public final class RIO
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
RIO.REROOTING |
Modifier and Type | Field and Description |
---|---|
static int |
DEFAULT_RANGE |
Modifier and Type | Method and Description |
---|---|
static IntMatrix |
calculateOrthologTable(Phylogeny[] analyzed_gene_trees,
boolean sort) |
static 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 |
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 |
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 |
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 |
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 |
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 |
executeAnalysis(Phylogeny[] gene_trees,
Phylogeny species_tree) |
static 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 |
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) |
Phylogeny[] |
getAnalyzedGeneTrees() |
BasicDescriptiveStatistics |
getDuplicationsStatistics() |
int |
getExtNodesOfAnalyzedGeneTrees()
Returns the numbers of number of ext nodes in gene trees analyzed (after
stripping).
|
SDIutil.TaxonomyComparisonBase |
getGSDIRtaxCompBase() |
int |
getIntNodesOfAnalyzedGeneTrees()
Returns the numbers of number of int nodes in gene trees analyzed (after
stripping).
|
java.lang.StringBuilder |
getLog() |
Phylogeny |
getMinDuplicationsGeneTree() |
IntMatrix |
getOrthologTable() |
java.util.List<PhylogenyNode> |
getRemovedGeneTreeNodes() |
Phylogeny |
getSpeciesTree() |
public static final int DEFAULT_RANGE
public final Phylogeny[] getAnalyzedGeneTrees()
public final BasicDescriptiveStatistics getDuplicationsStatistics()
public final int getExtNodesOfAnalyzedGeneTrees()
public final SDIutil.TaxonomyComparisonBase getGSDIRtaxCompBase()
public final int getIntNodesOfAnalyzedGeneTrees()
public final java.lang.StringBuilder getLog()
public final Phylogeny getMinDuplicationsGeneTree()
public final IntMatrix getOrthologTable()
public final java.util.List<PhylogenyNode> getRemovedGeneTreeNodes()
public final Phylogeny getSpeciesTree()
public static final IntMatrix calculateOrthologTable(Phylogeny[] analyzed_gene_trees, boolean sort) throws RIOException
RIOException
public static final 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) throws java.io.IOException, SDIException, RIOException
java.io.IOException
SDIException
RIOException
public static final 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) throws java.io.IOException, SDIException, RIOException
java.io.IOException
SDIException
RIOException
public static final 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) throws java.io.IOException, SDIException, RIOException
java.io.IOException
SDIException
RIOException
public static final 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) throws java.io.IOException, SDIException, RIOException
java.io.IOException
SDIException
RIOException
public static final 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) throws java.io.IOException, SDIException, RIOException
java.io.IOException
SDIException
RIOException
public static final 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) throws java.io.IOException, SDIException, RIOException
java.io.IOException
SDIException
RIOException
public static final RIO executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree) throws java.io.IOException, SDIException, RIOException
java.io.IOException
SDIException
RIOException
public static final 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) throws java.io.IOException, SDIException, RIOException
java.io.IOException
SDIException
RIOException
public static final 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) throws java.io.IOException, SDIException, RIOException
java.io.IOException
SDIException
RIOException