Package org.forester.sdi

Class GSDIR

java.lang.Object

org.forester.sdi.GSDIR

All Implemented Interfaces:

GSDII

public class GSDIR
extends java.lang.Object
implements GSDII

Constructor Summary

Constructors

Constructor	Description
GSDIR(Phylogeny gene_tree, Phylogeny species_tree, boolean strip_gene_tree, boolean strip_species_tree, boolean transfer_taxonomy)

Method Summary

Modifier and Type	Method	Description
BasicDescriptiveStatistics	getDuplicationsSumStats()
static java.util.List<java.lang.Integer>	getIndexesOfShortestTree(java.util.List<Phylogeny> assigned_trees)
java.util.Set<PhylogenyNode>	getMappedExternalSpeciesTreeNodes()
int	getMinDuplicationsSum()
Phylogeny	getMinDuplicationsSumGeneTree()
java.util.SortedSet<java.lang.String>	getReMappedScientificNamesFromGeneTree()
int	getSpeciationsSum()
java.util.List<PhylogenyNode>	getStrippedExternalGeneTreeNodes()
java.util.List<PhylogenyNode>	getStrippedSpeciesTreeNodes()
SDIutil.TaxonomyComparisonBase	getTaxCompBase()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GSDIR

public GSDIR(Phylogeny gene_tree,
             Phylogeny species_tree,
             boolean strip_gene_tree,
             boolean strip_species_tree,
             boolean transfer_taxonomy)
      throws SDIException

Throws:

SDIException

Method Detail

getDuplicationsSumStats

public BasicDescriptiveStatistics getDuplicationsSumStats()

getMappedExternalSpeciesTreeNodes

public java.util.Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes()

Specified by:

getMappedExternalSpeciesTreeNodes in interface GSDII

getMinDuplicationsSum

public int getMinDuplicationsSum()

getMinDuplicationsSumGeneTree

public Phylogeny getMinDuplicationsSumGeneTree()

getReMappedScientificNamesFromGeneTree

public final java.util.SortedSet<java.lang.String> getReMappedScientificNamesFromGeneTree()

Specified by:

getReMappedScientificNamesFromGeneTree in interface GSDII

getSpeciationsSum

public int getSpeciationsSum()

Specified by:

getSpeciationsSum in interface GSDII

getStrippedExternalGeneTreeNodes

public java.util.List<PhylogenyNode> getStrippedExternalGeneTreeNodes()

Specified by:

getStrippedExternalGeneTreeNodes in interface GSDII

getStrippedSpeciesTreeNodes

public java.util.List<PhylogenyNode> getStrippedSpeciesTreeNodes()

Specified by:

getStrippedSpeciesTreeNodes in interface GSDII

getTaxCompBase

public SDIutil.TaxonomyComparisonBase getTaxCompBase()

Specified by:

getTaxCompBase in interface GSDII

getIndexesOfShortestTree

public static final java.util.List<java.lang.Integer> getIndexesOfShortestTree(java.util.List<Phylogeny> assigned_trees)