Uses of Class
org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION

Packages that use NHXParser.TAXONOMY_EXTRACTION

Package	Description
org.forester.archaeopteryx
org.forester.io.parsers.nexus
org.forester.io.parsers.nhx
org.forester.io.parsers.util
org.forester.phylogeny
org.forester.sdi

Uses of NHXParser.TAXONOMY_EXTRACTION in org.forester.archaeopteryx

Methods in org.forester.archaeopteryx with parameters of type NHXParser.TAXONOMY_EXTRACTION

Modifier and Type	Method and Description
static Phylogeny[]	AptxUtil.readPhylogeniesFromUrl(URL url, boolean phyloxml_validate_against_xsd, boolean replace_underscores, boolean internal_numbers_are_confidences, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean midpoint_reroot)

Uses of NHXParser.TAXONOMY_EXTRACTION in org.forester.io.parsers.nexus

Methods in org.forester.io.parsers.nexus with parameters of type NHXParser.TAXONOMY_EXTRACTION

Modifier and Type	Method and Description
void	NexusPhylogeniesParser.setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)

Uses of NHXParser.TAXONOMY_EXTRACTION in org.forester.io.parsers.nhx

Methods in org.forester.io.parsers.nhx that return NHXParser.TAXONOMY_EXTRACTION

Modifier and Type	Method and Description
NHXParser.TAXONOMY_EXTRACTION	NHXParser.getTaxonomyExtraction()
static NHXParser.TAXONOMY_EXTRACTION	NHXParser.TAXONOMY_EXTRACTION.valueOf(String name) Returns the enum constant of this type with the specified name.
static NHXParser.TAXONOMY_EXTRACTION[]	NHXParser.TAXONOMY_EXTRACTION.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in org.forester.io.parsers.nhx with parameters of type NHXParser.TAXONOMY_EXTRACTION

Modifier and Type	Method and Description
static void	NHXParser.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	NHXParser.setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)

Uses of NHXParser.TAXONOMY_EXTRACTION in org.forester.io.parsers.util

Methods in org.forester.io.parsers.util with parameters of type NHXParser.TAXONOMY_EXTRACTION

Modifier and Type	Method and Description
static String	ParserUtils.extractTaxonomyCodeFromNodeName(String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static String	ParserUtils.extractTaxonomyDataFromNodeName(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static String	ParserUtils.extractUniprotTaxonomyIdFromNodeName(String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)

Uses of NHXParser.TAXONOMY_EXTRACTION in org.forester.phylogeny

Methods in org.forester.phylogeny with parameters of type NHXParser.TAXONOMY_EXTRACTION

Modifier and Type	Method and Description
static PhylogenyNode	PhylogenyNode.createInstanceFromNhxString(String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static PhylogenyNode	PhylogenyNode.createInstanceFromNhxString(String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores)

Uses of NHXParser.TAXONOMY_EXTRACTION in org.forester.sdi

Methods in org.forester.sdi with parameters of type NHXParser.TAXONOMY_EXTRACTION

Modifier and Type	Method and Description
static Phylogeny	SDIutil.parseSpeciesTree(Phylogeny gene_tree, File species_tree_file, boolean replace_undescores_in_nhx_trees, boolean ignore_quotes_in_nhx_trees, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees)