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[r27352] by bugman

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

If set to zero, all printouts are suppressed.

2015-01-29 13:16:23 Tree
[r27351] by bugman

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

2015-01-29 12:38:31 Tree
[r27350] by bugman

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

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

2015-01-29 12:37:46 Tree
[r27349] by bugman

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

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

2015-01-29 12:34:38 Tree
[r27348] by bugman

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.

2015-01-29 12:33:32 Tree
[r27347] by bugman

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

This function still does not work correctly.

2015-01-29 12:26:00 Tree
[r27346] by bugman

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.

2015-01-29 12:24:59 Tree
[r27345] by bugman

Simplified the Test_coordinates.test_common_residues unit test by removing many residues.

This is from the _lib._structure._internal.test_coordinates unit test module.

2015-01-29 12:23:58 Tree
[r27344] by bugman

Created the Test_align_protein.test_align_multiple_from_pairwise unit test.

This is in the _lib._sequence_alignment.test_align_protein unit test module. This test checks the
operation of the lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function, which
does not yet exist.

2015-01-28 17:24:15 Tree
[r27343] by bugman

Modified the lib.structure.internal.coordinates.common_residues() function.

It now accepts the seq argument which will caused the gapped sequence strings to be returned. This
is to allow for checking in the unit tests.

2015-01-28 14:15:13 Tree
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