relax SVN archive

Fix for the Needleman-Wunsch sequence alignment algorithm when the substitution matrix is absent.

Added more printouts to the Test_align_protein.test_align_pairwise unit test.

This is the test of the module _lib._sequence_alignment.test_align_protein.

Created a unit test for lib.sequence_alignment.align_protein.align_pairwise().

This is to test the pairwise alignment of two protein sequences using the Needleman-Wunsch sequence
alignment algorithm, BLOSUM62 substitution matrix, and gap penalty of 10.0.

Created the lib.sequence_alignment.align_protein module for the sequence alignment of proteins.

This general module currently implements the align_pairwise() function for the pairwise alignment of
protein sequences. It provides the infrastructure for specifying gap starting and extension
penalties, choosing the alignment algorithm (currently only the Needleman-Wunsch sequence alignment
algorithm as 'NW70'), and choosing the substitution matrix (currently only BLOSUM62). The function
provides lots of printouts for user feedback.

Modification of the Needleman-Wunsch sequence alignment algorithm implementation.

This is in the lib.sequence_alignment.needleman_wunsch functions. Scoring matrices are now
supported, as well as a user supplied non-integer gap penalty. The algorithm for walking through
the traceback matrix has been fixed for a bug under certain conditions.

Fix for the lib.sequence_alignment.substitution_matrices.BLOSUM62_SEQ string.

Corrected the spelling of the BLOSUM62 matrix in lib.sequence_alignment.substitution_matrices.

Created the lib.sequence_alignment.substitution_matrices module.

This is for storing substitution matrices for use in sequence alignment. The module currently only
includes the BLOSSUM62 matrix.

Created a unit test for checking the Needleman-Wunsch sequence alignment algorithm.

This uses the DNA data from the example in the Wikipedia article at
https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm. The test shows that the
implementation of the lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function is
correct.

Implementation of the Needleman-Wunsch sequence alignment algorithm.

This is located in the lib.sequence_alignment.needleman_wunsch module. This is implemented as
described in the Wikipedia article https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm.