Package org.forester.sdi
Class GSDIR
- java.lang.Object
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- org.forester.sdi.GSDIR
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description BasicDescriptiveStatistics
getDuplicationsSumStats()
static java.util.List<java.lang.Integer>
getIndexesOfShortestTree(java.util.List<Phylogeny> assigned_trees)
java.util.Set<PhylogenyNode>
getMappedExternalSpeciesTreeNodes()
int
getMinDuplicationsSum()
Phylogeny
getMinDuplicationsSumGeneTree()
java.util.SortedSet<java.lang.String>
getReMappedScientificNamesFromGeneTree()
int
getSpeciationsSum()
java.util.List<PhylogenyNode>
getStrippedExternalGeneTreeNodes()
java.util.List<PhylogenyNode>
getStrippedSpeciesTreeNodes()
SDIutil.TaxonomyComparisonBase
getTaxCompBase()
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Constructor Detail
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GSDIR
public GSDIR(Phylogeny gene_tree, Phylogeny species_tree, 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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getDuplicationsSumStats
public BasicDescriptiveStatistics getDuplicationsSumStats()
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getMappedExternalSpeciesTreeNodes
public java.util.Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes()
- Specified by:
getMappedExternalSpeciesTreeNodes
in interfaceGSDII
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getMinDuplicationsSum
public int getMinDuplicationsSum()
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getMinDuplicationsSumGeneTree
public Phylogeny getMinDuplicationsSumGeneTree()
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getReMappedScientificNamesFromGeneTree
public final java.util.SortedSet<java.lang.String> getReMappedScientificNamesFromGeneTree()
- Specified by:
getReMappedScientificNamesFromGeneTree
in interfaceGSDII
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getSpeciationsSum
public 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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getIndexesOfShortestTree
public static final java.util.List<java.lang.Integer> getIndexesOfShortestTree(java.util.List<Phylogeny> assigned_trees)
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