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

Description

static enum

NHXParser.TAXONOMY_EXTRACTION
Field Summary

Fields

Modifier and Type

Field

Description

static final Pattern

MB_BL_PATTERN

static final Pattern

MB_PROB_PATTERN

static final Pattern

MB_PROB_SD_PATTERN

static final Pattern

NUMBERS_ONLY_PATTERN

static final boolean

REPLACE_UNDERSCORES_DEFAULT
Constructor Summary

Constructors

Constructor

Description

NHXParser()
Method Summary

Modifier and Type

Method

Description

String

getName()

final NHXParser.TAXONOMY_EXTRACTION

getTaxonomyExtraction()

final boolean

hasNext()

final Phylogeny

next()

final Phylogeny[]

parse()

static final Phylogeny[]

parse(Object nhx_source)

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)

final void

reset()

final void

setAllowErrorsInDistanceToParent(boolean allow_errors_in_distance_to_parent)

final void

setGuessRootedness(boolean guess_rootedness)

final void

setIgnoreQuotes(boolean ignore_quotes)

final void

setReplaceUnderscores(boolean replace_underscores)

final void

setSource(Object nhx_source)

final 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 Details
- 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 Details
- NHXParser
  
  public NHXParser()
Method Details
- 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

Class NHXParser

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

MB_BL_PATTERN

MB_PROB_PATTERN

MB_PROB_SD_PATTERN

NUMBERS_ONLY_PATTERN

REPLACE_UNDERSCORES_DEFAULT

Constructor Details

NHXParser

Method Details

getName

getTaxonomyExtraction

hasNext

next

parse

reset

setGuessRootedness

setIgnoreQuotes

setReplaceUnderscores

setSource

setTaxonomyExtraction

setAllowErrorsInDistanceToParent

parse

parseNHX