relax SVN archive

Fix for a fatal bug introduced in the last commit (r27398).

The data store ds.sequence_alignment object is now being treated as special and is blacklisted.

The object is now explicitly recreated in the data store from_xml() method.

Fixes for the sequence alignment objects for the relax data store.

The Sequence_alignments(RelaxListType) and Alignment(Element) classes were not being set up
correctly. The container names and descriptions were missing.

Implemented the backend of the structure.sequence_alignment user function.

This checks some of the input parameters, assembles the structural objects then the atomic
coordinate information, performs the multiple sequence alignment, and then stores the results.

Spun out the atomic assembly code of the assemble_coord_array() function.

The code from the lib.structure.internal.coordinates.assemble_coord_array() function has been
shifted to the new assemble_atomic_coordinates(). This is to simplify assemble_coord_array() as
well as to isolate the individual functionality for reuse.

Modified the assemble_coordinates() function of the pipe_control.structure.main module.

The function has been renamed to assemble_structural_objects(). The call to the
lib.structure.internal.coordinates.assemble_coord_array() function has also been shifted out of
assemble_structural_objects() to simplify the logic and decrease the amount of arguments passed
around.

Created the frontend for the structure.sequence_alignment user function.

This is based on the structure.align user function with the 3D superimposition arguments removed and
new arguments added for selecting the MSA algorithm and the pairwise alignment algorithm (despite
only NW70 being currently implemented).

Important formatting improvement for the description in the GUI user function windows.

Previously lists, item lists, and prompt items were spaced with one empty line at the top and two at
the bottom. The two empty lines at the bottom was an accident caused by how the list text elements
were built up. Now the final newline character is stripped so that the top and bottom of the lists
only consist of one empty line. The change can give a lot more room in the GUI window.

Modified the Structure.test_sequence_alignment_molecules system test.

Changed and expanded the arguments to the yet to be implemented structure.sequence_alignment user
function.

Renamed the Sequence.test_align_molecules system test to Structure.test_sequence_alignment_molecules.

As the sequence alignment is dependent on the structural data in the relax data store, the user
function for sequence alignment would be better named as structure.sequence_alignment. The
sequence.align user function is not appropriate as all other sequence user functions relate to the
molecule, residue, and spin data structure of each data pipe rather than to the structural data.