relax SVN archive

Implemented the data_store.seq_align.Sequence_alignments.find_alignment() method.

This will only return an alignment if all alignment input data and alignment settings match exactly.

Code rearrangement in the _data_store.test_seq_align unit test module.

The ID generation has been shifted into the generate_ids() method to be used by multiple tests.

Added the Test_seq_align.test_find_alignment and Test_seq_align.test_find_missing_alignment unit tests.

These are in the _data_store.test_seq_align unit test module. They check the functionality of the
currently unimplemented Sequence_alignment.find_alignment() method which will be used to return
pre-existing alignments.

Fixes for the data_store.seq_align.Alignment.generate_id() method.

These problems were identified by the _data_store.test_seq_align module
Test_seq_align.test_alignment_addition unit test.

Created the Test_seq_align.test_alignment_addition unit test.

This is in the _data_store.test_seq_align unit test module. This tests the setup of the sequence
alignment object via the data_store.seq_align.Sequence_alignment.add() method.

Spelling mistake in the Sequence_alignments class name.

Added the seq_align module to the data_store package __all__ list.

Created the new relax data store object for saving sequence alignments.

This is in the new data_store.seq_align module via the Seqence_alignments object, subclassed from
RelaxListType, for holding all alignments and the Alignment Element object, subclassed from Element,
for holding each individual alignment. The objects are currently unused.

Large speed up of the mol-res-spin selection object.

The Selection.contains_mol(), Selection.contains_res() and Selection.contains_spin() methods of the
lib.selection module have been redesigned for speed. Instead of setting a number of flags and
performing bit operations at the end of the method to return the correct Boolean value, each of the
multiple checks now simply returns a Boolean value, avoiding all subsequent checks. The check list
order has also been rearranged so that the least expensive checks are to the top and the most time
intensive checks are last.

Modified the Structure.test_align_molecules_end_truncation system test.

The calmodulin bound calciums are now deleted prior to the structure.align user function call. This
prevents these being labelled as '*' residues and aligning with real amino acids via the central
star multiple sequence alignment (MSA) algorithm.