Example usage for org.apache.commons.lang ArrayUtils subarray

List of usage examples for org.apache.commons.lang ArrayUtils subarray

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Introduction

In this page you can find the example usage for org.apache.commons.lang ArrayUtils subarray.

Prototype

public static boolean[] subarray(boolean[] array, int startIndexInclusive, int endIndexExclusive)

Source Link

Document

Produces a new boolean array containing the elements between the start and end indices.

Usage

From source file:org.apache.velocity.io.UnicodeInputStreamTestCase.java

protected byte[] readAllBytes(final InputStream inputStream, final String enc) throws Exception {
    InputStreamReader isr = null;

    byte[] res = new byte[0];

    try {/*  w ww.j  a  v a2s. c  om*/
        byte[] buf = new byte[1024];
        int read = 0;

        while ((read = inputStream.read(buf)) >= 0) {
            res = ArrayUtils.addAll(res, ArrayUtils.subarray(buf, 0, read));
        }
    } finally {

        if (isr != null) {
            isr.close();
        }
    }

    return res;
}

From source file:org.beanfuse.persist.hibernate.EntityDaoHibernate.java

public List load(String entityName, String keyName, Object[] values) {
    StringBuilder hql = new StringBuilder();
    hql.append("select entity from ").append(entityName).append(" as entity where entity.").append(keyName)
            .append(" in (:keyName)");
    Map parameterMap = new HashMap(1);
    if (values.length < 500) {
        parameterMap.put("keyName", values);
        EntityQuery query = new EntityQuery(hql.toString());
        query.setParams(parameterMap);//from  w  w  w. j  av  a2  s  . co  m
        return (List) search(query);
    } else {
        EntityQuery query = new EntityQuery(hql.toString());
        query.setParams(parameterMap);
        List rs = new ArrayList();
        int i = 0;
        while (i < values.length) {
            int end = i + 500;
            if (end > values.length) {
                end = values.length;
            }
            parameterMap.put("keyName", ArrayUtils.subarray(values, i, end));
            rs.addAll(search(query));
            i += 500;
        }
        return rs;
    }
}

From source file:org.beangle.model.persist.hibernate.HibernateEntityDao.java

public <T> List<T> get(String entityName, String keyName, Object... values) {
    StringBuilder hql = new StringBuilder();
    hql.append("select entity from ").append(entityName).append(" as entity where entity.").append(keyName)
            .append(" in (:keyName)");
    Map<String, Object> parameterMap = CollectUtils.newHashMap();
    if (values.length < 500) {
        parameterMap.put("keyName", values);
        QueryBuilder<T> query = OqlBuilder.hql(hql.toString());
        return search(query.params(parameterMap).build());
    } else {// ww w.ja v a  2  s .com
        QueryBuilder<T> query = OqlBuilder.hql(hql.toString());
        List<T> rs = CollectUtils.newArrayList();
        int i = 0;
        while (i < values.length) {
            int end = i + 500;
            if (end > values.length) {
                end = values.length;
            }
            parameterMap.put("keyName", ArrayUtils.subarray(values, i, end));
            rs.addAll(search(query.params(parameterMap).build()));
            i += 500;
        }
        return rs;
    }
}

From source file:org.broadinstitute.gatk.tools.walkers.haplotypecaller.LDMerger.java

protected VariantContext createMergedVariantContext(final VariantContext thisVC, final VariantContext nextVC,
        final byte[] ref, final GenomeLoc refLoc) {
    final int thisStart = thisVC.getStart();
    final int nextStart = nextVC.getStart();
    byte[] refBases = new byte[] {};
    byte[] altBases = new byte[] {};
    refBases = ArrayUtils.addAll(refBases, thisVC.getReference().getBases());
    altBases = ArrayUtils.addAll(altBases, thisVC.getAlternateAllele(0).getBases());
    int locus;/* w  w  w.java  2 s .c o  m*/
    for (locus = thisStart + refBases.length; locus < nextStart; locus++) {
        final byte refByte = ref[locus - refLoc.getStart()];
        refBases = ArrayUtils.add(refBases, refByte);
        altBases = ArrayUtils.add(altBases, refByte);
    }
    refBases = ArrayUtils.addAll(refBases, ArrayUtils.subarray(nextVC.getReference().getBases(),
            locus > nextStart ? 1 : 0, nextVC.getReference().getBases().length)); // special case of deletion including the padding base of consecutive indel
    altBases = ArrayUtils.addAll(altBases, nextVC.getAlternateAllele(0).getBases());

