org.biojavax.bio.phylo.io.phylip

Interface PHYLIPFileListener

All Known Implementing Classes:

PHYLIPFileBuilder

public interface PHYLIPFileListener

Listens to events fired by the PHYLIP parser. Use these events to handle data directly or construct objects.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Method Summary

Methods

Modifier and Type	Method and Description
void	endFile() Finished reading a file.
void	receiveSequence(java.lang.String sequence) Receive sequence data for the current sequence.
void	setCurrentSequenceName(java.lang.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.

Method Detail

startFile

void startFile()

About to start a new file.

endFile

void endFile()
             throws ParseException

Finished reading a file.

Throws:

ParseException

setSequenceCount

void setSequenceCount(int count)

Set the number of sequences in the alignment.

Parameters:

count - the expected number of sequences

setSitesCount

void setSitesCount(int count)

Set the number of sites in the alignment

Parameters:

count - the expected number of sites

setCurrentSequenceName

void setCurrentSequenceName(java.lang.String name)

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

Parameters:

name - the label for the current sequence

receiveSequence

void receiveSequence(java.lang.String sequence)

Receive sequence data for the current sequence.

Parameters:

sequence - sequence text for the current sequence