broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO Class Reference

Inheritance diagram for broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO:

Collaboration diagram for broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO:

Public Member Functions
MultipleAlignment	load (String source) throws IOException, ParseException
MultipleAlignment	load (String fileName, List< String > sequencesToLoad) throws IOException, ParseException
MultipleAlignment	load (InputStream in) throws IOException, ParseException
MultipleAlignment	load (InputStream in, List< String > sequencesToLoad) throws IOException
void	setSpacing (int spacing)
void	write (BufferedWriter bw, MultipleAlignment ma) throws IOException
void	write (BufferedWriter bw, MultipleAlignment ma, List< String > order) throws IOException
String	getPreferredFileExtension ()

Member Function Documentation

String broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO.getPreferredFileExtension

(

)

Implements broad.core.multiplealignment.MultipleAlignmentIO.

MultipleAlignment broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO.load

(

String

source

)

throws IOException, ParseException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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MultipleAlignment broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO.load

(

InputStream

in

)

throws IOException, ParseException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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

Implements broad.core.multiplealignment.MultipleAlignmentIO.

void broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO.setSpacing

(

int

spacing

)

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

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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void broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO.write	(	BufferedWriter	bw,
		MultipleAlignment	ma,
		List< String >	order
	)		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/PhylipInterleavedMultipleAlignmentIO.java