Index (PhyloLib 1.0.0 API)

A B C D E F G H I J K L M N O P R S T U V W _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

add(Edge) - Method in class pt.ist.phylolib.data.tree.Tree: Adds a given edge to this tree.
Algorithm - Class in pt.ist.phylolib.command.algorithm: Responsible for calculating a phylogenetic tree from a distance matrix.
Algorithm() - Constructor for class pt.ist.phylolib.command.algorithm.Algorithm
ALGORITHM - Enum constant in enum class pt.ist.phylolib.cli.Command
ArgumentException - Exception Class in pt.ist.phylolib.exception: Wraps all exceptions derived from command line arguments related issues.
ArgumentException(String) - Constructor for exception class pt.ist.phylolib.exception.ArgumentException
Arguments - Class in pt.ist.phylolib.cli: Represents the parsed arguments of the program as commands and respective parameters.
Arguments() - Constructor for class pt.ist.phylolib.cli.Arguments
Asymmetric - Class in pt.ist.phylolib.data.matrix: Responsible for parsing distance matrices from and to Strings in an asymmetric format.
Asymmetric() - Constructor for class pt.ist.phylolib.data.matrix.Asymmetric
AUTO_HEAP_DENSE_MAX_BYTES - Static variable in class pt.ist.phylolib.data.matrix.MatrixStoragePlanner: A conservative automatic heap-storage budget of 320 MiB leaves process headroom for array headers, parser buffers, and other application data.

B

Bounded(double) - Constructor for record class pt.ist.phylolib.data.matrix.DistanceScope.Bounded: Creates an instance of a Bounded record class.

C

choose(int, boolean, DistanceScope, boolean) - Method in class pt.ist.phylolib.data.matrix.MatrixStoragePlanner
CL - Class in pt.ist.phylolib.command.algorithm.gcp: Responsible for calculating a phylogenetic tree from a distance matrix using the Complete-Linkage algorithm.
CL() - Constructor for class pt.ist.phylolib.command.algorithm.gcp.CL
Command - Enum Class in pt.ist.phylolib.cli: Enumerates the available commands with their respective repeatability and class.
COMMAND - Static variable in interface pt.ist.phylolib.command.ICommand
configureRequiredDistanceScope(Options) - Method in class pt.ist.phylolib.command.algorithm.Algorithm: Configures a scope that depends on user input before the matrix is loaded.
configureRequiredDistanceScope(Options) - Method in class pt.ist.phylolib.command.algorithm.goeburst.GoeBURST
Context - Class in pt.ist.phylolib.data: Maintains the shared data context for the program, storing references to the current Dataset, Matrix, and Tree.
Context() - Constructor for class pt.ist.phylolib.data.Context
correct(double) - Method in class pt.ist.phylolib.command.correction.Correction: Corrects the given phylogenetic distance.
correct(double) - Method in class pt.ist.phylolib.command.correction.JukesCantor
correct(Matrix.ICorrection) - Method in class pt.ist.phylolib.data.matrix.Matrix: Gets a distance matrix corrected according to the given correction formula.
Correction - Class in pt.ist.phylolib.command.correction: Responsible for correcting a distance matrix into another.
Correction() - Constructor for class pt.ist.phylolib.command.correction.Correction
CORRECTION - Enum constant in enum class pt.ist.phylolib.cli.Command
covers(DistanceScope) - Method in interface pt.ist.phylolib.data.matrix.DistanceScope: Returns whether this available scope contains every distance required by requiredScope.

