Author: bugman
Date: Sat Jun 28 23:34:34 2008
New Revision: 6542
URL: http://svn.gna.org/viewcvs/relax?rev=6542&view=rev
Log:
Renaming of most of the XML related methods.
The follow have changed:
xml_create_element() -> to_xml()
xml_read_element() -> from_xml()
xml_write() -> to_xml()
xml_read() -> from_xml()
Modified:
1.3/data/__init__.py
1.3/data/align_tensor.py
1.3/data/diff_tensor.py
1.3/data/mol_res_spin.py
1.3/data/pipe_container.py
1.3/generic_fns/results.py
Modified: 1.3/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/__init__.py?rev=6542&r1=6541&r2=6542&view=diff
==============================================================================
--- 1.3/data/__init__.py (original)
+++ 1.3/data/__init__.py Sat Jun 28 23:34:34 2008
@@ -160,7 +160,7 @@
self.current_pipe = pipe_name
- def xml_read(self, file, verbosity=1):
+ def from_xml(self, file, verbosity=1):
"""Parse a XML document representation of a data pipe, and load it
into the relax data store.
@param file: The open file object.
@@ -180,10 +180,10 @@
relax_version = str(relax_node.getAttribute('version'))
# Fill the pipe.
- self[self.current_pipe].xml_read_element(relax_node)
-
-
- def xml_write(self, file):
+ self[self.current_pipe].from_xml(relax_node)
+
+
+ def to_xml(self, file):
"""Create a XML document representation of the current data pipe.
This method creates the top level XML document including all the
information needed
@@ -217,7 +217,7 @@
pipe_element.setAttribute('type', self[self.current_pipe].pipe_type)
# Fill the data pipe XML element.
- self[self.current_pipe].xml_create_element(self.xmldoc, pipe_element)
+ self[self.current_pipe].to_xml(self.xmldoc, pipe_element)
# Write out the XML file.
file.write(self.xmldoc.toprettyxml(indent=' '))
Modified: 1.3/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/align_tensor.py?rev=6542&r1=6541&r2=6542&view=diff
==============================================================================
--- 1.3/data/align_tensor.py (original)
+++ 1.3/data/align_tensor.py Sat Jun 28 23:34:34 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2004, 2006-2007 Edward d'Auvergne
#
+# Copyright (C) 2003-2004, 2006-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -559,7 +559,7 @@
self.append(AlignTensorData(name))
- def xml_create_element(self, doc, element):
+ def to_xml(self, doc, element):
"""Create an XML element for the alignment tensors.
@param doc: The XML document object.
Modified: 1.3/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/diff_tensor.py?rev=6542&r1=6541&r2=6542&view=diff
==============================================================================
--- 1.3/data/diff_tensor.py (original)
+++ 1.3/data/diff_tensor.py Sat Jun 28 23:34:34 2008
@@ -840,7 +840,7 @@
xml_to_object(diff_tensor_node, self)
- def xml_create_element(self, doc, element):
+ def to_xml(self, doc, element):
"""Create an XML element for the diffusion tensor.
@param doc: The XML document object.
Modified: 1.3/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/mol_res_spin.py?rev=6542&r1=6541&r2=6542&view=diff
==============================================================================
--- 1.3/data/mol_res_spin.py (original)
+++ 1.3/data/mol_res_spin.py Sat Jun 28 23:34:34 2008
@@ -205,7 +205,7 @@
xml_to_object(spin_node, self[-1])
- def xml_create_element(self, doc, element):
+ def to_xml(self, doc, element):
"""Create XML elements for each spin.
@param doc: The XML document object.
@@ -452,7 +452,7 @@
self[-1].spin.from_xml(spin_nodes)
- def xml_create_element(self, doc, element):
+ def to_xml(self, doc, element):
"""Create XML elements for each residue.
@param doc: The XML document object.
@@ -476,7 +476,7 @@
fill_object_contents(doc, res_element, object=self[i],
blacklist=['name', 'num', 'spin'] + self[i].__class__.__dict__.keys())
# Add the residue data.
- self[i].spin.xml_create_element(doc, res_element)
+ self[i].spin.to_xml(doc, res_element)
@@ -649,7 +649,7 @@
self[-1].res.from_xml(res_nodes)
- def xml_create_element(self, doc, element):
+ def to_xml(self, doc, element):
"""Create XML elements for each molecule.
@param doc: The XML document object.
@@ -672,4 +672,4 @@
fill_object_contents(doc, mol_element, object=self[i],
blacklist=['name', 'res'] + self[i].__class__.__dict__.keys())
# Add the residue data.
- self[i].res.xml_create_element(doc, mol_element)
+ self[i].res.to_xml(doc, mol_element)
Modified: 1.3/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/pipe_container.py?rev=6542&r1=6541&r2=6542&view=diff
==============================================================================
--- 1.3/data/pipe_container.py (original)
+++ 1.3/data/pipe_container.py Sat Jun 28 23:34:34 2008
@@ -93,6 +93,40 @@
return text
+ def from_xml(self, relax_node):
+ """Read a pipe container XML element and place the contents into
this pipe.
