Author: bugman
Date: Thu Dec 30 15:15:01 2010
New Revision: 12037
URL: http://svn.gna.org/viewcvs/relax?rev=12037&view=rev
Log:
Changed the ds.relax_gui.file_setting data structure to be a container class.
The structure is now called ds.relax_gui.free_file_format and it is a
container with variables for
each column type and the column separator.
Modified:
branches/bieri_gui/data/gui.py
branches/bieri_gui/gui_bieri/analyses/auto_model_free.py
branches/bieri_gui/gui_bieri/execution/calc_noe.py
branches/bieri_gui/gui_bieri/execution/calc_rx.py
branches/bieri_gui/gui_bieri/relax_gui.py
branches/bieri_gui/gui_bieri/settings.py
branches/bieri_gui/gui_bieri/user_functions/base.py
Modified: branches/bieri_gui/data/gui.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/data/gui.py?rev=12037&r1=12036&r2=12037&view=diff
==============================================================================
--- branches/bieri_gui/data/gui.py (original)
+++ branches/bieri_gui/data/gui.py Thu Dec 30 15:15:01 2010
@@ -40,6 +40,9 @@
# Add the analysis list object.
self.analyses = Analyses()
+ # The free format file settings.
+ self.free_file_format = Free_file_format()
+
# Set the name and description.
self.name = 'relax_gui'
self.desc = 'The relax GUI information store.'
@@ -52,17 +55,20 @@
@type gui_node: xml.dom.minicompat.Element instance
"""
- # Add the analysis list object.
+ # Init.
self.analyses = Analyses()
+ self.free_file_format = Free_file_format()
- # Get the analyses node.
+ # Get the analyses node and recreate the analyses structure.
analyses_nodes = gui_node.getElementsByTagName('analyses')
-
- # Recreate the analyses structure.
self.analyses.from_xml(analyses_nodes[0])
+ # Get the file settings node and recreate the structure.
+ format_nodes = gui_node.getElementsByTagName('free_file_format')
+ self.free_file_format.from_xml(format_nodes[0])
+
# Recreate all the other data structures.
- xml_to_object(gui_node, self, blacklist=['analyses'])
+ xml_to_object(gui_node, self, blacklist=['analyses',
'free_file_format'])
@@ -116,3 +122,33 @@
# Recreate the analysis container.
cont.from_xml(node)
+
+
+class Free_file_format(Element):
+ """Container for the free format file settings (column numbers, column
separators, etc.)."""
+
+ def __init__(self):
+ """Set up the initial values."""
+
+ # Execute the base class __init__() method.
+ super(Free_file_format, self).__init__(name='free_file_format',
desc='The column numbers and separator for the free format file.')
+
+ # Reset.
+ self.reset()
+
+
+ def reset(self):
+ """Reset all variables to the initial values."""
+
+ # The default column numbers.
+ self.spin_id_col = None
+ self.mol_name_col = 1
+ self.res_num_col = 2
+ self.res_name_col = 3
+ self.spin_num_col = 4
+ self.spin_name_col = 5
+ self.data_col = 6
+ self.err_col = 7
+
+ # The column separator (set to None for white space).
+ self.sep = None
Modified: branches/bieri_gui/gui_bieri/analyses/auto_model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/analyses/auto_model_free.py?rev=12037&r1=12036&r2=12037&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/analyses/auto_model_free.py (original)
+++ branches/bieri_gui/gui_bieri/analyses/auto_model_free.py Thu Dec 30
15:15:01 2010
@@ -673,19 +673,11 @@
if not self.data.paramfiles1[2] == '': # R2 file of frq 1
sequence_file = self.data.paramfiles1[2]
- # Import parameter file settings.
- param = ds.relax_gui.file_setting
-
- # Read parameter file parameters and convert them to integers if not
None.
- param_tmp = param
- for i in range(0, len(param_tmp)):
- if str(param_tmp[i]) in ['', '0', 'None']:
- param_tmp[i] = None
- else:
- param_tmp[i] = int(param_tmp[i])
+ # Alias the free file format data structure.
+ format = ds.relax_gui.free_file_format
# The sequence data (file name, dir, mol_name_col, res_num_col,
res_name_col, spin_num_col, spin_name_col, sep). These are the arguments to
the sequence.read() user function, for more information please see the
documentation for that function.