D

Data - Enum Class in pt.ist.phylolib.cli: Enumerates the available data types with their respective option and class.
Dataset - Class in pt.ist.phylolib.data.dataset: Represents a phylogenetic dataset as profiles.
Dataset(List<Profile>) - Constructor for class pt.ist.phylolib.data.dataset.Dataset: Creates a phylogenetic dataset corresponding to the given profiles.
DATASET - Enum constant in enum class pt.ist.phylolib.cli.Data
DATASET - Enum constant in enum class pt.ist.phylolib.cli.Option
DatasetParser - Class in pt.ist.phylolib.data.dataset: Responsible for parsing phylogenetic datasets from Strings.
DatasetParser() - Constructor for class pt.ist.phylolib.data.dataset.DatasetParser
DENSE - Enum constant in enum class pt.ist.phylolib.data.matrix.MatrixStoragePlanner.Storage
dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.CL
dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.GloballyClosestPairs: Calculates the dissimilarity between a given previously existing node and a given node created by joining two existing nodes.
dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.SL
dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.UPGMA
dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.UPGMC
dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.WPGMA
dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.WPGMC
distance() - Method in record class pt.ist.phylolib.data.tree.Edge: Returns the value of the distance record component.
distance(int, int) - Method in class pt.ist.phylolib.data.matrix.Matrix
distance(int, int) - Method in class pt.ist.phylolib.data.matrix.ThresholdSparseMatrix
distance(Profile, Profile) - Method in class pt.ist.phylolib.command.distance.Distance: Calculates the phylogenetic distance between the two given profiles.
distance(Profile, Profile) - Method in class pt.ist.phylolib.command.distance.GrapeTree
distance(Profile, Profile) - Method in class pt.ist.phylolib.command.distance.Hamming
distance(Profile, Profile) - Method in class pt.ist.phylolib.command.distance.Kimura
Distance - Class in pt.ist.phylolib.command.distance: Responsible for calculating a distance matrix from a phylogenetic dataset.
Distance() - Constructor for class pt.ist.phylolib.command.distance.Distance
DISTANCE - Enum constant in enum class pt.ist.phylolib.cli.Command
DISTANCE - Enum constant in enum class pt.ist.phylolib.cli.Format
distanceScope() - Method in class pt.ist.phylolib.data.matrix.Matrix: Describes which pairwise distances this matrix retains.
DistanceScope - Interface in pt.ist.phylolib.data.matrix: The pairwise distance range required by an algorithm or retained by a matrix.
DistanceScope.Bounded - Record Class in pt.ist.phylolib.data.matrix: Distances through this finite, non-negative bound are available.
DistanceScope.Complete - Enum Class in pt.ist.phylolib.data.matrix: Every pairwise distance is available.

E

Edge - Record Class in pt.ist.phylolib.data.tree: Represents an edge as from and to nodes with a distance between them.
Edge(int, int, double) - Constructor for record class pt.ist.phylolib.data.tree.Edge: Creates an instance of a Edge record class.
edges() - Method in class pt.ist.phylolib.data.tree.Tree
Edmonds - Class in pt.ist.phylolib.command.algorithm.edmonds: Responsible for calculating a phylogenetic tree from a distance matrix using the Edmonds algorithm.
Edmonds() - Constructor for class pt.ist.phylolib.command.algorithm.edmonds.Edmonds
elements - Variable in class pt.ist.phylolib.command.algorithm.nj.NeighbourJoining.Cluster
equals(Object) - Method in record class pt.ist.phylolib.data.matrix.DistanceScope.Bounded: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class pt.ist.phylolib.data.tree.Edge: Indicates whether some other object is "equal to" this one.
error(String, Object...) - Static method in class pt.ist.phylolib.logging.Log: Logs the given error message.
estimateDenseBytes(int, boolean) - Static method in class pt.ist.phylolib.data.matrix.MatrixStoragePlanner: Estimates raw primitive-double storage.
exception(Exception) - Static method in class pt.ist.phylolib.logging.Log: Logs the given exception.

F

FAILED - Static variable in interface pt.ist.phylolib.data.IReader
FAILED - Static variable in interface pt.ist.phylolib.data.IWriter
FASTA - Class in pt.ist.phylolib.data.dataset: Responsible for parsing phylogenetic datasets from Strings in FASTA format.
FASTA() - Constructor for class pt.ist.phylolib.data.dataset.FASTA
File - Class in pt.ist.phylolib.data: Represents a file as a data type processor and a path.
File(Object, Path) - Constructor for class pt.ist.phylolib.data.File: Creates a file corresponding to the given data type processor and path.
FILE - Enum constant in enum class pt.ist.phylolib.cli.Format
FINISHED - Static variable in interface pt.ist.phylolib.command.ICommand
FINISHED - Static variable in interface pt.ist.phylolib.data.IReader
FINISHED - Static variable in interface pt.ist.phylolib.data.IWriter
FLAG - Enum constant in enum class pt.ist.phylolib.cli.Format
FORCE_DENSE - Enum constant in enum class pt.ist.phylolib.cli.Option
format() - Method in enum class pt.ist.phylolib.cli.Option
Format - Enum Class in pt.ist.phylolib.cli: Enumerates the available formats with their respective regex.
from() - Method in record class pt.ist.phylolib.data.tree.Edge: Returns the value of the from record component.

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 class pt.ist.phylolib.cli.Command: Gets the command corresponding to the given name.
get(String) - Static method in enum class 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(Option) - Method in class pt.ist.phylolib.cli.Options: Returns the value for the given Option without removing it.
get(Options) - Method in interface pt.ist.phylolib.command.ICommand.IGetter: Gets the input data from the given options.
getCurrentCommand() - Method in class pt.ist.phylolib.data.Context: Gets the current command being executed.
getDataset(Options) - Method in class pt.ist.phylolib.data.Context: Returns the dataset, updating it if a dataset option is provided.
getMatrix(Options) - Method in class pt.ist.phylolib.data.Context: Returns the matrix, updating it if a matrix option is provided.
getTree(Options) - Method in class pt.ist.phylolib.data.Context: Returns the tree, updating it if a tree option is provided.
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
GoeBURST() - Constructor for class pt.ist.phylolib.command.algorithm.goeburst.GoeBURST
GoeBURSTFullMST - Class in pt.ist.phylolib.command.algorithm.goeburst: Builds a complete goeBURST Full MST from an LV/Hamming-style distance matrix.
GoeBURSTFullMST() - Constructor for class pt.ist.phylolib.command.algorithm.goeburst.GoeBURSTFullMST
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

H

Hamming - Class in pt.ist.phylolib.command.distance: Responsible for calculating a distance matrix from a phylogenetic dataset using the Hamming distance calculation.
Hamming() - Constructor for class pt.ist.phylolib.command.distance.Hamming
hashCode() - Method in record class pt.ist.phylolib.data.matrix.DistanceScope.Bounded: Returns a hash code value for this object.
hashCode() - Method in record class pt.ist.phylolib.data.tree.Edge: Returns a hash code value for this object.

I

ICommand<T,R> - Interface in pt.ist.phylolib.command: Responsible for the common operations of a command.
ICommand.IGetter<T> - Interface in pt.ist.phylolib.command: Represents the input data getter for a command.
id() - Method in class pt.ist.phylolib.data.dataset.Profile
ids() - Method in class pt.ist.phylolib.data.dataset.Dataset
ids() - Method in class pt.ist.phylolib.data.matrix.Matrix
ids() - Method in class pt.ist.phylolib.data.tree.Tree
info(String, Object...) - Static method in class pt.ist.phylolib.logging.Log: Logs the given info message.
init(Iterator<String>) - Method in class pt.ist.phylolib.data.dataset.DatasetParser: Initializes the state of the processor by parsing the first lines of the dataset.
init(Iterator<String>) - Method in class pt.ist.phylolib.data.dataset.FASTA
init(Context, Options) - Method in class pt.ist.phylolib.command.algorithm.goeburst.GoeBURST
init(Context, Options) - Method in interface pt.ist.phylolib.command.ICommand: Initializes this command with the given context and options.
init(Context, Options) - Method in class pt.ist.phylolib.command.optimization.Optimization
INSTANCE - Enum constant in enum class pt.ist.phylolib.data.matrix.DistanceScope.Complete
InvalidCommandException - Exception Class in pt.ist.phylolib.exception: Represents an error derived from the definition of an invalid command in the command line arguments.
InvalidCommandException(String) - Constructor for exception class pt.ist.phylolib.exception.InvalidCommandException
InvalidTypeException - Exception Class in pt.ist.phylolib.exception: Represents an error derived from the definition of an invalid command type in the command line arguments.
InvalidTypeException(String, String) - Constructor for exception class pt.ist.phylolib.exception.InvalidTypeException
IReader<T> - Interface in pt.ist.phylolib.data: Responsible for the reading of data from files.
isRepeatable() - Method in enum class pt.ist.phylolib.cli.Command: Checks whether or not this Command is repeatable.
IWriter<T> - Interface in pt.ist.phylolib.data: Responsible for the writing of data into files.

J

join(int, Matrix, Tree, Edge) - Method in class pt.ist.phylolib.command.optimization.LBR
join(int, Matrix, Tree, Edge) - Method in class pt.ist.phylolib.command.optimization.Optimization: Gets an edge that connects the two clusters of a given tree.
JukesCantor - Class in pt.ist.phylolib.command.correction: Responsible for correcting a distance matrix into another using the Jukes-Cantor correction formula.
JukesCantor() - Constructor for class pt.ist.phylolib.command.correction.JukesCantor

K

keys() - Method in class pt.ist.phylolib.cli.Options: Returns a Set object with the keys for these options.
Kimura - Class in pt.ist.phylolib.command.distance: Responsible for calculating a distance matrix from a phylogenetic dataset using the Kimura distance calculation.
Kimura() - Constructor for class pt.ist.phylolib.command.distance.Kimura

L

lambda(NeighbourJoining.Cluster, NeighbourJoining.Cluster) - Method in class pt.ist.phylolib.command.algorithm.nj.NeighbourJoining: Gets the proportion of a given cluster according to another.
lambda(NeighbourJoining.Cluster, NeighbourJoining.Cluster) - Method in class pt.ist.phylolib.command.algorithm.nj.SaitouNei
lambda(NeighbourJoining.Cluster, NeighbourJoining.Cluster) - Method in class pt.ist.phylolib.command.algorithm.nj.StudierKepler
lambda(NeighbourJoining.Cluster, NeighbourJoining.Cluster) - Method in class pt.ist.phylolib.command.algorithm.nj.UNJ
LBR - Class in pt.ist.phylolib.command.optimization: Responsible for optimizing a phylogenetic tree into another using the Local Branch Recrafting algorithm.
LBR() - Constructor for class pt.ist.phylolib.command.optimization.LBR
length(double) - Method in class pt.ist.phylolib.command.algorithm.nj.NeighbourJoining: Gets the length corresponding to the given distance.
length(double) - Method in class pt.ist.phylolib.command.algorithm.nj.SaitouNei
length(double) - Method in class pt.ist.phylolib.command.algorithm.nj.StudierKepler
length(double) - Method in class pt.ist.phylolib.command.algorithm.nj.UNJ
locus(int) - Method in class pt.ist.phylolib.data.dataset.Profile
log - Static variable in interface pt.ist.phylolib.data.IReader
Log - Class in pt.ist.phylolib.logging: Responsible for the logging of information in the program.
Log() - Constructor for class pt.ist.phylolib.logging.Log
LVS - Enum constant in enum class pt.ist.phylolib.cli.Option

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 class pt.ist.phylolib.cli.Format: Checks whether a String matches this format.
Matrix - Class in pt.ist.phylolib.data.matrix
Matrix(boolean, String[], double[][]) - Constructor for class pt.ist.phylolib.data.matrix.Matrix
Matrix(boolean, String[], double[][], DistanceScope) - Constructor for class pt.ist.phylolib.data.matrix.Matrix
Matrix(boolean, String[], Matrix.IDistance) - Constructor for class pt.ist.phylolib.data.matrix.Matrix
Matrix(boolean, String[], Matrix.IDistance, DistanceScope) - Constructor for class pt.ist.phylolib.data.matrix.Matrix
MATRIX - Enum constant in enum class pt.ist.phylolib.cli.Data
MATRIX - Enum constant in enum class 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
MatrixStoragePlanner - Class in pt.ist.phylolib.data.matrix: Selects matrix storage from the available distance scope and a deterministic estimate of complete heap-backed storage.
MatrixStoragePlanner() - Constructor for class pt.ist.phylolib.data.matrix.MatrixStoragePlanner
MatrixStoragePlanner(long) - Constructor for class pt.ist.phylolib.data.matrix.MatrixStoragePlanner: Exposed to make automatic-storage policy testable without allocations.
MatrixStoragePlanner.Storage - Enum Class in pt.ist.phylolib.data.matrix
maxDistance() - Method in record class pt.ist.phylolib.data.matrix.DistanceScope.Bounded: Returns the value of the maxDistance record component.
MissingInputException - Exception Class 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 class pt.ist.phylolib.exception.MissingInputException
MissingTypeException - Exception Class 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 class 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

N

NATURAL - Enum constant in enum class pt.ist.phylolib.cli.Format
NeighbourJoining - Class in pt.ist.phylolib.command.algorithm.nj: Responsible for calculating a phylogenetic tree from a distance matrix using the Neighbour Joining algorithm.
NeighbourJoining() - Constructor for class pt.ist.phylolib.command.algorithm.nj.NeighbourJoining
NeighbourJoining.Cluster - Class in pt.ist.phylolib.command.algorithm.nj: Represents a cluster as the amount of elements in it, the total length of the cluster and the distances to other clusters.
Newick - Class in pt.ist.phylolib.data.tree: Responsible for parsing phylogenetic trees from and to Strings in Newick format.
Newick() - Constructor for class pt.ist.phylolib.data.tree.Newick
Nexus - Class in pt.ist.phylolib.data.tree: Responsible for parsing phylogenetic trees from and to Strings in Nexus format.
Nexus() - Constructor for class pt.ist.phylolib.data.tree.Nexus
NoCommandException - Exception Class in pt.ist.phylolib.exception: Represents an error derived from the definition of no command in the command line arguments.
NoCommandException() - Constructor for exception class pt.ist.phylolib.exception.NoCommandException

O

Optimization - Class in pt.ist.phylolib.command.optimization: Responsible for optimizing a phylogenetic tree into another.
Optimization() - Constructor for class pt.ist.phylolib.command.optimization.Optimization
OPTIMIZATION - Enum constant in enum class pt.ist.phylolib.cli.Command
option() - Method in enum class pt.ist.phylolib.cli.Data
Option - Enum Class in pt.ist.phylolib.cli: Enumerates the available options with their respective alias and format.
options() - Method in class pt.ist.phylolib.cli.Parameters
Options - Class in pt.ist.phylolib.cli: Represents the options of a command as keys and values.
Options() - Constructor for class pt.ist.phylolib.cli.Options
OUT - Enum constant in enum class pt.ist.phylolib.cli.Option

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>, Options) - Method in class pt.ist.phylolib.data.dataset.DatasetParser
parse(Stream<String>, Options) - Method in interface pt.ist.phylolib.data.IReader: Parses the input data into an object.
parse(Stream<String>, Options) - Method in class pt.ist.phylolib.data.matrix.SymmetryParser
parse(Stream<String>, Options) - Method in class pt.ist.phylolib.data.tree.Newick
parse(Stream<String>, Options) - Method in class pt.ist.phylolib.data.tree.Nexus
parse(Stream<String>, DistanceScope, boolean) - Method in class pt.ist.phylolib.data.matrix.MatrixParser: Parses with the scope and storage override supplied by matrix loading.
parse(Stream<String>, DistanceScope, boolean) - Method in class pt.ist.phylolib.data.matrix.SymmetryParser
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: Converts the data to a String (In-Memory).
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.Algorithm
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.
processImpl(Matrix) - Method in class pt.ist.phylolib.command.algorithm.Algorithm: Processes the matrix to create a phylogenetic tree.
processImpl(Matrix) - Method in class pt.ist.phylolib.command.algorithm.edmonds.Edmonds
processImpl(Matrix) - Method in class pt.ist.phylolib.command.algorithm.gcp.GloballyClosestPairs
processImpl(Matrix) - Method in class pt.ist.phylolib.command.algorithm.goeburst.GoeBURST
processImpl(Matrix) - Method in class pt.ist.phylolib.command.algorithm.goeburst.GoeBURSTFullMST
processImpl(Matrix) - Method in class pt.ist.phylolib.command.algorithm.nj.NeighbourJoining
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.
put(Option, String) - Method in class pt.ist.phylolib.cli.Options: Programmatically sets an option value (for internal use).

R

read(Options, T, Data) - Static method in interface pt.ist.phylolib.data.IReader: Reads data from an option of the given data type in the given options.
READ - Static variable in interface pt.ist.phylolib.data.IReader
readMatrix(Options, Matrix, DistanceScope, boolean) - Static method in interface pt.ist.phylolib.data.IReader: Reads a matrix using an explicit distance scope without overloading the generic reader API with matrix-only state.
reduce(Set<Edge>, Tree, Edge, Edge) - Method in class pt.ist.phylolib.command.optimization.LBR
reduce(Set<Edge>, Tree, Edge, Edge) - Method in class pt.ist.phylolib.command.optimization.Optimization: Reduces the given set of edges by removing the given edge and adds another given edge to the tree.
remove(Option) - Method in class pt.ist.phylolib.cli.Options: Returns the value and removes the association for the given Option.
remove(Edge) - Method in class pt.ist.phylolib.data.tree.Tree: Removes a given edge from this tree.
RepeatedCommandException - Exception Class in pt.ist.phylolib.exception: Represents an error derived from the definition of an unrepeatable command more than once in the command line arguments.
RepeatedCommandException(String) - Constructor for exception class pt.ist.phylolib.exception.RepeatedCommandException
requiredDistanceScope() - Method in class pt.ist.phylolib.command.algorithm.Algorithm: Declares the distance scope this algorithm needs.
requiredDistanceScope() - Method in class pt.ist.phylolib.command.algorithm.goeburst.GoeBURST
requiredDistanceScope() - Method in class pt.ist.phylolib.command.algorithm.goeburst.GoeBURSTFullMST
retainedThreshold() - Method in class pt.ist.phylolib.data.matrix.ThresholdSparseMatrix
rootAtMidpoint() - Method in class pt.ist.phylolib.data.tree.Tree: Roots this tree at the topological midpoint of the longest path between two labelled profiles.
run(Arguments, Context, Command, ICommand.IGetter<T>, BiConsumer<Options, R>) - Static method in interface pt.ist.phylolib.command.ICommand: Runs the specified command with that input getter and output setter for the given arguments and context.

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.
setCurrentCommand(ICommand<?, ?>) - Method in class pt.ist.phylolib.data.Context: Sets the current command being executed.
setMatrix(Options, Matrix) - Method in class pt.ist.phylolib.data.Context: Writes the given matrix using the provided options and updates the context.
setTree(Options, Tree) - Method in class pt.ist.phylolib.data.Context: Writes the given tree using the provided options and updates the context.
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
size() - Method in class pt.ist.phylolib.data.matrix.ThresholdSparseMatrix
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
storagePlanner() - Method in class pt.ist.phylolib.data.matrix.SymmetryParser: A protected seam keeps parser tests small while production uses the common large-matrix limit.
streamParse(Matrix, BufferedWriter) - Method in class pt.ist.phylolib.data.matrix.SymmetryParser
streamParse(Tree, BufferedWriter) - Method in class pt.ist.phylolib.data.tree.Newick
streamParse(Tree, BufferedWriter) - Method in class pt.ist.phylolib.data.tree.Nexus
streamParse(T, BufferedWriter) - Method in interface pt.ist.phylolib.data.IWriter: Writes the data directly to a buffered writer (Streaming).
StudierKepler - 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 Kepler.
StudierKepler() - Constructor for class pt.ist.phylolib.command.algorithm.nj.StudierKepler
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.Matrix: Indicates whether this matrix is represented as symmetric.
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

T

THRESHOLD_SPARSE - Enum constant in enum class pt.ist.phylolib.data.matrix.MatrixStoragePlanner.Storage
ThresholdSparseMatrix - Class in pt.ist.phylolib.data.matrix: A threshold-filtered distance matrix.
ThresholdSparseMatrix(boolean, String[], int[][], double[][], double) - Constructor for class pt.ist.phylolib.data.matrix.ThresholdSparseMatrix
TIMING - Static variable in interface pt.ist.phylolib.command.ICommand
to() - Method in record class pt.ist.phylolib.data.tree.Edge: Returns the value of the to record component.
toString() - Method in enum class pt.ist.phylolib.cli.Command
toString() - Method in enum class pt.ist.phylolib.cli.Data
toString() - Method in enum class pt.ist.phylolib.cli.Option
toString() - Method in record class pt.ist.phylolib.data.matrix.DistanceScope.Bounded: Returns a string representation of this record class.
toString() - Method in record class pt.ist.phylolib.data.tree.Edge: Returns a string representation of this record class.
Tree - Class in pt.ist.phylolib.data.tree: Represents a phylogenetic tree as a set of profiles identified by their ids and the edges that connect those profiles.
Tree(String[]) - Constructor for class pt.ist.phylolib.data.tree.Tree: Creates a phylogenetic tree corresponding to the given set of ids with no edges connecting them.
Tree(String[], List<Edge>) - Constructor for class pt.ist.phylolib.data.tree.Tree: Creates a phylogenetic tree corresponding to the given set of ids and edges.
TREE - Enum constant in enum class pt.ist.phylolib.cli.Data
TREE - Enum constant in enum class pt.ist.phylolib.cli.Option
TreeParser - Class in pt.ist.phylolib.data.tree: Responsible for parsing phylogenetic trees from and to Strings.
TreeParser() - Constructor for class pt.ist.phylolib.data.tree.TreeParser
type() - Method in class pt.ist.phylolib.cli.Parameters
type(String) - Method in enum class pt.ist.phylolib.cli.Command: Gets the constructor of the specified type for this command.
type(String) - Method in enum class pt.ist.phylolib.cli.Data: Gets the constructor of the specified processor type for this data type.
Types - Class in pt.ist.phylolib.reflection: Responsible for the use of reflection to search for types of a command or data.
Types() - Constructor for class pt.ist.phylolib.reflection.Types

