Package org.forester.io.parsers.nhx
Class NHXParser
- java.lang.Object
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- org.forester.io.parsers.nhx.NHXParser
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- All Implemented Interfaces:
IteratingPhylogenyParser
,PhylogenyParser
public final class NHXParser extends java.lang.Object implements PhylogenyParser, IteratingPhylogenyParser
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
NHXParser.TAXONOMY_EXTRACTION
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Field Summary
Fields Modifier and Type Field Description static java.util.regex.Pattern
MB_BL_PATTERN
static java.util.regex.Pattern
MB_PROB_PATTERN
static java.util.regex.Pattern
MB_PROB_SD_PATTERN
static java.util.regex.Pattern
NUMBERS_ONLY_PATTERN
static boolean
REPLACE_UNDERSCORES_DEFAULT
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Constructor Summary
Constructors Constructor Description NHXParser()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getName()
NHXParser.TAXONOMY_EXTRACTION
getTaxonomyExtraction()
boolean
hasNext()
Phylogeny
next()
Phylogeny[]
parse()
static Phylogeny[]
parse(java.lang.Object nhx_source)
static void
parseNHX(java.lang.String s, PhylogenyNode node_to_annotate, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores, boolean allow_errors_in_distance_to_parent, boolean replace_bell)
void
reset()
void
setAllowErrorsInDistanceToParent(boolean allow_errors_in_distance_to_parent)
void
setGuessRootedness(boolean guess_rootedness)
void
setIgnoreQuotes(boolean ignore_quotes)
void
setReplaceUnderscores(boolean replace_underscores)
void
setSource(java.lang.Object nhx_source)
void
setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
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Field Detail
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MB_BL_PATTERN
public static final java.util.regex.Pattern MB_BL_PATTERN
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MB_PROB_PATTERN
public static final java.util.regex.Pattern MB_PROB_PATTERN
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MB_PROB_SD_PATTERN
public static final java.util.regex.Pattern MB_PROB_SD_PATTERN
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NUMBERS_ONLY_PATTERN
public static final java.util.regex.Pattern NUMBERS_ONLY_PATTERN
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REPLACE_UNDERSCORES_DEFAULT
public static final boolean REPLACE_UNDERSCORES_DEFAULT
- See Also:
- Constant Field Values
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Method Detail
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getName
public java.lang.String getName()
- Specified by:
getName
in interfacePhylogenyParser
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getTaxonomyExtraction
public final NHXParser.TAXONOMY_EXTRACTION getTaxonomyExtraction()
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hasNext
public final boolean hasNext()
- Specified by:
hasNext
in interfaceIteratingPhylogenyParser
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next
public final Phylogeny next() throws NHXFormatException, java.io.IOException
- Specified by:
next
in interfaceIteratingPhylogenyParser
- Throws:
NHXFormatException
java.io.IOException
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parse
public final Phylogeny[] parse() throws java.io.IOException
- Specified by:
parse
in interfacePhylogenyParser
- Throws:
java.io.IOException
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reset
public final void reset() throws NHXFormatException, java.io.IOException
- Specified by:
reset
in interfaceIteratingPhylogenyParser
- Throws:
NHXFormatException
java.io.IOException
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setGuessRootedness
public final void setGuessRootedness(boolean guess_rootedness)
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setIgnoreQuotes
public final void setIgnoreQuotes(boolean ignore_quotes)
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setReplaceUnderscores
public final void setReplaceUnderscores(boolean replace_underscores)
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setSource
public final void setSource(java.lang.Object nhx_source) throws NHXFormatException, java.io.IOException
- Specified by:
setSource
in interfaceIteratingPhylogenyParser
- Specified by:
setSource
in interfacePhylogenyParser
- Throws:
NHXFormatException
java.io.IOException
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setTaxonomyExtraction
public final void setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
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setAllowErrorsInDistanceToParent
public final void setAllowErrorsInDistanceToParent(boolean allow_errors_in_distance_to_parent)
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parse
public static final Phylogeny[] parse(java.lang.Object nhx_source) throws NHXFormatException, java.io.IOException
- Throws:
NHXFormatException
java.io.IOException
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parseNHX
public static final void parseNHX(java.lang.String s, PhylogenyNode node_to_annotate, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores, boolean allow_errors_in_distance_to_parent, boolean replace_bell) throws NHXFormatException, PhyloXmlDataFormatException
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