org.forester.io.parsers.nhx

Class NHXParser

java.lang.Object

org.forester.io.parsers.nhx.NHXParser

All Implemented Interfaces:

IteratingPhylogenyParser, PhylogenyParser

public final class NHXParser
extends Object
implements PhylogenyParser, IteratingPhylogenyParser

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NHXParser.TAXONOMY_EXTRACTION

Field Summary

Fields

Modifier and Type	Field and Description
static Pattern	MB_BL_PATTERN
static Pattern	MB_PROB_PATTERN
static Pattern	MB_PROB_SD_PATTERN
static Pattern	NUMBERS_ONLY_PATTERN
static boolean	REPLACE_UNDERSCORES_DEFAULT

Constructor Summary

Constructors

Constructor and Description
NHXParser()

Method Summary

Modifier and Type	Method and Description
String	getName()
NHXParser.TAXONOMY_EXTRACTION	getTaxonomyExtraction()
boolean	hasNext()
Phylogeny	next()
Phylogeny[]	parse()
static Phylogeny[]	parse(Object nhx_source)
static void	parseNHX(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(Object nhx_source)
void	setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)

Methods inherited from class java.lang.Object

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

Field Detail

MB_BL_PATTERN

public static final Pattern MB_BL_PATTERN

MB_PROB_PATTERN

public static final Pattern MB_PROB_PATTERN

MB_PROB_SD_PATTERN

public static final Pattern MB_PROB_SD_PATTERN

NUMBERS_ONLY_PATTERN

public static final Pattern NUMBERS_ONLY_PATTERN

REPLACE_UNDERSCORES_DEFAULT

public static final boolean REPLACE_UNDERSCORES_DEFAULT

See Also:

Constant Field Values

Constructor Detail

NHXParser

public NHXParser()

Method Detail

getName

public String getName()

Specified by:

getName in interface PhylogenyParser

getTaxonomyExtraction

public final NHXParser.TAXONOMY_EXTRACTION getTaxonomyExtraction()

hasNext

public final boolean hasNext()

Specified by:

hasNext in interface IteratingPhylogenyParser

next

public final Phylogeny next()
                     throws NHXFormatException,
                            IOException

Specified by:

next in interface IteratingPhylogenyParser

Throws:

NHXFormatException

IOException

parse

public final Phylogeny[] parse()
                        throws IOException

Specified by:

parse in interface PhylogenyParser

Throws:

IOException

reset

public final void reset()
                 throws NHXFormatException,
                        IOException

Specified by:

reset in interface IteratingPhylogenyParser

Throws:

NHXFormatException

IOException

setGuessRootedness

public final void setGuessRootedness(boolean guess_rootedness)

setIgnoreQuotes

public final void setIgnoreQuotes(boolean ignore_quotes)

setReplaceUnderscores

public final void setReplaceUnderscores(boolean replace_underscores)

setSource

public final void setSource(Object nhx_source)
                     throws NHXFormatException,
                            IOException

Specified by:

setSource in interface IteratingPhylogenyParser

Specified by:

setSource in interface PhylogenyParser

Throws:

NHXFormatException

IOException

setTaxonomyExtraction

public final void setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)

setAllowErrorsInDistanceToParent

public final void setAllowErrorsInDistanceToParent(boolean allow_errors_in_distance_to_parent)

parse

public static final Phylogeny[] parse(Object nhx_source)
                               throws NHXFormatException,
                                      IOException

Throws:

NHXFormatException

IOException

parseNHX

public static final void parseNHX(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

Throws:

NHXFormatException

PhyloXmlDataFormatException