Uses of Class
org.forester.rio.RIO.REROOTING

Packages that use RIO.REROOTING

Package	Description
org.forester.rio

Uses of RIO.REROOTING in org.forester.rio

Methods in org.forester.rio that return RIO.REROOTING

Modifier and Type	Method and Description
static RIO.REROOTING	RIO.REROOTING.valueOf(String name) Returns the enum constant of this type with the specified name.
static RIO.REROOTING[]	RIO.REROOTING.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in org.forester.rio with parameters of type RIO.REROOTING

Modifier and Type	Method and Description
static 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 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 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 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 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 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 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 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)