org.biojavax.bio.phylo.io.nexus

Class NexusFileBuilder

java.lang.Object

org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract

org.biojavax.bio.phylo.io.nexus.NexusFileBuilder

All Implemented Interfaces:

NexusFileListener

public class NexusFileBuilder
extends NexusFileListener.Abstract

Builds a Nexus file by listening to events.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.bio.phylo.io.nexus.NexusFileListener

NexusFileListener.Abstract

Constructor Summary

Constructors

Constructor and Description
NexusFileBuilder()

Method Summary

Modifier and Type	Method and Description
void	beginFileComment() This method will get called when a comment is started on the file, and not any block within it.
protected void	blockEnded(NexusBlockParser blockParser) This method gets called when the block parser is expected to have finished parsing a block.
void	endFile() Finished reading a file.
void	endFileComment() This method will get called when a comment is ended on the file, and not any block within it.
void	fileCommentText(String comment) This method will get called when comment text is found on the file, and not any block within it.
NexusFile	getNexusFile() Obtain the constructed file.
void	setDefaultBlockParsers() Causes the default block parsers to be assigned.
void	startFile() About to start a new file.

Methods inherited from class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract

beginComment, commentText, endBlock, endComment, endTokenGroup, getBlockParser, parseToken, setBlockParser, startBlock, wantsBracketsAndBraces

Methods inherited from class java.lang.Object

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

Constructor Detail

NexusFileBuilder

public NexusFileBuilder()

Method Detail

setDefaultBlockParsers

public void setDefaultBlockParsers()

Description copied from interface: NexusFileListener

Causes the default block parsers to be assigned. This is called by the constructor of the abstract implementation. If it is not called, then at least the unknown block parser must be set by other means.

Specified by:

setDefaultBlockParsers in interface NexusFileListener

Overrides:

setDefaultBlockParsers in class NexusFileListener.Abstract

blockEnded

protected void blockEnded(NexusBlockParser blockParser)

Description copied from class: NexusFileListener.Abstract

This method gets called when the block parser is expected to have finished parsing a block.

Specified by:

blockEnded in class NexusFileListener.Abstract

Parameters:

blockParser - the parser that has finished.

startFile

public void startFile()

Description copied from interface: NexusFileListener

About to start a new file.

endFile

public void endFile()

Description copied from interface: NexusFileListener

Finished reading a file.

getNexusFile

public NexusFile getNexusFile()

Obtain the constructed file.

Returns:

the constructed file.

beginFileComment

public void beginFileComment()

Description copied from class: NexusFileListener.Abstract

This method will get called when a comment is started on the file, and not any block within it.

Specified by:

beginFileComment in class NexusFileListener.Abstract

fileCommentText

public void fileCommentText(String comment)

Description copied from class: NexusFileListener.Abstract

This method will get called when comment text is found on the file, and not any block within it.

Specified by:

fileCommentText in class NexusFileListener.Abstract

Parameters:

comment - the comment text.

endFileComment

public void endFileComment()

Description copied from class: NexusFileListener.Abstract

This method will get called when a comment is ended on the file, and not any block within it.

Specified by:

endFileComment in class NexusFileListener.Abstract