relax SVN archive

Created the lib.sequence.aa_codes_three_to_one() function.

The lib.sequence module now contains the AA_CODES dictionary which is a translation table for the 3
letter amino acid codes to the one letter codes. The new aa_codes_three_to_one() function performs
the conversion.

Copyright notice updates to 2015.

The sequence alignment arguments are now passed all the way to the internal structural object backend.

These are the arguments of the structure.align user function.

Removed the 'algorithm' argument from the Structure.test_align_CaM_BLOSUM62 system test script.

This is for the structure.align user function. The argument has not been implemented to save room
in the GUI, and as 'NW70' is currently the only choice.

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().