Example usage for java.util HashMap keySet

List of usage examples for java.util HashMap keySet

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Introduction

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

Prototype

public Set<K> keySet()

Source Link

Document

Returns a Set view of the keys contained in this map.

Usage

From source file:com.act.reachables.Network.java

public static JSONObject edgeObj(Edge e, HashMap<Node, Integer> order) throws JSONException {
    JSONObject eo = new JSONObject();
    if (order != null) {
        // 1. when printing a graph (and not a tree), the source and target nodeMapping are identified
        // by the array index they appear in the nodeMapping JSONArray. Those indices are contained in the order-map.
        // 2. such an ordering is not required when we are working with trees, so these fields not output there.
        eo.put("source", order.get(e.src)); // required, and have to lookup its order in the node spec
        eo.put("target", order.get(e.dst)); // required, and have to lookup its order in the node spec
    }/* w ww.  ja  v a2 s .  c  o m*/
    // eo.put("source_id", e.src.id); // only informational
    // eo.put("target_id", e.dst.id); // only informational
    // eo.put("value", 1); // weight of edge: not really needed
    HashMap<String, Serializable> attr = e.getAttr();
    for (String k : attr.keySet()) {
        // only output the fields relevant to the reachables tree structures
        if (k.equals("under_root") || k.equals("functionalCategory") || k.equals("importantAncestor"))
            eo.put(k, attr.get(k).toString());
    }
    return eo;
}

From source file:com.act.reachables.Network.java

public static JSONObject nodeObj(MongoDB db, Node n) throws JSONException {
    Chemical thisChemical = db.getChemicalFromChemicalUUID(n.id);
    JSONObject no = thisChemical == null ? new JSONObject()
            : new JSONObject(ComputeReachablesTree.getExtendedChemicalInformationJSON(thisChemical));
    no.put("id", n.id);
    HashMap<String, Serializable> attr = n.getAttr();
    for (String k : attr.keySet()) {
        // only output the fields relevants to the reachables tree structure
        if (k.equals("NameOfLen20") || k.equals("ReadableName") || k.equals("Synonyms") || k.equals("InChI")
                || k.equals("InChiKEY") || k.equals("parent") || k.equals("under_root")
                || k.equals("num_children") || k.equals("subtreeVendorsSz") || k.equals("subtreeSz")
                || k.equals("SMILES"))
            no.put(k, attr.get(k).toString());

        if (k.equals("has"))
            no.put(k, attr.get(k));/*ww  w  .  ja  v a2  s.  c  o m*/
    }
    // Object v;
    // String label = "" + ((v = n.getAttribute("canonical")) != null ? v : n.id );
    // no.put("name", label ); // required
    // String layer = "" + ((v = n.getAttribute("globalLayer")) != null ? v : 1);
    // no.put("group", layer ); // required: node color by group
    return no;
}

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

public static ArrayList<AbstractJobType> getSubset(HashMap<String, String> jobIdList) {

    ArrayList<AbstractJobType> abstractJobTypeList = new ArrayList<AbstractJobType>();

    for (String jobId : jobIdList.keySet()) {
        AbstractJobType tmpAbstractJobType = CoreFactory.getInstance().getMonitoringOperations().getJobQueue()
                .get(jobId).getAbstractJobType();
        abstractJobTypeList.add(tmpAbstractJobType);
    }/*from   w  w w  . ja va  2  s. c  o  m*/

    return abstractJobTypeList;
}

From source file:org.grameenfoundation.consulteca.utils.HttpHelpers.java

private static void addHeaders(HttpGet httpGet, HashMap<String, String> headers) {
    if (headers == null) {
        return;/*from  w  ww .  j  a  v a 2  s  .com*/
    }

    Set<String> keys = headers.keySet();
    for (String key : keys) {
        httpGet.addHeader(key, headers.get(key));
    }
}

