Package org.forester.sdi
Class GSDI
- java.lang.Object
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- org.forester.sdi.GSDI
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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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getDuplicationsSum()
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()
SDIutil.TaxonomyComparisonBase
getTaxCompBase()
java.lang.String
toString()
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Constructor Detail
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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
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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
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Method Detail
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getDuplicationsSum
public int getDuplicationsSum()
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getMappedExternalSpeciesTreeNodes
public java.util.Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes()
- Specified by:
getMappedExternalSpeciesTreeNodes
in interfaceGSDII
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getReMappedScientificNamesFromGeneTree
public final java.util.SortedSet<java.lang.String> getReMappedScientificNamesFromGeneTree()
- Specified by:
getReMappedScientificNamesFromGeneTree
in interfaceGSDII
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getSpeciationOrDuplicationEventsSum
public final int getSpeciationOrDuplicationEventsSum()
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getSpeciationsSum
public final int getSpeciationsSum()
- Specified by:
getSpeciationsSum
in interfaceGSDII
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getStrippedExternalGeneTreeNodes
public java.util.List<PhylogenyNode> getStrippedExternalGeneTreeNodes()
- Specified by:
getStrippedExternalGeneTreeNodes
in interfaceGSDII
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getStrippedSpeciesTreeNodes
public java.util.List<PhylogenyNode> getStrippedSpeciesTreeNodes()
- Specified by:
getStrippedSpeciesTreeNodes
in interfaceGSDII
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getTaxCompBase
public SDIutil.TaxonomyComparisonBase getTaxCompBase()
- Specified by:
getTaxCompBase
in interfaceGSDII
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toString
public final java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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