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

Class TreesBlockParser

java.lang.Object

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

org.biojavax.bio.phylo.io.nexus.TreesBlockParser

All Implemented Interfaces:

NexusBlockParser

public class TreesBlockParser
extends NexusBlockParser.Abstract

Parses Nexus taxa blocks.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff, Tiago Antao

Nested Class Summary

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

NexusBlockParser.Abstract

Field Summary

Fields inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser

UNKNOWN_BLOCK

Constructor Summary

Constructors

Constructor	Description
TreesBlockParser(TreesBlockListener blockListener)	Delegates to NexusBlockParser.Abstract.

Method Summary

Modifier and Type	Method	Description
void	beginComment()	Opening a comment tag.
void	commentText(String comment)	Receiving free text inside a comment tag.
void	endComment()	Closing a comment tag.
void	endTokenGroup()	Closing a line (semi-colon encountered).
void	parseToken(String token)	Notifies the parser of the next token.
void	resetStatus()	This function is called when the parser is reset before starting a new block.

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

endBlock, getBlockListener, getBlockName, startBlock, wantsBracketsAndBraces

Methods inherited from class java.lang.Object

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

Constructor Detail

TreesBlockParser

public TreesBlockParser(TreesBlockListener blockListener)

Delegates to NexusBlockParser.Abstract.

Parameters:

blockListener - the listener to send parse events to.

Method Detail

beginComment

public void beginComment()

Description copied from interface: NexusBlockParser

Opening a comment tag.

Specified by:

beginComment in interface NexusBlockParser

Overrides:

beginComment in class NexusBlockParser.Abstract

commentText

public void commentText(String comment)
                 throws ParseException

Description copied from interface: NexusBlockParser

Receiving free text inside a comment tag.

Specified by:

commentText in interface NexusBlockParser

Overrides:

commentText in class NexusBlockParser.Abstract

Parameters:

comment - the text of the comment.

Throws:

ParseException

endComment

public void endComment()

Description copied from interface: NexusBlockParser

Closing a comment tag.

Specified by:

endComment in interface NexusBlockParser

Overrides:

endComment in class NexusBlockParser.Abstract

resetStatus

public void resetStatus()

Description copied from class: NexusBlockParser.Abstract

This function is called when the parser is reset before starting a new block.

Specified by:

resetStatus in class NexusBlockParser.Abstract

parseToken

public void parseToken(String token)
                throws ParseException

Description copied from interface: NexusBlockParser

Notifies the parser of the next token. Comment tokens will already have been parsed out and sent separately to the text() method of the listener. Quoted strings will have been parsed and underscores converted. What this token contains is the full string, after removal of quotes if necessary. The token will never be only whitespace.

Specified by:

parseToken in interface NexusBlockParser

Specified by:

parseToken in class NexusBlockParser.Abstract

Parameters:

token - the token to parse.

Throws:

ParseException - if the token is unparseable.

endTokenGroup

public void endTokenGroup()

Description copied from interface: NexusBlockParser

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

Specified by:

endTokenGroup in interface NexusBlockParser

Overrides:

endTokenGroup in class NexusBlockParser.Abstract