Implemented better visualisation of changes in the protein. Added IVS and EX

notation. Implemented the detection of the addition or removal of restriction 
sites. Added additional information about the transcript under scrutiny (if
any), like the g. and c. positions of the exons, as well as the CDS start
and stop.

install.sh:
- Added a rewrite rule to link to the bug tracker.

Db.txt:
- Updated the definition of the GBInfo table.

errorcodes.txt:
- Added a new error (EPOS).

templates/base/images:
- Made new images for the template (temporary).

style.css:
- Added a new class to make a form button look like a clickable link (used in
  check.html).
- Added a new <td> class for right aligned text.

check.html:
- Made a lot of output conditional, depending on what Mutalyzer returns.
- Made the submit forms conditional, depending on the method of retrieval:
  - GET ->  No forms.
  - POST -> Full output.
- Added exon and CDS information.
- Added restriction site information, coupled to the `raw variants'.
- Added a download link for the reference sequence.
- Made the affected transcripts clickable (post to Mutalyzer).
- Added highlighting of changed amino acids for the protein changes.

gbupload.html:
- Added a conditional output section for uploaded sequences.

menu.html:
- Changed the logos.
- Added a link to the bug tracker.

index.html:
- Cleaned up the layout (indenting).
- Added link to Gen2Phen.

Mutator.py:
- Implemented the detection of the addition or removal of restriction sites.
  - Of each raw variant and its flanking sequences, two sets of restriction
    sites is constructed. One for the original subsequence and one for the
    mutated subsequence.
  - Additions and deletions can be detected by using the minus operator for
    sets.
- Changed the `visualisation' output list from a bare list to a list of 
  triples.
- Added verbose output to all raw variants.

Parser.py:
- Added productions for the EX and IVS position notations.

Output.py:
- Added a function that returns the data at the index in a list. Neither the
  list, nor the index need to be present, in which case None will be returned.
  This is convenient in index.py.

GBparser.py:
- Added a version variable to the record class (not used yet).
- Fixed a bug in matching transcripts and CDS by using a locus tag.

Retriever.py:
- Added return values for downloadrecord() and uploadrecord(), so they can be
  used in index.py.

GenRecord.py:
- Added translate and transcribe variables to the Locus class, to be used to
  skip translation of non coding transcripts and to skip the processing of 
  incomplete transcripts as a whole.

Web.py:
- Revived the old tal parser to return a more basic html page (used when GET
  instead of POST is used in index.py). Mainly for LOVD.

Scheduler.py:
- Testing.

Crossmap.py:
- Updated comment.
- Added:
  - getSpliceSite(), get the g. position of a splice site.
  - numberOfIntrons(), get the number of introns in a transcript.
  - numberOfExons(), get the number of exons in a transcript.

index.py:
- check():
  - Removed checks by using the getIndexedOutput() function.
  - Added a call to the `old' tal parser in case of a GET request.
  - Added more output (exon/CDS info, restriction sites, ...).
- upload():
  - Implemented calls to the uploadrecord() and downloadrecord() functions of
    the Retriever module.

Mutalyzer.py:
- Implemented a new protein visualisation function that highlights the changes.
- Used __toProtDescr() (and therefore the findInFrameDescription() and 
  findFrameShift() functions) to return the extent of the change, as well as a
  description of it. The extent is coded as a triple: (from, original end,
  variant end). This is used for the new visualisation.
- Added a check for an inversion of length 1 (actually a substitution).
- Added translation from EX and IVS positions (and ranges) to standard HGVS 
  positions.
- Added a check for out of boundary positions (outside the reference sequence).
- Added exon and CDS information to the output.
- Made the translation of a CDS depend on the translate member variable of the
  Locus class.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@66 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1