relax SVN archive

Deleted the Test_coordinates.test_common_residues unit test.

This is from the _lib._structure._internal.test_coordinates unit test module. The
lib.structure.internal.coordinates.common_residues() function no longer exists.

The assemble_coord_array() function is now using the central star multiple sequence alignment.

This is the function from the lib.structure.internal.coordinates module used to assemble common
atomic coordinate information, used by the structure.align, structure.atomic_fluctuations,
structure.com, structure.displacement, structure.find_pivot, structure.mean, structure.rmsd,
structure.superimpose and structure.web_of_motion user functions.

The non-functional lib.structure.internal.coordinates.common_residues() function has been removed as
the lib.sequence_alignment.msa.central_star() function performs this functionality correctly.

Fixes for the unit tests of the _lib._sequence_alignment.test_needleman_wunsch module.

The lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function now returns the
alignment score.

Fixes for the unit tests of the _lib._sequence_alignment.test_align_protein module.

The Test_align_protein.test_align_pairwise_PAM250 unit test was accidentally duplicated due to a
copy and paste error. And the lib.sequence_alignment.align_protein.align_pairwise() function now
also returns the alignment score.

Complete implementation of the central star multiple sequence alignment algorithm.

This includes all the four major steps - pairwise alignment between all sequence pairs, finding the
central sequence, iteratively aligning the sequences to the gapped central sequence, and introducing
gaps in previous alignments during the iterative alignment.

The correctness of the implementation is verified by the Test_msa.test_central_star unit test of the
_lib._sequence_alignment.test_msa module.

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.