBuilder.append("\\textbf{"); } spreadBuilder.append(decimalFormatter.format(mean.evaluate(spreadMap.get(heuristic))) + " (" + decimalFormatter.format(standardDeviation.evaluate(spreadMap.get(heuristic))) + ")"); if (bold) { spreadBuilder.append("}"); } coverageBuilder.append(" & "); bold = heuristic.equals(bestHeuristicCoverage) || !coverageResult.get(heuristic).get(bestHeuristicCoverage); if (bold) { coverageBuilder.append("\\textbf{"); } coverageBuilder .append(decimalFormatter.format(mean.evaluate(coverageMap.get(heuristic)))) .append(" (") .append(decimalFormatter .format(standardDeviation.evaluate(coverageMap.get(heuristic)))) .append(")"); if (bold) { coverageBuilder.append("}"); } } IGDWriter.write(igdBuilder + "\\\\\n"); spreadWriter.write(spreadBuilder + "\\\\\n"); GDWriter.write(gdBuilder + "\\\\\n"); coverageWriter.write(coverageBuilder + "\\\\\n"); } latexTableBuilder.append("\t\t\\bottomrule\n").append("\t\\end{tabulary}\n") .append("\\end{table}\n\n"); } latexTableBuilder.append("\\end{landscape}\n\n").append("\\end{document}"); String latexTable = latexTableBuilder.toString(); IGDWriter.write(latexTable); spreadWriter.write(latexTable); GDWriter.write(latexTable); coverageWriter.write(latexTable); } } }
From source file:com.hygenics.parser.MainApp.java
/** * The entire programs main method.// w w w. j a v a 2 s.c om * * @param args */ public static void main(String[] args) { final Logger log = LoggerFactory.getLogger(MainApp.class); log.info("Starting Parse @ " + Calendar.getInstance().getTime().toString()); ClassPathXmlApplicationContext context = new ClassPathXmlApplicationContext( ("file:" + System.getProperty("beansfile").trim())); log.info("Found beans @ " + System.getProperty("beansfile").trim()); log.info("Starting"); ArrayList<String> results = null; String activity = null; log.info("Obtaining Activities"); ActivitiesStack stack = (ActivitiesStack) context.getBean("ActivitiesStack"); // integers keeping track of bean number to pull (e.g. DumpToText0 or // DumpToText1) // in keeping with the spirit of dumping out data int n = 0, srn = 0, mv = 0, cen = 0, pps = 0, sb = 0, kv = 0, cf = 0, zip = 0, bm = 0, dump = 0, kettle = 0, execute = 0, transfer = 0, sqls = 0, job = 0, parsepages = 0, getpages = 0, map = 0, js = 0, sdump = 0, transforms = 0, execs = 0, gim = 0, ems = 0, jd = 0; Pattern p = Pattern.compile("[A-Za-z]+[0-9]+"); Matcher m; // start stack init log.info("Stack Initialized with Size of " + stack.getSize() + " @ " + Calendar.getInstance().getTime().toString()); while (stack.getSize() > 0) { // pop activity form stack activity = stack.Pop(); log.info("Activities Remaining " + stack.getSize()); m = p.matcher(activity); log.info("\n\nACTIVITY: " + activity + "\n\n"); if (activity.toLowerCase().contains("manualrepconn")) { log.info("Manual Transformation Started @ " + Calendar.getInstance().getTime().toString()); ManualReplacement mrp = (ManualReplacement) context.getBean("ManualRepConn"); mrp.run(); log.info("Manual Transformation Finished @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("cleanfolder")) { log.info("Folder Cleanup Started @ " + Calendar.getInstance().getTime().toString()); CleanFolder c; if (cf == 0 || context.containsBean("CleanFolder")) { c = (CleanFolder) ((context.containsBean("CleanFolder")) ? context.getBean("CleanFolder") : context.getBean("CleanFolder" + cf)); } else { c = (CleanFolder) context.getBean("CleanFolder" + cf); } c.run(); cf++; log.info("File Cleanup Complete @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("zip")) { log.info("Zip File Creation Started @ " + Calendar.getInstance().getTime().toString()); Archiver a; if (zip == 0 || context.containsBean("Zip")) { a = (Archiver) ((context.containsBean("Zip")) ? context.getBean("Zip") : context.getBean("Zip" + zip)); } else { a = (Archiver) context.getBean("Zip" + zip); } a.run(); zip++; log.info("Zip File Creation Complete @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("transfer")) { log.info("File Transfer Started @ " + Calendar.getInstance().getTime().toString()); Upload