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Doxygen
Generates documentation from source code. Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D. Doxygen can help users in three ways: (i) it can generate an on-line documentation browser (in HTML) and/or an off-line reference manual (in LaTeX) from a set of documented source files; (ii) users can configure Doxygen to extract the code structure from undocumented source files; (iii) users can also use doxygen for creating normal documentation.
Sphinx
Aims to create intelligent documentation. Sphinx was originally created for the Python documentation. This tool translates a set of reStructuredText source files into various output formats, automatically producing cross-references, indices etc. Sphinx can generate a nicely-organized arrangement of HTML files (in some other directory) for easy browsing and navigation from a directory containing a bunch of reST-formatted documents. From the same source, it can also generate a LaTeX file that users can compile into a PDF version of the documents, or a PDF file directly using rst2pdf.
Javadoc
Generates HTML pages of API (Application Programming Interface) documentation from Java source files. The Javadoc tool parses the declarations and documentation comments in a set of Java source files and produces a corresponding set of HTML pages describing (by default) the public and protected classes, nested classes (but not anonymous inner classes), interfaces, constructors, methods, and fields. The users can use it to generate the API documentation or the implementation documentation for a set of source files. The Javadoc tool can be applied to entire packages, individual source files, or both.
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