Rewrote the GBparser module to cope with multiple linking methods (to link

mRNA and CDS fields). Added a SNP converter. Implemented a first check for
variants that hit splice sites. Added a chromosomal position for NC slices.
Added a check for the use of intronic positions in a transcript reference 
sequence.

mutalyzer.conf:
- Added variables for splice site mutation detection.

Mutator.py:
- Merged the restriction sites (added, deleted) in one object.

Output.py:
- Changed the return type of getIndexedOutput() and getOutput() from None to
  an empty list for convenience.

Config.py:
- Added variables for splice site mutation detection.

GBparser.py:
- Completely rewrote this module.
  - Will now collect all CDS, mRNA and exon information.
  - Tries to match a CDS and mRNA based upon the range.
    - When this succeeds, try to match on protein, locus tag or product name.
    - If all fails and there is only one option left, link it.
  - Will remove genes that are not fully annotated (half outside the record
    for example).

Retriever.py:
- Added a snpConvert() function.
- Added a check for uploaded records or slices that have no sequence in them
  (a complete contig for example).

GenRecord.py:
- Added variables to cope with chromosomal coordinates.
- Added a toChromPos() function to convert a g. notation to a g. on a
  chromosome.
- Added a addToChromDescription() function to generate a chromosomal
  description of a variant.
- Modified some warnings concerning missing mRNA or missing CDS.
- Added a checkIntron() function that gives a warning when a variant hits a
  splice site.

Web.py:
- Added a nomenclature version variable.
- Added a urlEncode() function to generate valid links.

File.py:
- Made the getMimeType() function public.

Mutalyzer.py:
- Added a __intronicPosition() function that checks whether the user used an
  intronic position.
- Added checks for illegal use of intronic positions.
- Fixed a bug in the __toProtDescr() function.
- Added more checks for the translation and transcription of transcripts.
- Added a better CDS start site mutation detection.
- Added a chromosomal description if available.
- Added more information to the legend (product and linking method).
- Merged the restriction sites (added, deleted) in one object.

handler.py:
- Added guessing of mime types for downloadable files (it used to default to
  text/plain).

index.py:
- Added a snp() function to interface with the snp() function of the Retriever.
- Added a checkForward() function to accommodate for HTTP GET links.
- Removed the `version' variable from all functions, it is now moved to the
  menu.

check.html:
- Modified to cope with the new functionality.

gbupload.html:
- Restructured the layout.

snp.html:
- New page for the SNP converter.

menu.html:
- Modified to cope with the new functionality.

style.css:
- Modified to make some better tables and helper boxes.

index.html:
- Completely rewritten it.

parse.html:
- Restructured the layout to make it uniform with the name checker.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@73 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1