+
+ @param relax_node: The relax XML node.
+ @type relax_node: xml.dom.minidom.Element instance
+ """
+
+ # Test if empty.
+ if not self.is_empty():
+ raise RelaxFromXMLNotEmptyError, self.__class__.__name__
+
+ # Get the global data node, and fill the contents of the pipe.
+ global_node = relax_node.getElementsByTagName('global')[0]
+ xml_to_object(global_node, self)
+
+ # Get the hybrid node (and its sub-node), and recreate the hybrid
object.
+ hybrid_node = relax_node.getElementsByTagName('hybrid')[0]
+ pipes_node = hybrid_node.getElementsByTagName('pipes')[0]
+ setattr(self, 'hybrid_pipes',
node_value_to_python(pipes_node.childNodes[0]))
+
+ # Get the diffusion tensor data node and, if it exists, fill the
contents.
+ diff_tensor_node = relax_node.getElementsByTagName('diff_tensor')[0]
+ if diff_tensor_node:
+ # Create the diffusion tensor object.
+ self.diff_tensor = DiffTensorData()
+
+ # Fill its contents.
+ self.diff_tensor.from_xml(diff_tensor_node)
+
+ # Recreate the molecule, residue, and spin data structure.
+ mol_nodes = relax_node.getElementsByTagName('mol')
+ self.mol.from_xml(mol_nodes)
+
+
def is_empty(self):
"""Method for testing if the data pipe is empty.
@@ -133,7 +167,7 @@
return True
- def xml_create_element(self, doc, element):
+ def to_xml(self, doc, element):
"""Create a XML element for the current data pipe.
@param doc: The XML document object.
@@ -153,18 +187,18 @@
# Add the diffusion tensor data.
if hasattr(self, 'diff_tensor'):
- self.diff_tensor.xml_create_element(doc, element)
+ self.diff_tensor.to_xml(doc, element)
# Add the alignment tensor data.
if hasattr(self, 'align_tensors'):
- self.align_tensors.xml_create_element(doc, element)
+ self.align_tensors.to_xml(doc, element)
# Add the structural data, if it exists.
if hasattr(self, 'structure'):
self.xml_create_str_element(doc, element)
# Add the molecule-residue-spin data.
- self.mol.xml_create_element(doc, element)
+ self.mol.to_xml(doc, element)
def xml_create_hybrid_element(self, doc, element):
@@ -208,37 +242,3 @@
# Set the structural attributes.
str_element.setAttribute('desc', 'Structural information')
str_element.setAttribute('id', ds[ds.current_pipe].structure.id)
-
-
- def xml_read_element(self, relax_node):
- """Read a pipe container XML element and place the contents into
this pipe.
-
- @param relax_node: The relax XML node.
- @type relax_node: xml.dom.minidom.Element instance
- """
-
- # Test if empty.
- if not self.is_empty():
- raise RelaxFromXMLNotEmptyError, self.__class__.__name__
-
- # Get the global data node, and fill the contents of the pipe.
- global_node = relax_node.getElementsByTagName('global')[0]
- xml_to_object(global_node, self)
-
- # Get the hybrid node (and its sub-node), and recreate the hybrid
object.
- hybrid_node = relax_node.getElementsByTagName('hybrid')[0]
- pipes_node = hybrid_node.getElementsByTagName('pipes')[0]
- setattr(self, 'hybrid_pipes',
node_value_to_python(pipes_node.childNodes[0]))
-
- # Get the diffusion tensor data node and, if it exists, fill the
contents.
- diff_tensor_node = relax_node.getElementsByTagName('diff_tensor')[0]
- if diff_tensor_node:
- # Create the diffusion tensor object.
- self.diff_tensor = DiffTensorData()
-
- # Fill its contents.
- self.diff_tensor.from_xml(diff_tensor_node)
-
- # Recreate the molecule, residue, and spin data structure.
- mol_nodes = relax_node.getElementsByTagName('mol')
- self.mol.from_xml(mol_nodes)
Modified: 1.3/generic_fns/results.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/results.py?rev=6542&r1=6541&r2=6542&view=diff
==============================================================================
--- 1.3/generic_fns/results.py (original)
+++ 1.3/generic_fns/results.py Sat Jun 28 23:34:34 2008
@@ -91,7 +91,7 @@
# Specific results writing function.
if format == 'xml':
- write_function = ds.xml_write
+ write_function = ds.to_xml
elif format == 'columnar':
write_function = get_specific_fn('write_columnar_results',
ds[ds.current_pipe].pipe_type, raise_error=False)
else:
@@ -127,7 +127,7 @@
# XML results.
if format == 'xml':
- read_function = ds.xml_read(file)
+ read_function = ds.from_xml(file)
# Columnar results.
elif format == 'columnar':
@@ -164,7 +164,7 @@
# Specific results writing function.
if format == 'xml':
- write_function = ds.xml_write
+ write_function = ds.to_xml
elif format == 'columnar':
write_function = get_specific_fn('write_columnar_results',
ds[ds.current_pipe].pipe_type, raise_error=False)
else:
r6542 - in /1.3: data/ generic_fns/