htsjdk.samtools.util

Class SortingLongCollection

java.lang.Object

htsjdk.samtools.util.SortingLongCollection

public class SortingLongCollection
extends java.lang.Object

Accumulate a list of longs that can then be sorted in natural order and iterated over. If there are more values accumulated than a specified maximum, values are spilled to disk.

Note that because this class returns primitive longs rather than Longs, it does not conform to any of the Collection iteration interfaces. Use as follows:

1. ctor 2. call add() as many times as desired. 3. call doneAddingStartIteration(). 4. call hasNext() and next() until exhausted or had enough. 5. optionally call cleanup() to free space in temporary directory as soon as possible.

If there are few enough values so that they all can be kept in RAM, then the array is sorted and iterated over trivially.

If there are more values that can fit in RAM, then values are sorted and written to a temp file when the max number to be stored in RAM is reached. Multiple temp files are then merged during iteration via PriorityQueue.

c.f. SortingCollection for more details.

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_ITEMS_IN_RAM
static int	SIZEOF

Constructor Summary

Constructors

Constructor and Description
SortingLongCollection(int maxValuesInRam, java.io.File... tmpDir) Prepare to accumulate values to be sorted

Method Summary

Methods

Modifier and Type	Method and Description
void	add(long value) Add a value to the collection.
void	cleanup() Delete any temporary files.
void	doneAddingStartIteration() This method must be called after done adding, and before calling hasNext() or next().
boolean	hasNext() Call only after doneAddingStartIteration() has been called.
long	next() Call only if hasNext() == true.

Methods inherited from class java.lang.Object

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

Field Detail

SIZEOF

public static final int SIZEOF

See Also:

Constant Field Values

MAX_ITEMS_IN_RAM

public static final int MAX_ITEMS_IN_RAM

Constructor Detail

SortingLongCollection

public SortingLongCollection(int maxValuesInRam,
                     java.io.File... tmpDir)

Prepare to accumulate values to be sorted

Parameters:

maxValuesInRam - how many values to accumulate before spilling to disk

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

Method Detail

add

public void add(long value)

Add a value to the collection.

Parameters:

value -

doneAddingStartIteration

public void doneAddingStartIteration()

This method must be called after done adding, and before calling hasNext() or next().

cleanup

public void cleanup()

Delete any temporary files. After this method is called, no other method calls should be made on this object.

hasNext

public boolean hasNext()

Call only after doneAddingStartIteration() has been called.

Returns:

true if there is another value to be gotten.

next

public long next()

Call only if hasNext() == true.

Returns:

next value from collection, in natural sort order.