relax SVN archive

Added the sequence alignment arguments to the back end of the structure.align user function.

This is to allow the code in trunk to be functional before the sequence alignment before
superimposition has been implemented.

Added the sequence alignment arguments to the structure.align user function front end.

This includes the 'matrix', 'gap_open_penalty', 'gap_extend_penalty', 'end_gap_open_penalty', and
'end_gap_extend_penalty' arguments. The 'algorithm' argument has not been added to save room, as
there is only one choice of 'NW70'. A paragraph has been added to the user function description to
explain the sequence alignment part of the user function.

Small docstring expansion for lib.sequence_alignment.align_protein.align_pairwise().

Created the Test_align_protein.test_align_pairwise_PAM250 unit test.

This is in the unit test module _lib._sequence_alignment.test_align_protein. It check the protein
alignment function lib.sequence_alignment.align_protein.align_pairwise() together with the PAM250
substitution matrix.

Bug fix for the Needleman-Wunsch sequence alignment algorithm.

Part of the scoring system was functioning incorrectly when the gap penalty scores were non-integer,
as some scores were being stored in an integer array. Now the array is a float array.

Added support for the PAM250 substitution matrix to the protein pairwise sequence alignment function.

This is the function lib.sequence_alignment.align_protein.align_pairwise().

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.