java.lang.Object

org.forester.sdi.GSDIR

All Implemented Interfaces:: GSDII

public class GSDIR extends 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 final List<Integer>

getIndexesOfShortestTree(List<Phylogeny> assigned_trees)

Set<PhylogenyNode>

getMappedExternalSpeciesTreeNodes()

int

getMinDuplicationsSum()

Phylogeny

getMinDuplicationsSumGeneTree()

final SortedSet<String>

getReMappedScientificNamesFromGeneTree()

int

getSpeciationsSum()

List<PhylogenyNode>

getStrippedExternalGeneTreeNodes()

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 Details
- 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 Details
- getDuplicationsSumStats
  
  public BasicDescriptiveStatistics getDuplicationsSumStats()
- getMappedExternalSpeciesTreeNodes
  
  public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes()
  
  Specified by:
  
  getMappedExternalSpeciesTreeNodes in interface GSDII
- getMinDuplicationsSum
  
  public int getMinDuplicationsSum()
- getMinDuplicationsSumGeneTree
  
  public Phylogeny getMinDuplicationsSumGeneTree()
- getReMappedScientificNamesFromGeneTree
  
  public final SortedSet<String> getReMappedScientificNamesFromGeneTree()
  
  Specified by:
  
  getReMappedScientificNamesFromGeneTree in interface GSDII
- getSpeciationsSum
  
  public 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
- getIndexesOfShortestTree
  
  public static final List<Integer> getIndexesOfShortestTree(List<Phylogeny> assigned_trees)

Class GSDIR

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

GSDIR

Method Details

getDuplicationsSumStats

getMappedExternalSpeciesTreeNodes

getMinDuplicationsSum

getMinDuplicationsSumGeneTree

getReMappedScientificNamesFromGeneTree

getSpeciationsSum

getStrippedExternalGeneTreeNodes

getStrippedSpeciesTreeNodes

getTaxCompBase

getIndexesOfShortestTree