| Lattice Microbes 2.5
    This is for whole cell modeling | 
| Public Member Functions | |
| __init__ (self, src, with_function_signature=False, with_type_info=False, with_constructor_list=False, with_attribute_list=False, with_overloaded_functions=False, textwidth=80, quiet=False) | |
| generate (self) | |
| write (self, fname) | |
| parse (self, node) | |
| parse_Document (self, node) | |
| parse_Text (self, node) | |
| parse_Comment (self, node) | |
| parse_Element (self, node) | |
| subnode_parse (self, node, pieces=None, indent=0, ignore=[], restrict=None) | |
| surround_parse (self, node, pre_char, post_char) | |
| get_specific_subnodes (self, node, name, recursive=0) | |
| get_specific_nodes (self, node, names) | |
| add_text (self, value) | |
| start_new_paragraph (self) | |
| add_line_with_subsequent_indent (self, line, indent=4) | |
| extract_text (self, node) | |
| get_function_signature (self, node) | |
| make_constructor_list (self, constructor_nodes, classname) | |
| make_attribute_list (self, node) | |
| get_memberdef_nodes_and_signatures (self, node, kind) | |
| handle_typical_memberdefs_no_overload (self, signature, memberdef_nodes) | |
| handle_typical_memberdefs (self, signature, memberdef_nodes) | |
| do_linebreak (self, node) | |
| do_ndash (self, node) | |
| do_mdash (self, node) | |
| do_emphasis (self, node) | |
| do_bold (self, node) | |
| do_computeroutput (self, node) | |
| do_heading (self, node) | |
| do_verbatim (self, node) | |
| do_blockquote (self, node) | |
| do_hruler (self, node) | |
| do_includes (self, node) | |
| do_para (self, node) | |
| do_itemizedlist (self, node) | |
| do_orderedlist (self, node) | |
| do_listitem (self, node) | |
| do_parameterlist (self, node) | |
| do_parameteritem (self, node) | |
| do_parameternamelist (self, node) | |
| do_parametername (self, node) | |
| do_parameterdescription (self, node) | |
| do_simplesect (self, node) | |
| do_compounddef (self, node) | |
| do_memberdef (self, node) | |
| do_sectiondef (self, node) | |
| do_header (self, node) | |
| do_member (self, node) | |
| do_doxygenindex (self, node) | |
| Public Attributes | |
| with_function_signature = with_function_signature | |
| with_type_info = with_type_info | |
| with_constructor_list = with_constructor_list | |
| with_attribute_list = with_attribute_list | |
| with_overloaded_functions = with_overloaded_functions | |
| textwidth = textwidth | |
| quiet = quiet | |
| int | indent = 0 | 
| str | listitem = '' | 
| list | pieces = [] | 
| my_dir = os.path.dirname(f.name) | |
| xmldoc = minidom.parse(f).documentElement | |
| space_re = re.compile(r'\s+') | |
| lead_spc = re.compile(r'^(%feature\S+\s+\S+\s*?)"\s+(\S)') | |
| int | multi = 0 | 
| list | ignores | 
Converts Doxygen generated XML files into a file containing
docstrings that can be used by SWIG-1.3.x that have support for
feature("docstring").  Once the data is parsed it is stored in
self.pieces.
 | doxy2swig.Doxy2SWIG.__init__ | ( | self, | |
| src, | |||
| with_function_signature = False, | |||
| with_type_info = False, | |||
| with_constructor_list = False, | |||
| with_attribute_list = False, | |||
| with_overloaded_functions = False, | |||
| textwidth = 80, | |||
| quiet = False ) | 
Initialize the instance given a source object.  `src` can
be a file or filename.  If you do not want to include function
definitions from doxygen then set
`include_function_definition` to `False`.  This is handy since
this allows you to use the swig generated function definition
using %feature("autodoc", [0,1]).
