Uses of Class
org.forester.rio.RIOException
Packages that use RIOException
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Uses of RIOException in org.forester.rio
Methods in org.forester.rio that throw RIOExceptionModifier and TypeMethodDescriptionstatic final IntMatrixRIO.calculateOrthologTable(Phylogeny[] analyzed_gene_trees, boolean sort) static final RIORIO.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 RIORIO.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 RIORIO.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 RIORIO.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 RIORIO.executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy) static final RIORIO.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 RIORIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree) static final RIORIO.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 RIORIO.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)