Example usage for java.util HashMap values

List of usage examples for java.util HashMap values

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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:com.soomla.levelup.LevelUp.java

private static void applyMissionsStateToJSON(JSONObject modelJSON, JSONObject stateJSON) {
    JSONObject missionsStateJSON = new JSONObject();
    HashMap<String, JSONObject> missions = getMissions(modelJSON);
    for (JSONObject missionJSON : missions.values()) {
        JSONObject missionValuesJSON = new JSONObject();
        try {//ww  w. j  a va  2 s.  c  o m
            String missionId = missionJSON.getString("itemId");
            missionValuesJSON.put("timesCompleted", MissionStorage.getTimesCompleted(missionId));

            missionsStateJSON.put(missionId, missionValuesJSON);
        } catch (JSONException e) {
            SoomlaUtils.LogDebug(TAG, "Unable to get Missions state: " + e.getLocalizedMessage());
        }
    }

    try {
        stateJSON.put("missions", missionsStateJSON);
    } catch (JSONException e) {
        SoomlaUtils.LogDebug(TAG, "Unable to set Missions state: " + e.getLocalizedMessage());
    }
}

From source file:com.likya.myra.jef.utils.JobQueueOperations.java

@SuppressWarnings("unchecked")
public static Collection<AbstractJobType> getJobList(HashMap<String, AbstractJobType> abstractJobTypeList,
        Predicate predicate) {/*from www . j  av a2  s  .  c o m*/

    Collection<AbstractJobType> filteredList = CollectionUtils.select(abstractJobTypeList.values(), predicate);

    return filteredList;
}

From source file:com.soomla.levelup.LevelUp.java

public static HashMap<String, JSONObject> getGates(JSONObject model) {
    HashMap<String, JSONObject> resultHash = new HashMap<String, JSONObject>();

    HashMap<String, JSONObject> worldJSONs = getWorlds(model);

    for (JSONObject worldJSON : worldJSONs.values()) {
        JSONObject gateJSON = worldJSON.optJSONObject("gate");

        if (gateJSON != null) {
            String objectId = gateJSON.optString("itemId");
            if (!TextUtils.isEmpty(objectId)) {
                resultHash.put(objectId, gateJSON);
            }/*from ww w.ja va 2  s  .  c  om*/
        }
    }

    HashMap<String, JSONObject> missionJSONs = getMissions(model);
    for (JSONObject missionJSON : missionJSONs.values()) {
        JSONObject gateJSON = missionJSON.optJSONObject("gate");

        if (gateJSON != null) {
            String objectId = gateJSON.optString("itemId");
            if (!TextUtils.isEmpty(objectId)) {
                resultHash.put(objectId, gateJSON);
            }
        }
    }

    findInternalLists(resultHash, new String[] { "GatesListAND", "GatesListOR" }, "gates");

    return resultHash;
}

From source file:com.soomla.levelup.LevelUp.java

private static void applyWorldsStateToJSON(JSONObject modelJSON, JSONObject stateJSON) {
    JSONObject worldsStateJSON = new JSONObject();
    JSONObject levelsStateJSON = new JSONObject();

    HashMap<String, JSONObject> worlds = getWorlds(modelJSON);
    for (JSONObject worldJSON : worlds.values()) {
        JSONObject worldValuesJSON = new JSONObject();
        try {/*from   w w  w. j  a  va  2  s  . c  o m*/
            String worldId = worldJSON.getString("itemId");
            worldValuesJSON.put("completed", WorldStorage.isCompleted(worldId));
            worldValuesJSON.put("assignedReward", WorldStorage.getAssignedReward(worldId));

            worldsStateJSON.put(worldId, worldValuesJSON);

            if (worldJSON.getString("className").equals("Level")) {
                JSONObject levelValuesJSON = new JSONObject();
                levelValuesJSON.put("started", LevelStorage.getTimesStarted(worldId));
                levelValuesJSON.put("played", LevelStorage.getTimesPlayed(worldId));
                levelValuesJSON.put("timesCompleted", LevelStorage.getTimesCompleted(worldId));
                levelValuesJSON.put("slowest", LevelStorage.getSlowestDurationMillis(worldId));
                levelValuesJSON.put("fastest", LevelStorage.getFastestDurationMillis(worldId));

                levelsStateJSON.put(worldId, levelValuesJSON);
            }
        } catch (JSONException e) {
            SoomlaUtils.LogDebug(TAG, "Unable to get Worlds state: " + e.getLocalizedMessage());
        }
    }

    try {
        stateJSON.put("worlds", worldsStateJSON);
        stateJSON.put("levels", levelsStateJSON);
    } catch (JSONException e) {
        SoomlaUtils.LogDebug(TAG, "Unable to set Worlds state: " + e.getLocalizedMessage());
    }
}

From source file:com.likya.myra.jef.utils.JobQueueOperations.java

public static ArrayList<SortType> createProrityIndex(HashMap<String, JobImpl> jobQueue) {

