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

Introduction

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

Prototype

public static double[] addAll(double[] array1, double[] array2)

Source Link

Document

Adds all the elements of the given arrays into a new array.

Usage

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;
    }/*w w w .  j a  v a2 s .c  om*/
    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.broadinstitute.sting.utils.variant.GATKVariantContextUtils.java

public static Pair<int[], byte[]> getNumTandemRepeatUnits(final byte[] refBases, final byte[] altBases,
        final byte[] remainingRefContext) {
    /* we can't exactly apply same logic as in basesAreRepeated() to compute tandem unit and number of repeated units.
      Consider case where ref =ATATAT and we have an insertion of ATAT. Natural description is (AT)3 -> (AT)2.
    *///  w  w  w  . j a  v  a 2  s  .c o  m

    byte[] longB;
    // find first repeat unit based on either ref or alt, whichever is longer
    if (altBases.length > refBases.length)
        longB = altBases;
    else
        longB = refBases;

    // see if non-null allele (either ref or alt, whichever is longer) can be decomposed into several identical tandem units
    // for example, -*,CACA needs to first be decomposed into (CA)2
    final int repeatUnitLength = findRepeatedSubstring(longB);
    final byte[] repeatUnit = Arrays.copyOf(longB, repeatUnitLength);

    final int[] repetitionCount = new int[2];
    // look for repetitions forward on the ref bases (i.e. starting at beginning of ref bases)
    int repetitionsInRef = findNumberofRepetitions(repeatUnit, refBases, true);
    repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext),
            true) - repetitionsInRef;
    repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext),
            true) - repetitionsInRef;

    return new Pair<int[], byte[]>(repetitionCount, repeatUnit);

}

From source file:org.broadleafcommerce.common.copy.MultiTenantCopyContext.java

public Field[] getAllFields(Class<?> targetClass) {
    Field[] allFields = new Field[] {};
    boolean eof = false;
    Class<?> currentClass = targetClass;
    while (!eof) {
        Field[] fields = currentClass.getDeclaredFields();
        allFields = (Field[]) ArrayUtils.addAll(allFields, fields);
        if (currentClass.getSuperclass() != null) {
            currentClass = currentClass.getSuperclass();
        } else {/*from  w w w.  jav  a 2  s .c  o m*/
            eof = true;
        }
    }

    return allFields;
}

From source file:org.broadleafcommerce.openadmin.server.dao.DynamicEntityDaoImpl.java

protected void buildPropertiesFromPolymorphicEntities(Class<?>[] entities, ForeignKey foreignField,
        String[] additionalNonPersistentProperties, ForeignKey[] additionalForeignFields,
        MergedPropertyType mergedPropertyType, Boolean populateManyToOneFields, String[] includeFields,
        String[] excludeFields, String configurationKey, String ceilingEntityFullyQualifiedClassname,
        Map<String, FieldMetadata> mergedProperties, List<Class<?>> parentClasses, String prefix,
        Boolean isParentExcluded) {
    for (Class<?> clazz : entities) {
        String cacheKey = getCacheKey(foreignField, additionalNonPersistentProperties, additionalForeignFields,
                mergedPropertyType, populateManyToOneFields, clazz, configurationKey, isParentExcluded);

        Map<String, FieldMetadata> cacheData = null;
        synchronized (DynamicDaoHelperImpl.LOCK_OBJECT) {
            if (useCache()) {
                cacheData = METADATA_CACHE.get(cacheKey);
            }/*from w  w  w .jav  a 2  s  .  c o m*/

