The code is included in the seq.alg module and it is documented (with an
example) in seqalg.rst. The main new functions are:
- clip_start = seq.alg.ClipAlignment(aln)
- d_map = seq.alg.CreateDistanceMap(aln)
- var_map = seq.alg.CreateVarianceMap(d_map)
- dist_to_mean = seq.alg.CreateDist2Mean(d_map)

This allows the easy usage of the alignment algorithms on the c-level.
The storage to the info object has been removed.

export them to Python

wrong branch, big sorry

This reverts commit e77d08a6.

starting and ending gaps penalty. good when 1 sequence is much
smaller then the other or you expect the 2 sequences just to overlap
a bit.

extend Conservation function to set conservation score of stretches with many gaps to zero; added documentation

changed cmake scripts to allow building as subproject / moved common configuration from startup scripts to separate script

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2676 5a81b35b-ba03-0410-adc8-b2c5c5119f08

Note to self: Don't commit anything before 8 in the morning!


git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2506 5a81b35b-ba03-0410-adc8-b2c5c5119f08

These two algorithms are not tested enough to leave them in.
I will readd them once I find the time to properly test
them.

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2500 5a81b35b-ba03-0410-adc8-b2c5c5119f08

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/branches/new_shell@2368 5a81b35b-ba03-0410-adc8-b2c5c5119f08

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2333 5a81b35b-ba03-0410-adc8-b2c5c5119f08

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