- data.seq_args = [sequence_file, None, None, param_tmp[1],
param_tmp[2], param_tmp[3], param_tmp[4], None]
+ data.seq_args = [sequence_file, None, format.mol_name_col,
format.res_num_col, format.res_name_col, format.spin_num_col,
format.spin_name_col, format.sep]
# Import golbal settings.
global_settings = ds.relax_gui.global_setting
@@ -730,11 +722,11 @@
# Append the relaxation data if present.
if not files[1] == '':
- data.relax_data.append(['R1', str(frq), float(frq)*1e6,
files[1], None, None, param_tmp[1], param_tmp[2], param_tmp[3], param_tmp[4],
param_tmp[5], param_tmp[6], None])
+ data.relax_data.append(['R1', str(frq), float(frq)*1e6,
files[1], None, format.mol_name_col, format.res_num_col, format.res_name_col,
format.spin_num_col, format.spin_name_col, format.data_col, format.err_col,
format.sep])
if not files[2] == '':
- data.relax_data.append(['R2', str(frq), float(frq)*1e6,
files[2], None, None, param_tmp[1], param_tmp[2], param_tmp[3], param_tmp[4],
param_tmp[5], param_tmp[6], None])
+ data.relax_data.append(['R2', str(frq), float(frq)*1e6,
files[2], None, format.mol_name_col, format.res_num_col, format.res_name_col,
format.spin_num_col, format.spin_name_col, format.data_col, format.err_col,
format.sep])
if not files[0] == '':
- data.relax_data.append(['NOE', str(frq), float(frq)*1e6,
files[0], None, None, param_tmp[1], param_tmp[2], param_tmp[3], param_tmp[4],
param_tmp[5], param_tmp[6], None])
+ data.relax_data.append(['NOE', str(frq), float(frq)*1e6,
files[0], None, format.mol_name_col, format.res_num_col, format.res_name_col,
format.spin_num_col, format.spin_name_col, format.data_col, format.err_col,
format.sep])
# Unresolved resiudes
file = DummyFileObject()
Modified: branches/bieri_gui/gui_bieri/execution/calc_noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/execution/calc_noe.py?rev=12037&r1=12036&r2=12037&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/execution/calc_noe.py (original)
+++ branches/bieri_gui/gui_bieri/execution/calc_noe.py Thu Dec 30 15:15:01
2010
@@ -52,12 +52,6 @@
hetero = global_setting[2]
prot = global_setting[3]
- intcol = int(file_setting[5])
- mol_name = int(file_setting[0])
- res_num = int(file_setting[1])
- res_name = int(file_setting[2])
- spin_num = int(file_setting[3])
- spin_name = int(file_setting[4])
resultsdir = str(target_dir)
gracedir = str(target_dir) + sep + 'grace'
save_file = str(target_dir) + sep + 'noe.' + str(nmr_freq) + '.out'
Modified: branches/bieri_gui/gui_bieri/execution/calc_rx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/execution/calc_rx.py?rev=12037&r1=12036&r2=12037&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/execution/calc_rx.py (original)
+++ branches/bieri_gui/gui_bieri/execution/calc_rx.py Thu Dec 30 15:15:01 2010
@@ -53,12 +53,6 @@
hetero = global_setting[2]
prot = global_setting[3]
- intcol = int(file_setting[5])
- mol_name = int(file_setting[0])
- res_num = int(file_setting[1])
- res_name = int(file_setting[2])
- spin_num = int(file_setting[3])
- spin_name = int(file_setting[4])
resultsdir = str(target_dir)
gracedir = str(target_dir) + sep + 'grace'
savefile = str(target_dir) + sep + 'r' + str(r1_r2) + '.' +
str(nmr_freq) + '.out'
Modified: branches/bieri_gui/gui_bieri/relax_gui.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/relax_gui.py?rev=12037&r1=12036&r2=12037&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/relax_gui.py (original)
+++ branches/bieri_gui/gui_bieri/relax_gui.py Thu Dec 30 15:15:01 2010
@@ -420,7 +420,6 @@
ds.relax_gui.results_rx = []
ds.relax_gui.results_model_free = []
ds.relax_gui.global_setting = ['1.02 * 1e-10', '-172 * 1e-6', 'N',
'H', '11', 'newton', '500']
- ds.relax_gui.file_setting = [1, 2, 3, 4, 5, 6, 7]
# Table of relax Results
ds.relax_gui.table_residue = []
@@ -529,7 +528,7 @@
global global_setting #import global variable
