Author: bugman
Date: Thu Jan 20 23:48:24 2011
New Revision: 12391
URL: http://svn.gna.org/viewcvs/relax?rev=12391&view=rev
Log:
Merged revisions
9878-9890,9987,9989,10085,10092-10093,10206-10238,10246-10265,10268-10293,10295,10332-10403,10406-10430,10437-10442,10444,10446-10449,10452-10460,10463,10465-10610,10613-10625,10633-10644,10647-10651,10654-10667,10673,10677-10679,10682-10683,10685-10686,10695-10698,10701-10702,10706,10875,10887-10936,10959-10960,10991-10995,10997-10998,11003,11052,11060-11069,11073-11084,11101-11143,11178-11184,11191-11205,11213-11218,11343-11365,11370-11380,11386,11535-11539,11548-11551,11553-11564,11569-11570,11575,11577-11586,11590,11593,11596,11599-11606,11610-11617,11620-11626,11690,11700-11704,11707-11757,11759,11761-11800,11802-11804,11806-11810,11822-11825,11836,11845-11846,11881-11885,11897-11899,11901-11903,11922-11965,11968-11978,11980-12059,12080-12086,12166,12169-12171,12193-12201,12228,12327,12336,12345
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bieri_gui
........
r9878 | bugman | 2009-11-19 10:39:59 +0100 (Thu, 19 Nov 2009) | 5 lines
Added a directory for holding Michael Bieri's GUI for relax.
The original post for this GUI is
https://mail.gna.org/public/relax-devel/2009-11/msg00005.html.
........
r9879 | bugman | 2009-11-19 10:43:44 +0100 (Thu, 19 Nov 2009) | 6 lines
Initial commit of Michael Bieri's GUI code.
This is the code found in file #7341
(https://gna.org/support/download.php?file_id=7341) attached to
task #6847 (https://gna.org/task/?6847#comment4).
........
r9880 | bugman | 2009-11-19 10:44:36 +0100 (Thu, 19 Nov 2009) | 3 lines
The wrong README file was committed in the previous commit!
........
r9881 | bugman | 2009-11-19 11:15:13 +0100 (Thu, 19 Nov 2009) | 3 lines
Command line opts for launching the GUI mode (-g, --gui) and the specific
Bieri GUI model (-b, --bieri).
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r9882 | bugman | 2009-11-19 11:15:52 +0100 (Thu, 19 Nov 2009) | 3 lines
Renamed bieri_gui to gui_bieri.
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r9883 | bugman | 2009-11-19 11:18:50 +0100 (Thu, 19 Nov 2009) | 3 lines
Converted the relaxGUI code into a Python package.
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r9884 | bugman | 2009-11-19 11:19:51 +0100 (Thu, 19 Nov 2009) | 3 lines
Removed some *.pyc files that were accidentally committed to the repository.
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r9885 | bugman | 2009-11-19 11:22:18 +0100 (Thu, 19 Nov 2009) | 3 lines
Renamed the relaxGUI module to match the relax naming conventions.
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r9886 | bugman | 2009-11-19 11:35:08 +0100 (Thu, 19 Nov 2009) | 5 lines
Added support for launching the Bieri GUI.
The presence of the wx Python module is now being tested, and an
appropriate error message printed when missing.
........
r9887 | bugman | 2009-11-19 11:51:21 +0100 (Thu, 19 Nov 2009) | 5 lines
Modifications to the start of the GUI launching.
Much work is still needed to make this clean!
........
r9888 | bugman | 2009-11-19 11:56:43 +0100 (Thu, 19 Nov 2009) | 3 lines
Fixed all the paths to the images used by the GUI.
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r9889 | bugman | 2009-11-19 14:38:22 +0100 (Thu, 19 Nov 2009) | 3 lines
Made the Bieri GUI launch in a directory independent manner.
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r9890 | semor | 2009-11-19 20:05:50 +0100 (Thu, 19 Nov 2009) | 3 lines
Converted tab characters to 8 spaces...
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r9987 | bugman | 2009-11-27 10:15:16 +0100 (Fri, 27 Nov 2009) | 6 lines
Removed the SVN executable properties from the files of the Bieri GUI.
These were identified by Seb
(https://mail.gna.org/public/relax-devel/2009-11/msg00048.html,
Message-id: <4B060899.3040002@xxxxxxxxx>).
