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
Parses Nexus taxa blocks.
- Since:
- 1.6
- Author:
- Richard Holland, Tobias Thierer, Jim Balhoff, Tiago Antao
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
NexusBlockParser.Abstract
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Field Summary
Fields inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
UNKNOWN_BLOCK
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Constructor Summary
ConstructorsConstructorDescriptionTreesBlockParser
(TreesBlockListener blockListener) Delegates to NexusBlockParser.Abstract. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Opening a comment tag.void
commentText
(String comment) Receiving free text inside a comment tag.void
Closing a comment tag.void
Closing a line (semi-colon encountered).void
parseToken
(String token) Notifies the parser of the next token.void
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
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Constructor Details
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TreesBlockParser
Delegates to NexusBlockParser.Abstract.- Parameters:
blockListener
- the listener to send parse events to.
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Method Details
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beginComment
Description copied from interface:NexusBlockParser
Opening a comment tag.- Specified by:
beginComment
in interfaceNexusBlockParser
- Overrides:
beginComment
in classNexusBlockParser.Abstract
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commentText
Description copied from interface:NexusBlockParser
Receiving free text inside a comment tag.- Specified by:
commentText
in interfaceNexusBlockParser
- Overrides:
commentText
in classNexusBlockParser.Abstract
- Parameters:
comment
- the text of the comment.- Throws:
ParseException
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endComment
Description copied from interface:NexusBlockParser
Closing a comment tag.- Specified by:
endComment
in interfaceNexusBlockParser
- Overrides:
endComment
in classNexusBlockParser.Abstract
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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 classNexusBlockParser.Abstract
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parseToken
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 interfaceNexusBlockParser
- Specified by:
parseToken
in classNexusBlockParser.Abstract
- Parameters:
token
- the token to parse.- Throws:
ParseException
- if the token is unparseable.
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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 interfaceNexusBlockParser
- Overrides:
endTokenGroup
in classNexusBlockParser.Abstract
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