de.jstacs.data
Class SampleKMerEnumerator

java.lang.Object
  de.jstacs.data.SampleKMerEnumerator

All Implemented Interfaces:

RecyclableSequenceEnumerator, Enumeration<Sequence>

public class SampleKMerEnumerator
extends Object
implements RecyclableSequenceEnumerator

Class for an RecyclableSequenceEnumerator of Sequences that enumerates all k-mers that exist in a given Sample, optionally ignoring reverse complements.

Author:

Jens Keilwagen, Jan Grau

Constructor Summary

SampleKMerEnumerator(Sample data, int k, boolean eliminateRevComp)
Constructs a new SampleKMerEnumerator from a Sample data by extracting all k-mers.

Method Summary

boolean	hasMoreElements()
Sequence	nextElement()
void	reset() This method enables the user to reuse this enumerator.

Methods inherited from class java.lang.Object

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

Constructor Detail

SampleKMerEnumerator

public SampleKMerEnumerator(Sample data,
                            int k,
                            boolean eliminateRevComp)
                     throws OperationNotSupportedException

Constructs a new SampleKMerEnumerator from a Sample data by extracting all k-mers.

Parameters:

data - the data to extract the k-mers from

k - the length of the k-mers

eliminateRevComp - whether to ignore the reverse complement of already existing k-mers

Throws:

OperationNotSupportedException - if a Sequence in data does not support to compute the reverse complement but eliminateRevComp is true

Method Detail

reset

public void reset()

Description copied from interface: RecyclableSequenceEnumerator

This method enables the user to reuse this enumerator.

Specified by:

reset in interface RecyclableSequenceEnumerator

hasMoreElements

public boolean hasMoreElements()

Specified by:

hasMoreElements in interface Enumeration<Sequence>

nextElement

public Sequence nextElement()

Specified by:

nextElement in interface Enumeration<Sequence>