Author: bugman
Date: Fri Aug 16 20:30:10 2013
New Revision: 20624
URL: http://svn.gna.org/viewcvs/relax?rev=20624&view=rev
Log:
Merged revisions 20579,20598-20619 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/peak_intensities
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r20579 | bugman | 2013-08-13 11:58:38 +0200 (Tue, 13 Aug 2013) | 6 lines
Modification of the spectrum.read_intensities user function front end.
The heteronuc and proton arguments have been eliminated. Instead the new
dim argument is used to
associate the data with the spins of any dimension in the peak list.
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r20598 | bugman | 2013-08-15 12:01:52 +0200 (Thu, 15 Aug 2013) | 3 lines
Replaced the 'heteronuc' and 'proton' arguments of the
spectrum.read_intensities user function backend with 'dim'.
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r20599 | bugman | 2013-08-16 17:15:24 +0200 (Fri, 16 Aug 2013) | 6 lines
Created the new lib.spectrum.objects module.
This will hold temporary data structures for representing peak lists and
other spectral data. The
module currently contains the Peak_list class which is used to hold peak
list data.
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r20600 | bugman | 2013-08-16 17:18:21 +0200 (Fri, 16 Aug 2013) | 3 lines
Started to shift the spectrum.read_intensities user function backend to use
lib.spectrum.peak_list.
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r20601 | bugman | 2013-08-16 17:49:45 +0200 (Fri, 16 Aug 2013) | 3 lines
The pipe_control.spectrum.read_intensities() function now works with the
Peak_list object.
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r20602 | bugman | 2013-08-16 17:50:26 +0200 (Fri, 16 Aug 2013) | 3 lines
The Peak_list object is now used by the
lib.spectrum.peak_list.read_peak_list() function.
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r20603 | bugman | 2013-08-16 18:28:25 +0200 (Fri, 16 Aug 2013) | 3 lines
Fix for the lib.spectrum.objects.Peak_list object - the Assignment object
was not initialised.
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r20604 | bugman | 2013-08-16 18:31:04 +0200 (Fri, 16 Aug 2013) | 3 lines
Small fix for how pipe_control.spectrum.read() uses the Peak_list object.
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r20605 | bugman | 2013-08-16 18:31:40 +0200 (Fri, 16 Aug 2013) | 3 lines
The lib.software.sparky.read_list_intensity() function now operates on the
Peak_list object.
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r20606 | bugman | 2013-08-16 18:42:46 +0200 (Fri, 16 Aug 2013) | 3 lines
Changed the spectrum.read_intensities dim argument default to w2 and
improved the long description.
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r20607 | bugman | 2013-08-16 18:44:54 +0200 (Fri, 16 Aug 2013) | 5 lines
Fix for the assignment handling in the lib.software.sparky.read_peak_list()
function.
The first element is usually the indirect dimension or w2.
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r20608 | bugman | 2013-08-16 18:48:15 +0200 (Fri, 16 Aug 2013) | 5 lines
Fix for many of the Peak_list system tests for the user function argument
changes.
The heteronuc and proton arguments have been replaced by the dim argument.
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r20609 | bugman | 2013-08-16 18:57:15 +0200 (Fri, 16 Aug 2013) | 3 lines
The lib.software.xeasy.read_list_intensity() function now operates on the
Peak_list object.
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r20610 | bugman | 2013-08-16 18:58:58 +0200 (Fri, 16 Aug 2013) | 3 lines
Small docstring change for lib.software.sparky.read_list_intensity().
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r20611 | bugman | 2013-08-16 19:02:03 +0200 (Fri, 16 Aug 2013) | 3 lines
The lib.software.nmrview.read_list_intensity() function now operates on the
Peak_list object.
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r20612 | bugman | 2013-08-16 19:14:57 +0200 (Fri, 16 Aug 2013) | 3 lines
The lib.spectrum.peak_list.intensity_generic() function now operates on the
Peak_list object.
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r20613 | bugman | 2013-08-16 19:16:39 +0200 (Fri, 16 Aug 2013) | 5 lines
Fixes for the pipe_control.spectrum.read() function.
An error was referencing a now non-existent variable and the docstring has
been fixed.
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r20614 | bugman | 2013-08-16 19:17:01 +0200 (Fri, 16 Aug 2013) | 3 lines
Removal of a now unused list variable.
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r20615 | bugman | 2013-08-16 19:34:45 +0200 (Fri, 16 Aug 2013) | 6 lines
The Peak_list object can now store peak intensity names.
This is for peak lists such as from NMRPipe seriersTab files where the peak
list covers multiple
spectra.
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r20616 | bugman | 2013-08-16 19:42:56 +0200 (Fri, 16 Aug 2013) | 3 lines
The NMRPipe seriesTab peak lists are now supported through the Peak_list
object.
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r20617 | bugman | 2013-08-16 19:54:36 +0200 (Fri, 16 Aug 2013) | 3 lines
Unit test fixes for the spectrum.read_intensities user function argument
changes.
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r20618 | bugman | 2013-08-16 19:56:45 +0200 (Fri, 16 Aug 2013) | 3 lines
Fixes for a few system tests for the spectrum.read_intensities user
function argument changes.
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r20619 | bugman | 2013-08-16 20:11:07 +0200 (Fri, 16 Aug 2013) | 3 lines
Fixes for a few GUI tests for the spectrum.read_intensities user function
argument changes.
........
Added:
trunk/lib/spectrum/objects.py
- copied unchanged from r20619,
branches/peak_intensities/lib/spectrum/objects.py
Modified:
trunk/ (props changed)
trunk/lib/software/nmrpipe.py
trunk/lib/software/nmrview.py
trunk/lib/software/sparky.py
trunk/lib/software/xeasy.py
trunk/lib/spectrum/__init__.py
trunk/lib/spectrum/peak_list.py
trunk/pipe_control/spectrum.py
trunk/test_suite/gui_tests/noe.py
trunk/test_suite/gui_tests/rx.py
trunk/test_suite/system_tests/peak_lists.py
trunk/test_suite/system_tests/scripts/1UBQ_relax_fit.py
trunk/test_suite/system_tests/scripts/noe.py
trunk/test_suite/unit_tests/_prompt/test_spectrum.py
trunk/user_functions/spectrum.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/software/nmrpipe.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/software/nmrpipe.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/lib/software/nmrview.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/software/nmrview.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/lib/software/sparky.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/software/sparky.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/lib/software/xeasy.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/software/xeasy.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/lib/spectrum/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/__init__.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/lib/spectrum/peak_list.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/peak_list.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/spectrum.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/test_suite/gui_tests/noe.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/noe.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/test_suite/gui_tests/rx.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/rx.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/test_suite/system_tests/peak_lists.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/test_suite/system_tests/scripts/1UBQ_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/1UBQ_relax_fit.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/test_suite/system_tests/scripts/noe.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/noe.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/test_suite/unit_tests/_prompt/test_spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_prompt/test_spectrum.py?rev=20624&r1=20623&r2=20624&view=diff
Modified: trunk/user_functions/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/spectrum.py?rev=20624&r1=20623&r2=20624&view=diff
r20624 - in /trunk: ./ lib/software/ lib/spectrum/ pipe_control/ test_suite/gui_tests/ test_suite/system_tests/ test_suite/s...