Uses of Class
org.forester.sdi.SDIException
Packages that use SDIException
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Uses of SDIException in org.forester.rio
Methods in org.forester.rio that throw SDIExceptionModifier and TypeMethodDescriptionstatic final RIO
RIO.executeAnalysis
(File gene_trees_file, File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy) static final RIO
RIO.executeAnalysis
(File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy) static final RIO
RIO.executeAnalysis
(File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy) static final RIO
RIO.executeAnalysis
(IteratingPhylogenyParser p, File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy) static final RIO
RIO.executeAnalysis
(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy) static final RIO
RIO.executeAnalysis
(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy) static final RIO
RIO.executeAnalysis
(Phylogeny[] gene_trees, Phylogeny species_tree) static final RIO
RIO.executeAnalysis
(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy) static final RIO
RIO.executeAnalysis
(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, 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 SDIExceptionModifier and TypeMethodDescriptionstatic final SDIutil.TaxonomyComparisonBase
SDIutil.determineTaxonomyComparisonBase
(Phylogeny gene_tree) 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 final 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) Constructors in org.forester.sdi that throw SDIExceptionModifierConstructorDescriptionGSDI
(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) Constructor which sets the gene tree and the species tree to be compared.