    ArrayList<SortType> jobQueueArray = new ArrayList<SortType>();

    JobImpl job = null;//from w ww  . j a  v a 2  s .  c  o  m

    Iterator<JobImpl> jobsIterator = jobQueue.values().iterator();

    while (jobsIterator.hasNext()) {

        job = jobsIterator.next();

        AbstractJobType abstractJobType = job.getAbstractJobType();

        SortType mySortType = new SortType(abstractJobType.getId(),
                abstractJobType.getBaseJobInfos().getJobPriority().intValue());
        jobQueueArray.add(mySortType);
    }

    return jobQueueArray;
}

From source file:com.soomla.levelup.LevelUp.java

private static void findInternalLists(HashMap<String, JSONObject> objects, String[] listClasses,
        String listName) {//from   w w w. ja v a  2 s .  com
    try {
        List<String> classes = Arrays.asList(listClasses);
        for (JSONObject objectJSON : objects.values()) {
            findInternalLists(objects, classes, listName, objectJSON);
        }
    } catch (JSONException e) {
        SoomlaUtils.LogError(TAG,
                "couldn't get internal lists for " + listName + ". error: " + e.getLocalizedMessage());
    }
}

From source file:com.jajja.jorm.Database.java

/**
 * Closes and destroys all transactions for the current thread.
 *//*from  w w  w.  j  a v  a  2 s. c om*/
public static void close() {
    HashMap<String, Transaction> map = instance.getTransactions();
    for (Transaction transaction : map.values()) {
        transaction.destroy();
    }
    map.clear();
    instance.transactions.remove();
}

From source file:DIA_Umpire_Quant.DIA_Umpire_ProtQuant.java

/**
 * @param args the command line arguments
 *//*w w w.  j  av a 2  s. com*/
public static void main(String[] args) throws FileNotFoundException, IOException, Exception {
    System.out.println(
            "=================================================================================================");
    System.out.println(
            "DIA-Umpire protein quantitation module (version: " + UmpireInfo.GetInstance().Version + ")");
    if (args.length != 1) {
        System.out.println(
                "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_PortQuant.jar diaumpire_module.params");
        return;
    }
    try {
        ConsoleLogger.SetConsoleLogger(Level.INFO);
        ConsoleLogger.SetFileLogger(Level.DEBUG,
                FilenameUtils.getFullPath(args[0]) + "diaumpire_orotquant.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 Combined_Prot = "";
    boolean DefaultProtFiltering = true;

    float Freq = 0f;
    int TopNPep = 6;
    int TopNFrag = 6;
    String FilterWeight = "GW";
    float MinWeight = 0.9f;

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

    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 "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 "ProteinFDR": {
                tandemPara.ProtFDR = 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;
            }
            //<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();

    //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<>();
    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.ClearAssignPeakCluster();
                    FileList.add(DiaFile);
                    HashMap<String, FragmentPeak> FragMap = new HashMap<>();
                    IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap);
                }
            }
        }

        //<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 (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.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:eu.planets_project.tb.impl.serialization.ExperimentRecord.java

/**
 * Factory that does everything required when importing an experiment from an ExperimentRecord.
 * //w  w  w. j  av a2  s . c  o m
 * FIXME Test this comment loader!
 * 
 * @param er
 * @return
 */
static public long importExperimentRecord(ExperimentRecord er) {
    // Persist the experiment:
    long eid = edao.persistExperiment(er.experiment);
    // Also remember the comments, to make it easier to patch up the lists:
    HashMap<Long, Comment> cmts = new HashMap<Long, Comment>();

    // Persist the comments, using the correct experiment ID:
    for (CommentImpl c : er.comments) {
        // Update the comments to the new experiment id:
        c.setExperimentID(eid);
        // Persist the comments:
        long cid = cmp.persistComment(c);
        // Retrieve it again, for cross-reference resolution:
        cmts.put(new Long(c.getXmlCommentID()), cmp.findComment(cid));
    }

    // Go through the comments and correct the parent IDs:
    for (Comment c1 : cmts.values()) {
        // For this old identifier, look for it's parent comment:
        Comment c2 = cmts.get(c1.getParentID());
        if (c2 != null) {
            // Update the parent ID to the new comment ID:
            c1.setParentID(c2.getCommentID());
            // Don't forget to persist the id changes to the DB:
            cmp.updateComment(c1);
        }
    }

    // return the experiment id:
    return eid;
}

From source file:org.apache.hadoop.hbase.backup.util.BackupUtils.java

/**
 * Get the min value for all the Values a map.
 * @param map map//w w  w  .  j av a2s  .c  o m
 * @return the min value
 */
public static <T> Long getMinValue(HashMap<T, Long> map) {
    Long minTimestamp = null;
    if (map != null) {
        ArrayList<Long> timestampList = new ArrayList<Long>(map.values());
        Collections.sort(timestampList);
        // The min among all the RS log timestamps will be kept in backup system table table.
        minTimestamp = timestampList.get(0);
    }
    return minTimestamp;
}