- geneCollapseThreshold - Static variable in class rapgreen.TreeReconciler
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Gene tree branch collapse threshold, in term of branch support, initialized to 0.95
- geneDepthThreshold - Static variable in class rapgreen.TreeReconciler
-
Depth threshold, under which no duplications are predicted (polymorphism / sequencing error).
- geneFiles - Static variable in class rapgreen.RapGreen
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Input gene files
- generalFile - Static variable in class rapgreen.PhylogeneticMapping
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General stats file
- geneTree - Variable in class rapgreen.TreeReconciler
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The gene tree
- get5LettersCode(String) - Method in class rapgreen.SpeciesDictionary
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Get the 5 letters code from the numerical code
- getDepth(Tree) - Method in class rapgreen.Tree
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Return the depth of the leaf in this tree, 1.0 per level if no branch length, sum of branch lengths otherwise.
- getDepths(Vector, double) - Method in class rapgreen.Tree
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Fill a vector with every depths of each leaf of the tree, from this node, adding save
- getDuplications(Vector) - Method in class rapgreen.Tree
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Fill a vector with every duplication node of this tree.
- getLosses(Vector) - Method in class rapgreen.Tree
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Fill a vector with every losses node of this tree.
- getNbRedundancy() - Method in class rapgreen.Tree
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Return the number of redundant nodes.
- getNbUltraparalogGroups(Hashtable) - Method in class rapgreen.Tree
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Fill a table with the number of ultraparalogous groups for each taxon
- getNewick() - Method in class rapgreen.Tree
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Return the newick representation of this node
- getNHXNewick(Tree, Hashtable, String) - Method in class rapgreen.Tree
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Return the newick representation of this node
- getNode(double, String) - Method in class rapgreen.Tree
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Return the node corresponding to length and label
- getNodes() - Method in class rapgreen.Tree
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Return a vector containing all tree nodes under this node, this node included
- getNumericalCode(String) - Method in class rapgreen.SpeciesDictionary
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Get the numerical code from the 5 letters code
- getRootedTrees() - Method in class rapgreen.Tree
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Return every possible rooted trees, from this tree, cloning the structures
- getScientificName(String) - Method in class rapgreen.SpeciesDictionary
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Get the scientific name from the 5 letters code
- getScientificNameFromNumerical(String) - Method in class rapgreen.SpeciesDictionary
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Get the scientific name from the 5 letters code
- getSimpleNewick() - Method in class rapgreen.Tree
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Return the simple (no length, no support) newick representation of this node
- getSpeciations(Vector) - Method in class rapgreen.Tree
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Fill a vector with every speciations of leaves node of this tree.
- globalPretreatment() - Method in class rapgreen.Tree
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Fill the Vector, Hashtable and pointer fields, for species trees
- globalTable - Static variable in class rapgreen.TreeStats
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- taxaTranslationTable - Static variable in class rapgreen.RapGreen
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Table of taxa translation, for prefixed sequence names
- taxaTranslationVector - Static variable in class rapgreen.RapGreen
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Vector of taxa translation, for prefixed sequence names
- taxonomicPretreatment() - Method in class rapgreen.Tree
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Fill the Vector, Hashtable and pointer fields, in order to compare and a gene tree with a pattern tree.
- tDupWeight - Static variable in class rapgreen.TreeScoring
-
Global scoring attributs
- Temp - Class in rapgreen
-
- Temp() - Constructor for class rapgreen.Temp
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- threshold - Static variable in class rapgreen.TreeClustering
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Cutting threshold
- toCut - Static variable in class rapgreen.TreeClustering
-
- toNewick(int, String, StringBuffer, SpeciesDictionary) - Method in class rapgreen.TreeReader
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Private parser of a node, from a starting point in a newick string, to an ending point returned in an Integer object.
- toPhyloXMLString(StringBuffer) - Method in class rapgreen.Tree
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Specialized phyloXML string conversion method
- toPhyloXMLString(SpeciesDictionary) - Method in class rapgreen.Tree
-
Specialized phyloXML string conversion method, used with a dictionary in order to generate a global species tree from NCBI files
- toSimpleNewick(int, String, StringBuffer, SpeciesDictionary) - Method in class rapgreen.TreeReader
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Private parser of a node, from a starting point in a newick string, to an ending point returned in an Integer object.
- toString() - Method in class rapgreen.Tree
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Standard string conversion method
- trace() - Method in class rapgreen.Tree
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Compute the trace of a duplication node (intersection / union of species under the two sons)
- traceVector() - Method in class rapgreen.Tree
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Compute the species intersection of this node
- trashFile - Static variable in class rapgreen.PhylogeneticMapping
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Trash file
- Tree - Class in rapgreen
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Global class of tree management.
- Tree(String) - Constructor for class rapgreen.Tree
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Generic constructor of a tree, from a newick string
- Tree(Vector, String, double, String) - Constructor for class rapgreen.Tree
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Generic constructor of a node, directly from fields
- Tree(Vector, String, double, String, String) - Constructor for class rapgreen.Tree
-
Generic constructor of a node, directly from fields
- Tree(Tree) - Constructor for class rapgreen.Tree
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Cloning contructor, clone only basic fields, not the pretreatment fields
- tree - Variable in class rapgreen.TreeScoring
-
The reference tree
- TreeClustering - Class in rapgreen
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- TreeClustering() - Constructor for class rapgreen.TreeClustering
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- TreeColoring - Class in rapgreen
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- TreeColoring() - Constructor for class rapgreen.TreeColoring
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- treeDirectory - Static variable in class rapgreen.PhylogeneticMapping
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Input tree files
- treeFile - Static variable in class rapgreen.TreeClustering
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Input tree file
- treeFile - Static variable in class rapgreen.TreeFilter
-
Input tree file
- treeFile - Static variable in class rapgreen.TreeStats
-
Input tree file
- treeFileName - Static variable in class rapgreen.PhylogeneticMapping
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Input cluster file parsed names
- TreeFilter - Class in rapgreen
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- TreeFilter() - Constructor for class rapgreen.TreeFilter
-
- treeIndex - Variable in class rapgreen.TreeReader
-
The index
- TreeReader - Class in rapgreen
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Tree file reading class.
- TreeReader(File, int) - Constructor for class rapgreen.TreeReader
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Generic constructor, from several formats
- TreeReader(File, SpeciesDictionary, int) - Constructor for class rapgreen.TreeReader
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Generic constructor, from several formats, filling a species dictionary
- TreeReader(File, SpeciesDictionary, Hashtable, int) - Constructor for class rapgreen.TreeReader
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Generic constructor, from several formats, filling a species dictionary, and an ID index
- TreeReader(File, SpeciesDictionary, Hashtable, int, int) - Constructor for class rapgreen.TreeReader
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Generic constructor, from several formats, filling a species dictionary, and an ID index
- TreeReconciler - Class in rapgreen
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Tree reconciliation class.
- TreeReconciler(Tree, Tree) - Constructor for class rapgreen.TreeReconciler
-
Standard constructor, from species and gene trees, constructing reconciled tree.
- trees - Variable in class rapgreen.TreeReader
-
Trees
- TreeScoring - Class in rapgreen
-
Tree scoring class.
- TreeScoring(Tree) - Constructor for class rapgreen.TreeScoring
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Generic constructor
- TreeStats - Class in rapgreen
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- TreeStats() - Constructor for class rapgreen.TreeStats
-
- TreeWriter - Class in rapgreen
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Tree file writing class.
- TreeWriter(Tree) - Constructor for class rapgreen.TreeWriter
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Generic constructor, from several formats