Uses of Class
org.forester.io.parsers.nhx.NHXFormatException

Packages that use NHXFormatException

Package	Description
org.forester.io.parsers.nexus
org.forester.io.parsers.nhx
org.forester.phylogeny
org.forester.phylogeny.data
org.forester.tools

Uses of NHXFormatException in org.forester.io.parsers.nexus

Methods in org.forester.io.parsers.nexus that throw NHXFormatException

Modifier and Type	Method	Description
Phylogeny	NexusPhylogeniesParser.next()

Uses of NHXFormatException in org.forester.io.parsers.nhx

Methods in org.forester.io.parsers.nhx that throw NHXFormatException

Modifier and Type	Method	Description
Phylogeny	NHXParser.next()
static Phylogeny[]	NHXParser.parse(java.lang.Object nhx_source)
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.reset()
void	NHXParser.setSource(java.lang.Object nhx_source)

Uses of NHXFormatException in org.forester.phylogeny

Methods in org.forester.phylogeny that throw NHXFormatException

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)

Uses of NHXFormatException in org.forester.phylogeny.data

Constructors in org.forester.phylogeny.data that throw NHXFormatException

Constructor	Description
Event(java.lang.String nhx)

Uses of NHXFormatException in org.forester.tools

Methods in org.forester.tools that throw NHXFormatException

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)