Index

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G

get(double) - Method in interface pt.ist.phylolib.data.matrix.Matrix.ICorrection

Corrects the given phylogenetic distance.

get(int, int) - Method in interface pt.ist.phylolib.data.matrix.Matrix.IDistance

Calculates the phylogenetic distance between two given profiles.

get(Class<?>) - Static method in class pt.ist.phylolib.reflection.Types

Gets the names and constructors of the types inside specific packages that inherit from a specific type.

get(String) - Static method in enum pt.ist.phylolib.cli.Command

Gets the command corresponding to the given name.

get(String) - Static method in enum pt.ist.phylolib.cli.Option

Gets the option corresponding to the given name or alias.

get(String, Data) - Static method in class pt.ist.phylolib.data.File

Gets a file corresponding to the given file option and data type.

get(Options) - Method in interface pt.ist.phylolib.command.ICommand.IGetter

Gets the input data from the given options.

getDataset(Options) - Method in class pt.ist.phylolib.data.Context

Returns and updates the dataset with the given options.

getMatrix(Options) - Method in class pt.ist.phylolib.data.Context

Returns and updates the matrix with the given options.

getTree(Options) - Method in class pt.ist.phylolib.data.Context

Reads and updates the tree with the given options.

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

Responsible for calculating a phylogenetic tree from a distance matrix using the Globally Closest Pairs algorithm.

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

GoeBURST - Class in pt.ist.phylolib.command.algorithm.goeburst

Responsible for calculating a phylogenetic tree from a distance matrix using the goeBURST algorithm.

GoeBURST() - Constructor for class pt.ist.phylolib.command.algorithm.goeburst.GoeBURST

GrapeTree - Class in pt.ist.phylolib.command.distance

Responsible for calculating a distance matrix from a phylogenetic dataset using the GrapeTree distance calculation.

GrapeTree() - Constructor for class pt.ist.phylolib.command.distance.GrapeTree

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