Example usage for java.util HashMap values

Introduction

In this page you can find the example usage for java.util HashMap values.

Prototype

public Collection<V> values() 

Source Link

Document

Returns a Collection view of the values contained in this map.

Usage

From source file:DIA_Umpire_To_Skyline.DIA_Umpire_To_Skyline.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_To_Skyline (version: " + UmpireInfo.GetInstance().Version + ")");
    if (args.length < 1) {
        System.out.println(
                "command format error, it should be like: java -jar -Xmx20G DIA_Umpire_To_Skyline.jar Path NoThreads");
        System.out.println("command : java -jar -Xmx20G DIA_Umpire_To_Skyline.jar Path [Option]\n");
        System.out.println("\nOptions");
        System.out.println("\t-t\tNo. of threads, Ex: -t4 (using four threads, default value)");
        System.out.println(
                "\t-cP\tPath of msconvert.exe for mzXML conversion, Ex: -cP (using four threads, default value)");
        return;
    }
    try {
        ConsoleLogger.SetConsoleLogger(Level.DEBUG);
        ConsoleLogger.SetFileLogger(Level.DEBUG,
                FilenameUtils.getFullPath(args[0]) + "diaumpire_to_skyline.log");
    } catch (Exception e) {
        System.out.println("Logger initialization failed");
    }

    Logger.getRootLogger().info("Path:" + args[0]);
    String msconvertpath = "C:/inetpub/tpp-bin/msconvert";

    String WorkFolder = args[0];
    int NoCPUs = 4;

    for (int i = 1; i < args.length; i++) {
        if (args[i].startsWith("-")) {
            if (args[i].startsWith("-cP")) {
                msconvertpath = args[i].substring(3);
                Logger.getRootLogger().info("MSConvert path: " + msconvertpath);
            }
            if (args[i].startsWith("-t")) {
                NoCPUs = Integer.parseInt(args[i].substring(2));
                Logger.getRootLogger().info("No. of threads: " + NoCPUs);
            }
        }
    }

    HashMap<String, File> AssignFiles = new HashMap<>();

    try {
        File folder = new File(WorkFolder);
        if (!folder.exists()) {
            Logger.getRootLogger().info("Path: " + folder.getAbsolutePath() + " cannot be found.");
        }
        for (final File fileEntry : folder.listFiles()) {
            if (fileEntry.isFile() && fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml")
                    && !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("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());
        }

        ExecutorService executorPool = null;
        executorPool = Executors.newFixedThreadPool(3);

        for (File fileEntry : AssignFiles.values()) {
            String mzXMLFile = fileEntry.getAbsolutePath();
            FileThread thread = new FileThread(mzXMLFile, NoCPUs, msconvertpath);
            executorPool.execute(thread);
        }
        executorPool.shutdown();
        try {
            executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
        } catch (InterruptedException e) {
            Logger.getRootLogger().info("interrupted..");
        }
    } catch (Exception e) {
        Logger.getRootLogger().error(e.getMessage());
        throw e;
    }
    Logger.getRootLogger().info("Job done");
    Logger.getRootLogger().info(
            "=================================================================================================");

}

---

From source file:edu.usc.squash.Main.java

public static void main(String[] args) {
    Stack<Module> modulesStack;
    Module module;/*ww  w .ja  v a 2 s . c o  m*/

    if (parseInputs(args) == false) {
        System.exit(-1); //The input files do not exist
    }

    String separator = "----------------------------------------------";
    System.out.println("Squash v2.0");
    System.out.println(separator);
    long start = System.currentTimeMillis();

    // Parsing the input library
    Library library = QLib.readLib(libraryPath);
    library.setCurrentECC(currentECC);

    HashMap<String, Module> modules = parseQASMHF(library);
    Module mainModule = modules.get("main");

