Example usage for java.util HashMap get

List of usage examples for java.util HashMap get

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Introduction

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

Prototype

public V get(Object key)

Source Link

Document

Returns the value to which the specified key is mapped, or null if this map contains no mapping for the key.

Usage

From source file:com.act.lcms.db.analysis.StandardIonAnalysis.java

/**
 * This function returns the best SNR values and their times for each metlin ion based on the StandardIonResult
 * datastructure and plots diagnostics./*w ww . j  a  v a2s.c  om*/
 * @param lcmsDir The directory where the LCMS scan data can be found.
 * @param db The DB connection to query.
 * @param positiveStandardWell This is the positive standard well against which the snr comparison is done.
 * @param negativeStandardWells These are the negative standard wells which are used for benchmarking.
 * @param plateCache A hash of Plates already accessed from the DB.
 * @param chemical This is chemical of interest we are running ion analysis against.
 * @param plottingDir This is the directory where the plotting diagnostics will live.
 * @param restrictedTimeWindows This map of ion to list of doubles represent time windows over which the analysis has
 *                              to be done.
 * @return The StandardIonResult datastructure which contains the standard ion analysis results.
 * @throws Exception
 */
public static StandardIonResult getSnrResultsForStandardWellComparedToValidNegativesAndPlotDiagnostics(
        File lcmsDir, DB db, StandardWell positiveStandardWell, List<StandardWell> negativeStandardWells,
        HashMap<Integer, Plate> plateCache, String chemical, String plottingDir,
        Map<String, List<Double>> restrictedTimeWindows) throws Exception {
    Plate plate = plateCache.get(positiveStandardWell.getPlateId());

    if (plate == null) {
        plate = Plate.getPlateById(db, positiveStandardWell.getPlateId());
        plateCache.put(plate.getId(), plate);
    }

    List<Pair<String, Double>> searchMZs;
    Pair<String, Double> searchMZ = Utils.extractMassFromString(db, chemical);
    if (searchMZ != null) {
        searchMZs = Collections.singletonList(searchMZ);
    } else {
        throw new RuntimeException("Could not find Mass Charge value for " + chemical);
    }

    List<StandardWell> allWells = new ArrayList<>();
    allWells.add(positiveStandardWell);
    allWells.addAll(negativeStandardWells);

    ChemicalToMapOfMetlinIonsToIntensityTimeValues peakData = AnalysisHelper.readStandardWellScanData(db,
            lcmsDir, searchMZs, ScanData.KIND.STANDARD, plateCache, allWells, false, null, null,
            USE_SNR_FOR_LCMS_ANALYSIS, positiveStandardWell.getChemical());

    if (peakData == null || peakData.getIonList().size() == 0) {
        return null;
    }

    LinkedHashMap<String, XZ> snrResults = WaveformAnalysis
            .performSNRAnalysisAndReturnMetlinIonsRankOrderedBySNR(peakData, chemical, restrictedTimeWindows);

    String bestMetlinIon = AnalysisHelper.getBestMetlinIonFromPossibleMappings(snrResults);

    Map<String, String> plottingFileMappings = peakData
            .plotPositiveAndNegativeControlsForEachMetlinIon(searchMZ, plottingDir, chemical, allWells);

    StandardIonResult result = new StandardIonResult();
    result.setChemical(chemical);
    result.setAnalysisResults(snrResults);
    result.setStandardWellId(positiveStandardWell.getId());
    result.setPlottingResultFilePaths(plottingFileMappings);
    result.setBestMetlinIon(bestMetlinIon);
    return result;
}

From source file:com.ibm.bi.dml.runtime.matrix.WriteCSVMR.java

public static JobReturn runJob(MRJobInstruction inst, String[] inputs, InputInfo[] inputInfos, long[] rlens,
        long[] clens, int[] brlens, int[] bclens, String csvWriteInstructions, int numReducers, int replication,
        byte[] resultIndexes, String[] outputs) throws Exception {
    JobConf job = new JobConf(WriteCSVMR.class);
    job.setJobName("WriteCSV-MR");

    byte[] realIndexes = new byte[inputs.length];
    for (byte b = 0; b < realIndexes.length; b++)
        realIndexes[b] = b;/*from w  ww.j  a  va  2s  .com*/

    //set up the input files and their format information
    MRJobConfiguration.setUpMultipleInputs(job, realIndexes, inputs, inputInfos, brlens, bclens, true,
            ConvertTarget.CSVWRITE);

    //set up the dimensions of input matrices
    MRJobConfiguration.setMatricesDimensions(job, realIndexes, rlens, clens);

    //set up the block size
    MRJobConfiguration.setBlocksSizes(job, realIndexes, brlens, bclens);

    MRJobConfiguration.setCSVWriteInstructions(job, csvWriteInstructions);

    //set up the replication factor for the results
    job.setInt("dfs.replication", replication);

    //set up preferred custom serialization framework for binary block format
    if (MRJobConfiguration.USE_BINARYBLOCK_SERIALIZATION)
        MRJobConfiguration.addBinaryBlockSerializationFramework(job);

    long maxRlen = 0;
    for (long rlen : rlens)
        if (rlen > maxRlen)
            maxRlen = rlen;

    //set up the number of reducers (according to output size)
    int numRed = determineNumReducers(rlens, clens,
            ConfigurationManager.getConfig().getIntValue(DMLConfig.NUM_REDUCERS), (int) maxRlen);
    job.setNumReduceTasks(numRed);

    byte[] resultDimsUnknown = new byte[resultIndexes.length];
    MatrixCharacteristics[] stats = new MatrixCharacteristics[resultIndexes.length];
    OutputInfo[] outputInfos = new OutputInfo[outputs.length];
    HashMap<Byte, Integer> indexmap = new HashMap<Byte, Integer>();
    for (int i = 0; i < stats.length; i++) {
        indexmap.put(resultIndexes[i], i);
        resultDimsUnknown[i] = (byte) 0;
        stats[i] = new MatrixCharacteristics();
        outputInfos[i] = OutputInfo.CSVOutputInfo;
    }
    CSVWriteInstruction[] ins = MRInstructionParser.parseCSVWriteInstructions(csvWriteInstructions);
    for (CSVWriteInstruction in : ins)
        stats[indexmap.get(in.output)].set(rlens[in.input], clens[in.input], -1, -1);

    // Print the complete instruction
    if (LOG.isTraceEnabled())
        inst.printCompleteMRJobInstruction(stats);

    //set up what matrices are needed to pass from the mapper to reducer
    MRJobConfiguration.setUpOutputIndexesForMapper(job, realIndexes, "", "", csvWriteInstructions,
            resultIndexes);

    //set up the multiple output files, and their format information
    MRJobConfiguration.setUpMultipleOutputs(job, resultIndexes, resultDimsUnknown, outputs, outputInfos, true,
            true);

    // configure mapper and the mapper output key value pairs
    job.setMapperClass(CSVWriteMapper.class);
    job.setMapOutputKeyClass(TaggedFirstSecondIndexes.class);
    job.setMapOutputValueClass(MatrixBlock.class);

    //configure reducer
    job.setReducerClass(CSVWriteReducer.class);
    job.setOutputKeyComparatorClass(TaggedFirstSecondIndexes.Comparator.class);
    job.setPartitionerClass(TaggedFirstSecondIndexes.FirstIndexRangePartitioner.class);
    //job.setOutputFormat(UnPaddedOutputFormat.class);

    MatrixCharacteristics[] inputStats = new MatrixCharacteristics[inputs.length];
    for (int i = 0; i < inputs.length; i++) {
        inputStats[i] = new MatrixCharacteristics(rlens[i], clens[i], brlens[i], bclens[i]);
    }

    //set unique working dir
    MRJobConfiguration.setUniqueWorkingDir(job);

    RunningJob runjob = JobClient.runJob(job);

    /* Process different counters */

    Group group = runjob.getCounters().getGroup(MRJobConfiguration.NUM_NONZERO_CELLS);
    for (int i = 0; i < resultIndexes.length; i++) {
        // number of non-zeros
        stats[i].setNonZeros(group.getCounter(Integer.toString(i)));
    }

    return new JobReturn(stats, outputInfos, runjob.isSuccessful());
}

From source file:de.adesso.referencer.search.helper.ElasticConfig.java

public static String buildSearchQuery(HashMap<String, String> fieldvalue) {
    String result = null;// w  w  w  .  ja  v a  2 s .c  om
    if (fieldvalue == null)
        return null;
    if (fieldvalue.size() <= 0)
        return null;
    result = "{\"query\": { \"bool\": {\"must\": [";
    String matchString = null;
    for (String s : fieldvalue.keySet()) {
        matchString = buildMatchString(s, fieldvalue.get(s));
        if (matchString != null)
            result += "\n" + matchString + ",";
    }
    result = result.substring(0, result.length() - 1) + "\n";
    result += "]}}}";
    return result;
}

