Uses of Class
org.forester.io.parsers.nhx.NHXFormatException
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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 -
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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()
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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)
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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)
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Uses of NHXFormatException in org.forester.phylogeny.data
Constructors in org.forester.phylogeny.data that throw NHXFormatException Constructor Description Event(java.lang.String nhx)
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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)
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