Uses of Class
org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException
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Uses of PhyloXmlDataFormatException in org.forester.application
Methods in org.forester.application that throw PhyloXmlDataFormatException Modifier and Type Method Description static void
phyloxml_converter. main(java.lang.String[] args)
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Uses of PhyloXmlDataFormatException in org.forester.archaeopteryx.webservices
Methods in org.forester.archaeopteryx.webservices that throw PhyloXmlDataFormatException Modifier and Type Method Description static void
WebserviceUtil. processInstructions(PhylogeniesWebserviceClient client, Phylogeny phylogeny)
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Uses of PhyloXmlDataFormatException in org.forester.io.parsers.nhx
Methods in org.forester.io.parsers.nhx that throw PhyloXmlDataFormatException 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)
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Uses of PhyloXmlDataFormatException in org.forester.io.parsers.phyloxml
Methods in org.forester.io.parsers.phyloxml that throw PhyloXmlDataFormatException Modifier and Type Method Description double
XmlElement. getValueAsDouble()
int
XmlElement. getValueAsInt()
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Uses of PhyloXmlDataFormatException in org.forester.io.parsers.phyloxml.data
Methods in org.forester.io.parsers.phyloxml.data that throw PhyloXmlDataFormatException Modifier and Type Method Description PhylogenyData
AccessionParser. parse(XmlElement element)
PhylogenyData
AnnotationParser. parse(XmlElement element)
PhylogenyData
BinaryCharactersParser. parse(XmlElement element)
PhylogenyData
BranchWidthParser. parse(XmlElement element)
PhylogenyData
ColorParser. parse(XmlElement element)
PhylogenyData
ConfidenceParser. parse(XmlElement element)
PhylogenyData
DateParser. parse(XmlElement element)
PhylogenyData
DistributionParser. parse(XmlElement element)
DomainArchitecture
DomainArchitectureParser. parse(XmlElement element)
PhylogenyData
EventParser. parse(XmlElement element)
PhylogenyData
IdentifierParser. parse(XmlElement element)
PhylogenyData
PhylogenyDataPhyloXmlParser. parse(XmlElement element)
PhylogenyData
PointParser. parse(XmlElement element)
PhylogenyData
PolygonParser. parse(XmlElement element)
PhylogenyData
PropertyParser. parse(XmlElement element)
ProteinDomain
ProteinDomainParser. parse(XmlElement element)
PhylogenyData
ReferenceParser. parse(XmlElement element)
Sequence
SequenceParser. parse(XmlElement element)
SequenceRelation
SequenceRelationParser. parse(XmlElement element)
Taxonomy
TaxonomyParser. parse(XmlElement element)
PhylogenyData
UriParser. parse(XmlElement element)
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Uses of PhyloXmlDataFormatException in org.forester.io.parsers.util
Methods in org.forester.io.parsers.util that throw PhyloXmlDataFormatException Modifier and Type Method Description static java.lang.String
ParserUtils. extractTaxonomyDataFromNodeName(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
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Uses of PhyloXmlDataFormatException in org.forester.phylogeny
Methods in org.forester.phylogeny that throw PhyloXmlDataFormatException Modifier and Type Method Description static PhylogenyNode
PhylogenyNode. createInstanceFromNhxString(java.lang.String nhx)
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)
static void
PhylogenyMethods. setTaxonomyCode(PhylogenyNode node, java.lang.String taxonomy_code)
Convenience method to set the taxonomy code of a phylogeny node.static void
PhylogenyMethods. transferNodeNameToField(Phylogeny phy, PhylogenyMethods.PhylogenyNodeField field, boolean external_only)
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Uses of PhyloXmlDataFormatException in org.forester.phylogeny.data
Methods in org.forester.phylogeny.data that throw PhyloXmlDataFormatException Modifier and Type Method Description void
Reference. setDoi(java.lang.String doi)
void
Taxonomy. setRank(java.lang.String rank)
void
Sequence. setSymbol(java.lang.String symbol)
void
Taxonomy. setTaxonomyCode(java.lang.String taxonomy_code)
void
Sequence. setType(java.lang.String type)
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Uses of PhyloXmlDataFormatException in org.forester.sdi
Methods in org.forester.sdi that throw PhyloXmlDataFormatException 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)
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Uses of PhyloXmlDataFormatException in org.forester.tools
Methods in org.forester.tools that throw PhyloXmlDataFormatException Modifier and Type Method Description static java.lang.String
PhylogenyDecorator. decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose)
static java.lang.String
PhylogenyDecorator. decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, java.util.Map<java.lang.String,java.lang.String> intermediate_map, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose)
static void
PhylogenyDecorator. decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map, boolean picky)
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