de.charite.compbio.jannovar.impl.parse.gtfgff

Class GFFParser

java.lang.Object

de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser

public class GFFParser
extends Object

A class for parsing a stream of GFFRecord objects from a GTF or GFF file. This class is state-ful and not thread safe.

Author:

Manuel Holtgrewe

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GFFParser.GFFVersion Enum type for describing the GFF version

Constructor Summary

Constructors

Constructor and Description
GFFParser(File file) Initialize with a file, gzip compression is automatically recognized.
GFFParser(InputStream stream) Initialize from a InputStream, gzip compression is automatically recognized.

Method Summary

Modifier and Type	Method and Description
GFFParser.GFFVersion	getGFFVersion()
FeatureRecord	next() Reads next record from the GFF file and return it, null when the file is at its end.

Methods inherited from class java.lang.Object

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

Constructor Detail

GFFParser

public GFFParser(File file)
          throws IOException

Initialize with a file, gzip compression is automatically recognized.

Parameters:

file - The file to read from

Throws:

IOException - on I/O problems

GFFParser

public GFFParser(InputStream stream)
          throws IOException

Initialize from a InputStream, gzip compression is automatically recognized.

Parameters:

stream - InputStream to read from

Throws:

IOException - on I/O problems

Method Detail

next

public FeatureRecord next()
                   throws IOException

Reads next record from the GFF file and return it, null when the file is at its end.

Returns:

GFFRecord or null

Throws:

IOException - on problems with reading the GFF files

getGFFVersion

public GFFParser.GFFVersion getGFFVersion()

Returns:

GFF version detected from the stream