From source file:net.mutil.util.HttpUtil.java

public static String connServerForResultPost(String strUrl, HashMap<String, String> entityMap)
        throws ClientProtocolException, IOException {
    String strResult = "";
    URL url = new URL(HttpUtil.getPCURL() + strUrl);
    HttpURLConnection conn = (HttpURLConnection) url.openConnection();
    conn.setRequestMethod("POST");
    StringBuilder entitySb = new StringBuilder("");

    Object[] entityKeys = entityMap.keySet().toArray();
    for (int i = 0; i < entityKeys.length; i++) {
        String key = (String) entityKeys[i];
        if (i == 0) {
            entitySb.append(key + "=" + entityMap.get(key));
        } else {/*from   ww  w  .  j a v  a 2  s .c  o m*/
            entitySb.append("&" + key + "=" + entityMap.get(key));
        }
    }
    byte[] entity = entitySb.toString().getBytes("UTF-8");
    System.out.println(url.toString() + entitySb.toString());
    conn.setConnectTimeout(5000);
    conn.setDoOutput(true);
    conn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");
    conn.setRequestProperty("Content-Length", String.valueOf(entity.length));
    conn.getOutputStream().write(entity);
    if (conn.getResponseCode() == 200) {
        InputStream inputstream = conn.getInputStream();
        StringBuffer buffer = new StringBuffer();
        byte[] b = new byte[4096];
        for (int n; (n = inputstream.read(b)) != -1;) {
            buffer.append(new String(b, 0, n));
        }
        strResult = buffer.toString();
    }
    return strResult;
}

From source file:org.hfoss.posit.web.Communicator.java

/**
 * cleanup the item key,value pairs so that we can receive and save to the internal database
 * @param rMap//from  w  ww  .  j a va2  s.  co m
 */
public static void cleanupOnReceive(HashMap<String, Object> rMap) {
    rMap.put(PositDbHelper.FINDS_SYNCED, PositDbHelper.FIND_IS_SYNCED);
    rMap.put(PositDbHelper.FINDS_GUID, rMap.get("barcode_id"));
    //rMap.put(PositDbHelper.FINDS_GUID, rMap.get("barcode_id"));

    rMap.put(PositDbHelper.FINDS_PROJECT_ID, projectId);
    if (rMap.containsKey("add_time")) {
        rMap.put(PositDbHelper.FINDS_TIME, rMap.get("add_time"));
        rMap.remove("add_time");
    }
    if (rMap.containsKey("images")) {
        if (Utils.debug)
            Log.d(TAG, "contains image key");
        rMap.put(PositDbHelper.PHOTOS_IMAGE_URI, rMap.get("images"));
        rMap.remove("images");
    }
}

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

public static HashMap<String, AbstractJobType> toAbstractJobTypeList(HashMap<String, JobImpl> jobQueue) {

    HashMap<String, AbstractJobType> tmpList = new HashMap<String, AbstractJobType>();

    Iterator<String> jobsIterator = jobQueue.keySet().iterator();

    while (jobsIterator.hasNext()) {
        String jobKey = jobsIterator.next();
        tmpList.put(jobKey, jobQueue.get(jobKey).getAbstractJobType());
    }//w  w  w  . j a v  a  2s.c  o m

    return tmpList;
}

From source file:Main.java

public static HashMap<String, List<Object[]>> getUnitDataMapList(List<Object[]> list, int[] indexnum) {
    HashMap<String, List<Object[]>> dataMap = new HashMap<String, List<Object[]>>();
    for (int i = 0; i < list.size(); i++) {
        StringBuffer returnStringBuffer = new StringBuffer();
        for (int ai = 0; ai < indexnum.length; ai++) {
            int index = indexnum[ai];
            Object obj = list.get(i)[index];
            String gunit = obj.toString();
            if (ai == 0) {
                returnStringBuffer.append(gunit);
            } else {
                returnStringBuffer.append("(" + gunit + ")");
            }//from w w  w  .j  av  a  2  s .  c o m

