htsjdk.samtools.util

Class DiskBackedQueue<E>

java.lang.Object

htsjdk.samtools.util.DiskBackedQueue<E>

All Implemented Interfaces:

java.lang.Iterable<E>, java.util.Collection<E>, java.util.Queue<E>

public class DiskBackedQueue<E>
extends java.lang.Object
implements java.util.Queue<E>

A single-ended FIFO queue. Writes elements to temporary files when the queue gets too big. External references to elements in this queue are NOT guaranteed to be valid, due to the disk write/read

NB: The queue becomes read-only after the first time that an on-disk record is "next up" to be read (i.e. has been loaded into headRecord). Max size is therefore non-deterministic. This avoids issues arising from conflicts between the input and output streams. This could perhaps be avoided by creating a version of BAMRecordCodec that operates on RandomAccessFiles or channels.

Created by bradt on 4/28/14.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	add(E record) Add the record to the tail of the queue, spilling to disk if necessary Must check that (canAdd() == true) before calling this method
boolean	addAll(java.util.Collection<? extends E> c) Add all elements from collection c to this DiskBackedQueue Must check that (canAdd() == true) before calling this method
boolean	canAdd()
void	clear()
boolean	contains(java.lang.Object o) Not supported.
boolean	containsAll(java.util.Collection<?> c) Not supported.
E	element()
protected void	finalize() Clean up disk resources in case clear() has not been explicitly called (as would be preferable) Closes the input and output streams associated with this DiskBackedQueue and deletes the temporary file
int	getNumRecordsOnDisk()
boolean	headRecordIsFromDisk()
boolean	isEmpty()
java.util.Iterator<E>	iterator() Not supported at this time
static <T> DiskBackedQueue<T>	newInstance(SortingCollection.Codec<T> codec, int maxRecordsInRAM, java.util.List<java.io.File> tmpDir) Syntactic sugar around the ctor, to save some typing of type parameters
boolean	offer(E e)
E	peek()
E	poll()
E	remove()
boolean	remove(java.lang.Object o) Not supported.
boolean	removeAll(java.util.Collection<?> c) Not supported.
boolean	retainAll(java.util.Collection<?> c) Not supported.
int	size() Return the total number of elements in the queue, both in memory and on disk
java.lang.Object[]	toArray() Not supported at this time
<T1> T1[]	toArray(T1[] a) Not supported at this time

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.Collection

equals, hashCode

Method Detail

newInstance

public static <T> DiskBackedQueue<T> newInstance(SortingCollection.Codec<T> codec,
                                 int maxRecordsInRAM,
                                 java.util.List<java.io.File> tmpDir)

Syntactic sugar around the ctor, to save some typing of type parameters

Parameters:

codec - For writing records to file and reading them back into RAM

maxRecordsInRAM - how many records to accumulate in memory before spilling to disk

tmpDir - Where to write files of records that will not fit in RAM

canAdd

public boolean canAdd()

getNumRecordsOnDisk

public int getNumRecordsOnDisk()

headRecordIsFromDisk

public boolean headRecordIsFromDisk()

add

public boolean add(E record)
            throws java.lang.IllegalStateException

Add the record to the tail of the queue, spilling to disk if necessary Must check that (canAdd() == true) before calling this method

Specified by:

add in interface java.util.Collection<E>

Specified by:

add in interface java.util.Queue<E>

Parameters:

record - The record to be added to the queue

Returns:

true (if add successful)

Throws:

java.lang.IllegalStateException - if the queue cannot be added to

offer

public boolean offer(E e)

Specified by:

offer in interface java.util.Queue<E>

remove

public E remove()

Specified by:

remove in interface java.util.Queue<E>

poll

public E poll()

Specified by:

poll in interface java.util.Queue<E>

element

public E element()

Specified by:

element in interface java.util.Queue<E>

peek

public E peek()

Specified by:

peek in interface java.util.Queue<E>

size

public int size()

Return the total number of elements in the queue, both in memory and on disk

Specified by:

size in interface java.util.Collection<E>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface java.util.Collection<E>

addAll

public boolean addAll(java.util.Collection<? extends E> c)

Add all elements from collection c to this DiskBackedQueue Must check that (canAdd() == true) before calling this method

Specified by:

addAll in interface java.util.Collection<E>

Parameters:

c - the collection of elements to add

Returns:

true if this collection changed as a result of the call

Throws:

java.lang.IllegalStateException - if the queue cannot be added to

clear

public void clear()

Specified by:

clear in interface java.util.Collection<E>

finalize

protected void finalize()
                 throws java.lang.Throwable

Clean up disk resources in case clear() has not been explicitly called (as would be preferable) Closes the input and output streams associated with this DiskBackedQueue and deletes the temporary file

Overrides:

finalize in class java.lang.Object

Throws:

java.lang.Throwable

remove

public boolean remove(java.lang.Object o)

Not supported. Cannot access particular elements, as some elements may have been written to disk

Specified by:

remove in interface java.util.Collection<E>

Throws:

java.lang.UnsupportedOperationException

removeAll

public boolean removeAll(java.util.Collection<?> c)

Not supported. Cannot access particular elements, as some elements may have been written to disk

Specified by:

removeAll in interface java.util.Collection<E>

Throws:

java.lang.UnsupportedOperationException

retainAll

public boolean retainAll(java.util.Collection<?> c)

Not supported. Cannot access particular elements, as some elements may have been written to disk

Specified by:

retainAll in interface java.util.Collection<E>

Throws:

java.lang.UnsupportedOperationException

contains

public boolean contains(java.lang.Object o)

Not supported. It is not possible to check for the presence of a particular element, as some elements may have been written to disk

Specified by:

contains in interface java.util.Collection<E>

Throws:

java.lang.UnsupportedOperationException

containsAll

public boolean containsAll(java.util.Collection<?> c)

Not supported. It is not possible to check for the presence of a particular element, as some elements may have been written to disk

Specified by:

containsAll in interface java.util.Collection<E>

Throws:

java.lang.UnsupportedOperationException

iterator

public java.util.Iterator<E> iterator()

Not supported at this time

Specified by:

iterator in interface java.lang.Iterable<E>

Specified by:

iterator in interface java.util.Collection<E>

Throws:

java.lang.UnsupportedOperationException

toArray

public java.lang.Object[] toArray()

Not supported at this time

Specified by:

toArray in interface java.util.Collection<E>

Throws:

java.lang.UnsupportedOperationException

toArray

public <T1> T1[] toArray(T1[] a)

Not supported at this time

Specified by:

toArray in interface java.util.Collection<E>

Throws:

java.lang.UnsupportedOperationException