relax SVN archive

Fix for the Test_msa.test_central_star unit test.

This is from the _lib._sequence_alignment.test_msa unit test module. Some of the real gap matrix
indices were incorrect.

The protein pairwise sequence alignment function now returns the alignment score.

This is in the lib.sequence_alignment.align_protein.align_pairwise() function. The score from the
Needleman-Wunsch sequence alignment algorithm is simply passed along.

The Needleman-Wunsch sequence alignment algorithm now calculates and returns an alignment score.

This is in the lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function. The score
is calculated as the sum of the Needleman-Wunsch matrix elements along the traceback path.

Added the verbosity argument to lib.sequence_alignment.align_protein.align_pairwise().

If set to zero, all printouts are suppressed.

Import fix for the _lib._sequence_alignment.test_align_protein unit test module.

Initial lib.sequence_alignment.msa.central_star() function.

This was moved from lib.sequence_alignment.align_protein.align_multiple_from_pairwise().

Added the lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function.

This should have been committed earlier. The function is only partly implemented.

Renamed the Test_align_protein.test_align_multiple_from_pairwise unit test.

This is now the Test_msa.test_central_star unit test of the _lib._sequence_alignment.test_msa unit
test module (it was originally in the _lib._sequence_alignment.test_align_protein unit test module).
This is in preparation for converting the
lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function into the
lib.sequence_alignment.msa.central_star() function.

Attempt at fixing the lib.structure.internal.coordinates.common_residues() function.

This function still does not work correctly.

Expanded the docstring of the Test_align_protein.test_align_multiple_from_pairwise unit test.

This is from the _lib._sequence_alignment.test_align_protein unit test module.