Uses of Class
org.forester.sdi.SDIException
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Packages that use SDIException Package Description org.forester.rio org.forester.sdi -
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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)
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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.
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