Package org.biojavax.bio.phylo.io.phylip

Class PHYLIPFileBuilder

java.lang.Object

org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder

All Implemented Interfaces:

PHYLIPFileListener

public class PHYLIPFileBuilder
extends Object
implements PHYLIPFileListener

Builds a PHYLIP file by listening to events.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Constructor Summary

Constructors

Constructor	Description
PHYLIPFileBuilder()

Method Summary

Modifier and Type	Method	Description
void	endFile()	Finished reading a file.
Alignment	getAlignment()
void	receiveSequence(String sequence)	Receive sequence data for the current sequence.
void	setCurrentSequenceName(String name)	Set the name of the sequence which is about to be received.
void	setSequenceCount(int count)	Set the number of sequences in the alignment.
void	setSitesCount(int count)	Set the number of sites in the alignment
void	startFile()	About to start a new file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PHYLIPFileBuilder

public PHYLIPFileBuilder()

Method Detail

startFile

public void startFile()

Description copied from interface: PHYLIPFileListener

About to start a new file.

Specified by:

startFile in interface PHYLIPFileListener

endFile

public void endFile()
             throws ParseException

Description copied from interface: PHYLIPFileListener

Finished reading a file.

Specified by:

endFile in interface PHYLIPFileListener

Throws:

ParseException

setSequenceCount

public void setSequenceCount(int count)

Description copied from interface: PHYLIPFileListener

Set the number of sequences in the alignment.

Specified by:

setSequenceCount in interface PHYLIPFileListener

Parameters:

count - the expected number of sequences

setSitesCount

public void setSitesCount(int count)

Description copied from interface: PHYLIPFileListener

Set the number of sites in the alignment

Specified by:

setSitesCount in interface PHYLIPFileListener

Parameters:

count - the expected number of sites

setCurrentSequenceName

public void setCurrentSequenceName(String name)

Description copied from interface: PHYLIPFileListener

Set the name of the sequence which is about to be received. If the name has already been seen, the sequence should be appended.

Specified by:

setCurrentSequenceName in interface PHYLIPFileListener

Parameters:

name - the label for the current sequence

receiveSequence

public void receiveSequence(String sequence)

Description copied from interface: PHYLIPFileListener

Receive sequence data for the current sequence.

Specified by:

receiveSequence in interface PHYLIPFileListener

Parameters:

sequence - sequence text for the current sequence

getAlignment

public Alignment getAlignment()