Index

A C D E F G H I J K L M N O P R S T U V W _
All Classes All Packages

S

SaitouNei - Class in pt.ist.phylolib.command.algorithm.nj

Responsible for calculating a phylogenetic tree from a distance matrix using the Neighbour Joining algorithm by Saitou and Nei.

SaitouNei() - Constructor for class pt.ist.phylolib.command.algorithm.nj.SaitouNei

select(Set<Edge>) - Method in class pt.ist.phylolib.command.optimization.LBR

select(Set<Edge>) - Method in class pt.ist.phylolib.command.optimization.Optimization

Selects an edge of the given set of edges to be removed from the phylogenetic tree.

setMatrix(Options, Matrix) - Method in class pt.ist.phylolib.data.Context

Writes and updates the matrix with the given options.

setTree(Options, Tree) - Method in class pt.ist.phylolib.data.Context

Writes and updates the tree with the given options.

size() - Method in class pt.ist.phylolib.data.dataset.Dataset

size() - Method in class pt.ist.phylolib.data.dataset.Profile

size() - Method in class pt.ist.phylolib.data.matrix.Matrix

SL - Class in pt.ist.phylolib.command.algorithm.gcp

Responsible for calculating a phylogenetic tree from a distance matrix using the Single-Linkage algorithm.

SL() - Constructor for class pt.ist.phylolib.command.algorithm.gcp.SL

SNP - Class in pt.ist.phylolib.data.dataset

Responsible for parsing phylogenetic datasets from Strings in SNP format.

SNP() - Constructor for class pt.ist.phylolib.data.dataset.SNP

STARTED - Static variable in interface pt.ist.phylolib.command.ICommand

STARTED - Static variable in interface pt.ist.phylolib.data.IReader

STARTED - Static variable in interface pt.ist.phylolib.data.IWriter

StudierKeppler - Class in pt.ist.phylolib.command.algorithm.nj

Responsible for calculating a phylogenetic tree from a distance matrix using the Neighbour Joining algorithm by Studier and Keppler.

StudierKeppler() - Constructor for class pt.ist.phylolib.command.algorithm.nj.StudierKeppler

symmetric() - Method in class pt.ist.phylolib.command.distance.Distance

Checks the symmetry of the distance matrix calculated by this distance command.

symmetric() - Method in class pt.ist.phylolib.command.distance.GrapeTree

symmetric() - Method in class pt.ist.phylolib.command.distance.Hamming

symmetric() - Method in class pt.ist.phylolib.command.distance.Kimura

symmetric() - Method in class pt.ist.phylolib.data.matrix.Asymmetric

symmetric() - Method in class pt.ist.phylolib.data.matrix.Symmetric

symmetric() - Method in class pt.ist.phylolib.data.matrix.SymmetryParser

Checks the symmetry of this distance matrix processor.

Symmetric - Class in pt.ist.phylolib.data.matrix

Responsible for parsing distance matrices from and to Strings in a symmetric format.

Symmetric() - Constructor for class pt.ist.phylolib.data.matrix.Symmetric

SymmetryParser - Class in pt.ist.phylolib.data.matrix

Responsible for parsing distance matrices from and to Strings.

SymmetryParser() - Constructor for class pt.ist.phylolib.data.matrix.SymmetryParser

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