Index

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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

InvalidCommandException - Exception 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 pt.ist.phylolib.exception.InvalidCommandException

InvalidTypeException - Exception 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 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 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.

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