    //Finding max{A_L_i}
    int childModulesLogicalAncillaReq;
    int moduleAncillaReq;

    modulesStack = new Stack<Module>();

    modulesStack.add(mainModule);
    while (!modulesStack.isEmpty()) {
        module = modulesStack.peek();
        if (!module.isVisited() && module.isChildrenVisited()) {
            //Finding the maximum 
            childModulesLogicalAncillaReq = 0;
            for (Module child : module.getDFG().getModules()) {
                childModulesLogicalAncillaReq = Math.max(childModulesLogicalAncillaReq, child.getAncillaReq());
            }
            moduleAncillaReq = module.getAncillaQubitNo() + childModulesLogicalAncillaReq;
            module.setAncillaReq(moduleAncillaReq);
            //            System.out.println("Module "+module.getName()+" requires "+moduleAncillaReq+" ancilla.");

            modulesStack.pop();
            module.setVisited();
        } else if (module.isVisited()) {
            modulesStack.pop();
        } else if (!module.isChildrenVisited()) {
            modulesStack.addAll(module.getDFG().getModules());
            module.setChildrenVisited();
        }
    }

    int totalLogicalAncilla = mainModule.getAncillaReq();

    System.out.println("A_L_i_max: " + totalLogicalAncilla);

    final int Q_L = mainModule.getDataQubitNo();

    /* 
     * In order traversal of modules
     */
    //Making sure all of the modules are unvisited
    for (Module m : modules.values()) {
        m.setUnvisited();
    }
    modulesStack = new Stack<Module>();

    modulesStack.add(mainModule);
    while (!modulesStack.isEmpty()) {
        module = modulesStack.peek();
        if (!module.isVisited() && module.isChildrenVisited()) {
            System.out.println(separator);

            mapModule(module, k, physicalAncillaBudget, totalLogicalAncilla, Q_L, beta_pmd, alpha_int,
                    gamma_memory, library);

            modulesStack.pop();
            module.setVisited();
        } else if (module.isVisited()) {
            modulesStack.pop();
        } else if (!module.isChildrenVisited()) {
            modulesStack.addAll(module.getDFG().getModules());
            module.setChildrenVisited();
        }
    }

    System.out.println(separator);
    double runtime = (System.currentTimeMillis() - start) / 1000.0;
    System.out.println("B_P: " + B_P);
    System.out.println("Total Runtime:\t" + runtime + " sec");
}

---

From source file:DIA_Umpire_Quant.DIA_Umpire_LCMSIDGen.java

/**
 * @param args the command line arguments
 *//*  w  ww.j  a  va 2 s . c  om*/
public static void main(String[] args) throws FileNotFoundException, IOException, Exception {
    System.out.println(
            "=================================================================================================");
    System.out.println("DIA-Umpire LCMSID geneartor (version: " + UmpireInfo.GetInstance().Version + ")");
    if (args.length != 1) {
        System.out.println(
                "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_LCMSIDGen.jar diaumpire_module.params");
        return;
    }
    try {
        ConsoleLogger.SetConsoleLogger(Level.INFO);
        ConsoleLogger.SetFileLogger(Level.DEBUG,
                FilenameUtils.getFullPath(args[0]) + "diaumpire_lcmsidgen.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;

    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 "DecoyPrefix": {
                if (!"".equals(value)) {
                    tandemPara.DecoyPrefix = value;
                }
                break;
            }
            case "PeptideFDR": {
                tandemPara.PepFDR = Float.parseFloat(value);
                break;
            }
            }
        }
    }
    //</editor-fold>

    //Initialize PTM manager using compomics library
    PTMManager.GetInstance();

    //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());
    }

    //process each DIA file to genearate untargeted identifications
    for (File fileEntry : AssignFiles.values()) {
        String mzXMLFile = fileEntry.getAbsolutePath();
        if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) {
            long time = System.currentTimeMillis();

            DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs);
            FileList.add(DiaFile);
            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 + "....");

            DiaFile.ParsePepXML(tandemPara, null);
            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(mzXMLFile + " 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))));
        }
        Logger.getRootLogger().info("Job done");
        Logger.getRootLogger().info(
                "=================================================================================================");
    }
}

---

From source file:Pathway2RDFv2.java

public static void main(String[] args) throws ParserConfigurationException, SAXException, IOException,
        ServiceException, ClassNotFoundException, IDMapperException, ParseException {

    int softwareVersion = 0;
    int schemaVersion = 0;
    int latestRevision = 0;

