bpp-core3 Documentation

This library contains Bio++ core interfaces, classes and functions. It provides a general interface called bpp::Clonable, which allows dynamic copy of objects. Wrapper classes for numbers, strings and vectors that implement this interface are provided, and called respectively bpp::Number, bpp::BppString and bpp::BppVector.

The bpp::Exception class is the most general exception class used in Bio++, and provides only a single text information. Several more specialized exception classes are also provided, like

• bpp::IOException for input/output errors, usually when reading from or writing to files,
• bpp::NullPointerException when a NULL pointer is unexpectedly provided,
• bpp::BadNumberException and bpp::BadIntegerException, dealing with number problems (bounds, format, etc),
• and more...

This library also includes several submodules:

• The Text module contains: functions to deal with character strings (bpp::StringTokenizer and the bpp::TextTools static class), like pattern matching, concatenation, number conversion, etc.
• The Graphics module provides support for graphical output. This includes the general bpp::GraphicDevice interface, with currently three implementations for XFig (bpp::XFigGraphicDevice), SVG (bpp::SVGGraphicDevice) and PGF (bpp::PGFGraphicDevice) formats. Classes to deal with colors and fonts were created (see bpp::RGBColor, bpp::ColorSet, bpp::ColorTools and bpp::Font).
• The App module contains classes and tools that provide powerful methods to parse command-line options and more.
• The Numeric module is quite large and provides interfaces, classes and functions for numerical calculus. The tools included are general enough to be useful beyond biology. The originality of this module, unless many existing libraries, is to be fully object-oriented. Available methods include:
  • Vector operations, based on the stl::vector class, see bpp::VectorTools,
  • Matrix data and operations, see the bpp::Matrix interface and bpp::MatrixTools class,
  • Functions are implemented using several general classes:
    • the bpp::Function interface and its derivatives,
    • the bpp::Parameter, bpp::Constraint and bpp::ParameterList classes, and the bpp::Parametrizable interface provide a very general way to deal with parameters
    • Function operations, see the bpp::Optimizer interface, and the bpp::AbstractNumericalDerivative class for numerical differenciation,
    • Discrete probability distributions are implemented via the bpp::DiscreteDistribution interface
    • Several random numbers generators are available through the bpp::RandomNumberFactory interface, and the bpp::RandomTools static class provides useful methods to deal with random numbers.