handling for incomplete and poorly annotated GenBank files.

menu.html:
- Template for all pages. Includes a menu and such.

index.html:
- The main page.

base/:
- Pictures, javascript, stylesheet, etc.

interface.js:
- Temporary script for gbupload.html.

download.html:
- Adjusted to work with the menu.html template.

gbupload.html:
- Adjusted to work with the menu.html template.

check.html:
- Extended the template to use more variables to increase flexibility.

index.py:
- Removed the capturing of the Mutalyzer output in the check() function,
  replaced it with retrieval of data from the Output object. 
- Added a new index() function (see index.html).
- Implemented the upload() function (see gbupload.html), currently it can only
  retrieve genes and chromosome slices from the NCBI.

Web.py:
- Enabled the parsing of the menu.html template in the tal() function.

handler.py:
- Modified to work with the new tal() function of Web.py.

Output.py:
- getMessages() now returns a list of messages, instead of printing it to 
  standard output.

mail.txt:
- Template message for finished batch jobs.

Mutalyzer.py:
- __bprint() now puts the visualisation of a protein in the Output object, 
  instead of printing it to standard output.
- Made a new protein printing function that can highlight the changes, it is
  not used yet.
- Added a __cdsLen() function that is used to see if a variant leads to a
  frameshift or not.
- Added extention of a protein in the protein description function.
- Added some error handling for `?' as a position.
- Added error messages for invalid genes and transcript variants in the 
  input (suggesting possible options).
- DNA / protein descriptions are now stored in the Output object.  
- Added a legend.

GenRecord.py:
- Added functions listLoci() and listGenes() for suggestions when invalid 
  input is given.
- Added a preprocessing step in the GenBank file parsing to deal with 
  missing locus tags (not functional yet).
- Added some error handling for incomplete transcripts.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@52 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1