Uses of Class
org.forester.sdi.SDIException

Packages that use SDIException

Package	Description
org.forester.rio
org.forester.sdi

Uses of SDIException in org.forester.rio

Methods in org.forester.rio that throw SDIException

Modifier and Type	Method	Description
static RIO	RIO.executeAnalysis(java.io.File gene_trees_file, java.io.File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(IteratingPhylogenyParser p, java.io.File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree)
static RIO	RIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)

Uses of SDIException in org.forester.sdi

Methods in org.forester.sdi that throw SDIException

Modifier and Type	Method	Description
static SDIutil.TaxonomyComparisonBase	SDIutil.determineTaxonomyComparisonBase(Phylogeny gene_tree)
Phylogeny[]	SDIR.infer(Phylogeny gene_tree, Phylogeny species_tree, boolean minimize_mapping_cost, boolean minimize_sum_of_dup, boolean minimize_height, boolean return_trees, int max_trees_to_return)	Infers gene duplications on a possibly unrooted gene Phylogeny gene_tree.
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)

Constructors in org.forester.sdi that throw SDIException

Constructor	Description
GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree)
GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree, boolean transfer_taxonomy)
GSDIR(Phylogeny gene_tree, Phylogeny species_tree, boolean strip_gene_tree, boolean strip_species_tree, boolean transfer_taxonomy)
SDI(Phylogeny gene_tree, Phylogeny species_tree)	Constructor which sets the gene tree and the species tree to be compared.