            if (cacheData == null) {
                Map<String, FieldMetadata> props = getPropertiesForEntityClass(clazz, foreignField,
                        additionalNonPersistentProperties, additionalForeignFields, mergedPropertyType,
                        populateManyToOneFields, includeFields, excludeFields, configurationKey,
                        ceilingEntityFullyQualifiedClassname, parentClasses, prefix, isParentExcluded);
                //first check all the properties currently in there to see if my entity inherits from them
                for (Class<?> clazz2 : entities) {
                    if (!clazz2.getName().equals(clazz.getName())) {
                        for (Map.Entry<String, FieldMetadata> entry : props.entrySet()) {
                            FieldMetadata metadata = entry.getValue();
                            try {
                                if (Class.forName(metadata.getInheritedFromType()).isAssignableFrom(clazz2)) {
                                    String[] both = (String[]) ArrayUtils.addAll(metadata.getAvailableToTypes(),
                                            new String[] { clazz2.getName() });
                                    metadata.setAvailableToTypes(both);
                                }
                            } catch (ClassNotFoundException e) {
                                throw new RuntimeException(e);
                            }
                        }
                    }
                }
                METADATA_CACHE.put(cacheKey, props);
                cacheData = props;
            }
        }
        //clone the metadata before passing to the system
        Map<String, FieldMetadata> clonedCache = new HashMap<String, FieldMetadata>(cacheData.size());
        for (Map.Entry<String, FieldMetadata> entry : cacheData.entrySet()) {
            clonedCache.put(entry.getKey(), entry.getValue().cloneFieldMetadata());
        }
        mergedProperties.putAll(clonedCache);
    }
}

From source file:org.broadleafcommerce.openadmin.server.dao.DynamicEntityDaoImpl.java

@Override
public Field[] getAllFields(Class<?> targetClass) {
    Field[] allFields = new Field[] {};
    boolean eof = false;
    Class<?> currentClass = targetClass;
    while (!eof) {
        Field[] fields = currentClass.getDeclaredFields();
        allFields = (Field[]) ArrayUtils.addAll(allFields, fields);
        if (currentClass.getSuperclass() != null) {
            currentClass = currentClass.getSuperclass();
        } else {//from   ww  w.j a va  2 s  .c om
            eof = true;
        }
    }

    return allFields;
}

From source file:org.broadleafcommerce.openadmin.server.service.persistence.entitymanager.HibernateCleaner.java

protected Field[] getFields(Class<?> clazz) {
    Field[] fields = new Field[] {};
    Class<?> myClass = clazz;
    boolean eof = false;
    while (!eof) {
        Field[] temp = myClass.getDeclaredFields();
        fields = (Field[]) ArrayUtils.addAll(temp, fields);
        if (myClass.getSuperclass() != null) {
            myClass = myClass.getSuperclass();
        } else {/*from   ww  w .  j  a v a  2 s.c  o m*/
            eof = true;
        }
    }

    return fields;
}

From source file:org.carewebframework.api.spring.FrameworkAppContext.java

/**
 * Adds one or more locations to the list of current locations to search for configuration
 * files./*from  ww  w .  j  av  a 2 s .c o  m*/
 * 
 * @param location One or more locations to search.
 */
public void addConfigLocation(String... location) {
    setConfigLocations((String[]) ArrayUtils.addAll(getConfigLocations(), location));
}

From source file:org.carewebframework.maven.plugin.theme.AbstractThemeProcessor.java

protected void addConfigEntry(String insertionTag, String... params) {
    params = (String[]) ArrayUtils
            .addAll(new String[] { theme.getThemeName(), theme.getThemeVersion(), getThemeBase() }, params);
    mojo.addConfigEntry(insertionTag, params);
}

From source file:org.carewebframework.ui.spring.FrameworkAppContext.java

/**
 * For the root container, adds the usual defaults to any custom locations. For a child
 * container, returns just the usual defaults.
 *//*w ww. ja  v a 2s  .com*/
@Override
protected String[] getDefaultConfigLocations() {
    return desktop == null
            ? (String[]) ArrayUtils.addAll(Constants.DEFAULT_LOCATIONS, super.getDefaultConfigLocations())
            : Constants.DEFAULT_LOCATIONS;
}

From source file:org.cesecore.audit.impl.queued.AuditLogProcessQueue.java

public byte[] dependencyData(final AuditLogProcess process) throws IOException {
    byte[] data = {};
    synchronized (pullLock) {
        for (final Iterator<AuditLogData> it = logs.iterator(); it.hasNext();) {
            final AuditLogData auditLogData = it.next();
            if (auditLogData.getSequenceNumber() < process.getAuditLogData().getSequenceNumber()) {
                data = ArrayUtils.addAll(auditLogData.getBytes(), data);
                it.remove();//from   w  ww.  jav a 2s . c o m
            } else {
                break;
            }
        }
    }
    return data;
}