    BioDataSource.init();//  w  ww. ja  va  2  s.  c o  m
    Class.forName("org.bridgedb.rdb.IDMapperRdb");
    File dir = new File("/Users/andra/Downloads/bridge");
    File[] bridgeDbFiles = dir.listFiles();
    IDMapperStack mapper = new IDMapperStack();
    for (File bridgeDbFile : bridgeDbFiles) {
        System.out.println(bridgeDbFile.getAbsolutePath());
        mapper.addIDMapper("idmapper-pgdb:" + bridgeDbFile.getAbsolutePath());
    }

    Model bridgeDbmodel = ModelFactory.createDefaultModel();
    InputStream in = new FileInputStream("/tmp/BioDataSource.ttl");
    bridgeDbmodel.read(in, "", "TURTLE");

    WikiPathwaysClient client = new WikiPathwaysClient(
            new URL("http://www.wikipathways.org/wpi/webservice/webservice.php"));

    basicCalls.printMemoryStatus();

    //Map wikipathway organisms to NCBI organisms
    HashMap<String, String> organismTaxonomy = wpRelatedCalls.getOrganismsTaxonomyMapping();
    //HashMap<String, String> miriamSources = new HashMap<String, String>();
    //      HashMap<String, Str ing> miriamLinks = basicCalls.getMiriamUriBridgeDb();

    //Document wikiPathwaysDom = basicCalls.openXmlFile(args[0]);
    Document wikiPathwaysDom = basicCalls.openXmlFile("/tmp/WpGPML.xml");

    //initiate the Jena model to be populated
    Model model = ModelFactory.createDefaultModel();
    Model voidModel = ModelFactory.createDefaultModel();

    voidModel.setNsPrefix("xsd", XSD.getURI());
    voidModel.setNsPrefix("void", Void.getURI());
    voidModel.setNsPrefix("wprdf", "http://rdf.wikipathways.org/");
    voidModel.setNsPrefix("pav", Pav.getURI());
    voidModel.setNsPrefix("prov", Prov.getURI());
    voidModel.setNsPrefix("dcterms", DCTerms.getURI());
    voidModel.setNsPrefix("biopax", Biopax_level3.getURI());
    voidModel.setNsPrefix("gpml", Gpml.getURI());
    voidModel.setNsPrefix("wp", Wp.getURI());
    voidModel.setNsPrefix("foaf", FOAF.getURI());
    voidModel.setNsPrefix("hmdb", "http://identifiers.org/hmdb/");
    voidModel.setNsPrefix("freq", Freq.getURI());
    voidModel.setNsPrefix("dc", DC.getURI());
    setModelPrefix(model);

    //Populate void.ttl
    Calendar now = Calendar.getInstance();
    Literal nowLiteral = voidModel.createTypedLiteral(now);
    Literal titleLiteral = voidModel.createLiteral("WikiPathways-RDF VoID Description", "en");
    Literal descriptionLiteral = voidModel
            .createLiteral("This is the VoID description for a WikiPathwyas-RDF dataset.", "en");
    Resource voidBase = voidModel.createResource("http://rdf.wikipathways.org/");
    Resource identifiersOrg = voidModel.createResource("http://identifiers.org");
    Resource wpHomeBase = voidModel.createResource("http://www.wikipathways.org/");
    Resource authorResource = voidModel
            .createResource("http://semantics.bigcat.unimaas.nl/figshare/search_author.php?author=waagmeester");
    Resource apiResource = voidModel
            .createResource("http://www.wikipathways.org/wpi/webservice/webservice.php");
    Resource mainDatadump = voidModel.createResource("http://rdf.wikipathways.org/wpContent.ttl.gz");
    Resource license = voidModel.createResource("http://creativecommons.org/licenses/by/3.0/");
    Resource instituteResource = voidModel.createResource("http://dbpedia.org/page/Maastricht_University");
    voidBase.addProperty(RDF.type, Void.Dataset);
    voidBase.addProperty(DCTerms.title, titleLiteral);
    voidBase.addProperty(DCTerms.description, descriptionLiteral);
    voidBase.addProperty(FOAF.homepage, wpHomeBase);
    voidBase.addProperty(DCTerms.license, license);
    voidBase.addProperty(Void.uriSpace, voidBase);
    voidBase.addProperty(Void.uriSpace, identifiersOrg);
    voidBase.addProperty(Pav.importedBy, authorResource);
    voidBase.addProperty(Pav.importedFrom, apiResource);
    voidBase.addProperty(Pav.importedOn, nowLiteral);
    voidBase.addProperty(Void.dataDump, mainDatadump);
    voidBase.addProperty(Voag.frequencyOfChange, Freq.Irregular);
    voidBase.addProperty(Pav.createdBy, authorResource);
    voidBase.addProperty(Pav.createdAt, instituteResource);
    voidBase.addLiteral(Pav.createdOn, nowLiteral);
    voidBase.addProperty(DCTerms.subject, Biopax_level3.Pathway);
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/ncbigene/2678"));
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/pubmed/15215856"));
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/hmdb/HMDB02005"));
    voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://rdf.wikipathways.org/WP15"));
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/obo.chebi/17242"));

