com.pacbio.secondary.vis.data.session

Class ReferenceSequenceStorage

java.lang.Object

com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage

public class ReferenceSequenceStorage
extends java.lang.Object

Author:

mmilletti

Constructor Summary

Constructors

Constructor and Description
ReferenceSequenceStorage()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	acceptNewDataAndClear(GenomicViewDetailsData view, int view_contig, Interval view_visible_range, java.lang.String data)
void	clear()
char[]	getDNASequence(Interval int_visible_range)
char	getDNASequence(long pos)
byte[]	getReference_data()
Locus	getReference_locus()
boolean	intersects(int viewContig, Interval int_visible_range)
boolean	isFasta_file_exists()
boolean	setReference_data(byte[] data)
boolean	setReference_data(javax.activation.DataHandler dataHandler) Deprecated.
void	setReference_locus(Locus reference_locus)
int	size()

Methods inherited from class java.lang.Object

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

Constructor Detail

ReferenceSequenceStorage

public ReferenceSequenceStorage()

Method Detail

getReference_locus

public Locus getReference_locus()

setReference_locus

public void setReference_locus(Locus reference_locus)

getReference_data

public byte[] getReference_data()

isFasta_file_exists

public boolean isFasta_file_exists()

clear

public void clear()

size

public int size()

intersects

public boolean intersects(int viewContig,
                 Interval int_visible_range)

getDNASequence

public char[] getDNASequence(Interval int_visible_range)

Parameters:

int_visible_range -

Returns:

getDNASequence

public char getDNASequence(long pos)

Parameters:

int_visible_range -

Returns:

acceptNewDataAndClear

public boolean acceptNewDataAndClear(GenomicViewDetailsData view,
                            int view_contig,
                            Interval view_visible_range,
                            java.lang.String data)

setReference_data

public boolean setReference_data(byte[] data)

setReference_data

@Deprecated
public boolean setReference_data(javax.activation.DataHandler dataHandler)

Deprecated.