Example usage for java.util Collections nCopies

List of usage examples for java.util Collections nCopies

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Introduction

In this page you can find the example usage for java.util Collections nCopies.

Prototype

public static <T> List<T> nCopies(int n, T o)

Source Link

Document

Returns an immutable list consisting of n copies of the specified object.

Usage

From source file:eionet.cr.dao.virtuoso.VirtuosoStagingDatabaseDAO.java

@Override
public void delete(List<String> dbNames) throws DAOException {

    if (dbNames == null || dbNames.isEmpty()) {
        return;//w  w w .j  a v a 2  s.c o m
    }

    Connection conn = null;
    try {
        conn = getSQLConnection();
        conn.setAutoCommit(false);

        // First, ensure the given databases are present in staging databases table (to avoid deleting other databases).
        String questionMarks = StringUtils.join(Collections.nCopies(dbNames.size(), "?"), ',');
        String sql = COUNT_EXISTING_DBS_SQL.replace("?", questionMarks);
        int count = NumberUtils.toInt(SQLUtil.executeSingleReturnValueQuery(sql, dbNames, conn).toString());
        if (dbNames.size() > count) {
            throw new DAOException("At least one of the given databases is unknown");
        }

        // Second, delete the databases themselves.
        deleteDatabases(dbNames, conn);

        // Third, delete rows from the staging databases table.
        sql = DELETE_DB_SQL.replace("?", questionMarks);
        SQLUtil.executeUpdate(sql, dbNames, conn);

        conn.commit();
    } catch (SQLException e) {
        SQLUtil.rollback(conn);
        throw new DAOException(e.getMessage(), e);
    } finally {
        SQLUtil.close(conn);
    }
}

From source file:org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculatorUnitTest.java

private static int[] PLsForObviousCall(final int ploidy, final int numAlleles, final int[] alleleCounts,
        final int PL) {
    final GenotypeLikelihoodCalculator glCalc = GL_CALCS.getInstance(ploidy, numAlleles);
    final int[] result = Collections.nCopies(glCalc.genotypeCount(), PL).stream().mapToInt(n -> n).toArray();
    result[glCalc.alleleCountsToIndex(alleleCounts)] = 0;
    return result;
}

From source file:org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculatorUnitTest.java

@Test
public void testManyRefSamplesDontKillGoodVariant() {
    final AlleleFrequencyCalculator afCalc = new AlleleFrequencyCalculator(1, 0.1, 0.1, DEFAULT_PLOIDY);
    final List<Allele> alleles = Arrays.asList(A, B);
    final Genotype AA = genotypeWithObviousCall(DIPLOID, BIALLELIC, new int[] { 0, 2 }, EXTREMELY_CONFIDENT_PL);
    final Genotype AB = genotypeWithObviousCall(DIPLOID, BIALLELIC, new int[] { 0, 1, 1, 1 },
            EXTREMELY_CONFIDENT_PL);/* w w  w.j a  v  a 2  s .c o m*/
    for (final int numRef : new int[] { 1, 10, 100, 1000, 10000, 100000 }) {
        final List<Genotype> genotypeList = new ArrayList<>(Collections.nCopies(numRef, AA));
        genotypeList.add(AB);
        final VariantContext vc = makeVC(alleles, genotypeList);
        final double log10PRef = afCalc.getLog10PNonRef(vc).getLog10LikelihoodOfAFEq0();
        Assert.assertTrue(log10PRef < (-EXTREMELY_CONFIDENT_PL / 10) + Math.log10(numRef) + 1);
    }
}

From source file:org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculatorUnitTest.java

private static Genotype makeGenotype(final int ploidy, int... pls) {
    return new GenotypeBuilder("sample" + sampleNameCounter++)
            .alleles(Collections.nCopies(ploidy, Allele.NO_CALL)).PL(pls).make();
}

From source file:org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationUnitTest.java

