Package com.compomics.util.general

General, top-level tasks that are used throughout the other packages in the util section.
  • Class Summary 
    Class Description
    BoxedObject<K>
    Convenience class allowing the boxing of an object.
    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).
    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.