Package com.compomics.util.general

The classes in this package focus mainly on very general, top-level tasks that are used throughout the other packages in the util section.

See: Description

Class Summary

Class	Description
CommandLineParser	This class provides a generic interface for the parsing of command-line arguments, options and flags.
DefaultOutputLoggerImplementation	This class implements a default logger (for debugging purposes).
ExceptionHandler	Handles exception for a given application.
FileLoggerImplementation	This class implements the Logger interface for logging to a file.
IsotopicDistribution	This class calculates the isotopic distribution based on a molecular formula.
IsotopicDistributionSpectrum	This class is an implementation of the SpectrumFile specific for the isotopic distribution Created by IntelliJ IDEA.
IsotopicElement	This class represents the isotopically different element with the occurrence and the dalton difference between this and the natural variant.
MassCalc	This class takes care of mass calculation, based on a sequence in IUPAC format.
Translate	This class allows the user to translate a DNA sequence into 6 reading frames.

Exception Summary

Exception	Description
UnknownElementMassException	This class implements an Exception, thrown when a MassCalc instance is confronted with an element symbol it cannot retrieve in its element lists.

Package com.compomics.util.general Description

The classes in this package focus mainly on very general, top-level tasks that are used throughout the other packages in the util section.