Package org.forester.io.parsers.nexus
Class NexusPhylogeniesParser
- java.lang.Object
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- org.forester.io.parsers.nexus.NexusPhylogeniesParser
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- All Implemented Interfaces:
IteratingPhylogenyParser,PhylogenyParser
public final class NexusPhylogeniesParser extends java.lang.Object implements IteratingPhylogenyParser, PhylogenyParser
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Constructor Summary
Constructors Constructor Description NexusPhylogeniesParser()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.StringgetName()booleanhasNext()Phylogenynext()Phylogeny[]parse()voidreset()voidsetIgnoreQuotes(boolean ignore_quotes_in_nh_data)voidsetReplaceUnderscores(boolean replace_underscores)voidsetSource(java.lang.Object nexus_source)voidsetTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
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Method Detail
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getName
public java.lang.String getName()
- Specified by:
getNamein interfacePhylogenyParser
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hasNext
public final boolean hasNext()
- Specified by:
hasNextin interfaceIteratingPhylogenyParser
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next
public final Phylogeny next() throws NHXFormatException, java.io.IOException
- Specified by:
nextin interfaceIteratingPhylogenyParser- Throws:
NHXFormatExceptionjava.io.IOException
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parse
public final Phylogeny[] parse() throws java.io.IOException
- Specified by:
parsein interfacePhylogenyParser- Throws:
java.io.IOException
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reset
public final void reset() throws java.io.FileNotFoundException, java.io.IOException- Specified by:
resetin interfaceIteratingPhylogenyParser- Throws:
java.io.FileNotFoundExceptionjava.io.IOException
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setIgnoreQuotes
public final void setIgnoreQuotes(boolean ignore_quotes_in_nh_data)
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setReplaceUnderscores
public final void setReplaceUnderscores(boolean replace_underscores)
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setSource
public final void setSource(java.lang.Object nexus_source) throws PhylogenyParserException, java.io.IOException- Specified by:
setSourcein interfaceIteratingPhylogenyParser- Specified by:
setSourcein interfacePhylogenyParser- Throws:
PhylogenyParserExceptionjava.io.IOException
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setTaxonomyExtraction
public final void setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
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