org.forester.sdi
Class GSDI

java.lang.Object
  org.forester.sdi.SDI
      org.forester.sdi.GSDI

public final class GSDI
extends SDI

Nested Class Summary

Nested classes/interfaces inherited from class org.forester.sdi.SDI

SDI.TaxonomyComparisonBase

Constructor Summary

GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree)

Method Summary

static SDI.TaxonomyComparisonBase	determineTaxonomyComparisonBase(Phylogeny gene_tree)
java.util.Set<PhylogenyNode>	getMappedExternalSpeciesTreeNodes()
java.util.SortedSet<java.lang.String>	getReMappedScientificNamesFromGeneTree()
int	getSpeciationOrDuplicationEventsSum()
int	getSpeciationsSum()
java.util.List<PhylogenyNode>	getStrippedExternalGeneTreeNodes()
java.util.List<PhylogenyNode>	getStrippedSpeciesTreeNodes()
SDI.TaxonomyComparisonBase	getTaxCompBase()
java.lang.String	toString()

Methods inherited from class org.forester.sdi.SDI

computeMappingCostL, getDuplicationsSum, getGeneTree, getSpeciesTree

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

Method Detail

getSpeciationOrDuplicationEventsSum

public final int getSpeciationOrDuplicationEventsSum()

getSpeciationsSum

public final int getSpeciationsSum()

getReMappedScientificNamesFromGeneTree

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

getTaxCompBase

public SDI.TaxonomyComparisonBase getTaxCompBase()

getStrippedSpeciesTreeNodes

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

getMappedExternalSpeciesTreeNodes

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

determineTaxonomyComparisonBase

public static SDI.TaxonomyComparisonBase determineTaxonomyComparisonBase(Phylogeny gene_tree)

getStrippedExternalGeneTreeNodes

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

toString

public final java.lang.String toString()

Overrides:

toString in class SDI