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

P

Parameters - Class in pt.ist.phylolib.cli

Represents the parameters of a command as a type and a set of options.

Parameters(Constructor<?>, Options) - Constructor for class pt.ist.phylolib.cli.Parameters

Creates the parameters of a command corresponding to a given type of command and respective options.

parse(String[]) - Static method in class pt.ist.phylolib.cli.Arguments

Parses the given command line arguments into an Arguments object.

parse(Iterator<String>) - Method in class pt.ist.phylolib.data.dataset.DatasetParser

Parses one profile from the given Strings.

parse(Iterator<String>) - Method in class pt.ist.phylolib.data.dataset.FASTA

parse(Iterator<String>) - Method in class pt.ist.phylolib.data.dataset.ML

parse(Iterator<String>) - Method in class pt.ist.phylolib.data.dataset.SNP

parse(Stream<String>) - Method in class pt.ist.phylolib.data.dataset.DatasetParser

parse(Stream<String>) - Method in interface pt.ist.phylolib.data.IReader

Parses the input data into an object.

parse(Stream<String>) - Method in class pt.ist.phylolib.data.matrix.SymmetryParser

parse(Stream<String>) - Method in class pt.ist.phylolib.data.tree.Newick

parse(Stream<String>) - Method in class pt.ist.phylolib.data.tree.Nexus

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

parse(Tree) - Method in class pt.ist.phylolib.data.tree.Newick

parse(Tree) - Method in class pt.ist.phylolib.data.tree.Nexus

parse(T) - Method in interface pt.ist.phylolib.data.IWriter

Parses the output data into a String.

path() - Method in class pt.ist.phylolib.data.File

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

process(Matrix) - Method in class pt.ist.phylolib.command.algorithm.edmonds.Edmonds

process(Matrix) - Method in class pt.ist.phylolib.command.algorithm.gcp.GloballyClosestPairs

process(Matrix) - Method in class pt.ist.phylolib.command.algorithm.goeburst.GoeBURST

process(Matrix) - Method in class pt.ist.phylolib.command.algorithm.nj.NeighbourJoining

process(Matrix) - Method in class pt.ist.phylolib.command.correction.Correction

process(Tree) - Method in class pt.ist.phylolib.command.optimization.Optimization

process(T) - Method in interface pt.ist.phylolib.command.ICommand

Processes this command's input data into an output data.

processor() - Method in class pt.ist.phylolib.data.File

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

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

Represents a profile as an id and a set of loci.

Profile(String, String) - Constructor for class pt.ist.phylolib.data.dataset.Profile

Creates a profile corresponding to the given id and loci represented by characters.

Profile(String, Stream<String>) - Constructor for class pt.ist.phylolib.data.dataset.Profile

Creates a profile corresponding to the given id and loci represented by ids.

pt.ist.phylolib - package pt.ist.phylolib

pt.ist.phylolib.cli - package pt.ist.phylolib.cli

pt.ist.phylolib.command - package pt.ist.phylolib.command

pt.ist.phylolib.command.algorithm - package pt.ist.phylolib.command.algorithm

pt.ist.phylolib.command.algorithm.edmonds - package pt.ist.phylolib.command.algorithm.edmonds

pt.ist.phylolib.command.algorithm.gcp - package pt.ist.phylolib.command.algorithm.gcp

pt.ist.phylolib.command.algorithm.goeburst - package pt.ist.phylolib.command.algorithm.goeburst

pt.ist.phylolib.command.algorithm.nj - package pt.ist.phylolib.command.algorithm.nj

pt.ist.phylolib.command.correction - package pt.ist.phylolib.command.correction

pt.ist.phylolib.command.distance - package pt.ist.phylolib.command.distance

pt.ist.phylolib.command.optimization - package pt.ist.phylolib.command.optimization

pt.ist.phylolib.data - package pt.ist.phylolib.data

pt.ist.phylolib.data.dataset - package pt.ist.phylolib.data.dataset

pt.ist.phylolib.data.matrix - package pt.ist.phylolib.data.matrix

pt.ist.phylolib.data.tree - package pt.ist.phylolib.data.tree

pt.ist.phylolib.exception - package pt.ist.phylolib.exception

pt.ist.phylolib.logging - package pt.ist.phylolib.logging

pt.ist.phylolib.reflection - package pt.ist.phylolib.reflection

put(String) - Method in class pt.ist.phylolib.cli.Options

Saves the association between the key-value option given as parameter.

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