java.lang.Object

org.forester.rio.RIO

public final class RIO extends Object

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

static enum

RIO.REROOTING
Field Summary

Fields

Modifier and Type

Field

Description

static final int

DEFAULT_RANGE
Method Summary

Modifier and Type

Method

Description

static final IntMatrix

calculateOrthologTable(Phylogeny[] analyzed_gene_trees, boolean sort)

static final 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

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

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

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

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

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

executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree)

static final 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

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)

final Phylogeny[]

getAnalyzedGeneTrees()

final BasicDescriptiveStatistics

getDuplicationsStatistics()

final int

getExtNodesOfAnalyzedGeneTrees()

Returns the numbers of number of ext nodes in gene trees analyzed (after stripping).

final SDIutil.TaxonomyComparisonBase

getGSDIRtaxCompBase()

final int

getIntNodesOfAnalyzedGeneTrees()

Returns the numbers of number of int nodes in gene trees analyzed (after stripping).

final StringBuilder

getLog()

final Phylogeny

getMinDuplicationsGeneTree()

final IntMatrix

getOrthologTable()

final List<PhylogenyNode>

getRemovedGeneTreeNodes()

final Phylogeny

getSpeciesTree()

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- DEFAULT_RANGE
  
  public static final int DEFAULT_RANGE
  See Also:
  
  Constant Field Values
Method Details
- getAnalyzedGeneTrees
  
  public final Phylogeny[] getAnalyzedGeneTrees()
- getDuplicationsStatistics
  
  public final BasicDescriptiveStatistics getDuplicationsStatistics()
- getExtNodesOfAnalyzedGeneTrees
  
  public final int getExtNodesOfAnalyzedGeneTrees()
  
  Returns the numbers of number of ext nodes in gene trees analyzed (after stripping).
  
  Returns:
  
  number of ext nodes in gene trees analyzed (after stripping)
- getGSDIRtaxCompBase
  
  public final SDIutil.TaxonomyComparisonBase getGSDIRtaxCompBase()
- getIntNodesOfAnalyzedGeneTrees
  
  public final int getIntNodesOfAnalyzedGeneTrees()
  
  Returns the numbers of number of int nodes in gene trees analyzed (after stripping).
  
  Returns:
  
  number of int nodes in gene trees analyzed (after stripping)
- getLog
  
  public final StringBuilder getLog()
- getMinDuplicationsGeneTree
  
  public final Phylogeny getMinDuplicationsGeneTree()
- getOrthologTable
  
  public final IntMatrix getOrthologTable()
- getRemovedGeneTreeNodes
  
  public final List<PhylogenyNode> getRemovedGeneTreeNodes()
- getSpeciesTree
  
  public final Phylogeny getSpeciesTree()
- calculateOrthologTable
  
  public static final IntMatrix calculateOrthologTable(Phylogeny[] analyzed_gene_trees, boolean sort) throws RIOException
  
  Throws:
  
  RIOException
- executeAnalysis
  
  public static final 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) throws IOException, SDIException, RIOException
  
  Throws:
  
  IOException
  
  SDIException
  
  RIOException
- executeAnalysis
  
  public static final 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) throws IOException, SDIException, RIOException
  
  Throws:
  
  IOException
  
  SDIException
  
  RIOException
- executeAnalysis
  
  public static final 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) throws IOException, SDIException, RIOException
  
  Throws:
  
  IOException
  
  SDIException
  
  RIOException
- executeAnalysis
  
  public static final 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) throws IOException, SDIException, RIOException
  
  Throws:
  
  IOException
  
  SDIException
  
  RIOException
- executeAnalysis
  
  public static final RIO executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws IOException, SDIException, RIOException
  
  Throws:
  
  IOException
  
  SDIException
  
  RIOException
- executeAnalysis
  
  public static final 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) throws IOException, SDIException, RIOException
  
  Throws:
  
  IOException
  
  SDIException
  
  RIOException
- executeAnalysis
  
  public static final RIO executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree) throws IOException, SDIException, RIOException
  
  Throws:
  
  IOException
  
  SDIException
  
  RIOException
- executeAnalysis
  
  public static final RIO executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws IOException, SDIException, RIOException
  
  Throws:
  
  IOException
  
  SDIException
  
  RIOException
- executeAnalysis
  
  public static final 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) throws IOException, SDIException, RIOException
  
  Throws:
  
  IOException
  
  SDIException
  
  RIOException

Class RIO

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

DEFAULT_RANGE

Method Details

getAnalyzedGeneTrees

getDuplicationsStatistics

getExtNodesOfAnalyzedGeneTrees

getGSDIRtaxCompBase

getIntNodesOfAnalyzedGeneTrees

getLog

getMinDuplicationsGeneTree

getOrthologTable

getRemovedGeneTreeNodes

getSpeciesTree

calculateOrthologTable

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis