Uses of Class
org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException

Packages that use PhyloXmlDataFormatException

Package	Description
org.forester.application
org.forester.archaeopteryx.webservices
org.forester.io.parsers.nhx
org.forester.io.parsers.phyloxml
org.forester.io.parsers.phyloxml.data
org.forester.io.parsers.util
org.forester.phylogeny
org.forester.phylogeny.data
org.forester.sdi
org.forester.tools

Uses of PhyloXmlDataFormatException in org.forester.application

Methods in org.forester.application that throw PhyloXmlDataFormatException

Modifier and Type	Method and Description
static void	phyloxml_converter.main(String[] args)

Uses of PhyloXmlDataFormatException in org.forester.archaeopteryx.webservices

Methods in org.forester.archaeopteryx.webservices that throw PhyloXmlDataFormatException

Modifier and Type	Method and Description
static 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 PhyloXmlDataFormatException

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)

Uses of PhyloXmlDataFormatException in org.forester.io.parsers.phyloxml

Methods in org.forester.io.parsers.phyloxml that throw PhyloXmlDataFormatException

Modifier and Type	Method and Description
double	XmlElement.getValueAsDouble()
int	XmlElement.getValueAsInt()

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 and Description
PhylogenyData	PropertyParser.parse(XmlElement element)
PhylogenyData	DistributionParser.parse(XmlElement element)
PhylogenyData	AnnotationParser.parse(XmlElement element)
PhylogenyData	EventParser.parse(XmlElement element)
Taxonomy	TaxonomyParser.parse(XmlElement element)
PhylogenyData	PolygonParser.parse(XmlElement element)
PhylogenyData	ColorParser.parse(XmlElement element)
PhylogenyData	ReferenceParser.parse(XmlElement element)
PhylogenyData	ConfidenceParser.parse(XmlElement element)
PhylogenyData	PhylogenyDataPhyloXmlParser.parse(XmlElement element)
DomainArchitecture	DomainArchitectureParser.parse(XmlElement element)
PhylogenyData	UriParser.parse(XmlElement element)
PhylogenyData	PointParser.parse(XmlElement element)
PhylogenyData	IdentifierParser.parse(XmlElement element)
PhylogenyData	DateParser.parse(XmlElement element)
PhylogenyData	BranchWidthParser.parse(XmlElement element)
PhylogenyData	AccessionParser.parse(XmlElement element)
SequenceRelation	SequenceRelationParser.parse(XmlElement element)
ProteinDomain	ProteinDomainParser.parse(XmlElement element)
Sequence	SequenceParser.parse(XmlElement element)
PhylogenyData	BinaryCharactersParser.parse(XmlElement element)

Uses of PhyloXmlDataFormatException in org.forester.io.parsers.util

Methods in org.forester.io.parsers.util that throw PhyloXmlDataFormatException

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

Uses of PhyloXmlDataFormatException in org.forester.phylogeny

Methods in org.forester.phylogeny that throw PhyloXmlDataFormatException

Modifier and Type	Method and Description
static 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 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

Modifier and Type	Method and Description
void	Reference.setDoi(String doi)
void	Taxonomy.setRank(String rank)
void	Sequence.setSymbol(String symbol)
void	Taxonomy.setTaxonomyCode(String taxonomy_code)
void	Sequence.setType(String type)

Uses of PhyloXmlDataFormatException in org.forester.sdi

Methods in org.forester.sdi that throw PhyloXmlDataFormatException

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)

Uses of PhyloXmlDataFormatException in org.forester.tools

Methods in org.forester.tools that throw PhyloXmlDataFormatException

Modifier and Type	Method and Description
static void	PhylogenyDecorator.decorate(Phylogeny phylogeny, Map<String,Map<String,String>> map, boolean picky)
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, 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)