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API Documentation

This document contains the API (Application Programming Interface) documentation for Biskit. Documentation for the Python objects defined by the project is divided into separate pages for each package, module, and class. The API documentation also includes two pages containing information about the project as a whole: a trees page, and an index page.

Object Documentation

Each Package Documentation page contains:

A description of the package.
A list of the modules and sub-packages contained by the package.
A summary of the classes defined by the package.
A summary of the functions defined by the package.
A summary of the variables defined by the package.
A detailed description of each function defined by the package.
A detailed description of each variable defined by the package.

Each Module Documentation page contains:

A description of the module.
A summary of the classes defined by the module.
A summary of the functions defined by the module.
A summary of the variables defined by the module.
A detailed description of each function defined by the module.
A detailed description of each variable defined by the module.

Each Class Documentation page contains:

A class inheritance diagram.
A list of known subclasses.
A description of the class.
A summary of the methods defined by the class.
A summary of the instance variables defined by the class.
A summary of the class (static) variables defined by the class.
A detailed description of each method defined by the class.
A detailed description of each instance variable defined by the class.
A detailed description of each class (static) variable defined by the class.

Project Documentation

The Trees page contains the module and class hierarchies:

The module hierarchy lists every package and module, with modules grouped into packages. At the top level, and within each package, modules and sub-packages are listed alphabetically.
The class hierarchy lists every class, grouped by base class. If a class has more than one base class, then it will be listed under each base class. At the top level, and under each base class, classes are listed alphabetically.

The Index page contains indices of terms and identifiers:

The term index lists every term indexed by any object's documentation. For each term, the index provides links to each place where the term is indexed.
The identifier index lists the (short) name of every package, module, class, method, function, variable, and parameter. For each identifier, the index provides a short description, and a link to its documentation.

The Table of Contents

The table of contents occupies the two frames on the left side of the window. The upper-left frame displays the project contents, and the lower-left frame displays the module contents:

Project Contents ...	API Documentation Frame
Module Contents ...

The project contents frame contains a list of all packages and modules that are defined by the project. Clicking on an entry will display its contents in the module contents frame. Clicking on a special entry, labeled "Everything," will display the contents of the entire project.

The module contents frame contains a list of every submodule, class, type, exception, function, and variable defined by a module or package. Clicking on an entry will display its documentation in the API documentation frame. Clicking on the name of the module, at the top of the frame, will display the documentation for the module itself.

The "frames" and "no frames" buttons below the top navigation bar can be used to control whether the table of contents is displayed or not.

The Navigation Bar

A navigation bar is located at the top and bottom of every page. It indicates what type of page you are currently viewing, and allows you to go to related pages. The following table describes the labels on the navigation bar. Note that not some labels (such as [Parent]) are not displayed on all pages.

Label	Highlighted when...	Links to...
[Parent]	(never highlighted)	the parent of the current package
[Package]	viewing a package	the package containing the current object
[Module]	viewing a module	the module containing the current object
[Class]	viewing a class	the class containing the current object
[Trees]	viewing the trees page	the trees page
[Index]	viewing the index page	the index page
[Help]	viewing the help page	the help page

The "show private" and "hide private" buttons below the top navigation bar can be used to control whether documentation for private objects is displayed. Private objects are usually defined as objects whose (short) names begin with a single underscore, but do not end with an underscore. For example, "_x", "__pprint", and "epydoc.epytext._tokenize" are private objects; but "re.sub", "__init__", and "type_" are not. However, if a module defines the "__all__" variable, then its contents are used to decide which objects are private.

A timestamp below the bottom navigation bar indicates when each page was last updated.