describe.py:
- Slicing of the LCS matrix went wrong in findMax(), the coordinates of {s2}
  should be reversed.
- Added a function visMatrix() that can print part of the LCS matrix, handy
  for debugging.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@602 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@601 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@600 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Mainly removal of the javascript code for the menu, this is now all CSS
driven and much simplified.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@599 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@598 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Calculating the LCS matrices only for the affected region.
- Reusing the LCS matrices.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@597 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

experimental service.

describe.py:
- Added an `unknown' type to the possible types of raw variants.
- Disabled the experimental LCSMatrix() code.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@596 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

describe.py:
- Added functionality to detect frame shifts.
- Modified the RawVar class to support protein descriptions.
- Added the core protein description function.

models.py:
- Modified the RawVar class to support protein descriptions.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@595 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Modified describe.py to comply with the preferred programming style.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@594 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@593 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@592 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

rpc.py:
- Added the function descriptionExtract().
- Standardised indentation.

models.py:
- Added a RawVar and an Allele class for the webservices.

describe.py:
- Made the RawVar class a child of models.RawVar. This is convenient for
  webservices since we can simply return this object.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@591 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@564 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

recommendations.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@563 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@562 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@561 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@559 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1