Uses of Enum Class
org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION
Packages that use NHXParser.TAXONOMY_EXTRACTION
Package
Description
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Uses of NHXParser.TAXONOMY_EXTRACTION in org.forester.archaeopteryx
Methods in org.forester.archaeopteryx with parameters of type NHXParser.TAXONOMY_EXTRACTIONModifier and TypeMethodDescriptionstatic final 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_EXTRACTIONModifier and TypeMethodDescriptionfinal 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_EXTRACTIONModifier and TypeMethodDescriptionNHXParser.getTaxonomyExtraction()
Returns the enum constant of this class with the specified name.static NHXParser.TAXONOMY_EXTRACTION[]
NHXParser.TAXONOMY_EXTRACTION.values()
Returns an array containing the constants of this enum class, in the order they are declared.Methods in org.forester.io.parsers.nhx with parameters of type NHXParser.TAXONOMY_EXTRACTIONModifier and TypeMethodDescriptionstatic final 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) final 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_EXTRACTIONModifier and TypeMethodDescriptionstatic final String
ParserUtils.extractTaxonomyCodeFromNodeName
(String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) static final String
ParserUtils.extractTaxonomyDataFromNodeName
(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) static final 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_EXTRACTIONModifier and TypeMethodDescriptionstatic 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_EXTRACTIONModifier and TypeMethodDescriptionstatic final 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)