u; if (transfer == 0 || context.containsBean("FileTransfer")) { u = (Upload) ((context.containsBean("FileTransfer")) ? context.getBean("FileTransfer") : context.getBean("FileTransfer" + transfer)); } else { u = (Upload) context.getBean("FileTransfer" + transfer); } u.run(); transfer++; log.info("File Transfer Complete @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("droptables")) { // drop tables log.info("Dropping Tables @ " + Calendar.getInstance().getTime().toString()); DropTables droptables = (DropTables) context.getBean("DropTables"); droptables.run(); droptables = null; log.info("Done Dropping Tables @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().equals("createtables")) { // create tables log.info("Creating Tables @ " + Calendar.getInstance().getTime().toString()); CreateTable create = (CreateTable) context.getBean("CreateTables"); create.run(); create = null; log.info("Done Creating Tables @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("createtableswithreference")) { // create tables log.info("Creating Tables @ " + Calendar.getInstance().getTime().toString()); CreateTablesWithReference create = (CreateTablesWithReference) context .getBean("CreateTablesWithReference"); create.run(); create = null; log.info("Done Creating Tables @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("truncate")) { // truncate table log.info("Truncating @ " + Calendar.getInstance().getTime().toString()); Truncate truncate = (Truncate) context.getBean("Truncate"); truncate.truncate(); truncate = null; log.info("Truncated @ " + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().equals("enforce")) { // enforce schema log.info("Enforcing Schema @" + Calendar.getInstance().getTime().toString()); ForceConformity ef = (ForceConformity) context.getBean("EnforceStandards"); ef.run(); log.info("Done Enforcing Schema @" + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().contains("enforcewithreference")) { // enforce schema ForceConformityWithReference ef = (ForceConformityWithReference) context .getBean("EnforceStandardsWithReference"); log.info("Enforcing Schema By Reference @" + Calendar.getInstance().getTime().toString()); ef.run(); log.info("Done Enforcing Schema @" + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().trim().equals("repconn")) { log.info("Replacing Transformation Connection Information @" + Calendar.getInstance().getTime().toString()); RepConn rep = (RepConn) context.getBean("repconn"); rep.run(); log.info("Finished Replacing Connection Information @" + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("job")) { // run a Pentaho job as opposed to a Pentaho Transformation log.info("Run Job kjb file @" + Calendar.getInstance().getTime().toString()); RunJob kjb = null; if (m.find()) { kjb = (RunJob) context.getBean(activity); } else { kjb = (RunJob) context.getBean("Job" + job); } kjb.run(); kjb = null; log.info("Pentaho Job Complete @" + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); } else if (activity.toLowerCase().compareTo("execute") == 0) { // Execute a process log.info("Executing Process @" + Calendar.getInstance().getTime().toString()); if (context.containsBean("Execute") && execs == 0) { ExecuteProcess proc = (ExecuteProcess) context.getBean(("Execute")); proc.Execute(); } else { ExecuteProcess proc = (ExecuteProcess) context.getBean(("Execute" + execute)); proc.Execute(); } execs++; log.info("Pages Obtained @" + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().contains("parsepageswithscala") || activity.toLowerCase().contains("parsepagesscala")) { //parse pages with scala log.info("Parsing Pages with Scala @ " + Calendar.getInstance().getTime().toString()); ScalaParseDispatcher pds = null; if (context.containsBean("ParsePagesScala" + pps)) { pds = (ScalaParseDispatcher) context.getBean("ParsePagesScala" + pps); } else if (context.containsBean("ParsePagesScala") && pps > 0) { pds = (ScalaParseDispatcher) context.getBean("ParsePagesScala"); } pps++; pds.run(); Runtime.getRuntime().gc(); log.info("Finished