java.lang.Object

org.forester.sdi.GSDI

All Implemented Interfaces:: GSDII

public final class GSDI extends Object implements GSDII

Constructor Summary

Constructors

Constructor

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

Description

int

getDuplicationsSum()

Set<PhylogenyNode>

getMappedExternalSpeciesTreeNodes()

final SortedSet<String>

getReMappedScientificNamesFromGeneTree()

final int

getSpeciationOrDuplicationEventsSum()

final int

getSpeciationsSum()

List<PhylogenyNode>

getStrippedExternalGeneTreeNodes()

List<PhylogenyNode>

getStrippedSpeciesTreeNodes()

SDIutil.TaxonomyComparisonBase

getTaxCompBase()

final String

toString()

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

Constructor Details
- 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 Details
- 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

Class GSDI

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

GSDI

GSDI

Method Details

getDuplicationsSum

getMappedExternalSpeciesTreeNodes

getReMappedScientificNamesFromGeneTree

getSpeciationOrDuplicationEventsSum

getSpeciationsSum

getStrippedExternalGeneTreeNodes

getStrippedSpeciesTreeNodes

getTaxCompBase

toString