Inheritance diagram for broad.core.annotation.RepeatMaskerAnnotationReader:

Collaboration diagram for broad.core.annotation.RepeatMaskerAnnotationReader:

Public Member Functions
	RepeatMaskerAnnotationReader ()

	RepeatMaskerAnnotationReader (BufferedReader br) throws ParseException, IOException

	RepeatMaskerAnnotationReader (String input) throws ParseException, IOException

void	load (BufferedReader br) throws IOException, ParseException

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

RepeatMaskerAnnotation	createAnnotation (GenomicAnnotation a)

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

Set< String >	getUniqueRepeatNames () throws IOException

Set< String >	getUniqueRepeatClasses () throws IOException

Set< String >	getUniqueRepeatFamilies () throws IOException

Constructor & Destructor Documentation

broad.core.annotation.RepeatMaskerAnnotationReader.RepeatMaskerAnnotationReader ( )

broad.core.annotation.RepeatMaskerAnnotationReader.RepeatMaskerAnnotationReader ( BufferedReader br ) throws ParseException, IOException

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broad.core.annotation.RepeatMaskerAnnotationReader.RepeatMaskerAnnotationReader ( String input ) throws ParseException, IOException

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Member Function Documentation

RepeatMaskerAnnotation broad.core.annotation.RepeatMaskerAnnotationReader.createAnnotation ( GenomicAnnotation a )

Set<String> broad.core.annotation.RepeatMaskerAnnotationReader.getUniqueRepeatClasses ( ) throws IOException

Set<String> broad.core.annotation.RepeatMaskerAnnotationReader.getUniqueRepeatFamilies ( ) throws IOException

Set<String> broad.core.annotation.RepeatMaskerAnnotationReader.getUniqueRepeatNames ( ) throws IOException

void broad.core.annotation.RepeatMaskerAnnotationReader.load ( BufferedReader br ) throws IOException, ParseException

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int broad.core.annotation.RepeatMaskerAnnotationReader.parse	(	BufferedReader	br,
		GenomicAnnotationFilter< RepeatMaskerAnnotation >	filter,
		AnnotationHandler	handler
	)		throws ParseException

int broad.core.annotation.RepeatMaskerAnnotationReader.parse	(	String	file,
		GenomicAnnotationFilter< RepeatMaskerAnnotation >	filter,
		AnnotationHandler	handler
	)		throws ParseException, IOException

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