relax SVN archive

Modified the Needleman-Wunsch sequence alignment algorithm.

The previous attempt was buggy. The algorithm has been modified to match the logic of the GPL
licenced EMBOSS software (http://emboss.sourceforge.net/) to allow for gap opening and extension
penalties, as well as end penalties. No code was copied, rather the algorithm for creating the
scoring and penalty matrices, as well as the traceback matrix.

Updated the gap penalties in the Test_align_protein.test_align_pairwise unit test.

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

Annotated the BLOSUM62 substitution matrix with the amino acid codes for easy reading.

The lib.sequence_alignment.align_protein.align_pairwise() function now returns data.

This includes both alignment strings as well as the gap matrix.

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.