 
| doxy2swig.Doxy2SWIG.add_line_with_subsequent_indent | ( | self, | |
| line, | |||
| indent = 4 ) | 
Add line of text and wrap such that subsequent lines are indented by `indent` spaces.
| doxy2swig.Doxy2SWIG.add_text | ( | self, | |
| value ) | 
Adds text corresponding to `value` into `self.pieces`.
| doxy2swig.Doxy2SWIG.do_blockquote | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_bold | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_compounddef | ( | self, | |
| node ) | 
This produces %feature("docstring") entries for classes, and handles
class, namespace and file memberdef entries specially to allow for 
overloaded functions. For other cases, passes parsing on to standard
handlers (which may produce unexpected results).
 | doxy2swig.Doxy2SWIG.do_computeroutput | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_doxygenindex | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_emphasis | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_header | ( | self, | |
| node ) | 
For a user defined section def a header field is present which should not be printed as such, so we comment it in the output.
| doxy2swig.Doxy2SWIG.do_heading | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_hruler | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_includes | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_itemizedlist | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_linebreak | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_listitem | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_mdash | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_member | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_memberdef | ( | self, | |
| node ) | 
Handle cases outside of class, struct, file or namespace. These are now dealt with by `handle_overloaded_memberfunction`. Do these even exist???
| doxy2swig.Doxy2SWIG.do_ndash | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_orderedlist | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_para | ( | self, | |
| node ) | 
This is the only place where text wrapping is automatically performed. Generally, this function parses the node (locally), wraps the text, and then adds the result to self.pieces. However, it may be convenient to allow the previous content of self.pieces to be included in the text wrapping. For this, use the following *convention*: If self.pieces ends with '', treat the _previous_ entry as part of the current paragraph. Else, insert new-line and start a new paragraph and "wrapping context". Paragraphs always end with ' \n', but if the parsed content ends with the special symbol '', this is passed on.
| doxy2swig.Doxy2SWIG.do_parameterdescription | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_parameteritem | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_parameterlist | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_parametername | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_parameternamelist | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_sectiondef | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_simplesect | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.do_verbatim | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.extract_text | ( | self, | |
| node ) | 
Return the string representation of the node or list of nodes by parsing the subnodes, but returning the result as a string instead of adding it to `self.pieces`. Note that this allows extracting text even if the node is in the ignore list.
| doxy2swig.Doxy2SWIG.generate | ( | self | ) | 
Parses the file set in the initialization. The resulting data is stored in `self.pieces`.
| doxy2swig.Doxy2SWIG.get_function_signature | ( | self, | |
| node ) | 
Returns the function signature string for memberdef nodes.
| doxy2swig.Doxy2SWIG.get_memberdef_nodes_and_signatures | ( | self, | |
| node, | |||
| kind ) | 
Collects the memberdef nodes and corresponding signatures that correspond to public function entries that are at most depth 2 deeper than the current (compounddef) node. Returns a dictionary with function signatures (what swig expects after the %feature directive) as keys, and a list of corresponding memberdef nodes as values.
| doxy2swig.Doxy2SWIG.get_specific_nodes | ( | self, | |
| node, | |||
| names ) | 
Given a node and a sequence of strings in `names`, return a dictionary containing the names as keys and child `ELEMENT_NODEs`, that have a `tagName` equal to the name.
| doxy2swig.Doxy2SWIG.get_specific_subnodes | ( | self, | |
| node, | |||
| name, | |||
| recursive = 0 ) | 
Given a node and a name, return a list of child `ELEMENT_NODEs`, that have a `tagName` matching the `name`. Search recursively for `recursive` levels.
| doxy2swig.Doxy2SWIG.handle_typical_memberdefs | ( | self, | |
| signature, | |||
| memberdef_nodes ) | 
Produces docstring entries containing an "Overloaded function" section with the documentation for each overload, if the function is overloaded and self.with_overloaded_functions is set. Else, produce normal documentation.
