• Laros's avatar
    Started on the TRM, therefore the separate files Db.txt and errorcodes.txt have · 0aa697dd
    Laros authored
    vanished. Fixed a large number of bugs.
    Db.txt, errorcodes.txt:
    - Renamed and converted to LaTeX.
    - Added references for the TRM.
    - Documented a large part of the modules.
    - 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.
    - 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().
    - Separated the visualisation of a parse error from the error message. The 
      visualisation is now put in the output object as "parseError".
    - Added documentation.
    - 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.
    - Added file type information (for lrg and gb files).
    - Added sanity checks for the snpConvert() function.
    - Added documentation.
    - Added a new type "construction" to the linking methods, meaning that the
      mRNA is generated from the CDS.
    - Added an email variable for output to the website.
    - Added error information, to hide parts of the output.
    - Added file type information (see Retriever.py) to make download links more
    - Modified the syntax checker to work with the new parser output (see
    - Fixed a bug (selecting the human build) in the position converter.
    - Renamed download() to webservices().
    - Renamed ConversionChecker to PositionConverter.
    - Added.
    - Modified the template to work with the new restriction site format and the
      new parse error format.
    - Made lots of things conditional.
    - Added.
    - Added an example.
    - 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