@DataProvider(name = "GLsWithNonInformative")
public Object[][] makeGLsWithNonInformative() {
    List<Object[]> tests = new ArrayList<Object[]>();

    final List<NonInformativeData> nonInformativeTests = new LinkedList<NonInformativeData>();
    nonInformativeTests.add(new NonInformativeData(Arrays.asList(AB1), NON_INFORMATIVE1, 1));
    nonInformativeTests.add(new NonInformativeData(Arrays.asList(AB2), NON_INFORMATIVE2, 2));
    nonInformativeTests.add(new NonInformativeData(Arrays.asList(AB2, BC2), NON_INFORMATIVE2, 2));

    for (final int nNonInformative : Arrays.asList(1, 10, 100)) {
        for (final NonInformativeData testData : nonInformativeTests) {
            final List<Genotype> samples = new ArrayList<Genotype>();
            samples.addAll(testData.called);
            samples.addAll(Collections.nCopies(nNonInformative, testData.nonInformative));

            final int nSamples = samples.size();
            List<AFCalculator> calcs = createAFCalculators(Arrays.asList(AFCalculatorImplementation.values()),
                    MAX_ALT_ALLELES, PLOIDY);

            final double[] priors = MathUtils.normalizeFromLog10(new double[2 * nSamples + 1], true); // flat priors

            for (AFCalculator model : calcs) {
                if (testData.nAltAlleles > 1 && model instanceof OriginalDiploidExactAFCalculator)
                    continue;

                final GetGLsTest onlyInformative = new GetGLsTest(model, testData.nAltAlleles, testData.called,
                        priors, "flat");

                for (int rotation = 0; rotation < nSamples; rotation++) {
                    Collections.rotate(samples, 1);
                    final GetGLsTest withNonInformative = new GetGLsTest(model, testData.nAltAlleles, samples,
                            priors, "flat");
                    tests.add(new Object[] { onlyInformative, withNonInformative });
                }//from  w  w  w . ja v a2  s .  c o m
            }
        }
    }

    return tests.toArray(new Object[][] {});
}

From source file:org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend.java

private String buildWriteKeysInsertStmt(int size) {
    StringBuilder stmtBuilder = new StringBuilder();
    stmtBuilder.append("INSERT INTO ");
    if (getKeyLoaderKeyIdSchema() != null) {
        stmtBuilder.append(getKeyLoaderKeyIdSchema());
        stmtBuilder.append('.');
    }/* ww  w . j a  v  a2 s  . c  om*/
    stmtBuilder.append(getKeyLoaderKeyIdTable());
    stmtBuilder.append(" (");
    stmtBuilder.append(getKeyLoaderKeyIdColumn());
    stmtBuilder.append(", ");
    stmtBuilder.append(getKeyLoaderKeyIdJoinKey());
    stmtBuilder.append(") ");
    stmtBuilder.append(" SELECT ");
    stmtBuilder.append(getDefaultKeyIdColumn());
    stmtBuilder.append(", ");
    stmtBuilder.append(getDefaultKeyIdJoinKey());
    stmtBuilder.append(" FROM ");
    if (getSchemaName() != null) {
        stmtBuilder.append(getSchemaName());
        stmtBuilder.append('.');
    }
    stmtBuilder.append(getDefaultKeyIdTable());
    stmtBuilder.append(" WHERE ");
    stmtBuilder.append(getDefaultKeyIdColumn());
    stmtBuilder.append(" IN (");
    stmtBuilder.append(StringUtils.join(Collections.nCopies(size, "?"), ','));
    stmtBuilder.append(')');
    String stmt = stmtBuilder.toString();
    return stmt;
}

From source file:edu.vt.vbi.patric.proteinfamily.FIGfamData.java

@SuppressWarnings("unchecked")
public void getGroupStats(ResourceRequest request, PrintWriter writer) throws IOException {

    DataApiHandler dataApi = new DataApiHandler(request);

    JSONObject figfams = new JSONObject();
    Set<String> figfamIdList = new HashSet<>();
    List<String> genomeIdList = new LinkedList<>();
    // get family Type
    final String familyType = request.getParameter("familyType");
    final String familyId = familyType + "_id";

    // get genome list in order
    String genomeIds = request.getParameter("genomeIds");
    try {//from  ww w.  j  av a  2s . com
        SolrQuery query = new SolrQuery("genome_id:(" + genomeIds.replaceAll(",", " OR ") + ")");
        query.addSort("genome_name", SolrQuery.ORDER.asc).addField("genome_id")
                .setRows(DataApiHandler.MAX_ROWS);

        LOGGER.trace("[{}] {}", SolrCore.GENOME.getSolrCoreName(), query);

        String apiResponse = dataApi.solrQuery(SolrCore.GENOME, query);
        Map resp = jsonReader.readValue(apiResponse);
        Map respBody = (Map) resp.get("response");

