relax SVN archive

Bug fix for the unit test for the unpickling and restoration of the relax data storage singleton.

The path has been changed to a relative path so that the unit tests can be run by themselves or as
part of relax.

Bug fix for the unit test for reading of the amino acid sequence out of a protein NOE data file.

The path has been changed to a relative path so that the unit tests can be run by themselves or as
part of relax.

Updated the prompt.align_tensor arg unit tests to use the DATA_TYPES structure.

Merged revisions 3809-3833 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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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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Final fix for the unit test of reading of the amino acid sequence out of a protein NOE data file.

Actually the read() function was not functional!!! So this is another fix.

Bug fix for the generic_fns.sequence.read() function, it's now functional!

The empty first containers are now taken into account.

Fix for the unit test of reading of the amino acid sequence out of a protein NOE data file.

Updated the docstring of generic_fns.sequence.read(). This is now in the epydoc format.

Updated the docstring of the generic_fns.sequence.validate_sequence() function.