relax SVN archive

Created the Structure.test_align_CaM_BLOSUM62 system test.

This will be used for expanding the functionality of the structure.align user function to perform
true sequence alignment via the new lib.sequence_alignment package. The test aligns 3 calmodulin
(CaM) structures from different organisms, hence the sequence numbering is different and the current
structure.align user function design fails. The structure.align user function has been expanded in
the test to include a number of arguments for advanced sequence alignment.

Added the end gap penalty arguments to lib.sequence_alignment.align_protein.align_pairwise().

The needleman_wunsch_align() function now accepts the end gap penalty arguments.

These are passed onto the needleman_wunsch_matrix() function.

Fix for the Needleman-Wunsch sequence alignment algorithm.

The start of the sequences are no longer truncated when starting gaps are encountered.

Created a unit test for demonstrating a failure in the Needleman-Wunsch sequence alignment algorithm.

The test is Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4b from the
_lib._sequence_alignment.test_needleman_wunsch module. The problem is that the start of the
alignment is truncated if any gaps are present.

Created the Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4 unit test.

This is in the unit test module _lib._sequence_alignment.test_needleman_wunsch. This tests the
Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.

Modified the Test_needleman_wunsch.test_needleman_wunsch_align_DNA unit test to pass.

This is from the unit test module _lib._sequence_alignment.test_needleman_wunsch. The DNA sequences
were simplified so that the behaviour can be better predicted.

Added the PAM 250 amino acid substitution matrix.

This was taken from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM250 and added to
lib.sequence_alignment.substitution_matrices.PAM250.

Added the header from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62.

This is to document the BLOSUM62 substitution matrix.

Added the NUC 4.4 nucleotide substitution matrix from ftp://ftp.ncbi.nih.gov/blast/matrices/.

Uracil was added to the table as a copy to T.