Beta-2 release.

Wrote documentation:
- Removed the bibliography database and replaced it with a (generated) bbl
  file.
- Wrote a number of new sections in the TRM.
- Modified the Makefile for the new bibliography method.

Mutalyzer.py:
- Added documentation.
- Reinstated the ``alternative protein'' (alternative start codon).
- Added the molType to the output object, this is needed in the check.html
  template.

Scheduler.py:
- Fixed a bug that made any position conversion batch job crash.

File.py:
- Fixed a bug that made every batch job with no errors in the input crash.

index.py:
- Added a variable genomicDNA to the arguments in the check() function.
- Fixed a bug in the syntaxCheck() function, that made the syntax checker
  crash.

check.html:
- Added a ``clear field'' button.
- Added different headers for genomic DNA and mRNA.
- Modified the ``alternative protein'' visualisation.

snp.html:
- Added a ``clear field'' button.

menu.html:
- Fixed a bug in the background image.
- Removed the link to HGVS_nomenclature_extension_proposal.pdf and made it an
  external link.
- Added a link to Mutalyzer 1.0.4.

menu.js:
- Added a clearForm() function that clears one element in a form.

converter.html:
- Added a ``clear field'' button.

parse.html:
- Added a ``clear field'' button.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@79 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1