    for (String organism : organismTaxonomy.values()) {
        voidBase.addProperty(DCTerms.subject,
                voidModel.createResource("http://dbpedia.org/page/" + organism.replace(" ", "_")));
    }
    voidBase.addProperty(Void.vocabulary, Biopax_level3.NAMESPACE);
    voidBase.addProperty(Void.vocabulary, voidModel.createResource(Wp.getURI()));
    voidBase.addProperty(Void.vocabulary, voidModel.createResource(Gpml.getURI()));
    voidBase.addProperty(Void.vocabulary, FOAF.NAMESPACE);
    voidBase.addProperty(Void.vocabulary, Pav.NAMESPACE);
    //Custom Properties
    String baseUri = "http://rdf.wikipathways.org/";
    NodeList pathwayElements = wikiPathwaysDom.getElementsByTagName("Pathway");

    //BioDataSource.init();
    for (int i = 0; i < pathwayElements.getLength(); i++) {
        Model pathwayModel = createPathwayModel();
        String wpId = pathwayElements.item(i).getAttributes().getNamedItem("identifier").getTextContent();
        String revision = pathwayElements.item(i).getAttributes().getNamedItem("revision").getTextContent();
        String pathwayOrganism = "";
        if (pathwayElements.item(i).getAttributes().getNamedItem("Organism") != null)
            pathwayOrganism = pathwayElements.item(i).getAttributes().getNamedItem("Organism").getTextContent()
                    .trim();
        if (Integer.valueOf(revision) > latestRevision) {
            latestRevision = Integer.valueOf(revision);
        }
        File f = new File("/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl");
        System.out.println(f.getName());
        if (!f.exists()) {

            Resource voidPwResource = wpRelatedCalls.addVoidTriples(voidModel, voidBase,
                    pathwayElements.item(i), client);
            Resource pwResource = wpRelatedCalls.addPathwayLevelTriple(pathwayModel, pathwayElements.item(i),
                    organismTaxonomy);

            // Get the comments
            NodeList commentElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Comment");
            wpRelatedCalls.addCommentTriples(pathwayModel, pwResource, commentElements, wpId, revision);
            // Get the Groups
            NodeList groupElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Group");
            for (int n = 0; n < groupElements.getLength(); n++) {
                wpRelatedCalls.addGroupTriples(pathwayModel, pwResource, groupElements.item(n), wpId, revision);
            }
            // Get all the Datanodes
            NodeList dataNodesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("DataNode");
            for (int j = 0; j < dataNodesElement.getLength(); j++) {
                wpRelatedCalls.addDataNodeTriples(pathwayModel, pwResource, dataNodesElement.item(j), wpId,
                        revision, bridgeDbmodel, mapper);
            }
            // Get all the lines
            NodeList linesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Line");
            for (int k = 0; k < linesElement.getLength(); k++) {
                wpRelatedCalls.addLineTriples(pathwayModel, pwResource, linesElement.item(k), wpId, revision);
            }
            //Get all the labels
            NodeList labelsElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Label");
            for (int l = 0; l < labelsElement.getLength(); l++) {
                wpRelatedCalls.addLabelTriples(pathwayModel, pwResource, labelsElement.item(l), wpId, revision);
            }
            NodeList referenceElements = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:PublicationXref");
            for (int m = 0; m < referenceElements.getLength(); m++) {
                wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements.item(m), wpId,
                        revision);
            }
            NodeList referenceElements2 = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:publicationXref");
            for (int m = 0; m < referenceElements2.getLength(); m++) {
                wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements2.item(m), wpId,
                        revision);
            }
            NodeList referenceElements3 = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:PublicationXRef");
            for (int m = 0; m < referenceElements3.getLength(); m++) {
                wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements3.item(m), wpId,
                        revision);
            }