        }
        String unit = returnStringBuffer.toString();
        if (dataMap.containsKey(unit)) {
            dataMap.get(unit).add((Object[]) list.get(i));
        } else {
            ArrayList<Object[]> rowdata = new ArrayList<Object[]>();
            rowdata.add((Object[]) list.get(i));
            dataMap.put(unit, rowdata);
        }
    }

    return dataMap;
}

From source file:com.nubits.nubot.trading.TradeUtils.java

/**
 *
 * @param args/*from   w  w  w.ja v a 2  s  . c o  m*/
 * @param encoding
 * @return
 */
public static String buildQueryString(HashMap<String, String> args, String encoding) {
    String result = new String();
    for (String hashkey : args.keySet()) {
        if (result.length() > 0) {
            result += '&';
        }
        try {
            result += URLEncoder.encode(hashkey, encoding) + "="
                    + URLEncoder.encode(args.get(hashkey), encoding);
        } catch (Exception ex) {
            LOG.severe(ex.toString());
        }
    }
    return result;
}

From source file:jsave.Utils.java

public static HashMap<String, Object> read_arraydesc(final RandomAccessFile raf) throws IOException, Exception {
    HashMap<String, Object> arraydesc = new HashMap<>();
    arraydesc.put("arrstart", read_long(raf));
    int arrStart = (int) arraydesc.get("arrstart");
    switch (arrStart) {
    case 8://from  w w  w. j  a  va2  s .co  m
        skip_bytes(raf, 4);
        arraydesc.put("nbytes", read_long(raf));
        arraydesc.put("nelements", read_long(raf));
        arraydesc.put("ndims", read_long(raf));
        skip_bytes(raf, 8);
        arraydesc.put("nmax", read_long(raf));
        int length = (int) arraydesc.get("nmax");
        int[] dims = new int[length];
        for (int i = 0; i < length; i++) {
            dims[i] = read_long(raf);
        }
        arraydesc.put("dims", dims);
        break;
    case 18:
        throw new UnsupportedOperationException("arrstart=18 is not supported");
        //warnings.warn("Using experimental 64-bit array read")
        //_skip_bytes(f, 8)

        //arraydesc['nbytes'] = _read_uint64(f)
        //arraydesc['nelements'] = _read_uint64(f)
        //arraydesc['ndims'] = _read_long(f)
        //_skip_bytes(f, 8)
        //arraydesc['nmax'] = 8
        //arraydesc['dims'] = []
        //for d in range(arraydesc['nmax']):
        //    v = _read_long(f)
        //    if v != 0:
        //        raise Exception("Expected a zero in ARRAY_DESC")
        //    arraydesc['dims'].append(_read_long(f))                
        //break;
    default:
        throw new Exception("Unknown ARRSTART: " + arraydesc.get("arrstart"));
    }

    return arraydesc;
}

From source file:fr.lissi.belilif.om2m.rest.WebServiceActions.java

/**
 * Do post./*from   w  w  w  .j av a2  s.  c o m*/
 *
 * @param uri
 *            the uri
 * @param body
 *            the body
 * @param headers
 *            the headers
 * @return the int
 * @throws ClientProtocolException
 *             the client protocol exception
 * @throws IOException
 *             Signals that an I/O exception has occurred.
 * @throws HttpResponseException
 *             the http response exception
 */
public static int doPost(String uri, String body, HashMap<String, String> headers)
        throws ClientProtocolException, IOException, HttpResponseException {
    // TODO delete before commit
    // System.out.println("doPost>> uri:"+uri +"\nbody:"+body+"\n");
    CloseableHttpClient httpclient = HttpClients.createDefault();
    int resp = -1;
    try {
        HttpPost httpPost = new HttpPost(uri);
        for (String key : headers.keySet()) {
            httpPost.addHeader(key, headers.get(key));
            // System.out.println("header:"+key+"/"+headers.get(key));

        }
        // System.out.println("doPost<<");
        httpPost.setEntity(new StringEntity(body));
        CloseableHttpResponse response = httpclient.execute(httpPost);
        resp = response.getStatusLine().getStatusCode();
        if (response.getStatusLine().getStatusCode() == HttpStatus.SC_CREATED) {
            response.close();
        } else {
            throw new HttpResponseException(response.getStatusLine().getStatusCode(),
                    response.getStatusLine().getReasonPhrase());
        }
    } finally {
        httpclient.close();
    }
    return resp;
}