Uses of Class
org.forester.rio.RIO
-
Packages that use RIO Package Description org.forester.rio -
-
Uses of RIO in org.forester.rio
Methods in org.forester.rio that return RIO 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)
-