Package org.biojavax.bio.phylo.io.nexus

Class NexusFileListener.Abstract

java.lang.Object

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

All Implemented Interfaces:

NexusFileListener

Direct Known Subclasses:

NexusFileBuilder

Enclosing interface:

NexusFileListener

public abstract static class NexusFileListener.Abstract
extends Object
implements NexusFileListener

Example abstract implementation which all others should extend.

Nested Class Summary

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

NexusFileListener.Abstract

Constructor Summary

Constructors

Constructor	Description
Abstract()

Method Summary

Modifier and Type	Method	Description
void	beginComment()	Opening a comment tag.
protected abstract void	beginFileComment()	This method will get called when a comment is started on the file, and not any block within it.
protected abstract void	blockEnded(NexusBlockParser blockParser)	This method gets called when the block parser is expected to have finished parsing a block.
void	commentText(String comment)	Receiving free text inside a comment tag.
void	endBlock()	Finished reading a block.
void	endComment()	Closing a comment tag.
protected abstract void	endFileComment()	This method will get called when a comment is ended on the file, and not any block within it.
void	endTokenGroup()	Closing a line (semi-colon encountered).
protected abstract void	fileCommentText(String comment)	This method will get called when comment text is found on the file, and not any block within it.
NexusBlockParser	getBlockParser(String blockName)	Gets the parser to use for a given block.
void	parseToken(String token)	Encountered a token.
void	setBlockParser(String blockName, NexusBlockParser parser)	Sets the parser to use for a given block.
void	setDefaultBlockParsers()	Causes the default block parsers to be assigned.
void	startBlock(String blockName)	About to start a new block.
boolean	wantsBracketsAndBraces()	Does the listener want to know about brackets and braces as separate tokens?

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojavax.bio.phylo.io.nexus.NexusFileListener

endFile, startFile

Constructor Detail

Abstract

public Abstract()

Method Detail

beginComment

public void beginComment()

Description copied from interface: NexusFileListener

Opening a comment tag.

Specified by:

beginComment in interface NexusFileListener

beginFileComment

protected abstract void beginFileComment()

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

commentText

public void commentText(String comment)
                 throws ParseException

Description copied from interface: NexusFileListener

Receiving free text inside a comment tag.

Specified by:

commentText in interface NexusFileListener

Parameters:

comment - the text of the comment.

Throws:

ParseException

fileCommentText

protected abstract void fileCommentText(String comment)

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

Parameters:

comment - the comment text.

endComment

public void endComment()

Description copied from interface: NexusFileListener

Closing a comment tag.

Specified by:

endComment in interface NexusFileListener

endFileComment

protected abstract void endFileComment()

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

endBlock

public void endBlock()

Description copied from interface: NexusFileListener

Finished reading a block.

Specified by:

endBlock in interface NexusFileListener

blockEnded

protected abstract void blockEnded(NexusBlockParser blockParser)

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

Parameters:

blockParser - the parser that has finished.

wantsBracketsAndBraces

public boolean wantsBracketsAndBraces()

Description copied from interface: NexusFileListener

Does the listener want to know about brackets and braces as separate tokens?

Specified by:

wantsBracketsAndBraces in interface NexusFileListener

Returns:

true if it does.

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

getBlockParser

public NexusBlockParser getBlockParser(String blockName)

Description copied from interface: NexusFileListener

Gets the parser to use for a given block.

Specified by:

getBlockParser in interface NexusFileListener

Parameters:

blockName - the name of the block. return parser the parser to use. Is never null.

endTokenGroup

public void endTokenGroup()

Description copied from interface: NexusFileListener

Closing a line (semi-colon encountered). This indicates that anything received after it is on the next logical line of the file.

Specified by:

endTokenGroup in interface NexusFileListener

parseToken

public void parseToken(String token)
                throws ParseException

Description copied from interface: NexusFileListener

Encountered a token.

Specified by:

parseToken in interface NexusFileListener

Parameters:

token - the token.

Throws:

ParseException - if the token is invalid.

setBlockParser

public void setBlockParser(String blockName,
                           NexusBlockParser parser)

Description copied from interface: NexusFileListener

Sets the parser to use for a given block.

Specified by:

setBlockParser in interface NexusFileListener

Parameters:

blockName - the name of the block.

parser - the parser to use. Use null to unset an existing one and use the default one for that block instead.

startBlock

public void startBlock(String blockName)

Description copied from interface: NexusFileListener

About to start a new block.

Specified by:

startBlock in interface NexusFileListener

Parameters:

blockName - the name of the new block.