org.forester.sdi

Class GSDI

java.lang.Object

org.forester.sdi.GSDI

All Implemented Interfaces:

GSDII

public final class GSDI
extends Object
implements GSDII

Constructor Summary

Constructors

Constructor and Description
GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree)
GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree, boolean transfer_taxonomy)

Method Summary

Modifier and Type	Method and Description
int	getDuplicationsSum()
Set<PhylogenyNode>	getMappedExternalSpeciesTreeNodes()
SortedSet<String>	getReMappedScientificNamesFromGeneTree()
int	getSpeciationOrDuplicationEventsSum()
int	getSpeciationsSum()
List<PhylogenyNode>	getStrippedExternalGeneTreeNodes()
List<PhylogenyNode>	getStrippedSpeciesTreeNodes()
SDIutil.TaxonomyComparisonBase	getTaxCompBase()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GSDI

public GSDI(Phylogeny gene_tree,
            Phylogeny species_tree,
            boolean most_parsimonious_duplication_model,
            boolean strip_gene_tree,
            boolean strip_species_tree)
     throws SDIException

Throws:

SDIException

GSDI

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

Throws:

SDIException

Method Detail

getDuplicationsSum

public int getDuplicationsSum()

getMappedExternalSpeciesTreeNodes

public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes()

Specified by:

getMappedExternalSpeciesTreeNodes in interface GSDII

getReMappedScientificNamesFromGeneTree

public final SortedSet<String> getReMappedScientificNamesFromGeneTree()

Specified by:

getReMappedScientificNamesFromGeneTree in interface GSDII

getSpeciationOrDuplicationEventsSum

public final int getSpeciationOrDuplicationEventsSum()

getSpeciationsSum

public final int getSpeciationsSum()

Specified by:

getSpeciationsSum in interface GSDII

getStrippedExternalGeneTreeNodes

public List<PhylogenyNode> getStrippedExternalGeneTreeNodes()

Specified by:

getStrippedExternalGeneTreeNodes in interface GSDII

getStrippedSpeciesTreeNodes

public List<PhylogenyNode> getStrippedSpeciesTreeNodes()

Specified by:

getStrippedSpeciesTreeNodes in interface GSDII

getTaxCompBase

public SDIutil.TaxonomyComparisonBase getTaxCompBase()

Specified by:

getTaxCompBase in interface GSDII

toString

public final String toString()

Overrides:

toString in class Object