Package fr.ens.biologie.genomique.eoulsan.modules.fastqc

Class SAMSequenceFile

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile

All Implemented Interfaces:

CounterSequenceFile, uk.ac.babraham.FastQC.Sequence.SequenceFile

public class SAMSequenceFile
extends Object
implements CounterSequenceFile

This class define a SequenceFile for SAM files.

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
SAMSequenceFile(DataFile inFile)	Public constructor.

Method Summary

Modifier and Type	Method	Description
long	getCount()	Get the count of the read entries.
File	getFile()
int	getPercentComplete()
boolean	hasNext()
boolean	isColorspace()
String	name()
uk.ac.babraham.FastQC.Sequence.Sequence	next()

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMSequenceFile

public SAMSequenceFile(DataFile inFile)
                throws IOException

Public constructor.

Parameters:

inFile - SAM input file

Throws:

IOException - if an error occurs when opening the file

Method Detail

getFile

public File getFile()

Specified by:

getFile in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

getPercentComplete

public int getPercentComplete()

Specified by:

getPercentComplete in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

hasNext

public boolean hasNext()

Specified by:

hasNext in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

isColorspace

public boolean isColorspace()

Specified by:

isColorspace in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

name

public String name()

Specified by:

name in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

next

public uk.ac.babraham.FastQC.Sequence.Sequence next()
                                             throws uk.ac.babraham.FastQC.Sequence.SequenceFormatException

Specified by:

next in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

Throws:

uk.ac.babraham.FastQC.Sequence.SequenceFormatException

getCount

public long getCount()

Description copied from interface: CounterSequenceFile

Get the count of the read entries.

Specified by:

getCount in interface CounterSequenceFile

Returns:

the count of the read entries