    int iii = 0;
    if (refBases.length == altBases.length) { // insertion + deletion of same length creates an MNP --> trim common prefix bases off the beginning of the allele
        while (iii < refBases.length && refBases[iii] == altBases[iii]) {
            iii++;
        }
        if (iii == refBases.length) {
            // we've become a null allele, such as with CA/C + A/AA -> CA/CA => after trimming there's nothing left
            // so return a null variant context so we can eliminate the variants from consideration
            return null;
        }
    }

    final Allele refAllele = Allele.create(ArrayUtils.subarray(refBases, iii, refBases.length), true);
    final Allele altAllele = Allele.create(ArrayUtils.subarray(altBases, iii, altBases.length), false);
    return new VariantContextBuilder("merged", thisVC.getChr(), thisVC.getStart() + iii, nextVC.getEnd(),
            Arrays.asList(refAllele, altAllele)).make();
}

From source file:org.broadinstitute.gatk.utils.activeregion.BandPassActivityProfileUnitTest.java

private double[] bandPassInOnePass(final BandPassActivityProfile profile, final double[] activeProbArray) {
    final double[] bandPassProbArray = new double[activeProbArray.length];

    // apply the band pass filter for activeProbArray into filteredProbArray
    final double[] GaussianKernel = profile.getKernel();
    for (int iii = 0; iii < activeProbArray.length; iii++) {
        final double[] kernel = ArrayUtils.subarray(GaussianKernel,
                Math.max(profile.getFilteredSize() - iii, 0),
                Math.min(GaussianKernel.length, profile.getFilteredSize() + activeProbArray.length - iii));
        final double[] activeProbSubArray = ArrayUtils.subarray(activeProbArray,
                Math.max(0, iii - profile.getFilteredSize()),
                Math.min(activeProbArray.length, iii + profile.getFilteredSize() + 1));
        bandPassProbArray[iii] = dotProduct(activeProbSubArray, kernel);
    }/*from w w w .jav a2s  . c om*/

    return bandPassProbArray;
}

From source file:org.broadinstitute.gatk.utils.haplotype.Haplotype.java

@Requires({ "refInsertLocation >= 0" })
public Haplotype insertAllele(final Allele refAllele, final Allele altAllele, final int refInsertLocation,
        final int genomicInsertLocation) {
    // refInsertLocation is in ref haplotype offset coordinates NOT genomic coordinates
    final int haplotypeInsertLocation = ReadUtils.getReadCoordinateForReferenceCoordinate(
            alignmentStartHapwrtRef, cigar, refInsertLocation, ReadUtils.ClippingTail.RIGHT_TAIL, true);
    final byte[] myBases = this.getBases();
    if (haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= myBases.length) { // desired change falls inside deletion so don't bother creating a new haplotype
        return null;
    }// w  ww.  j  av a2s.co  m

    byte[] newHaplotypeBases = new byte[] {};
    newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases,
            ArrayUtils.subarray(myBases, 0, haplotypeInsertLocation)); // bases before the variant
    newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, altAllele.getBases()); // the alt allele of the variant
    newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases,
            ArrayUtils.subarray(myBases, haplotypeInsertLocation + refAllele.length(), myBases.length)); // bases after the variant
    return new Haplotype(newHaplotypeBases);
}

From source file:org.broadinstitute.sting.utils.activeregion.ActivityProfile.java

