Started on the TRM, therefore the separate files Db.txt and errorcodes.txt have

vanished. Fixed a large number of bugs.

Db.txt, errorcodes.txt:
- Renamed and converted to LaTeX.

bibliography.bib:
- Added references for the TRM.

TechnicalReference.tex:
- Documented a large part of the modules.

Mutalyzer.py:
- Added a __formatRange() function for better output of a range.
- Added a __checkIntronPosition() function that checks the validity of an 
  intronic notation.
- Fixed a bug that made a change in the first 9 nucleotides result in an
  unknown protein description.
- Modified the error- and warning messages for large strings (see Mutator.py)
  and ranges.
- Added a filter for indexing by protein isoform.

Mutator.py:
- Replaced the calculation of restriction sites using sets with code that does
  so using multisets. This allows the deletion of a site while an other site
  with the same name remains to be detected. Restriction sites are also
  reported in a more compact way.
- Extracted the part of the visualisation where large strings are represented
  by their pre- and suffix and a number of omitted nucleotides. This is now
  available as a function visualiseLargeString().

Parser.py:
- Separated the visualisation of a parse error from the error message. The 
  visualisation is now put in the output object as "parseError".

Output.py:
- Added documentation.

GBparser.py:
- Moved the reverse-complement logic for the __findMismatch() function to the
  function itself.
- Added an extra check for retrieving slicing information.
- Added a filter for poorly annotated exons.
- Added documentation.

Retriever.py:
- Added file type information (for lrg and gb files).
- Added sanity checks for the snpConvert() function.
- Added documentation.

GenRecord.py:
- Added a new type "construction" to the linking methods, meaning that the
  mRNA is generated from the CDS.

Web.py:
- Added an email variable for output to the website.

index.py:
- Added error information, to hide parts of the output.
- Added file type information (see Retriever.py) to make download links more
  sensible.
- Modified the syntax checker to work with the new parser output (see
  Parser.py).
- Fixed a bug (selecting the human build) in the position converter.
- Renamed download() to webservices().
- Renamed ConversionChecker to PositionConverter.

disclaimer.html:
- Added.

check.html:
- Modified the template to work with the new restriction site format and the
  new parse error format.
- Made lots of things conditional.

skel.html:
- Added.

snp.html:
- Added an example.

menu.html:
- Modified the layout, added some links, etc.

Other templates:
- Mainly edited the layout and indentation.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@75 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1