net.sf.snver.pileup.meta
Class SAMSequenceVo

java.lang.Object
  net.sf.snver.pileup.meta.SAMSequenceVo

All Implemented Interfaces:

java.lang.Comparable<SAMSequenceVo>

public class SAMSequenceVo
extends java.lang.Object
implements java.lang.Comparable<SAMSequenceVo>

Facade Object to present the SAM Record

Created by IntelliJ IDEA. User: weicheng hu Date: 10/20/11 Time: 2:24 PM

Constructor Summary

SAMSequenceVo(net.sf.samtools.SAMRecord record)
Constructor

Method Summary

int	compareTo(SAMSequenceVo seq)
void	echo() Print the original record information
java.lang.String	getSequenceName() Get sequence name
boolean	isEmpty() Check base and score are empty
java.lang.String[]	pop() Return a Pair for a single base and score pair
void	print() Print some of information

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMSequenceVo

public SAMSequenceVo(net.sf.samtools.SAMRecord record)

Constructor

Parameters:

record - SAMRecord

Method Detail

echo

public void echo()

Print the original record information

print

public void print()

Print some of information

isEmpty

public boolean isEmpty()

Check base and score are empty

Returns:

boolean

pop

public java.lang.String[] pop()

Return a Pair for a single base and score pair

Returns:

String[]

compareTo

public int compareTo(SAMSequenceVo seq)

Specified by:

compareTo in interface java.lang.Comparable<SAMSequenceVo>

Parameters:

seq - SAMSequenceVo

Returns:

See Also:

Comparable.compareTo(Object)

getSequenceName

public java.lang.String getSequenceName()

Get sequence name

Returns:

String