EMBOSS: C2 Software Documentation

The source files have documentation in a format derived from JavaDoc with extensions developed at the Sanger Centre for other projects.

Issues:

1. There is a perl parser for the documentation comments in the source files. This checks the parameters and return type against the function definition and also reports errors if descriptions are missing. The log file fromthis parser is checked regularly.
2. The output from the parser is an HTML page with the documentation for all functions in one source file.
3. The same parser reads the include files and notes the documentation on the data types.
4. There is still a need to check the HTML output and to find ways to add new files automatically to the index pages.
5. The parser also writes an "EMBL" style flat file which is indexed by SRS as EFUNC and EDATA on the Sanger Centre SRS 6.0 server.
6. The SRS indexed source code in EFUNC is the easiest way to see the function documentation and sources and to navigate to other functions. See, for example, ajStrAss
7. The SRS EDATA index takes you from the data objects to the most important functions that use them.
8. The parser needs to be cleaned up and made available in the "scripts" directory.