........
r9989 | bugman | 2009-11-27 10:46:40 +0100 (Fri, 27 Nov 2009) | 3 lines
relax now launches when the wx python module is not installed.
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r10085 | bugman | 2009-12-11 11:42:24 +0100 (Fri, 11 Dec 2009) | 20 lines
Split up relax_gui.py to make it smaller.
This change was communicated by Michael Bieri
(https://gna.org/users/michaelbieri) in the posts
https://mail.gna.org/public/relax-devel/2009-12/msg00020.html (Message-id:
<4B217970.805@xxxxxx>) and
https://mail.gna.org/public/relax-devel/2009-12/msg00022.html (Message-id:
<4B21950C.5080803@xxxxxx>).
This enhances clarity allowing for a better understanding and to facilitate
manipulation. The
relax_gui.py module was split up as follows:
relax_gui.py
--> res/calc_modelfree.py (script to calculate model-free).
--> res/calc_noe.py (script to calculate noe).
--> res/calc_rx.py (script to calculate Rx).
--> res/project.py (script to open and save the project)
--> res/results_analysis.py (script to perform post-analysis: craete grace
plots, pymol macros...)
The res/filedialog.py, res/message.py, res/select_model_calc.py, and
res/settings.py have not yet
been created due to ambiguities as to their origin.
........
r10092 | bugman | 2009-12-14 14:41:14 +0100 (Mon, 14 Dec 2009) | 8 lines
Added the filedialog and message modules.
See Michael's post at
https://mail.gna.org/public/relax-devel/2009-12/msg00024.html (Message-id:
<4B25B6EE.6060505@xxxxxx>).
These are new files which replace functions within easygui.py.
........
r10093 | bugman | 2009-12-14 14:48:05 +0100 (Mon, 14 Dec 2009) | 8 lines
Added the select_model_calc modules.
See Michael's post at
https://mail.gna.org/public/relax-devel/2009-12/msg00024.html (Message-id:
<4B25B6EE.6060505@xxxxxx>).
This module is a dialog whereby users can choose the model-free model.
........
r10206 | bugman | 2010-01-14 11:13:05 +0100 (Thu, 14 Jan 2010) | 7 lines
Changed '/' to os.sep to make the Bieri GUI OS independent.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri). This change was
discussed in the tread starting
at https://mail.gna.org/public/relax-devel/2010-01/msg00007.html.
........
r10207 | bugman | 2010-01-14 11:50:27 +0100 (Thu, 14 Jan 2010) | 9 lines
Complete conversion from t[12x] and T[12x] notation to r[12x] and R[12x].
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri). This change was
discussed in the tread starting
at https://mail.gna.org/public/relax-devel/2010-01/msg00007.html.
These changes are far more extensive than that in patch_II, and cover 100%
of the code.
........
r10208 | bugman | 2010-01-14 14:43:03 +0100 (Thu, 14 Jan 2010) | 3 lines
Updated the copyright statements adding myself and this year.
........
r10209 | bugman | 2010-01-14 14:47:33 +0100 (Thu, 14 Jan 2010) | 9 lines
Added version information to the GUI. This includes a GUI version of 1.00.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
The change is different though as the relax 'version' module is being used
to obtain the relax
version.
........
r10210 | bugman | 2010-01-14 14:58:33 +0100 (Thu, 14 Jan 2010) | 8 lines
Fixes for the relaxGUI imports.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
Again this is different as the import statements were not clearly separated
and were messy.
........
r10211 | bugman | 2010-01-14 15:06:48 +0100 (Thu, 14 Jan 2010) | 3 lines
Another import fix as this was forgotten in the last commit.
........
r10212 | bugman | 2010-01-14 15:45:19 +0100 (Thu, 14 Jan 2010) | 9 lines
Clean up of the gui_bieri.res.results_analysis module (much code deletion)
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
This code appears to have been an unnecessary duplication of that in other
modules. It looks like a
remnant of the splitting up of relax_gui.py at revision r10085.
........
r10213 | bugman | 2010-01-14 16:06:06 +0100 (Thu, 14 Jan 2010) | 8 lines
Expansion and improvements to the menu bar of the main window.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
Many new entries have been created and menu hot keys have been added for
all entries.
........
r10214 | bugman | 2010-01-14 16:10:02 +0100 (Thu, 14 Jan 2010) | 8 lines
Added the missing import_seq(), settings(), param_file_setting() and
reset_setting() methods.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
This prevented relax from launching the GUI.
........
r10215 | bugman | 2010-01-14 17:27:17 +0100 (Thu, 14 Jan 2010) | 8 lines
Switched from using diropenbox() to opendir().
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
This will be a problem because in patch_II, opendir() is not defined in
gui_bieri.relax_gui.
........
r10216 | bugman | 2010-01-14 17:33:36 +0100 (Thu, 14 Jan 2010) | 8 lines
Switched from using msgbox() to using the specific dir_message() function.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
This will again be a problem because dir_message() is not defined in
gui_bieri.relax_gui.
........
r10217 | bugman | 2010-01-14 17:45:18 +0100 (Thu, 14 Jan 2010) | 11 lines
Changes to all the opening and saving file dialogs.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
The following have been changed:
filesavebox() -> savefile(),
fileopenbox() -> openfile(),
fileopenbox() -> multi_openfile(),
........
r10218 | bugman | 2010-01-14 17:46:33 +0100 (Thu, 14 Jan 2010) | 3 lines
Bug fix. Incorrect whitespace was introduced in the last revision (r10217).
........
r10219 | bugman | 2010-01-14 18:01:25 +0100 (Thu, 14 Jan 2010) | 19 lines
Reverted r10214 as the code was not placed in the correct spot!
The command used was:
svn merge -r10214:10213 .
.....
r10214 | bugman | 2010-01-14 16:10:02 +0100 (Thu, 14 Jan 2010) | 8 lines
Changed paths:
M /branches/bieri_gui/gui_bieri/relax_gui.py
Added the missing import_seq(), settings(), param_file_setting() and
reset_setting() methods.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
This prevented relax from launching the GUI.
.....
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r10220 | bugman | 2010-01-14 18:05:47 +0100 (Thu, 14 Jan 2010) | 30 lines
Properly introduced the import_seq(), settings(), param_file_setting() and
reset_setting() methods.
This is what r10214 should have been.
.....
r10219 | bugman | 2010-01-14 18:01:25 +0100 (Thu, 14 Jan 2010) | 19 lines
Changed paths:
M /branches/bieri_gui/gui_bieri/relax_gui.py
Reverted r10214 as the code was not placed in the correct spot!
The command used was:
svn merge -r10214:10213 .
.....
r10214 | bugman | 2010-01-14 16:10:02 +0100 (Thu, 14 Jan 2010) | 8
lines
Changed paths:
M /branches/bieri_gui/gui_bieri/relax_gui.py
Added the missing import_seq(), settings(), param_file_setting()
and reset_setting() methods.
This corresponds to one component of the patch_II file attached
to https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
This prevented relax from launching the GUI.
.....
.....
........
r10221 | bugman | 2010-01-14 19:05:43 +0100 (Thu, 14 Jan 2010) | 8 lines
Updated the global setting dialog.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
The gui_bieri.res.settings module is now in sync with patch_II.
........
r10222 | bugman | 2010-01-15 10:10:26 +0100 (Fri, 15 Jan 2010) | 9 lines
Improvements to how unresolved spin systems are handled.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
The situation of no unresolved spins is better handled, and the ';'
character is replaced by ','
internally.
........
r10223 | bugman | 2010-01-15 10:12:53 +0100 (Fri, 15 Jan 2010) | 6 lines
Simplified the whichmodel() function (not sure what the removed wx calls
did anyway).
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
........
r10224 | bugman | 2010-01-15 10:17:00 +0100 (Fri, 15 Jan 2010) | 6 lines
Increased the status bar width.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
........
r10225 | bugman | 2010-01-15 10:32:40 +0100 (Fri, 15 Jan 2010) | 9 lines
Added a series of global variables to be used throughout the GUI.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
These include the global_setting list, the file_setting list, the
sequencefile, and tables of
results.
........
r10226 | bugman | 2010-01-15 10:45:55 +0100 (Fri, 15 Jan 2010) | 6 lines
Comment improvements throughout relax_gui.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
........
r10227 | bugman | 2010-01-15 10:46:48 +0100 (Fri, 15 Jan 2010) | 6 lines
Added actions for the new menu entries.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
........
r10228 | bugman | 2010-01-15 10:51:59 +0100 (Fri, 15 Jan 2010) | 10 lines
Expanded the print out when exiting to include references and shifted to
using question().
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
The print out will need a bit of formatting, and it would be better if the
question() box is
eventually removed as asking the user if they would like to quit after the
user asked the program
to quit is annoying.
........
r10229 | bugman | 2010-01-15 10:54:54 +0100 (Fri, 15 Jan 2010) | 8 lines
relax execution now occurs automatically after clicking on the icon.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
Previously a confirmation was required.
........
r10230 | bugman | 2010-01-15 10:59:06 +0100 (Fri, 15 Jan 2010) | 6 lines
Modified how the r1_list and r2_list data structures are handled.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
........
r10231 | bugman | 2010-01-15 11:03:40 +0100 (Fri, 15 Jan 2010) | 6 lines
Expansion of exec_model_free() in preparation for rearrangements in the
calc_modelfree module.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
........
r10232 | bugman | 2010-01-15 11:04:37 +0100 (Fri, 15 Jan 2010) | 6 lines
Removed an event.Skip() call.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
........
r10233 | bugman | 2010-01-15 11:17:23 +0100 (Fri, 15 Jan 2010) | 6 lines
Shifted from using msgbox() to relax_run_ok() to indication proper
completion of the calculation.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
........
r10234 | bugman | 2010-01-15 11:23:13 +0100 (Fri, 15 Jan 2010) | 11 lines
Shift of the GUI calculation code to using the relax API (rather than
scripting).
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri). See the thread
starting at
https://mail.gna.org/public/relax-devel/2009-11/msg00045.html, specifically
the details in
https://mail.gna.org/public/relax-devel/2009-11/msg00056.html.
This includes a large rearrangement of the model-free code, which could not
be separated from the
shift to the relax API.
........
r10235 | bugman | 2010-01-15 11:24:40 +0100 (Fri, 15 Jan 2010) | 6 lines
Simplifications to the file dialog code.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
........
r10236 | bugman | 2010-01-15 11:25:21 +0100 (Fri, 15 Jan 2010) | 8 lines
Removed a number of calls to wx.PySimpleApp().
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
I'm guessing these were not necessary?
........
r10237 | bugman | 2010-01-15 11:30:17 +0100 (Fri, 15 Jan 2010) | 11 lines
A number of improvements to the final results analysis.
This corresponds to one component of the patch_II file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri).
This commit is the last of those from patch_II. This patch has now been
almost completely committed
to the branch in a series of individual commits (see r10206 to r10234,
https://mail.gna.org/public/relax-commits/2010-01/threads.html). The
rejected changes are listed at
https://mail.gna.org/public/relax-devel/2010-01/msg00016.html.
........
r10238 | bugman | 2010-01-15 12:40:52 +0100 (Fri, 15 Jan 2010) | 6 lines
Bug fix for the color_code_noe() method.
This was introduced by the breaking up of patch_II. The structure is now
called
self.structure_r21_copy_1_copy.
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r10246 | bugman | 2010-01-19 11:06:29 +0100 (Tue, 19 Jan 2010) | 8 lines
Names of buttons are enhanced and m2-m6 and final calculation is controlled
by local_tm variable.
This is the disable_models_patch file
(http://gna.org/support/download.php?file_id=7720) attached to
http://gna.org/task/?6847#comment19.
This is for feedback of successful local tm calculation.
........
r10247 | bugman | 2010-01-19 11:10:47 +0100 (Tue, 19 Jan 2010) | 9 lines
The GUI does not creat its own wx application anymore.
This is the stacking_problem_settings_patch file
(http://gna.org/support/download.php?file_id=7721)
attached to http://gna.org/task/?6847#comment19.
This caused the problem reported at
https://mail.gna.org/public/relax-devel/2010-01/msg00029.html,
where the dialog could not be opened.
........
r10248 | bugman | 2010-01-19 15:51:19 +0100 (Tue, 19 Jan 2010) | 6 lines
Added some initial Oxygen (http://www.oxygen-icons.org/) icons.
These are taken from Mandriva 2010's /usr/share/icons/oxygen/ directory and
are licenced unde the
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r12391 - in /1.3: ./ auto_analyses/ data/ graphics/oxygen_icons/ graphics/oxygen_icons/22x22/actions/ graphics/oxygen_icons/...