org.utgenome.gwt.utgb.client.bio
Class ReferenceSequence

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.ReferenceSequence

All Implemented Interfaces:

Serializable, OnGenome

public class ReferenceSequence
extends Object
implements OnGenome

reference genome sequence to which genome reads are aligned

Author:

leo

See Also:

Serialized Form

Field Summary

String	name
String	sequence
int	start

Constructor Summary

ReferenceSequence()

Method Summary

void	accept(OnGenomeDataVisitor visitor)
int	getEnd() return 1-based end position of the data.
String	getName()
int	getStart() return 1-based start position of the data.
int	length() return the length of the data

Methods inherited from class java.lang.Object

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

Field Detail

start

public int start

name

public String name

sequence

public String sequence

Constructor Detail

ReferenceSequence

public ReferenceSequence()

Method Detail

accept

public void accept(OnGenomeDataVisitor visitor)

Specified by:

accept in interface OnGenome

getStart

public int getStart()

Description copied from interface: OnGenome

return 1-based start position of the data. The interval represents [start, end). ([inclusive, exclusive))

Specified by:

getStart in interface OnGenome

Returns:

getEnd

public int getEnd()

Description copied from interface: OnGenome

return 1-based end position of the data. The interval represents [start, end). ([inclusive, exclusive))

Specified by:

getEnd in interface OnGenome

Returns:

getName

public String getName()

Specified by:

getName in interface OnGenome

length

public int length()

Description copied from interface: OnGenome

return the length of the data

Specified by:

length in interface OnGenome

Returns: