Graph grammar rule parser. More...

#include <Rule_GML_grammar.hh>

Inheritance diagram for ggl::Rule_GML_grammar:

Data Structures
struct	definition
	The definition of the GML grammar. More...

class	keys_map

struct	keyvalue_closure

struct	lt_edge

struct	lt_node

Public Member Functions
	Rule_GML_grammar (Rule::CoreGraph &toFill, std::string &ruleID, std::vector< sgm::Pattern_Interface::Match_Constraint * > &ruleConstraints, Rule::CopyAndPasteOperations &copyAndPaste, std::string &wildcard)

Static Public Member Functions
static std::pair< Rule, int >	parseRule (const std::string &GML_string) throw (Rule_GML_error)

Protected Types
typedef boost::tuple< int, int, std::string, std::string >	edge_t

typedef std::map< std::string, kv_values_t >	keys_map_t

enum	kv_values { Y_CONTXT = -3, N_CONTXT = -2, UNKNOWN = -1, INT_VAL = 0, STR_VAL = 1, DBL_VAL = 2, LST_VAL = 3, STRLST_VAL = 4 }
	enummeration of value types in gml key-value pairs More...

typedef enum kv_values	kv_values_t

typedef boost::tuple< int, std::string, std::string >	node_t

Static Protected Member Functions
static std::string	trimQuotes (const std::string &s)

Protected Attributes
Rule::CopyAndPasteOperations &	copyAndPaste
	The copy-and-Paste operation container to be filled. More...

boost::property_map < Rule::CoreGraph, Rule::EdgeContextProperty > ::type	edgeContext
	Access to the edge Rule context property_map of g2fill. More...

boost::property_map < Rule::CoreGraph, Rule::EdgeLabelProperty > ::type	edgeLabel
	Access to the edge label property_map of g2fill to set edge labels. More...

Rule::CoreGraph &	g2fill

boost::property_map < Rule::CoreGraph, Rule::NodeContextProperty > ::type	nodeContext
	Access to the node Rule context property_map of g2fill. More...

boost::property_map < Rule::CoreGraph, Rule::NodeLabelProperty > ::type	nodeLabel
	Access to the node label property_map of g2fill to set node labels. More...

boost::property_map < Rule::CoreGraph, Rule::NodeRightLabelProperty > ::type	nodeLabelRight

std::vector < sgm::Pattern_Interface::Match_Constraint * > &	ruleConstraints
	The additional constraints to be fulfilled by the rule to be filled. More...

std::string &	ruleID
	The rule id that is filled. More...

std::string &	wildcard
	The wildcard label that is filled if present. More...

Detailed Description

  Parses a GML string representation of a ggl::Rule object.

  Example :

      ====== RULE TO ENCODE =======================

        3(D) -1- 1(B)               3(E) -1- 1(B)
         |      /                    |        |
         2    3           ==>        4        3
         |  /                        |        |
        2(C) -0- 0(A)               2(C)     4(D)

      ======= RULE IN GML =========================

      rule [
              ruleID "Example rule"
              context [
                      node [ id 1 label "B" ]
                      node [ id 2 label "C" ]
                      edge [ source 1 target 3 label "-1-" ]
              ]
              left [
                      node [ id 0 label "A" ]
                      node [ id 3 label "D" ]
                      edge [ source 0 target 2 label "-0-" ]
                      edge [ source 1 target 2 label "-3-" ]
                      edge [ source 2 target 3 label "-2-" ]
              ]
              right [
                      node [ id 3 label "E" ]
                      node [ id 4 label "D" ]
                      edge [ source 2 target 3 label "-4-" ]
                      edge [ source 1 target 4 label "-3-" ]
              ]
      ]

      =============================================
    *

BNF grammar of GML (http://www.infosun.fim.uni-passau.de/Graphlet/GML/)

       gml            ::= keyvalues
       keyvalues      ::= keyvalue (keyvalue)
       keyvalue       ::= key value
       key            ::= ['a'-'z''A'-'Z']['a'-'z''A'-'Z''0'-'9']
       value          ::= real | integer | string | operator | list
       real           ::= sign? digit  '.' digit+ mantissa
       integer        ::= sign? digit+
       string         ::= '"' instring '"'
       operator       ::= '>' | '<' | '=' | '!'
       list           ::= '[' keyvalues ']'
       sign           ::= '+' | '-'
       digit          ::= ['0'-'9']
       mantissa       ::= ('E' | 'e') sign? digit+
       instring       ::= ASCII-{'&', '"'} | '&' ['a'-'z''A'-'Z']  ';'
    *

Author: Christoph Flamm (c) 2008 http://www.tbi.univie.ac.at/~xtof/; Martin Mann (c) 2008 http://www.bioinf.uni-freiburg.de/~mmann/

Definition at line 117 of file Rule_GML_grammar.hh.