U

UNJ - Class in pt.ist.phylolib.command.algorithm.nj: Responsible for calculating a phylogenetic tree from a distance matrix using the Unweighted Neighbour Joining algorithm.
UNJ() - Constructor for class pt.ist.phylolib.command.algorithm.nj.UNJ
UNUSED - Static variable in interface pt.ist.phylolib.command.ICommand
UPGMA - Class in pt.ist.phylolib.command.algorithm.gcp: Responsible for calculating a phylogenetic tree from a distance matrix using the Unweighted Pair Group Method with Arithmetic-mean algorithm.
UPGMA() - Constructor for class pt.ist.phylolib.command.algorithm.gcp.UPGMA
UPGMC - Class in pt.ist.phylolib.command.algorithm.gcp: Responsible for calculating a phylogenetic tree from a distance matrix using the Unweighted Pair Group Method with Centroid algorithm.
UPGMC() - Constructor for class pt.ist.phylolib.command.algorithm.gcp.UPGMC

V

valueOf(String) - Static method in enum class pt.ist.phylolib.cli.Command: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class pt.ist.phylolib.cli.Data: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class pt.ist.phylolib.cli.Format: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class pt.ist.phylolib.cli.Option: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class pt.ist.phylolib.data.matrix.DistanceScope.Complete: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class pt.ist.phylolib.data.matrix.MatrixStoragePlanner.Storage: Returns the enum constant of this class with the specified name.
values() - Static method in enum class pt.ist.phylolib.cli.Command: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class pt.ist.phylolib.cli.Data: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class pt.ist.phylolib.cli.Format: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class pt.ist.phylolib.cli.Option: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class pt.ist.phylolib.data.matrix.DistanceScope.Complete: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class pt.ist.phylolib.data.matrix.MatrixStoragePlanner.Storage: Returns an array containing the constants of this enum class, in the order they are declared.

W

warning(String, Object...) - Static method in class pt.ist.phylolib.logging.Log: Logs the given warning message.
weight(NeighbourJoining.Cluster) - Method in class pt.ist.phylolib.command.algorithm.nj.NeighbourJoining: Gets the weight of a given cluster.
weight(NeighbourJoining.Cluster) - Method in class pt.ist.phylolib.command.algorithm.nj.SaitouNei
weight(NeighbourJoining.Cluster) - Method in class pt.ist.phylolib.command.algorithm.nj.StudierKepler
weight(NeighbourJoining.Cluster) - Method in class pt.ist.phylolib.command.algorithm.nj.UNJ
WPGMA - Class in pt.ist.phylolib.command.algorithm.gcp: Responsible for calculating a phylogenetic tree from a distance matrix using the Weighted Pair Group Method with Arithmetic-mean algorithm.
WPGMA() - Constructor for class pt.ist.phylolib.command.algorithm.gcp.WPGMA
WPGMC - Class in pt.ist.phylolib.command.algorithm.gcp: Responsible for calculating a phylogenetic tree from a distance matrix using the Weighted Pair Group Method with Centroid algorithm.
WPGMC() - Constructor for class pt.ist.phylolib.command.algorithm.gcp.WPGMC
write(Options, T, Data) - Static method in interface pt.ist.phylolib.data.IWriter
WRITE - Static variable in interface pt.ist.phylolib.data.IWriter

_

_default() - Method in enum class pt.ist.phylolib.cli.Option

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