Package sequence

Class DiskSequence

java.lang.Object

sequence.DiskSequence

All Implemented Interfaces:

Sequence

public class DiskSequence
extends Object
implements Sequence

Constructor Summary

Constructors

Constructor	Description
DiskSequence(File file)

Method Summary

Modifier and Type	Method	Description
void	buildIndex(long k)	Builds the index based on the length of the k-mer.
void	clearTable(int k)	Clears table corresponding to the length of the k-mer.
void	close()
Base	getBase(long position)
List<Long>	getMatchingPositions(Sequence kmer)	Gets positions of the sequence that matches with k-mer.
long	getSize()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

DiskSequence

public DiskSequence(File file)
             throws FileNotFoundException,
                    SQLException,
                    ClassNotFoundException

Throws:

FileNotFoundException

SQLException

ClassNotFoundException

Method Detail

toString

public String toString()

Overrides:

toString in class Object

buildIndex

public void buildIndex(long k)
                throws Exception

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

Throws:

Exception - throws exception when errors occur on database end

clearTable

public void clearTable(int k)
                throws Exception

Clears table corresponding to the length of the k-mer.

Parameters:

k - length of the k-mer

Throws:

Exception - when there is no such table exists

getSize

public long getSize()

Specified by:

getSize in interface Sequence

Returns:

size of the sequence

close

public void close()
           throws Exception

Throws:

Exception

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

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