The classes Mutator, Output and Db are now derived classes of Config. The
class Retriever is a derived class of Output. This reduces the amount of
code and variable passing significantly.

mutalyzer.conf:
- Converted the dbName variable to a dbName list, to accommodate for more than
  one database.
- Added variables flanksize, maxvissize and flankclipsize for the visualisation
  in Mutator.py (instead of the previous alignment).

Mutalyzer.py:
- Resolved the range-swap issues.
- Resolved the reverse-complement (cosmetic) issues.
- Fixed a cosmetic bug in the __bprint() function.
- Added a new function __nsplice(), to accommodate for a CDS extension.
- Added a function __toProtDescr(), that gives a protein description in case
  of a simple substitution.
- Added functionality for n. m. and EST notations.
- Added functionality for other species (translation tables).
- Corrected the roll-rule for insertions.
- Added fallbacks for missing CDS and mRNA lists and positions (for an EST for
  example).
- Added an input check for wrong gene symbols.
- Added a temporary exception for in frame stop codons.

webservice.py:
- Added the private functions __checkBuild(), __checkChrom() and __checkPos()
  that do routine checks in a number of services.
- Added a 'build' variable to getTranscripts(), getTranscriptsRange() and
  getGeneName()
- Added exceptions that raise a Fault() object to make the client receive a
  SOAP exception.

UCSC_update.py:
- Added functionality for more than one database.

Variant_info.py:
- Added functionality for more than one database.
- Added functionality to deal with non-coding transcripts.

Genrecord.py:
- Made a RecordObj() object that consists of the old 'genelist' dictionary, 
  combined with 'mol_type' and 'organelle' variables. Also, a fake gene named
  'source' is included to accommodate for sequences that do not contain any
  annotated genes (an EST for example).
- The Locus object is extended with a 'txTable' variable to accommodate for
  different organelles (mitochondria) and other species.

Mutator.py:
- Replaced the alignment visualisation by a home-made one. Also see the
  variables that were added to the configuration file to alter the behaviour of
  this visualisation.
- Modified the shiftpos() function when inserting something on a splice site
  boundary (now it extends the exon).

Output.py:
- Minor modifications for the new inheritance scheme.

Config.py:
- Minor modifications for the new inheritance scheme.

Db.py:
- Minor modifications for the new inheritance scheme.
- Added functionality to handle multiple databases.
- Added an isChrom() function, used by the webservices check functions.

Crossmap.py:
- Made a change in the usage of the '__STOP' variable. It is set to
  transcription stop if there is no stop codon present. This makes conversion
  to an n. notation trivial.

Retriever.py:
- Minor modifications for the new inheritance scheme.
- Added a check for invalid accession numbers (or versions).
- Added a check for erroneous genbank files that can occur when the NCBI is
  overloaded. The erroneous file is purged and the user can try again.

templates/sp.py
- Modified the sample code to accommodate for the new 'build' variable.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@20 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1