        List<Genome> genomes = dataApi.bindDocuments((List<Map>) respBody.get("docs"), Genome.class);

        for (final Genome genome : genomes) {
            genomeIdList.add(genome.getId());
        }

        if (genomeIdList.size() == 25000) {
            query.setStart(25000);

            apiResponse = dataApi.solrQuery(SolrCore.GENOME, query);
            resp = jsonReader.readValue(apiResponse);
            respBody = (Map) resp.get("response");

            genomes = dataApi.bindDocuments((List<Map>) respBody.get("docs"), Genome.class);

            for (final Genome genome : genomes) {
                genomeIdList.add(genome.getId());
            }
        }
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    //      LOGGER.debug("genomeIdList: {}", genomeIdList);

    // getting genome counts per figfamID (figfam)
    // {stat:{field:{field:figfam_id,limit:-1,facet:{min:"min(aa_length)",max:"max(aa_length)",mean:"avg(aa_length)",ss:"sumsq(aa_length)",sum:"sum(aa_length)",dist:"percentile(aa_length,50,75,99,99.9)",field:{field:genome_id}}}}}

    try {
        long start = System.currentTimeMillis();
        SolrQuery query = new SolrQuery("annotation:PATRIC AND feature_type:CDS");
        //         query.addFilterQuery("end:[3200 TO 4300] OR end:[4400 TO 4490] OR end:[4990 TO 4999]");
        query.addFilterQuery(getSolrQuery(request));
        query.addFilterQuery("!" + familyId + ":\"\"");
        query.setRows(0).setFacet(true).set("facet.threads", 15);
        query.add("json.facet", "{stat:{type:field,field:genome_id,limit:-1,facet:{figfams:{type:field,field:"
                + familyId + ",limit:-1,sort:{index:asc}}}}}");

        LOGGER.trace("getGroupStats() 1/3: [{}] {}", SolrCore.FEATURE.getSolrCoreName(), query);
        String apiResponse = dataApi.solrQuery(SolrCore.FEATURE, query);

        long point = System.currentTimeMillis();
        LOGGER.debug("1st query: {} ms", (point - start));
        start = point;

        Map resp = jsonReader.readValue(apiResponse);
        Map facets = (Map) resp.get("facets");
        Map stat = (Map) facets.get("stat");

        final Map<String, String> figfamGenomeIdStr = new LinkedHashMap<>();
        final Map<String, Integer> figfamGenomeCount = new LinkedHashMap<>();

        final int genomeTotal = genomeIdList.size();
        final Map<String, Integer> genomePosMap = new LinkedHashMap<>();
        for (String genomeId : genomeIdList) {
            genomePosMap.put(genomeId, genomeIdList.indexOf(genomeId));
        }

        final Map<String, List> figfamGenomeIdCountMap = new ConcurrentHashMap<>();
        final Map<String, Set> figfamGenomeIdSet = new ConcurrentHashMap<>();

        List<Map> genomeBuckets = (List<Map>) stat.get("buckets");

        for (final Map bucket : genomeBuckets) {

            final String genomeId = (String) bucket.get("val");
            final List<Map> figfamBucket = (List<Map>) ((Map) bucket.get("figfams")).get("buckets");

            for (final Map figfam : figfamBucket) {
                final String figfamId = (String) figfam.get("val");
                final String genomeCount = String.format("%02x", (Integer) figfam.get("count"));

                if (figfamGenomeIdCountMap.containsKey(figfamId)) {
                    figfamGenomeIdCountMap.get(figfamId).set(genomePosMap.get(genomeId), genomeCount);
                } else {
                    final List<String> genomeIdCount = new LinkedList<>(Collections.nCopies(genomeTotal, "00"));
                    genomeIdCount.set(genomePosMap.get(genomeId), genomeCount);
                    figfamGenomeIdCountMap.put(figfamId, genomeIdCount);
                }

                if (figfamGenomeIdSet.containsKey(figfamId)) {
                    figfamGenomeIdSet.get(figfamId).add(genomeId);
                } else {
                    final Set<String> genomeIdSet = new HashSet<>();
                    genomeIdSet.add(genomeId);
                    figfamGenomeIdSet.put(figfamId, genomeIdSet);
                }
            }
        }

        for (String figfamId : figfamGenomeIdCountMap.keySet()) {
            final List genomeIdStr = figfamGenomeIdCountMap.get(figfamId);
            figfamGenomeIdStr.put(figfamId, StringUtils.join(genomeIdStr, ""));
            figfamGenomeCount.put(figfamId, figfamGenomeIdSet.get(figfamId).size());
        }

        point = System.currentTimeMillis();
        LOGGER.debug("1st query process : {} ms, figfamGenomeIdStr:{}, figfamGenomeCount:{}", (point - start),
                figfamGenomeIdStr.size(), figfamGenomeCount.size());

        long start2nd = System.currentTimeMillis();
        // 2nd query

        query.set("json.facet", "{stat:{type:field,field:" + familyId
                + ",limit:-1,facet:{min:\"min(aa_length)\",max:\"max(aa_length)\",mean:\"avg(aa_length)\",ss:\"sumsq(aa_length)\",sum:\"sum(aa_length)\"}}}");

        LOGGER.trace("getGroupStats() 2/3: [{}] {}", SolrCore.FEATURE.getSolrCoreName(), query);
        apiResponse = dataApi.solrQuery(SolrCore.FEATURE, query);

        point = System.currentTimeMillis();
        LOGGER.debug("2st query: {} ms", (point - start2nd));
        start2nd = point;

        resp = jsonReader.readValue(apiResponse);
        facets = (Map) resp.get("facets");
        stat = (Map) facets.get("stat");

        List<Map> buckets = (List<Map>) stat.get("buckets");

        for (Map bucket : buckets) {
            final String figfamId = (String) bucket.get("val");
            final int count = (Integer) bucket.get("count");

            double min, max, mean, sumsq, sum;
            if (bucket.get("min") instanceof Double) {
                min = (Double) bucket.get("min");
            } else if (bucket.get("min") instanceof Integer) {
                min = ((Integer) bucket.get("min")).doubleValue();
            } else {
                min = 0;
            }
            if (bucket.get("max") instanceof Double) {
                max = (Double) bucket.get("max");
            } else if (bucket.get("max") instanceof Integer) {
                max = ((Integer) bucket.get("max")).doubleValue();
            } else {
                max = 0;
            }
            if (bucket.get("mean") instanceof Double) {
                mean = (Double) bucket.get("mean");
            } else if (bucket.get("mean") instanceof Integer) {
                mean = ((Integer) bucket.get("mean")).doubleValue();
            } else {
                mean = 0;
            }
            if (bucket.get("ss") instanceof Double) {
                sumsq = (Double) bucket.get("ss");
            } else if (bucket.get("ss") instanceof Integer) {
                sumsq = ((Integer) bucket.get("ss")).doubleValue();
            } else {
                sumsq = 0;
            }
            if (bucket.get("sum") instanceof Double) {
                sum = (Double) bucket.get("sum");
            } else if (bucket.get("sum") instanceof Integer) {
                sum = ((Integer) bucket.get("sum")).doubleValue();
            } else {
                sum = 0;
            }

            //            LOGGER.debug("bucket:{}, sumsq:{}, count: {}", bucket, sumsq, count);
            double std;
            if (count > 1) {
                // std = Math.sqrt(sumsq / (count - 1));
                final double realSq = sumsq - (sum * sum) / count;
                std = Math.sqrt(realSq / (count - 1));
            } else {
                std = 0;
            }
            final JSONObject aaLength = new JSONObject();
            aaLength.put("min", min);
            aaLength.put("max", max);
            aaLength.put("mean", mean);
            aaLength.put("stddev", std);

            figfamIdList.add(figfamId);

            final JSONObject figfam = new JSONObject();
            figfam.put("genomes", figfamGenomeIdStr.get(figfamId));
            figfam.put("genome_count", figfamGenomeCount.get(figfamId));
            figfam.put("feature_count", count);
            figfam.put("stats", aaLength);

            figfams.put(figfamId, figfam);
        }

        point = System.currentTimeMillis();
        LOGGER.debug("2st query process: {} ms", (point - start2nd));
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    // getting distinct figfam_product
    if (!figfamIdList.isEmpty()) {

        figfamIdList.remove("");

        try {
            SolrQuery query = new SolrQuery("family_id:(" + StringUtils.join(figfamIdList, " OR ") + ")");
            query.addFilterQuery("family_type:" + familyType);
            query.addField("family_id,family_product").setRows(figfamIdList.size());

