Uses of Class
org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException
Packages that use PhyloXmlDataFormatException
Package
Description
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Uses of PhyloXmlDataFormatException in org.forester.application
Methods in org.forester.application that throw PhyloXmlDataFormatException -
Uses of PhyloXmlDataFormatException in org.forester.archaeopteryx.webservices
Methods in org.forester.archaeopteryx.webservices that throw PhyloXmlDataFormatExceptionModifier and TypeMethodDescriptionstatic void
WebserviceUtil.processInstructions
(PhylogeniesWebserviceClient client, Phylogeny phylogeny) -
Uses of PhyloXmlDataFormatException in org.forester.io.parsers.nhx
Methods in org.forester.io.parsers.nhx that throw PhyloXmlDataFormatExceptionModifier 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) -
Uses of PhyloXmlDataFormatException in org.forester.io.parsers.phyloxml
Methods in org.forester.io.parsers.phyloxml that throw PhyloXmlDataFormatExceptionModifier and TypeMethodDescriptiondouble
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 PhyloXmlDataFormatExceptionModifier and TypeMethodDescriptionAccessionParser.parse
(XmlElement element) AnnotationParser.parse
(XmlElement element) BinaryCharactersParser.parse
(XmlElement element) BranchWidthParser.parse
(XmlElement element) ColorParser.parse
(XmlElement element) ConfidenceParser.parse
(XmlElement element) DateParser.parse
(XmlElement element) DistributionParser.parse
(XmlElement element) DomainArchitectureParser.parse
(XmlElement element) EventParser.parse
(XmlElement element) IdentifierParser.parse
(XmlElement element) PhylogenyDataPhyloXmlParser.parse
(XmlElement element) PointParser.parse
(XmlElement element) PolygonParser.parse
(XmlElement element) PropertyParser.parse
(XmlElement element) ProteinDomainParser.parse
(XmlElement element) ReferenceParser.parse
(XmlElement element) SequenceParser.parse
(XmlElement element) SequenceRelationParser.parse
(XmlElement element) TaxonomyParser.parse
(XmlElement element) UriParser.parse
(XmlElement element) -
Uses of PhyloXmlDataFormatException in org.forester.io.parsers.util
Methods in org.forester.io.parsers.util that throw PhyloXmlDataFormatExceptionModifier and TypeMethodDescriptionstatic final String
ParserUtils.extractTaxonomyDataFromNodeName
(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) -
Uses of PhyloXmlDataFormatException in org.forester.phylogeny
Methods in org.forester.phylogeny that throw PhyloXmlDataFormatExceptionModifier and TypeMethodDescriptionstatic PhylogenyNode
PhylogenyNode.createInstanceFromNhxString
(String nhx) 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) static void
PhylogenyMethods.setTaxonomyCode
(PhylogenyNode node, String taxonomy_code) Convenience method to set the taxonomy code of a phylogeny node.static final void
PhylogenyMethods.transferNodeNameToField
(Phylogeny phy, PhylogenyMethods.PhylogenyNodeField field, boolean external_only) -
Uses of PhyloXmlDataFormatException in org.forester.phylogeny.data
Methods in org.forester.phylogeny.data that throw PhyloXmlDataFormatException -
Uses of PhyloXmlDataFormatException in org.forester.sdi
Methods in org.forester.sdi that throw PhyloXmlDataFormatExceptionModifier 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) -
Uses of PhyloXmlDataFormatException in org.forester.tools
Methods in org.forester.tools that throw PhyloXmlDataFormatExceptionModifier and TypeMethodDescriptionstatic String
PhylogenyDecorator.decorate
(Phylogeny phylogeny, Map<String, 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 String
PhylogenyDecorator.decorate
(Phylogeny phylogeny, Map<String, String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, Map<String, String> intermediate_map, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose) static void