umcg.genetica.io.gtf

Class GtfReader

java.lang.Object

umcg.genetica.io.gtf.GtfReader

All Implemented Interfaces:

Iterable<GffElement>, GffReaderInterface

public class GtfReader
extends Object
implements GffReaderInterface

Author:

Patrick Deelen

Constructor Summary

Constructors

Constructor and Description
GtfReader(File gftFile)
GtfReader(Reader gftReader)

Method Summary

Modifier and Type	Method and Description
void	close()
PerChrIntervalTree<GffElement>	createIntervalTree()
Iterator<GffElement>	iterator()
GffElement	nextElement()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

GtfReader

public GtfReader(File gftFile)
          throws FileNotFoundException

Throws:

FileNotFoundException

GtfReader

public GtfReader(Reader gftReader)

Method Detail

nextElement

public GffElement nextElement()
                       throws IOException

Specified by:

nextElement in interface GffReaderInterface

Returns:

next element null when done

Throws:

IOException

close

public void close()
           throws IOException

Specified by:

close in interface GffReaderInterface

Throws:

IOException

iterator

public Iterator<GffElement> iterator()

Specified by:

iterator in interface Iterable<GffElement>

createIntervalTree

public PerChrIntervalTree<GffElement> createIntervalTree()
                                                  throws Exception

Throws:

Exception