            LOGGER.debug("getGroupStats() 3/3: [{}] {}", SolrCore.FIGFAM_DIC.getSolrCoreName(), query);

            String apiResponse = dataApi.solrQuery(SolrCore.FIGFAM_DIC, query);

            Map resp = jsonReader.readValue(apiResponse);
            Map respBody = (Map) resp.get("response");

            List<Map> sdl = (List<Map>) respBody.get("docs");

            for (final Map doc : sdl) {
                final JSONObject figfam = (JSONObject) figfams.get(doc.get("family_id"));
                figfam.put("description", doc.get("family_product"));
                figfams.put(doc.get("family_id").toString(), figfam);
            }

            int i = 1;
            while (sdl.size() == 25000) {
                query.setStart(25000 * i);

                apiResponse = dataApi.solrQuery(SolrCore.FIGFAM_DIC, query);
                resp = jsonReader.readValue(apiResponse);
                respBody = (Map) resp.get("response");

                sdl = (List<Map>) respBody.get("docs");

                for (final Map doc : sdl) {
                    final JSONObject figfam = (JSONObject) figfams.get(doc.get("family_id"));
                    figfam.put("description", doc.get("family_product"));
                    figfams.put(doc.get("family_id").toString(), figfam);
                }
                i++;
            }
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
            LOGGER.debug("::getGroupStats() 3/3, params: {}", request.getParameterMap().toString());
        }
        figfams.writeJSONString(writer);
    }
}

From source file:org.openconcerto.sql.model.SQLRow.java

public Set<SQLRow> getDistantRows(final Path path) {
    // on veut tous les champs de la derniere table et rien d'autre
    final List<List<String>> fields = new ArrayList<List<String>>(
            Collections.nCopies(path.length() - 1, Collections.<String>emptyList()));
    fields.add(null);//from w w w  .ja va2 s . c  o m
    final Set<List<SQLRow>> s = this.getRowsOnPath(path, fields);
    final Set<SQLRow> res = new LinkedHashSet<SQLRow>(s.size());
    for (final List<SQLRow> l : s) {
        res.add(l.get(0));
    }
    return res;
}

From source file:gov.nih.nci.caarray.magetab.sdrf.SdrfDocument.java

private void addCharacteristic(List<String> row, Characteristic characteristic, boolean hasTerm,
        boolean hasUnit) {
    List<String> values = new LinkedList<String>();
    // Measurement characteristic: Add value, unit and the unit's term source.
    if (characteristic == null || characteristic.getTermOrDirectValue() == null) {
        values.add("");
        if (hasTerm) {
            values.add("");
        }//  www .  j a  va  2  s. co m
        if (hasUnit) {
            values.addAll(Collections.nCopies(2, ""));
        }
    } else {
        values.add(characteristic.getTermOrDirectValue());
        if (characteristic.getTerm() != null) {
            TermSource termSource = characteristic.getTerm().getTermSource();
            if (termSource == null || StringUtils.isBlank(termSource.getName())) {
                values.add("");
            } else {
                values.add(termSource.getName());
            }
        } else if (hasTerm) {
            values.add("");
        }
        OntologyTerm unit = characteristic.getUnit();
        if (unit != null) {
            values.add(unit.getValue());
            TermSource termSource = unit.getTermSource();
            if (termSource == null || StringUtils.isBlank(termSource.getName())) {
                values.add("");
            } else {
                values.add(termSource.getName());
            }
        } else if (hasUnit) {
            values.add("");
            values.add("");
        }
    }
    row.addAll(values);
}

From source file:eu.crisis_economics.abm.model.AbstractModel.java

/**
  * Selling price of goods manufactured by firms
  *//* w  ww .ja  v a 2  s .  co  m*/
@RecorderSource(value = "firmGoodsSellingPrice", collectionLengthMember = "getNumberOfFirmsForRecorderSampling()")
public List<Double> getFirmSellingPrices() {
    final List<Double> salePrices = new ArrayList<Double>();
    for (final MacroFirm firm : population.getAgentsOfType(MacroFirm.class))
        salePrices.add(firm.getGoodsSellingPrice());
    final List<Double> result = new ArrayList<Double>(Collections.nCopies(getNumberOfFirms(), 0.));
    for (int i = 0; i < salePrices.size(); ++i)
        result.set(i, salePrices.get(i));
    return result;
}