Package sequence

Class MemorySequence

java.lang.Object

sequence.MemorySequence

All Implemented Interfaces:

Sequence

public class MemorySequence
extends Object
implements Sequence

An immutable sequence that is stored completely in memory.

Author:

gerardlee

Method Summary

Modifier and Type	Method	Description
void	buildIndex(long k)	Builds the index based on the length of the k-mer.
static MemorySequence	fromString(String sequence)	Constructs a new MemorySequence from the input sequence string that contains A, G, T, and C.
Base	getBase(long position)
List<Long>	getMatchingPositions(Sequence kmer)	Gets positions of the sequence that matches with k-mer.
long	getSize()
static MemorySequence	random(int k)	Generates a random MemorySequence of length k.

Methods inherited from class java.lang.Object

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

Method Detail

fromString

public static MemorySequence fromString(String sequence)

Constructs a new MemorySequence from the input sequence string that contains A, G, T, and C. Note that there should be no white space between any of the bases.

Parameters:

sequence - input sequence

Returns:

new MemorySequence

random

public static MemorySequence random(int k)

Generates a random MemorySequence of length k.

Parameters:

k - length of the MemorySequence

Returns:

new MemorySequence

buildIndex

public void buildIndex(long k)

Description copied from interface: Sequence

Builds the index based on the length of the k-mer.

Specified by:

buildIndex in interface Sequence

Parameters:

k - length of the k-mer

getMatchingPositions

public List<Long> getMatchingPositions(Sequence kmer)
                                throws Exception

Description copied from interface: Sequence

Gets positions of the sequence that matches with k-mer. If an index has been built, then this method tries to use that index to perform faster look-up.

Specified by:

getMatchingPositions in interface Sequence

Parameters:

kmer - sub-sequence to search for

Returns:

list of matching starting positions in this sequence

Throws:

Exception - throws exception

getSize

public long getSize()

Specified by:

getSize in interface Sequence

Returns:

size of the sequence

getBase

public Base getBase(long position)

Specified by:

getBase in interface Sequence

Parameters:

position - the position of the sequence

Returns:

the base at the position provided