Uses of Class
org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION
-
-
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 Description static Phylogeny[]
AptxUtil. readPhylogeniesFromUrl(java.net.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 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 Description NHXParser.TAXONOMY_EXTRACTION
NHXParser. getTaxonomyExtraction()
static NHXParser.TAXONOMY_EXTRACTION
NHXParser.TAXONOMY_EXTRACTION. valueOf(java.lang.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 Description static void
NHXParser. 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
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 Description static java.lang.String
ParserUtils. extractTaxonomyCodeFromNodeName(java.lang.String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static java.lang.String
ParserUtils. extractTaxonomyDataFromNodeName(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static java.lang.String
ParserUtils. extractUniprotTaxonomyIdFromNodeName(java.lang.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 Description static PhylogenyNode
PhylogenyNode. createInstanceFromNhxString(java.lang.String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static PhylogenyNode
PhylogenyNode. createInstanceFromNhxString(java.lang.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 Description static Phylogeny
SDIutil. parseSpeciesTree(Phylogeny gene_tree, java.io.File species_tree_file, boolean replace_undescores_in_nhx_trees, boolean ignore_quotes_in_nhx_trees, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees)
-