relax SVN archive

Fix for the Noe.test_noe_analysis system test.

The grace plots of the peak intensities now have error bars.

Redesign and standardisation of the peak intensity data structure throughout all analyses in relax.

The various structures 'intensities', 'intensity_err', 'intensity_sim', 'sim_intensity', and
'intensity_bc' have all been renamed. The new structures are called 'peak_intensity',
'peak_intensity_err', 'peak_intensity_sim' and 'peak_intensity_bc'. This allows the structure to be
processed as a standard parameter in the specific analysis API. One very visible consequence is
that plots of peak intensities, as well as value files, will now have peak intensity errors.

For backwards compatibility, the relax data store method _back_compat_hook() has been modified to
catch all previous peak intensity object variants and to standardise and rename these to the new
object names.

As the parameter is now called 'peak_intensity' rather than 'intensities', all calls to the
grace.write and value.write for this parameter have been changed in the auto-analyses, the sample
scripts, the test suite and the manual.

Merged revisions 22550 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22550 | bugman | 2014-03-26 19:28:47 +0100 (Wed, 26 Mar 2014) | 10 lines

Changed the Noe auto-analysis to properly handle the peak intensity Grace plots.

This relates to bug #21863 (https://gna.org/bugs/?21863), the grace.write user function not being
able to write ref/sat plots as described in sample script noe.py.

Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat'
parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter.
The reference and saturated intensities will appear as two graph sets within that plot.
........

Merged revisions 22546-22549 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22546 | bugman | 2014-03-26 18:42:57 +0100 (Wed, 26 Mar 2014) | 6 lines

Fix for the line numbering for the NOE analysis sample script in the user manual.

The line numbering for the code snippets did not match that of the full sample script shown at the
start of that section of the NOE chapter.
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r22547 | bugman | 2014-03-26 19:01:15 +0100 (Wed, 26 Mar 2014) | 5 lines

Added a simple shell script to quickly grep the entire source tree while excluding .svn directories.

This will only work on POSIX systems (Linux and Macs).
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r22548 | bugman | 2014-03-26 19:20:09 +0100 (Wed, 26 Mar 2014) | 6 lines

Fix for the Noe.test_bug_21562_noe_replicate_fail system test.

The 'ref' and 'sat' parameters do not exist. Therefore the grace.write user function calls in the
system test script have been modified to output the 'intensities' parameter instead.
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r22549 | bugman | 2014-03-26 19:25:44 +0100 (Wed, 26 Mar 2014) | 6 lines

Complete rearrangement of the specific analysis code for the steady-state NOE.

This brings the code into line with the recent specific analysis code rearrangements, specifically
in the specific_analyses.relax_disp package.
........

Changed the Noe auto-analysis to properly handle the peak intensity Grace plots.

This relates to bug #21863 (https://gna.org/bugs/?21863), the grace.write user function not being
able to write ref/sat plots as described in sample script noe.py.

Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat'
parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter.
The reference and saturated intensities will appear as two graph sets within that plot.

Complete rearrangement of the specific analysis code for the steady-state NOE.

This brings the code into line with the recent specific analysis code rearrangements, specifically
in the specific_analyses.relax_disp package.

Fix for the Noe.test_bug_21562_noe_replicate_fail system test.

The 'ref' and 'sat' parameters do not exist. Therefore the grace.write user function calls in the
system test script have been modified to output the 'intensities' parameter instead.

Added a simple shell script to quickly grep the entire source tree while excluding .svn directories.

This will only work on POSIX systems (Linux and Macs).

Fix for the line numbering for the NOE analysis sample script in the user manual.

The line numbering for the code snippets did not match that of the full sample script shown at the
start of that section of the NOE chapter.

Merged revisions 22543-22544 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22543 | bugman | 2014-03-26 18:32:15 +0100 (Wed, 26 Mar 2014) | 10 lines

Changed the Noe.test_noe_analysis system test to handle the peak intensities correctly.

This relates to bug #21863 (https://gna.org/bugs/?21863), , the grace.write user function not being
able to write ref/sat plots as described in sample script noe.py.

Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat'
parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter.
The reference and saturated intensities will appear as two graph sets within that plot.
........
r22544 | bugman | 2014-03-26 18:38:41 +0100 (Wed, 26 Mar 2014) | 11 lines

Changed the Noe analysis sample script to properly handle the peak intensity Grace plots.

This relates to bug #21863 (https://gna.org/bugs/?21863), the grace.write user function not being
able to write ref/sat plots as described in sample script noe.py.

Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat'
parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter.
The reference and saturated intensities will appear as two graph sets within that plot. These
changes match those of the test suite.
........