This also enabled test_cleanup, test_nonstandard and test_aligntoseqres which
were previously skipped with 'make check' indep. of compound lib availability
(simply because unittests are launched with 'python' and not with 'ost').

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)

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.

Added new option "try_resnum_first" to AlignToSEQRES. Mainly for the MMCifParser to align seqres entries easier to the chains.

clustalw with external options, including unittest; renumbering accepts seq and aln as input;unit tests

clustalw with external options, including unittest; renumbering accepts seq and aln as input;unit tests

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

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2137 5a81b35b-ba03-0410-adc8-b2c5c5119f08