Author: bugman
Date: Thu Nov 22 18:16:02 2007
New Revision: 3834
URL: http://svn.gna.org/viewcvs/relax?rev=3834&view=rev
Log:
Merged revisions 3809-3833 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r3809 | bugman | 2007-11-22 11:24:17 +0100 (Thu, 22 Nov 2007) | 5 lines
Removed the return_data_types() function and converted data_types into a
permanent module constant.
This is in preparation to add file descriptors to the list.
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r3810 | bugman | 2007-11-22 11:26:04 +0100 (Thu, 22 Nov 2007) | 3 lines
Added the tmpfile() file descriptor to the 'DATA_TYPES' array.
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r3811 | bugman | 2007-11-22 11:27:39 +0100 (Thu, 22 Nov 2007) | 3 lines
Alphabetically sorted the initialisation of DATA_TYPES to bring some order
to the chaos.
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r3812 | bugman | 2007-11-22 11:31:00 +0100 (Thu, 22 Nov 2007) | 3 lines
Fixed all user function arg unit tests to use the new DATA_TYPES module
array.
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r3813 | bugman | 2007-11-22 11:37:47 +0100 (Thu, 22 Nov 2007) | 3 lines
Updated the sequence.write() user function for the new relax design.
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r3814 | bugman | 2007-11-22 11:40:59 +0100 (Thu, 22 Nov 2007) | 3 lines
Added unit tests for all arguments of the sequence.write() user function.
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r3815 | bugman | 2007-11-22 12:11:30 +0100 (Thu, 22 Nov 2007) | 3 lines
Wrote a unit test for the writing of an amino acid sequence to file.
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r3816 | bugman | 2007-11-22 12:21:41 +0100 (Thu, 22 Nov 2007) | 3 lines
Added a new RelaxError for invalid sequence data.
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r3817 | bugman | 2007-11-22 12:22:21 +0100 (Thu, 22 Nov 2007) | 3 lines
Small fix for RelaxInvalidSeqError.
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r3818 | bugman | 2007-11-22 12:36:59 +0100 (Thu, 22 Nov 2007) | 3 lines
Started to implement the read, sequence_exists, and valid_sequence
functions.
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r3819 | bugman | 2007-11-22 12:39:37 +0100 (Thu, 22 Nov 2007) | 3 lines
Updated the extract_data() for the new relax design (converted from a class
method to a function).
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r3820 | bugman | 2007-11-22 17:16:52 +0100 (Thu, 22 Nov 2007) | 3 lines
Fixed the path in the unit test for reading a protein sequence.
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r3821 | bugman | 2007-11-22 17:18:45 +0100 (Thu, 22 Nov 2007) | 3 lines
Added the missing import of relax_io.strip.
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r3822 | bugman | 2007-11-22 17:19:25 +0100 (Thu, 22 Nov 2007) | 3 lines
Converted the strip class method to a module function.
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r3823 | bugman | 2007-11-22 17:25:44 +0100 (Thu, 22 Nov 2007) | 3 lines
Fix for the generic_fns.sequence.read() function.
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r3824 | bugman | 2007-11-22 17:40:25 +0100 (Thu, 22 Nov 2007) | 2 lines
Renamed valid_sequence() to validate_sequence() and called it from within
the read() fn.
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r3825 | bugman | 2007-11-22 17:49:25 +0100 (Thu, 22 Nov 2007) | 3 lines
Completed the generic_fns.sequence.read() function.
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r3826 | bugman | 2007-11-22 17:50:39 +0100 (Thu, 22 Nov 2007) | 3 lines
Bug fix for the generic_fns.sequence.validate_sequence() function.
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r3827 | bugman | 2007-11-22 17:52:41 +0100 (Thu, 22 Nov 2007) | 5 lines
Another bug fix for the generic_fns.sequence.validate_sequence() function.
The mol, res, and spin column numbers are now passed into it.
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r3828 | bugman | 2007-11-22 17:55:19 +0100 (Thu, 22 Nov 2007) | 3 lines
Updated the docstring of the generic_fns.sequence.validate_sequence()
function.
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r3829 | bugman | 2007-11-22 18:01:07 +0100 (Thu, 22 Nov 2007) | 3 lines
Updated the docstring of generic_fns.sequence.read(). This is now in the
epydoc format.
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r3830 | bugman | 2007-11-22 18:02:47 +0100 (Thu, 22 Nov 2007) | 3 lines
Fix for the unit test of reading of the amino acid sequence out of a
protein NOE data file.
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r3831 | bugman | 2007-11-22 18:09:57 +0100 (Thu, 22 Nov 2007) | 5 lines
Bug fix for the generic_fns.sequence.read() function, it's now functional!
The empty first containers are now taken into account.
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r3832 | bugman | 2007-11-22 18:11:35 +0100 (Thu, 22 Nov 2007) | 3 lines
Actually the read() function was not functional!!! So this is another fix.
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r3833 | bugman | 2007-11-22 18:14:04 +0100 (Thu, 22 Nov 2007) | 3 lines
Final fix for the unit test of reading of the amino acid sequence out of a
protein NOE data file.
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Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/generic_fns/sequence.py
branches/N_state_model/prompt/sequence.py
branches/N_state_model/relax_errors.py
branches/N_state_model/relax_io.py
branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_molecule.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_residue.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_sequence.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_spin.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_state.py
branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/N_state_model/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/sequence.py?rev=3834&r1=3833&r2=3834&view=diff
Modified: branches/N_state_model/prompt/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/sequence.py?rev=3834&r1=3833&r2=3834&view=diff
Modified: branches/N_state_model/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_errors.py?rev=3834&r1=3833&r2=3834&view=diff
Modified: branches/N_state_model/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_io.py?rev=3834&r1=3833&r2=3834&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py?rev=3834&r1=3833&r2=3834&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/_prompt/test_molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_molecule.py?rev=3834&r1=3833&r2=3834&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/test_residue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_residue.py?rev=3834&r1=3833&r2=3834&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/_prompt/test_sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_sequence.py?rev=3834&r1=3833&r2=3834&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/test_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_spin.py?rev=3834&r1=3833&r2=3834&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/test_state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_state.py?rev=3834&r1=3833&r2=3834&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py?rev=3834&r1=3833&r2=3834&view=diff
r3834 - in /branches/N_state_model: ./ generic_fns/ prompt/ test_suite/unit_tests/ test_suite/unit_tests/_prompt/