/**
 * Band pass this ActivityProfile, producing a new profile that's band pass filtered
 * @return a new ActivityProfile that's the band-pass filtered version of this profile
 *//* w w w.j a v a2 s  .co m*/
public ActivityProfile bandPassFilter() {
    final Double[] activeProbArray = isActiveList.toArray(new Double[isActiveList.size()]);
    final Double[] filteredProbArray = new Double[activeProbArray.length];
    if (!presetRegions) {
        for (int iii = 0; iii < activeProbArray.length; iii++) {
            final Double[] kernel = (Double[]) ArrayUtils.subarray(GaussianKernel,
                    Math.max(FILTER_SIZE - iii, 0),
                    Math.min(GaussianKernel.length, FILTER_SIZE + activeProbArray.length - iii));
            final Double[] activeProbSubArray = (Double[]) ArrayUtils.subarray(activeProbArray,
                    Math.max(0, iii - FILTER_SIZE), Math.min(activeProbArray.length, iii + FILTER_SIZE + 1));
            filteredProbArray[iii] = MathUtils.dotProduct(activeProbSubArray, kernel);
        }
    }
    return new ActivityProfile(parser, presetRegions, Arrays.asList(filteredProbArray), regionStartLoc);
}

From source file:org.broadinstitute.sting.utils.haplotype.Haplotype.java

@Requires({ "refInsertLocation >= 0" })
public Haplotype insertAllele(final Allele refAllele, final Allele altAllele, final int refInsertLocation,
        final int genomicInsertLocation) {
    // refInsertLocation is in ref haplotype offset coordinates NOT genomic coordinates
    final int haplotypeInsertLocation = ReadUtils.getReadCoordinateForReferenceCoordinate(
            alignmentStartHapwrtRef, cigar, refInsertLocation, ReadUtils.ClippingTail.RIGHT_TAIL, true);
    final byte[] myBases = this.getBases();
    if (haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= myBases.length) { // desired change falls inside deletion so don't bother creating a new haplotype
        return null;
    }//from   ww w  .java  2  s  . c o m

    byte[] newHaplotypeBases = new byte[] {};
    newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases,
            ArrayUtils.subarray(myBases, 0, haplotypeInsertLocation)); // bases before the variant
    newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, altAllele.getBases()); // the alt allele of the variant
    newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases,
            ArrayUtils.subarray(myBases, haplotypeInsertLocation + refAllele.length(), myBases.length)); // bases after the variant
    return new Haplotype(newHaplotypeBases, new Event(refAllele, altAllele, genomicInsertLocation));
}

From source file:org.broadinstitute.sting.utils.Haplotype.java

@Requires({ "refInsertLocation >= 0" })
public Haplotype insertAllele(final Allele refAllele, final Allele altAllele, final int refInsertLocation) {
    // refInsertLocation is in ref haplotype offset coordinates NOT genomic coordinates
    final int haplotypeInsertLocation = ReadUtils.getReadCoordinateForReferenceCoordinate(
            alignmentStartHapwrtRef, cigar, refInsertLocation, ReadUtils.ClippingTail.RIGHT_TAIL, true);
    if (haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= bases.length) { // desired change falls inside deletion so don't bother creating a new haplotype
        return null;
    }//from w w w .jav a2s. co m
    byte[] newHaplotypeBases = new byte[] {};
    newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases,
            ArrayUtils.subarray(bases, 0, haplotypeInsertLocation)); // bases before the variant
    newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, altAllele.getBases()); // the alt allele of the variant
    newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases,
            ArrayUtils.subarray(bases, haplotypeInsertLocation + refAllele.length(), bases.length)); // bases after the variant
    return new Haplotype(newHaplotypeBases);
}

From source file:org.brushingbits.jnap.persistence.hibernate.DynaQueryBuilder.java

Object[] getPropertyValues(int size) {
    if ((propertyValueIndex + size) <= this.queryParams.length) {
        Object[] values = ArrayUtils.subarray(this.queryParams, propertyValueIndex, propertyValueIndex + size);
        propertyValueIndex += size;//from w  w w  .  j a  v  a 2 s . c o m
        return values;
    } else {
        throw new QueryException(
                format("The number of parameters ({0}) does not satisfy " + "DynaQuery expression",
                        Integer.toString(this.queryParams.length)),
                this.dynaQuery);
    }
}