            NodeList ontologyElements = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:openControlledVocabulary");
            for (int n = 0; n < ontologyElements.getLength(); n++) {
                wpRelatedCalls.addPathwayOntologyTriples(pathwayModel, pwResource, ontologyElements.item(n));
            }
            System.out.println(wpId);
            basicCalls.saveRDF2File(pathwayModel, "/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl",
                    "TURTLE");

            model.add(pathwayModel);
            pathwayModel.removeAll();
        }
    }
    Date myDate = new Date();
    SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd");
    String myDateString = sdf.format(myDate);
    FileUtils.writeStringToFile(new File("latestVersion.txt"),
            "v" + schemaVersion + "." + softwareVersion + "." + latestRevision + "_" + myDateString);
    basicCalls.saveRDF2File(model, "/tmp/wpContent_v" + schemaVersion + "." + softwareVersion + "."
            + latestRevision + "_" + myDateString + ".ttl", "TURTLE");
    basicCalls.saveRDF2File(voidModel, "/tmp/void.ttl", "TURTLE");
}

---

From source file:DIA_Umpire_Quant.DIA_Umpire_IntLibSearch.java

/**
 * @param args the command line arguments
 *///from   w  w w . ja va  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 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:DIA_Umpire_Quant.DIA_Umpire_ExtLibSearch.java

/**
 * @param args the command line arguments
 *//*from  ww  w  .java2  s .c  o  m*/
public static void main(String[] args) throws FileNotFoundException, IOException, Exception {
    System.out.println(
            "=================================================================================================");
    System.out.println("DIA-Umpire targeted re-extraction analysis using external library (version: "
            + UmpireInfo.GetInstance().Version + ")");
    if (args.length != 1) {
        System.out.println(
                "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_ExtLibSearch.jar diaumpire_module.params");
        return;
    }
    try {
        ConsoleLogger.SetConsoleLogger(Level.INFO);
        ConsoleLogger.SetFileLogger(Level.DEBUG,
                FilenameUtils.getFullPath(args[0]) + "diaumpire_extlibsearch.log");
    } catch (Exception e) {
    }

    Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version);
    Logger.getRootLogger().info("Parameter file:" + args[0]);

    BufferedReader reader = new BufferedReader(new FileReader(args[0]));
    String line = "";
    String WorkFolder = "";
    int NoCPUs = 2;

    String ExternalLibPath = "";
    String ExternalLibDecoyTag = "DECOY";

    float ExtProbThreshold = 0.99f;
    float RTWindow_Ext = -1f;

    TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600);
    HashMap<String, File> AssignFiles = new HashMap<>();

    //<editor-fold defaultstate="collapsed" desc="Reading parameter file">
    while ((line = reader.readLine()) != null) {
        line = line.trim();
        Logger.getRootLogger().info(line);
        if (!"".equals(line) && !line.startsWith("#")) {
            //System.out.println(line);
            if (line.equals("==File list begin")) {
                do {
                    line = reader.readLine();
                    line = line.trim();
                    if (line.equals("==File list end")) {
                        continue;
                    } else if (!"".equals(line)) {
                        File newfile = new File(line);
                        if (newfile.exists()) {
                            AssignFiles.put(newfile.getAbsolutePath(), newfile);
                        } else {
                            Logger.getRootLogger().info("File: " + newfile + " does not exist.");
                        }
                    }
                } while (!line.equals("==File list end"));
            }
            if (line.split("=").length < 2) {
                continue;
            }
            String type = line.split("=")[0].trim();
            String value = line.split("=")[1].trim();
            switch (type) {