| doxy2swig.Doxy2SWIG.handle_typical_memberdefs_no_overload | ( | self, | |
| signature, | |||
| memberdef_nodes ) | 
Produce standard documentation for memberdef_nodes.
| doxy2swig.Doxy2SWIG.make_attribute_list | ( | self, | |
| node ) | 
Produces the "Attributes" section in class docstrings for public member variables (attributes).
| doxy2swig.Doxy2SWIG.make_constructor_list | ( | self, | |
| constructor_nodes, | |||
| classname ) | 
Produces the "Constructors" section and the constructor signatures (since swig does not do so for classes) for class docstrings.
| doxy2swig.Doxy2SWIG.parse | ( | self, | |
| node ) | 
Parse a given node. This function in turn calls the `parse_<nodeType>` functions which handle the respective nodes.
| doxy2swig.Doxy2SWIG.parse_Comment | ( | self, | |
| node ) | 
Parse a `COMMENT_NODE`. This does nothing for now.
| doxy2swig.Doxy2SWIG.parse_Document | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.parse_Element | ( | self, | |
| node ) | 
Parse an `ELEMENT_NODE`. This calls specific `do_<tagName>` handers for different elements. If no handler is available the `subnode_parse` method is called. All tagNames specified in `self.ignores` are simply ignored.
| doxy2swig.Doxy2SWIG.parse_Text | ( | self, | |
| node ) | 
| doxy2swig.Doxy2SWIG.start_new_paragraph | ( | self | ) | 
Make sure to create an empty line. This is overridden, if the previous text ends with the special marker ''. In that case, nothing is done.
| doxy2swig.Doxy2SWIG.subnode_parse | ( | self, | |
| node, | |||
| pieces = None, | |||
| indent = 0, | |||
| ignore = [], | |||
| restrict = None ) | 
Parse the subnodes of a given node. Subnodes with tags in the `ignore` list are ignored. If pieces is given, use this as target for the parse results instead of self.pieces. Indent all lines by the amount given in `indent`. Note that the initial content in `pieces` is not indented. The final result is in any case added to self.pieces.
| doxy2swig.Doxy2SWIG.surround_parse | ( | self, | |
| node, | |||
| pre_char, | |||
| post_char ) | 
Parse the subnodes of a given node. Subnodes with tags in the `ignore` list are ignored. Prepend `pre_char` and append `post_char` to the output in self.pieces.
| doxy2swig.Doxy2SWIG.write | ( | self, | |
| fname ) | 
| list doxy2swig.Doxy2SWIG.ignores | 
| int doxy2swig.Doxy2SWIG.indent = 0 | 
| doxy2swig.Doxy2SWIG.lead_spc = re.compile(r'^(%feature\S+\s+\S+\s*?)"\s+(\S)') | 
| str doxy2swig.Doxy2SWIG.listitem = '' | 
| int doxy2swig.Doxy2SWIG.multi = 0 | 
| doxy2swig.Doxy2SWIG.my_dir = os.path.dirname(f.name) | 
| doxy2swig.Doxy2SWIG.pieces = [] | 
| doxy2swig.Doxy2SWIG.quiet = quiet | 
| doxy2swig.Doxy2SWIG.space_re = re.compile(r'\s+') | 
| doxy2swig.Doxy2SWIG.textwidth = textwidth | 
| doxy2swig.Doxy2SWIG.with_attribute_list = with_attribute_list | 
| doxy2swig.Doxy2SWIG.with_constructor_list = with_constructor_list | 
| doxy2swig.Doxy2SWIG.with_function_signature = with_function_signature | 
| doxy2swig.Doxy2SWIG.with_overloaded_functions = with_overloaded_functions | 
| doxy2swig.Doxy2SWIG.with_type_info = with_type_info | 
| doxy2swig.Doxy2SWIG.xmldoc = minidom.parse(f).documentElement |