if question('Do you realy want to change relax settings?'):
ds.relax_gui.global_setting = ['1.02 * 1e-10', '-172 * 1e-6',
'N', 'H', '11', 'newton', '500']
- ds.relax_gui.file_setting = [1, 2, 3, 4, 5, 6, 7]
+ ds.relax_gui.free_file_format.reset()
def settings(self, event): # set up for relax variables
Modified: branches/bieri_gui/gui_bieri/settings.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/settings.py?rev=12037&r1=12036&r2=12037&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/settings.py (original)
+++ branches/bieri_gui/gui_bieri/settings.py Thu Dec 30 15:15:01 2010
@@ -252,14 +252,13 @@
def accept_settings(self, event): # change settings
- ds.relax_gui.file_setting = []
- ds.relax_gui.file_setting.append(gui_to_int(self.mol_nam.GetValue()))
-
ds.relax_gui.file_setting.append(gui_to_int(self.res_num_col.GetValue()))
-
ds.relax_gui.file_setting.append(gui_to_int(self.res_nam_col.GetValue()))
-
ds.relax_gui.file_setting.append(gui_to_int(self.spin_num_col.GetValue()))
-
ds.relax_gui.file_setting.append(gui_to_int(self.spin_nam_col.GetValue()))
-
ds.relax_gui.file_setting.append(gui_to_int(self.value_col.GetValue()))
-
ds.relax_gui.file_setting.append(gui_to_int(self.error_col.GetValue()))
+ ds.relax_gui.free_file_format.mol_name_col =
gui_to_int(self.mol_nam.GetValue())
+ ds.relax_gui.free_file_format.res_num_col =
gui_to_int(self.res_num_col.GetValue())
+ ds.relax_gui.free_file_format.res_name_col =
gui_to_int(self.res_nam_col.GetValue())
+ ds.relax_gui.free_file_format.spin_num_col =
gui_to_int(self.spin_num_col.GetValue())
+ ds.relax_gui.free_file_format.spin_name_col =
gui_to_int(self.spin_nam_col.GetValue())
+ ds.relax_gui.free_file_format.data_col =
gui_to_int(self.value_col.GetValue())
+ ds.relax_gui.free_file_format.err_col =
gui_to_int(self.error_col.GetValue())
# Update the fields.
self.update()
@@ -274,10 +273,10 @@
def update(self):
"""Update all the fields."""
- self.mol_nam = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.file_setting[0]))
- self.res_num_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.file_setting[1]))
- self.res_nam_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.file_setting[2]))
- self.spin_num_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.file_setting[3]))
- self.spin_nam_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.file_setting[4]))
- self.value_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.file_setting[5]))
- self.error_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.file_setting[6]))
+ self.mol_nam = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.free_file_format.mol_name_col))
+ self.res_num_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.free_file_format.res_num_col))
+ self.res_nam_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.free_file_format.res_name_col))
+ self.spin_num_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.free_file_format.spin_num_col))
+ self.spin_nam_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.free_file_format.spin_name_col))
+ self.value_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.free_file_format.data_col))
+ self.error_col = wx.TextCtrl(self, -1,
int_to_gui(ds.relax_gui.free_file_format.err_col))
Modified: branches/bieri_gui/gui_bieri/user_functions/base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/user_functions/base.py?rev=12037&r1=12036&r2=12037&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/user_functions/base.py (original)
+++ branches/bieri_gui/gui_bieri/user_functions/base.py Thu Dec 30 15:15:01
2010
@@ -28,6 +28,7 @@
from wx.lib import buttons
# relax module imports.
+from data import Relax_data_store; ds = Relax_data_store()
from relax_errors import AllRelaxErrors, RelaxImplementError
# relax GUI module imports.
r12037 - in /branches/bieri_gui: data/ gui_bieri/ gui_bieri/analyses/ gui_bieri/execution/ gui_bieri/user_functions/