From source file:org.grameenfoundation.consulteca.utils.HttpHelpers.java

private static void addHeaders(HttpPost httpPost, HashMap<String, String> headers) {
    if (headers == null) {
        return;//from w  w w .  j  a va 2  s  .c om
    }

    Set<String> keys = headers.keySet();
    for (String key : keys) {
        httpPost.addHeader(key, headers.get(key));
    }
}

From source file:lineage.LineageEngine.java

/**
 * The main pipeline for reconstructing the cell lineage trees
 *//*  w w w.  j  a v  a 2 s . co m*/
public static void buildLineage(Args args) {

    // 1. load SNV data
    SNVDataStore db = new SNVDataStore(args.inputFileName, args.clustersFileName, args.normalSampleId);

    // 2. get the SNVs partitioned by group tag and create the appropriate SNV group objects
    HashMap<String, ArrayList<SNVEntry>> snvsByTag = db.getSomaticGroups();
    ArrayList<SNVGroup> groups = new ArrayList<SNVGroup>();
    for (String groupTag : snvsByTag.keySet()) {
        groups.add(new SNVGroup(groupTag, snvsByTag.get(groupTag), db.isRobustGroup(groupTag)));
    }
    if (groups.size() == 0) {
        logger.warning("All SNV groups have been filtered out.");
        return;
    }

    // 3. cluster SNVs in each group
    AAFClusterer clusterer = new AAFClusterer();
    for (SNVGroup group : groups) {
        if (args.clustersFileName == null) {
            Cluster[] clusters = clusterer.clusterSubPopulations(group, ClusteringAlgorithms.EM, 1);
            logger.fine("Clustering results for group: " + group.getTag());
            for (Cluster c : clusters) {
                logger.fine(c.toString());
            }
            group.setSubPopulations(clusters);
        } else {
            ArrayList<Cluster> groupClusters = db.getClusters().get(group.getTag());
            group.subPopulations = new Cluster[groupClusters.size()];
            group.subPopulations = groupClusters.toArray(group.subPopulations);
        }
    }

    // 4. construct the constraint network
    PHYNetwork constrNetwork = new PHYNetwork(groups, db.getNumSamples());
    logger.fine(constrNetwork.toString());

    // 5. find all the lineage trees that pass the VAF constraints
    ArrayList<PHYTree> spanningTrees = constrNetwork.getLineageTrees();
    logger.info("Found " + spanningTrees.size() + " valid tree(s)");

    if (spanningTrees.size() == 0) {
        logger.info("Adjusting the network...");
        // if no valid trees were found, fix the network 
        // remove group nodes that are not robust, complete edges
        int delta = 0;
        do {
            int numNodes = constrNetwork.numNodes;
            constrNetwork = constrNetwork.fixNetwork();
            spanningTrees = constrNetwork.getLineageTrees();
            delta = numNodes - constrNetwork.numNodes;
        } while ((delta != 0) && (spanningTrees.size() <= 0));
        if (spanningTrees.size() <= 0) {
            Parameters.ALL_EDGES = true;
            constrNetwork = new PHYNetwork(groups, db.getNumSamples());
            spanningTrees = constrNetwork.getLineageTrees();
        }
        logger.info("Found " + spanningTrees.size() + " valid trees after network adjustments");
    }

    // 6. evaluate/rank the trees
    if (spanningTrees.size() > 0) {
        constrNetwork.evaluateLineageTrees();
        logger.fine("Top tree\nError score: " + spanningTrees.get(0).getErrorScore());
        logger.fine(spanningTrees.get(0).toString());
    }

    // 7. result visualization
    if (args.showNetwork) {
        constrNetwork.displayNetwork();
    }
    if (spanningTrees.size() > 0) {
        for (int i = 0; i < args.numShow; i++) {
            if (spanningTrees.size() > i) {
                constrNetwork.displayTree(spanningTrees.get(i), db.getSampleNames(), null, null);
            } else {
                break;
            }
        }
        // 8. persistent storage
        if (args.numSave > 0) {
            writeTreesToTxtFile(constrNetwork, spanningTrees, db.getSampleNames(), args);
        }
    }
}

From source file:es.pode.soporte.auditoria.registrar.Registrar.java

/**
 * A partir de los datos enviados se recupera el tipo de bsqueda avanzada, simple, rbol curricular y tesauro
 * @param tabla Son los datos interceptados en formato HashMap
 * @return valores Los valores interceptados en formato String
 *               //from ww w.java  2s  .com
 */
private static String getValoresInterceptados(HashMap tabla) {

    StringBuffer valores = new StringBuffer();

    try {
        for (Iterator it = tabla.keySet().iterator(); it.hasNext();) {
            String s = (String) it.next();
            String s1 = (String) tabla.get(s);
            valores.append(s + ": " + s1 + "  ");
        }
    } catch (Exception e) {
        log.error("Error captura valores interceptados: " + e);
        valores.append(VACIO);
    }

    return valores.toString();
}

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());
    }/*from  w  ww  . java  2  s .c o m*/

    return tmpList;
}

From source file:LineageSimulator.java

public static void simulateLineageTrees(Args args) {
    int totalNumNodes = 0;
    // --- grow lineage trees --- //
    for (int t = 0; t < Parameters.NUM_TREES; t++) {
        // create the directory to store the results for each generated tree 
        File treeDir = new File(args.simPath + "/tree" + "_" + t);
        treeDir.mkdirs();/*from  w  w w  .j av  a 2s  .  c  o  m*/
        // initial tree (only contains the root)
        SimulatedTree lineageTree = new SimulatedTree();
        // -- expand the tree --
        int iter = 0;
        while (iter < Parameters.NUM_ITERATIONS || /* there must be a min number of undead nodes */
                lineageTree.getNumNodes() < lineageTree.getNumDeadNodes() + Parameters.MIN_NUM_NODES + 1) {
            if (lineageTree.getNumNodes() >= lineageTree.getNumDeadNodes() + Parameters.MAX_NUM_NODES + 1) {
                break;
            }
            lineageTree.grow();
            iter++;
        }
        writeOutputFile(treeDir.getAbsolutePath() + "/TREE_plain.txt", lineageTree.toString());
        if (args.generateDOT) {
            writeOutputFile(treeDir.getAbsolutePath() + "/TREE.dot", lineageTree.toDOT());
        }
        logger.fine("Generated tree " + t + " with " + lineageTree.getNumNodes() + " nodes.");
        totalNumNodes += lineageTree.getNumNodes();

        // --- sampling --- //
        for (int s = 0; s < Parameters.NUM_SAMPLES_ARRAY.length; s++) {
            int numSamples = Parameters.NUM_SAMPLES_ARRAY[s];
            ArrayList<TumorSample> samples = new ArrayList<TumorSample>();
            HashSet<CellPopulation> subclones = new HashSet<CellPopulation>();
            HashMap<Mutation.SNV, double[]> multiSampleFrequencies = new HashMap<Mutation.SNV, double[]>();

            // --- collect the samples from the tree ---
            if (Parameters.LOCALIZED_SAMPLING) {
                samples = lineageTree.getKLocalizedSamples(numSamples - 1);
            } else { // randomized
                for (int i = 1; i < numSamples; i++) {
                    samples.add(lineageTree.getSample());
                }
            }
            if (args.generateSampledDOT) {
                writeOutputFile(treeDir.getAbsolutePath() + "/TREE_s" + numSamples + ".dot",
                        lineageTree.toColoredDOT(samples));
            }
            lineageTree.resetColors();

