broad.core.multiplealignment.MAFIO Class Reference

Inheritance diagram for broad.core.multiplealignment.MAFIO:

Collaboration diagram for broad.core.multiplealignment.MAFIO:

Public Member Functions
	MAFIO (String alignmentFile, boolean keepFileHandle) throws IOException, ParseException
	MAFIO ()
String	getPreferredFileExtension ()
void	destroyFileHandle () throws IOException
MAFAlignment	load (List< String > sequencesToLoad, int start, int end) throws IOException, ParseException
MAFAlignment	createUnloadedAlignment (String fileName) throws IOException, ParseException
MAFAlignment	load (String fileName) throws IOException, ParseException
MAFAlignment	load (String fileName, List< String > sequencesToLoad) throws IOException, ParseException
MultipleAlignment	load (InputStream in) throws IOException, ParseException
MAFAlignment	load (String fileName, List< String > sequencesToLoad, int start, int end) throws IOException, ParseException
MultipleAlignment	load (InputStream in, List< String > sequencesToLoad) throws IOException, ParseException
void	write (BufferedWriter bw, MultipleAlignment ma) throws IOException
void	write (BufferedWriter bw, MultipleAlignment ma, List< String > sequenceOrder) throws IOException

Constructor & Destructor Documentation

broad.core.multiplealignment.MAFIO.MAFIO	(	String	alignmentFile,
		boolean	keepFileHandle
	)		throws IOException, ParseException

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broad.core.multiplealignment.MAFIO.MAFIO

(

)

Member Function Documentation

MAFAlignment broad.core.multiplealignment.MAFIO.createUnloadedAlignment

(

String

fileName

)

throws IOException, ParseException

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void broad.core.multiplealignment.MAFIO.destroyFileHandle

(

)

throws IOException

String broad.core.multiplealignment.MAFIO.getPreferredFileExtension

(

)

Implements broad.core.multiplealignment.MultipleAlignmentIO.

MAFAlignment broad.core.multiplealignment.MAFIO.load	(	List< String >	sequencesToLoad,
		int	start,
		int	end
	)		throws IOException, ParseException

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MAFAlignment broad.core.multiplealignment.MAFIO.load

(

String

fileName

)

throws IOException, ParseException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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MAFAlignment broad.core.multiplealignment.MAFIO.load	(	String	fileName,
		List< String >	sequencesToLoad
	)		throws IOException, ParseException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

MultipleAlignment broad.core.multiplealignment.MAFIO.load

(

InputStream

in

)

throws IOException, ParseException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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MAFAlignment broad.core.multiplealignment.MAFIO.load	(	String	fileName,
		List< String >	sequencesToLoad,
		int	start,
		int	end
	)		throws IOException, ParseException

MultipleAlignment broad.core.multiplealignment.MAFIO.load	(	InputStream	in,
		List< String >	sequencesToLoad
	)		throws IOException, ParseException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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void broad.core.multiplealignment.MAFIO.write	(	BufferedWriter	bw,
		MultipleAlignment	ma
	)		throws IOException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

void broad.core.multiplealignment.MAFIO.write	(	BufferedWriter	bw,
		MultipleAlignment	ma,
		List< String >	sequenceOrder
	)		throws IOException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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

• java/broad/core/multiplealignment/MAFIO.java