            case "Path": {
                WorkFolder = value;
                break;
            }
            case "path": {
                WorkFolder = value;
                break;
            }
            case "Thread": {
                NoCPUs = Integer.parseInt(value);
                break;
            }
            case "Fasta": {
                tandemPara.FastaPath = value;
                break;
            }
            case "DecoyPrefix": {
                if (!"".equals(value)) {
                    tandemPara.DecoyPrefix = value;
                }
                break;
            }
            case "ExternalLibPath": {
                ExternalLibPath = value;
                break;
            }
            case "ExtProbThreshold": {
                ExtProbThreshold = Float.parseFloat(value);
                break;
            }
            case "RTWindow_Ext": {
                RTWindow_Ext = Float.parseFloat(value);
                break;
            }
            case "ExternalLibDecoyTag": {
                ExternalLibDecoyTag = value;
                if (ExternalLibDecoyTag.endsWith("_")) {
                    ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1);
                }
                break;
            }
            }
        }
    }
    //</editor-fold>

    //Initialize PTM manager using compomics library
    PTMManager.GetInstance();

    //Check if the fasta file can be found
    if (!new File(tandemPara.FastaPath).exists()) {
        Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath
                + " cannot be found, the process will be terminated, please check.");
        System.exit(1);
    }

    //Generate DIA file list
    ArrayList<DIAPack> FileList = new ArrayList<>();

    File folder = new File(WorkFolder);
    if (!folder.exists()) {
        Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found.");
        System.exit(1);
    }
    for (final File fileEntry : folder.listFiles()) {
        if (fileEntry.isFile()
                && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml")
                        | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")
                && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml")
                && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) {
            AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry);
        }
        if (fileEntry.isDirectory()) {
            for (final File fileEntry2 : fileEntry.listFiles()) {
                if (fileEntry2.isFile()
                        && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml")
                                | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                        && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")
                        && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml")
                        && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) {
                    AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2);
                }
            }
        }
    }

    Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size());
    for (File fileEntry : AssignFiles.values()) {
        Logger.getRootLogger().info(fileEntry.getAbsolutePath());
    }

    for (File fileEntry : AssignFiles.values()) {
        String mzXMLFile = fileEntry.getAbsolutePath();
        if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) {
            DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs);
            Logger.getRootLogger().info(
                    "=================================================================================================");
            Logger.getRootLogger().info("Processing " + mzXMLFile);
            if (!DiaFile.LoadDIASetting()) {
                Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete");
                System.exit(1);
            }
            if (!DiaFile.LoadParams()) {
                Logger.getRootLogger().info("Loading parameters failed, job is incomplete");
                System.exit(1);
            }
            Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "....");

            //If the serialization file for ID file existed
            if (DiaFile.ReadSerializedLCMSID()) {
                DiaFile.IDsummary.ReduceMemoryUsage();
                DiaFile.IDsummary.FastaPath = tandemPara.FastaPath;
                FileList.add(DiaFile);
            }
        }
    }

    //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library">

    //External library search

    Logger.getRootLogger().info("Targeted extraction using external library");

    //Read exteranl library
    FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder,
            FilenameUtils.getBaseName(ExternalLibPath));
    if (ExlibManager == null) {
        ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath));

        //Import traML file
        ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag);
        //Check if there are decoy spectra
        ExlibManager.CheckDecoys();
        //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath);
        ExlibManager.WriteFragmentLibSerialization(WorkFolder);
    }
    Logger.getRootLogger()
            .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size());
    for (DIAPack diafile : FileList) {
        if (diafile.IDsummary == null) {
            diafile.ReadSerializedLCMSID();
        }
        //Generate RT mapping
        RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter());
        RTmap.GenerateModel();
        RTmap.GenerateMappedPepIon();

        diafile.BuildStructure();
        diafile.MS1FeatureMap.ReadPeakCluster();
        diafile.GenerateMassCalibrationRTMap();
        //Perform targeted re-extraction
        diafile.TargetedExtractionQuant(false, ExlibManager, ExtProbThreshold, RTWindow_Ext);
        diafile.MS1FeatureMap.ClearAllPeaks();
        diafile.IDsummary.ReduceMemoryUsage();
        //Remove target IDs below the defined probability threshold
        diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold);
        diafile.ExportID();
        diafile.ClearStructure();
        Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size()
                + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size());
    }

    //</editor-fold>

    Logger.getRootLogger().info("Job done");
    Logger.getRootLogger().info(
            "=================================================================================================");

}

---

From source file:Main.java

public static int getTotalValueCount(HashMap<String, Integer> hm) {
    int count = 0;
    for (Integer intVal : hm.values()) {
        count += intVal.intValue();/*www . j  av  a  2 s. com*/
    }
    return count;
}

---

From source file:org.apache.axis2.util.SchemaUtil.java

public static XmlSchema[] getAllSchemas(XmlSchema schema) {
    HashMap map = new HashMap();
    traverseSchemas(schema, map);//from  w  w  w. j a  v  a 2s .c om
    return (XmlSchema[]) map.values().toArray(new XmlSchema[map.values().size()]);
}

---

From source file:Main.java

public static void finishAllActivies(Activity activity) {
    try {//from w ww .j  a v a2s  .  c om
        Class<?> clazz_Activity = Class.forName("android.app.Activity");
        Field field_mMainThread = clazz_Activity.getDeclaredField("mMainThread");
        field_mMainThread.setAccessible(true);
        Object mMainThread = field_mMainThread.get(activity);

        Class<?> clazz_ActivityThread = Class.forName("android.app.ActivityThread");
        Field field_mActivities = clazz_ActivityThread.getDeclaredField("mActivities");
        field_mActivities.setAccessible(true);
        Object mActivities = field_mActivities.get(mMainThread);

        HashMap<?, ?> map = (HashMap<?, ?>) mActivities;
        Collection<?> collections = map.values();
        if (null != collections && !collections.isEmpty()) {
            Class<?> clazz_ActivityClientRecord = Class
                    .forName("android.app.ActivityThread$ActivityClientRecord");
            Field field_activitiy = clazz_ActivityClientRecord.getDeclaredField("activity");
            field_activitiy.setAccessible(true);

            Activity acti;
            for (Object obj : collections) {
                acti = (Activity) field_activitiy.get(obj);
                Log.d(TAG, "activity.name=" + acti.getClass().getName());
                if (null != acti && !acti.isFinishing()) {
                    Log.d(TAG, "activity.name=" + acti.getClass().getName() + " not finish.");
                    acti.finish();
                }
            }
        }
    } catch (NoSuchFieldException e) {
        e.printStackTrace();
    } catch (IllegalAccessException e) {
        e.printStackTrace();
    } catch (IllegalArgumentException e) {
        e.printStackTrace();
    } catch (ClassNotFoundException e) {
        e.printStackTrace();
    }
}

---

From source file:Main.java

@SuppressWarnings("unchecked")
static public LinkedHashMap<Object, Comparable> sortHashMapByValues(HashMap<Object, Comparable> passedMap) {
    ArrayList mapKeys = new ArrayList(passedMap.keySet());
    ArrayList mapValues = new ArrayList(passedMap.values());
    Collections.sort(mapValues);//from  w  w w  .  j a v a 2s. c  om
    Collections.sort(mapKeys);

    LinkedHashMap<Object, Comparable> sortedMap = new LinkedHashMap<Object, Comparable>();

    Iterator<Comparable> valueIt = mapValues.iterator();
    while (valueIt.hasNext()) {
        Comparable val = valueIt.next();
        Iterator keyIt = mapKeys.iterator();

        while (keyIt.hasNext()) {
            Object key = keyIt.next();
            Comparable comp = passedMap.get(key);

            if (comp.equals(val)) {
                passedMap.remove(key);
                mapKeys.remove(key);
                sortedMap.put(key, val);
                break;
            }

        }
    }
    return sortedMap;
}

---

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