relax SVN archive

Merged revisions 27426-27438 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27426 | bugman | 2015-01-31 13:13:38 +0100 (Sat, 31 Jan 2015) | 8 lines

Shifted the residue skipping data structure construction into the relax library.

The code was originally in pipe_control.structure.main.assemble_structural_coordinates() but has
been shifted into the new lib.sequence_alignment.msa.msa_residue_skipping() function. This will
also for greater code reuse. The lib.sequence_alignment.msa module is also a better location for
such functionality.
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r27427 | bugman | 2015-01-31 15:07:35 +0100 (Sat, 31 Jan 2015) | 6 lines

Renamed the Structure.test_sequence_alignment_molecules system test.

The new name is Structure.test_sequence_alignment_central_star_nw70_blosum62, to better reflect what
the test is doing.
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r27428 | bugman | 2015-01-31 15:15:17 +0100 (Sat, 31 Jan 2015) | 5 lines

Modified the Structure.test_sequence_alignment_central_star_nw70_blosum62 system test.

Some residues are now deleted so that the sequences are not identical.
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r27429 | bugman | 2015-01-31 15:17:09 +0100 (Sat, 31 Jan 2015) | 7 lines

Created the Structure.test_sequence_alignment_residue_number system test.

This will be used to test the structure.sequence_alignment user function together with the 'residue
number' MSA algorithm. This is simply a copy of the
Structure.test_sequence_alignment_central_star_nw70_blosum62 system test with a few small changes.
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r27430 | bugman | 2015-01-31 17:26:57 +0100 (Sat, 31 Jan 2015) | 3 lines

Corrections and simplifications for the Structure.test_sequence_alignment_residue_number system test.
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r27431 | bugman | 2015-01-31 17:33:38 +0100 (Sat, 31 Jan 2015) | 5 lines

Modified the structure.sequence_alignment user function arguments.

The pairwise_algorithm and matrix arguments can no be None, and they default to None.
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r27432 | bugman | 2015-01-31 17:54:04 +0100 (Sat, 31 Jan 2015) | 6 lines

Updated the Structure.test_align_CaM_BLOSUM62 system test script.

The MSA algorithm and pairwise alignment algorithms are now specified in the
structure.sequence_alignment user function calls.
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r27433 | bugman | 2015-01-31 17:56:51 +0100 (Sat, 31 Jan 2015) | 7 lines

Creation of the lib.sequence_alignment.msa.msa_general() function.

This consists of code from the structure.sequence_alignment user function backend function
pipe_control.structure.main.sequence_alignment() for selecting between the different sequence
alignment methods.
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r27434 | bugman | 2015-01-31 17:59:44 +0100 (Sat, 31 Jan 2015) | 6 lines

The structure.sequence_alignment user function now sets some arguments to None before storage.

This is for all arguments not used in the sequence alignment. For example the residue number based
alignment does not use the gap penalties, pairwise alignment algorithm or the substitution matrices.
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r27435 | bugman | 2015-02-02 09:11:41 +0100 (Mon, 02 Feb 2015) | 7 lines

Fix for the lib.sequence_alignment.msa.msa_residue_skipping() function.

The sequences argument for passing in the one letter codes has been removed. The per molecule loop
should be over the alignment strings rather than one letter codes, otherwise the loop will be too
short.
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r27436 | bugman | 2015-02-02 09:20:06 +0100 (Mon, 02 Feb 2015) | 9 lines

Fix for the internal structural object atomic coordinate assembly function.

This is the pipe_control.structure.main.assemble_structural_coordinates() function. The case of no
sequence alignment being required as only models are being handled is now functional. The strings
and gaps data structures passed into the lib.sequence_alignment.msa.msa_residue_skipping() function
for generating the residue skipping data structure are now set to the one letter codes and an empty
structure of zeros respectively.
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r27437 | bugman | 2015-02-02 16:44:46 +0100 (Mon, 02 Feb 2015) | 6 lines

Test data directory renaming.

The test_suite/shared_data/diffusion_tensor/spheroid directory has been renamed to spheroid_prolate.
This is in preparation for creating oblate spheroid diffusion relaxation data.
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r27438 | bugman | 2015-02-02 16:46:06 +0100 (Mon, 02 Feb 2015) | 5 lines

Creation of oblate spheroid diffusion relaxation data.

This will be used in the Structure.test_create_diff_tensor_pdb_oblate system test.
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Created the relax GUI prompt Destroy() method.

This is used to cleanly destroy the GUI prompt by first unregistering with the observer objects,
destroying then deleting the wx.py.shell.Shell instance, and finally destroying the window.

Temporary disabling of the memory management check in the GUI tests tearDown() method.

For some reason, it appears as if it is not possible to destroy wx Windows on MS Windows.

Fix for the GUI tests clean_up_windows() tearDown method.

After destroying all of the main GUI windows, a wx.Yield() call is made to flush the wxPython event
queue. This seems to help with the memory management.

Removed the wx.CallAfter() call in the GUI tests tearDown() method.

This was used to call the clean_up_windows() method. However the value of wx.Thread_IsMain() shows
that the tearDown() method executes in the main GUI thread. Therefore the wx.CallAfter() call for
avoiding racing conditions is not needed.

Changed the title for the user function GUI windows.

To better help identify what the window is, the title is now the user function name together with
text saying that it is a user function.

Popup menus are now properly destroyed in the GUI tests.

In many instances, the wx.Menu.Destroy() method was only being called when the GUI is shown. This
causes memory leaking in the GUI tests.

Added memory management checking to the GUI test suite tearDown() method.

If any top level windows are present, excluding the main GUI window and the relax controller, then a
RelaxError will be raised. Such a check will significantly help in future GUI coding, as now there
will be feedback if not all windows are properly destroyed.

The relax prompt window is now being destroyed by the GUI test suite tearDown() method.

The window is first closed in the tearDown() method and then destroyed in the clean_up_windows()
method.

Improved memory management for the GUI user function windows.

The Destroy() method will now destroy any Sequence or Sequence_2D windows used for the user function
arguments.