Parsing Pages with Scala @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("parsepages")) { // Parse Pages with java log.info("Parsing Individual Pages @" + Calendar.getInstance().getTime().toString()); if (context.containsBean("ParsePages") && parsepages == 0) { ParseDispatcher pd = (ParseDispatcher) context.getBean("ParsePages"); pd.run(); pd = null; } else { ParseDispatcher pd = (ParseDispatcher) context.getBean("ParsePages" + parsepages); pd.run(); pd = null; } parsepages++; log.info("Finished Parsing @" + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().contains("kvparser")) { // Parse Pages using the KV Parser log.info("Parsing Individual Pages with Key Value Pairs @" + Calendar.getInstance().getTime().toString()); if (context.containsBean("KVParser") && parsepages == 0) { KVParser pd = (KVParser) context.getBean("KVParser"); pd.run(); pd = null; } else { KVParser pd = (KVParser) context.getBean("KVParser" + kv); pd.run(); pd = null; } parsepages++; log.info("Finished Parsing @" + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().contains("parsewithsoup")) { // Parse Pages with Jsoup log.info("Parsing Pages with JSoup @ " + Calendar.getInstance().getTime().toString()); if (context.containsBean("ParseJSoup") && js == 0) { ParseJSoup psj = (ParseJSoup) context.getBean("ParseJSoup"); psj.run(); } else { ParseJSoup psj = (ParseJSoup) context.getBean("ParseJSoup" + Integer.toString(js)); psj.run(); } js++; log.info("Finished Parsing @" + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); log.info("Finished Parsing with JSoup @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("breakmultiplescala") || activity.toLowerCase().contains("breakmultiplewithscala")) { log.info("Breaking Records"); BreakMultipleScala bms = null; if (context.containsBean("BreakMultipleScala" + ems)) { bms = (BreakMultipleScala) context.getBean("BreakMultipleScala" + sb); } else { bms = (BreakMultipleScala) context.getBean("BreakMultipleScala"); } bms.run(); bms = null; sb++; Runtime.getRuntime().gc(); System.gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); log.info("Completed Breaking Tasks"); } else if (activity.toLowerCase().contains("breakmultiple")) { // break apart multi-part records log.info("Breaking apart Records (BreakMultiple) @" + Calendar.getInstance().getTime().toString()); if (context.containsBean("BreakMultiple") && bm == 0) { BreakMultiple br = (BreakMultiple) context.getBean(("BreakMultiple")); br.run(); br = null; } else { BreakMultiple br = (BreakMultiple) context.getBean(("BreakMultiple" + Integer.toString(bm))); br.run(); br = null; } bm++; log.info("Finished Breaking Apart Records @" + Calendar.getInstance().getTime().toString()); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().compareTo("mapper") == 0) { // remap data log.info("Mapping Records @" + Calendar.getInstance().getTime().toString()); if (context.containsBean("Mapper") && map == 0) { Mapper mp = (Mapper) context.getBean("Mapper"); mp.run(); mp = null; } else { Mapper mp = (Mapper) context.getBean("Mapper" + Integer.toString(map)); mp.run(); mp = null; } map++; log.info("Completed Mapping Records @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("getimages")) { // Get Images in a Separate Step log.info("Beggining Image Pull @ " + Calendar.getInstance().getTime().toString()); if (context.containsBean("getImages") && gim == 0) { GetImages gi = (GetImages) context.getBean("getImages"); gi.run(); log.info("Image Pull Complete @ " + Calendar.getInstance().getTime().toString()); gi = null; } else { GetImages gi = (GetImages) context.getBean("getImages"); gi.run(); log.info("Image Pull Complete @ " + Calendar.getInstance().getTime().toString()); gi = null; } gim++; Runtime.getRuntime().gc(); System.gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().compareTo("sql") == 0) { // execute a sql command log.info("Executing SQL Query @ " + Calendar.getInstance().getTime().toString()); if (context.containsBean("SQL") && sqls == 0) { ExecuteSQL sql; if (m.find()) { sql = (ExecuteSQL) context.getBean(activity); } else { sql = (ExecuteSQL) context.getBean("SQL"); } sql.execute(); sql = null; } else { ExecuteSQL sql; if (m.find()) { sql = (ExecuteSQL) context.getBean(activity); } else { sql = (ExecuteSQL) context.getBean("SQL" + sqls); } sql.execute(); sql = null; } sqls++; log.info("Finished SQL Query @ " + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); System.gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().compareTo("kettle") == 0) { // run one or more kettle transformation(s) log.info("Beginning Kettle Transformation @ " + Calendar.getInstance().getTime().toString()); RunTransformation rt = null; if (context.containsBean("kettle") && transforms == 0) { if (m.find()) { rt = (RunTransformation) context.getBean(activity); } else { rt = (RunTransformation) context.getBean(("kettle")); } rt.run(); rt = null; } else { if (m.find()) { rt = (RunTransformation) context.getBean(activity); } else { rt = (RunTransformation) context.getBean(("kettle" + kettle)); } rt.run(); rt = null; } transforms++; log.info("Ending Kettle Transformation @ " + Calendar.getInstance().getTime().toString()); Runtime.getRuntime().gc(); System.gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); kettle++; } else if (activity.toLowerCase().contains("dumptotext")) { // dump to a text file via java log.info("Dumping to Text @ " + Calendar.getInstance().getTime().toString()); DumptoText dtt = null; if (m.find()) { dtt = (DumptoText) context.getBean(activity); } else { dtt = (DumptoText) context.getBean("DumpToText" + dump); } dtt.run(); dump++; log.info("Completed Dump @ " + Calendar.getInstance().getTime().toString()); dtt = null; Runtime.getRuntime().gc(); System.gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().equals("jdump")) { log.info("Dumping via JDump @ " + Calendar.getInstance().getTime().toString()); if (jd == 0 && context.containsBean("JDump")) { JDump j = (JDump) context.getBean("JDump"); jd++; j.run(); } else { JDump j = (JDump) context.getBean("JDump" + jd); jd++; j.run(); } Runtime.getRuntime().gc(); System.gc(); log.info("Finished Dumping via JDump @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("jdumpwithreference")) { log.info("Dumping via JDump @ " + Calendar.getInstance().getTime().toString()); if (jd == 0 && context.containsBean("JDumpWithReference")) { JDumpWithReference j = (JDumpWithReference) context.getBean("JDumpWithReference"); jd++; j.run(); } else { JDumpWithReference j = (JDumpWithReference) context.getBean("JDumpWithReference" + jd); jd++; j.run(); } Runtime.getRuntime().gc(); System.gc(); log.info("Finished Dumping via JDump @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().compareTo("commanddump") == 0) { // dump to text using a client side sql COPY TO command log.info("Dumping via SQL @ " + Calendar.getInstance().getTime().toString()); CommandDump d = (CommandDump) context.getBean("dump"); d.run(); d = null; log.info("Completed Dump @ " + Calendar.getInstance().getTime().toString()); // most likely not needed by satisfies my paranoia Runtime.getRuntime().gc(); System.gc(); } else if (activity.toLowerCase().equals("specdump")) { // Specified Dump log.info("Dumping via Specified Tables, Files, and Attributes @ " + Calendar.getInstance().getTime().toString()); if (context.containsBean("SpecDump") && sdump == 0) { sdump++; SpecifiedDump sd = (SpecifiedDump) context.getBean("SpecDump"); sd.run(); sd = null; } else if (context.containsBean("SpecDump" + Integer.toString(sdump))) { SpecifiedDump sd = (SpecifiedDump) context.getBean("SpecDump" + Integer.toString(sdump)); sd.run(); sd = null; } sdump++; log.info("Completed Dumping via Specified Tables, Files, and Attributes @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("specdumpwithreference")) { // Specified Dump log.info("Dumping via Specified Tables, Files, and Attributes by Reference @ " + Calendar.getInstance().getTime().toString()); if (context.containsBean("SpecDumpWithReference") && sdump == 0) { sdump++; SpecDumpWithReference sd = (SpecDumpWithReference) context.getBean("SpecDumpWithReference"); sd.run(); sd = null; } else if (context.containsBean("SpecDumpWithReference" + Integer.toString(sdump))) { SpecDumpWithReference sd = (SpecDumpWithReference) context .getBean("SpecDumpWithReference" + Integer.toString(sdump)); sd.run(); sd = null; } else { log.info("Bean Not Found For " + activity); } sdump++; log.info("Completed Dumping via Specified Tables, Files, and Attributes @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().compareTo("email") == 0) { // email completion notice log.info("Sending Notice of Completion @ " + Calendar.getInstance().getTime().toString()); if (context.containsBean("Email") && ems == 0) { Send s = (Send) context.getBean("Email"); s.run(); s = null; } else { Send s = (Send) context.getBean("Email" + Integer.toString(ems)); s.run(); s = null; } ems++; Runtime.getRuntime().gc(); System.gc(); log.info("Completed Email @ " + Calendar.getInstance().getTime().toString()); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().equals("qa")) { // perform qa log.info("Performing Quality Assurance @ " + Calendar.getInstance().getTime().toString()); if (context.containsBean("QA")) { QualityAssurer qa = (QualityAssurer) context.getBean("QA"); qa.run(); qa = null; } // attempt to hint --> all tasks are really intense so anything // is nice Runtime.getRuntime().gc(); System.gc(); log.info("Completed QA @ " + Calendar.getInstance().getTime().toString()); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); } else if (activity.toLowerCase().equals("notify")) { log.info("Running Notification Tasks"); Notification nt = null; if (context.containsBean("Notify" + Integer.toString(n))) { nt = (Notification) context.getBean("Notify" + Integer.toString(n)); } else { nt = (Notification) context.getBean("Notify"); } nt.run(); nt = null; n++; if (context.containsBean("Email") && ems == 0) { Send s = (Send) context.getBean("Email"); s.run(); s = null; } else if (context.containsBean("Email" + ems)) { Send s = (Send) context.getBean("Email" + Integer.toString(ems)); s.run(); s = null; } ems++; Runtime.getRuntime().gc(); System.gc(); log.info("Free Memory: " + Runtime.getRuntime().freeMemory()); log.info("Completed Notification Tasks"); } else if (activity.toLowerCase().contains("move")) { log.info("Moving Files @ " + Calendar.getInstance().getTime().toString()); MoveFile mf = null; if (context.containsBean("Move" + Integer.toString(mv))) { mf = (MoveFile) context.getBean("Move" + Integer.toString(mv)); } else { mf = (MoveFile) context.getBean("Move"); } mf.run(); mv++; Runtime.getRuntime().gc(); log.info("Finished Moving Files @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("numericalcheck")) { log.info("Checking Counts"); NumericalChecker nc = (NumericalChecker) context.getBean("NumericalChecker"); nc.run(); Runtime.getRuntime().gc(); log.info("Finished Checking Counts @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("runscript")) { log.info("Running Script @ " + Calendar.getInstance().getTime().toString()); RunScript runner = null; if (context.containsBean("RunScript" + srn)) { runner = (RunScript) context.getBean("RunScript" + srn); } else { runner = (RunScript) context.getBean("RunScript"); } runner.run(); srn++; Runtime.getRuntime().gc(); log.info("Finished Running SCript @ " + Calendar.getInstance().getTime().toString()); } else if (activity.toLowerCase().contains("checkexistance")) { log.info("Checking Existance @ " + Calendar.getInstance().getTime().toString()); ExistanceChecker runner = null; if (context.containsBean("CheckExistance" + srn)) { runner = (ExistanceChecker) context.getBean("CheckExistance" + cen); } else { runner = (ExistanceChecker) context.getBean("CheckExistance"); } runner.run(); cen++; Runtime.getRuntime().gc(); log.info("Finished Checking Existance @ " + Calendar.getInstance().getTime().toString()); } else { log.info("Activity " + activity + " does not exist!"); } } log.info("Completed Parse @ " + Calendar.getInstance().getTime().toString()); context.destroy(); context.close(); }