            // --- populate the SNV VAFs for each sample ---
            for (int i = 1; i < numSamples; i++) { // + default normal sample 0
                TumorSample sample = samples.get(i - 1);
                HashMap<Mutation.SNV, Double> freqMap = sample.getSNVFrequencies();
                for (Mutation.SNV snv : freqMap.keySet()) {
                    if (multiSampleFrequencies.containsKey(snv)) {
                        multiSampleFrequencies.get(snv)[i] = freqMap.get(snv);
                    } else {
                        multiSampleFrequencies.put(snv, new double[numSamples]);
                        multiSampleFrequencies.get(snv)[i] = freqMap.get(snv);
                    }
                }
                subclones.addAll(sample.cellPopulationCounts.keySet());
            }
            HashMap<Mutation.SNV, String> binaryProfiles = null;
            if (args.outputSampleProfile) {
                binaryProfiles = getBinaryProfile(multiSampleFrequencies, numSamples);
            }
            // --- store true VAFs --- 
            String VAFFileName = treeDir.getAbsolutePath() + "/VAF_s" + numSamples + "_true.txt";
            writeVAFsToFile(VAFFileName, multiSampleFrequencies, binaryProfiles, numSamples);

            // --- generate VAFs with simulated coverage and sequencing error ---
            for (int c = 0; c < Parameters.COVERAGE_ARRAY.length; c++) {
                int coverage = Parameters.COVERAGE_ARRAY[c];
                VAFFileName = treeDir.getAbsolutePath() + "/VAF_s" + numSamples + "_" + coverage + "X.txt";
                HashMap<Mutation.SNV, double[]> noisyMultiSampleFrequencies = addNoise(multiSampleFrequencies,
                        coverage, numSamples);
                writeVAFsToFile(VAFFileName, noisyMultiSampleFrequencies, binaryProfiles, numSamples);
            }
            // --- store subclone information for evaluation ---
            String lineageFileName = treeDir.getAbsolutePath() + "/SUBCLONES_s" + numSamples + ".txt";
            writeSubclonesToFile(lineageFileName, subclones);
        }
        if ((t + 1) % 1 == 0)
            logger.info("[PROGRESS] Simulated " + (t + 1) + " trees.");
    }
    logger.info("[SUMMARY] Simulated " + Parameters.NUM_TREES + " trees. Average number of nodes / tree = "
            + (double) totalNumNodes / (Parameters.NUM_TREES));
}

From source file:bookChapter.theoretical.AnalyzeTheoreticalMSMSCalculation.java

private static String result(MSnSpectrum msms, double precursorTolerance, HashSet<DBEntry> peptideAndMass,
        double fragmentTolerance, int correctionFactor, boolean hasAllPossCharge)
        throws IllegalArgumentException, IOException, MzMLUnmarshallerException {
    String res = "";
    HashMap<Peptide, Boolean> allSelectedPeps = getSelectedTheoPeps(msms, precursorTolerance, peptideAndMass); // select peptides within a given precursor tolerance
    int scoredPeps = allSelectedPeps.size();
    ArrayList<Identify> sequestResults = new ArrayList<Identify>(),
            andromedaResults = new ArrayList<Identify>();
    // for every peptide... calculate each score...
    for (Peptide selectedPep : allSelectedPeps.keySet()) {
        Identify toCalculateSequest = new Identify(msms, selectedPep, fragmentTolerance, true,
                allSelectedPeps.get(selectedPep), scoredPeps, correctionFactor, hasAllPossCharge),
                toCalculateAndromeda = new Identify(msms, selectedPep, fragmentTolerance, false,
                        allSelectedPeps.get(selectedPep), scoredPeps, correctionFactor, hasAllPossCharge);
        if (toCalculateSequest.getScore() != Double.NEGATIVE_INFINITY) {
            sequestResults.add(toCalculateSequest);
            andromedaResults.add(toCalculateAndromeda);
        }/*w w w .j  a va2  s  .  c  om*/
    }
    if (!sequestResults.isEmpty()) {
        HashSet<Identify> theBestSEQUESTResults = getBestResult(sequestResults),
                theBestAndromedaResults = getBestResult(andromedaResults);
        res = printInfo(theBestAndromedaResults, theBestSEQUESTResults);
    }
    return res;
}