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)