Index

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M

main(String[]) - Static method in class pt.ist.phylolib.Main

Main - Class in pt.ist.phylolib

Main() - Constructor for class pt.ist.phylolib.Main

matches(String) - Method in enum pt.ist.phylolib.cli.Format

Checks whether or not a String matches this format.

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

Represents a distance matrix as a square or triangle depending on its symmetry and the ids of the profiles.

Matrix(boolean, String[], Double[][]) - Constructor for class pt.ist.phylolib.data.matrix.Matrix

Creates an eager distance matrix corresponding to the given symmetry, ids and phylogenetic distances.

Matrix(boolean, String[], Matrix.IDistance) - Constructor for class pt.ist.phylolib.data.matrix.Matrix

Create a lazy distance matrix corresponding to the given symmetry, ids and distance provider.

MATRIX - pt.ist.phylolib.cli.Data

MATRIX - pt.ist.phylolib.cli.Option

Matrix.ICorrection - Interface in pt.ist.phylolib.data.matrix

Represents a correction formula for a phylogenetic distance.

Matrix.IDistance - Interface in pt.ist.phylolib.data.matrix

Represents a phylogenetic distance provider between two profiles.

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

Responsible for parsing distance matrices from and to Strings.

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

MissingInputException - Exception in pt.ist.phylolib.exception

Represents an error derived from the definition of no input for a command in the command line arguments.

MissingInputException(String) - Constructor for exception pt.ist.phylolib.exception.MissingInputException

MissingTypeException - Exception in pt.ist.phylolib.exception

Represents an error derived from the definition of no type for a command in the command line arguments.

MissingTypeException(String) - Constructor for exception pt.ist.phylolib.exception.MissingTypeException

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

Responsible for parsing phylogenetic datasets from Strings in MLST or MLVA format.

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

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