Inheritance diagram for broad.pda.datastructures.AlignmentsReader:

Collaboration diagram for broad.pda.datastructures.AlignmentsReader:

Public Member Functions
	AlignmentsReader ()

	AlignmentsReader (Collection< Alignments > annot)

	AlignmentsReader (BufferedReader br) throws ParseException, IOException

	AlignmentsReader (String input) throws ParseException, IOException

void	load (BufferedReader br) throws IOException, ParseException

int	parse (BufferedReader br, GenomicAnnotationFilter< Alignments > filter, AnnotationHandler handler) throws ParseException

Alignments	createAnnotation (GenomicAnnotation a)

int	parse (String file, GenomicAnnotationFilter< Alignments > filter, AnnotationHandler handler) throws ParseException, IOException

void	write (BufferedWriter bw) throws IOException

Detailed Description

Author: engreitz Wrapper class to take advantage of all the code in AnnotationReader for Alignments

Constructor & Destructor Documentation

broad.pda.datastructures.AlignmentsReader.AlignmentsReader ( )

broad.pda.datastructures.AlignmentsReader.AlignmentsReader ( Collection< Alignments > annot )

broad.pda.datastructures.AlignmentsReader.AlignmentsReader ( BufferedReader br ) throws ParseException, IOException

broad.pda.datastructures.AlignmentsReader.AlignmentsReader ( String input ) throws ParseException, IOException

Alignments broad.pda.datastructures.AlignmentsReader.createAnnotation ( GenomicAnnotation a )

void broad.pda.datastructures.AlignmentsReader.load ( BufferedReader br ) throws IOException, ParseException

int broad.pda.datastructures.AlignmentsReader.parse	(	BufferedReader	br,
		GenomicAnnotationFilter< Alignments >	filter,
		AnnotationHandler	handler
	)		throws ParseException

int broad.pda.datastructures.AlignmentsReader.parse	(	String	file,
		GenomicAnnotationFilter< Alignments >	filter,
		AnnotationHandler	handler
	)		throws ParseException, IOException

void broad.pda.datastructures.AlignmentsReader.write ( BufferedWriter bw ) throws IOException

The documentation for this class was generated from the following file: