broad.core.multiplealignment.PhylipSequencialMultipleAlignmentIO Class Reference

Inheritance diagram for broad.core.multiplealignment.PhylipSequencialMultipleAlignmentIO:

Collaboration diagram for broad.core.multiplealignment.PhylipSequencialMultipleAlignmentIO:

Classes
class	PhylipSequenceIO

Public Member Functions
MultipleAlignment	load (String fileName) throws IOException
MultipleAlignment	load (InputStream in) throws IOException
MultipleAlignment	load (String fileName, List< String > sequencesToLoad) throws IOException
MultipleAlignment	load (InputStream in, List< String > sequencesToLoad) throws IOException
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.PhylipSequencialMultipleAlignmentIO.getPreferredFileExtension

(

)

Implements broad.core.multiplealignment.MultipleAlignmentIO.

MultipleAlignment broad.core.multiplealignment.PhylipSequencialMultipleAlignmentIO.load

(

String

fileName

)

throws IOException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

MultipleAlignment broad.core.multiplealignment.PhylipSequencialMultipleAlignmentIO.load

(

InputStream

in

)

throws IOException

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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

Implements broad.core.multiplealignment.MultipleAlignmentIO.

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

Implements broad.core.multiplealignment.MultipleAlignmentIO.

Here is the caller graph for this function:

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

Implements broad.core.multiplealignment.MultipleAlignmentIO.

Here is the call graph for this function:

---

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

• java/broad/core/multiplealignment/PhylipSequencialMultipleAlignmentIO.java