Package org.broadinstitute.hellbender.tools.dragstr

Class DragstrLocusCases

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<DragstrLocusCase>

org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases

All Implemented Interfaces:

Iterable<DragstrLocusCase>, Collection<DragstrLocusCase>, List<DragstrLocusCase>

public final class DragstrLocusCases
extends AbstractList<DragstrLocusCase>

Collection of Dragstr Locus cases constraint to a particular period and (minimum) repeat-length

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor	Description
DragstrLocusCases(int period, int repeatLength)	Creates a new collection with default initial capacity.
DragstrLocusCases(int initialCapacity, int period, int repeatLength)	Creates a new dragstr cases collection providing it period and repeat-length constraints.

Method Summary

Modifier and Type	Method	Description
boolean	add(DragstrLocusCase caze)	Adds a case to the collection.
boolean	addAll(Collection<? extends DragstrLocusCase> more)
boolean	addAll(DragstrLocusCases other)
DragstrLocusCase	get(int index)
int	getPeriod()
int	getRepeatLength()
DragstrLocusCases	qualifyingOnly(int minDepth, int minMQ, int maxSup)	Returns a new collection that contains only those cases are qualify for parameter estimation given the required constraints.
int	size()

Methods inherited from class java.util.AbstractList

add, addAll, clear, equals, hashCode, indexOf, iterator, lastIndexOf, listIterator, listIterator, remove, removeRange, set, subList

Methods inherited from class java.util.AbstractCollection

contains, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream, toArray

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface java.util.List

contains, containsAll, isEmpty, remove, removeAll, replaceAll, retainAll, sort, spliterator, toArray, toArray

Constructor Details

DragstrLocusCases

public DragstrLocusCases(int period,
 int repeatLength)

Creates a new collection with default initial capacity.

Parameters:

period - the collection cases period.

repeatLength - the collection cases (minimum) repeat-length.

DragstrLocusCases

public DragstrLocusCases(int initialCapacity,
 int period,
 int repeatLength)

Creates a new dragstr cases collection providing it period and repeat-length constraints.

Parameters:

initialCapacity - the expected maximum number of members in the collection.

period - the member case period constraint. Only cases with this period are allowed.

repeatLength - the member case repeat-length constraint. Only cases with a repeat-length as large are allowed.

Method Details

get

public DragstrLocusCase get(int index)

Specified by:

get in interface List<DragstrLocusCase>

Specified by:

get in class AbstractList<DragstrLocusCase>

add

public boolean add(DragstrLocusCase caze)

Adds a case to the collection.

This method makes sure that you don't add cases with a different period. The input repeat-length might be larger than the collection's to accomodate the special case of the "maximum" analyzed repeat-length.

Specified by:

add in interface Collection<DragstrLocusCase>

Specified by:

add in interface List<DragstrLocusCase>

Overrides:

add in class AbstractList<DragstrLocusCase>

Parameters:

caze - the case to add.

Returns:

always true.

Throws:

IllegalArgumentException - if the input is null or has the wrong period or repeat-length.

addAll

public boolean addAll(Collection<? extends DragstrLocusCase> more)

Specified by:

addAll in interface Collection<DragstrLocusCase>

Specified by:

addAll in interface List<DragstrLocusCase>

Overrides:

addAll in class AbstractCollection<DragstrLocusCase>

addAll

public boolean addAll(DragstrLocusCases other)

getPeriod

public int getPeriod()

getRepeatLength

public int getRepeatLength()

size

public int size()

Specified by:

size in interface Collection<DragstrLocusCase>

Specified by:

size in interface List<DragstrLocusCase>

Specified by:

size in class AbstractCollection<DragstrLocusCase>

qualifyingOnly

public DragstrLocusCases qualifyingOnly(int minDepth,
 int minMQ,
 int maxSup)

Returns a new collection that contains only those cases are qualify for parameter estimation given the required constraints.

Parameters:

minDepth - minimum depth admissible.

minMQ - minimum mapping quality admissible.

maxSup - maximum number of supplementary alignments admissible.

Returns:

never null.