Member Typedef Documentation

typedef boost::tuple<int,int,std::string,std::string> ggl::Rule_GML_grammar::edge_t

protected

Definition at line 136 of file Rule_GML_grammar.hh.

typedef std::map<std::string, kv_values_t> ggl::Rule_GML_grammar::keys_map_t

protected

Definition at line 145 of file Rule_GML_grammar.hh.

typedef enum kv_values ggl::Rule_GML_grammar::kv_values_t

protected

Definition at line 135 of file Rule_GML_grammar.hh.

typedef boost::tuple<int,std::string,std::string> ggl::Rule_GML_grammar::node_t

protected

Definition at line 137 of file Rule_GML_grammar.hh.

Member Enumeration Documentation

enum ggl::Rule_GML_grammar::kv_values

protected

Enumerator
Y_CONTXT
N_CONTXT
UNKNOWN
INT_VAL
STR_VAL
DBL_VAL
LST_VAL
STRLST_VAL

Definition at line 123 of file Rule_GML_grammar.hh.

Constructor & Destructor Documentation

ggl::Rule_GML_grammar::Rule_GML_grammar	(	Rule::CoreGraph &	toFill,
		std::string &	ruleID,
		std::vector< sgm::Pattern_Interface::Match_Constraint * > &	ruleConstraints,
		Rule::CopyAndPasteOperations &	copyAndPaste,
		std::string &	wildcard
	)

explicit

Constructs the definitions of a GML graph grammar to parse a GML graph string representation and to fill the encoded graph into a given boost graph object.

Parameters

toFill	the Rule core graph object to add nodes and edges to
ruleID	the Rule ID to set
ruleConstraints	the additional constraints that have to be met by the rule
copyAndPaste	the copy-and-Paste operation container to fill
wildcard	the wildcard string to be filled. NOTE: if no wildcard was parsed this string is not changed, so check for a change to know if a wildcard was parsed or not!

Member Function Documentation

static std::pair< Rule, int > ggl::Rule_GML_grammar::parseRule ( const std::string & GML_string ) throw (Rule_GML_error)

static

Parses a GML string and generates a Rule object

Parameters

GML_string the string to parse

Returns: pair.first = the graph encoding of the molecule pair.second = -1 if parsing was successfull, in error case it returns the string position that caused the parsing error

Exceptions

ggl::Rule_GML_error if parsing errors occur

static std::string ggl::Rule_GML_grammar::trimQuotes ( const std::string & s )

staticprotected

Trims leading and tailing quotes from a string

Parameters

s	the string to trim

Returns: the trimmed string

Field Documentation

Rule::CopyAndPasteOperations& ggl::Rule_GML_grammar::copyAndPaste

protected

Definition at line 248 of file Rule_GML_grammar.hh.

boost::property_map<Rule::CoreGraph , Rule::EdgeContextProperty>::type ggl::Rule_GML_grammar::edgeContext

mutableprotected

Definition at line 282 of file Rule_GML_grammar.hh.

boost::property_map<Rule::CoreGraph , Rule::EdgeLabelProperty>::type ggl::Rule_GML_grammar::edgeLabel

mutableprotected

Definition at line 276 of file Rule_GML_grammar.hh.

Rule::CoreGraph& ggl::Rule_GML_grammar::g2fill

protected

The boost core graph object that is filled to represent the next parsed Rule.

Definition at line 239 of file Rule_GML_grammar.hh.

boost::property_map<Rule::CoreGraph , Rule::NodeContextProperty>::type ggl::Rule_GML_grammar::nodeContext

mutableprotected

Definition at line 270 of file Rule_GML_grammar.hh.

boost::property_map<Rule::CoreGraph , Rule::NodeLabelProperty>::type ggl::Rule_GML_grammar::nodeLabel

mutableprotected

Definition at line 257 of file Rule_GML_grammar.hh.

boost::property_map<Rule::CoreGraph , Rule::NodeRightLabelProperty>::type ggl::Rule_GML_grammar::nodeLabelRight

mutableprotected

Access to the right node label property_map of g2fill to set changing node labels

Definition at line 264 of file Rule_GML_grammar.hh.

std::vector< sgm::Pattern_Interface::Match_Constraint* >& ggl::Rule_GML_grammar::ruleConstraints

protected

Definition at line 245 of file Rule_GML_grammar.hh.

std::string& ggl::Rule_GML_grammar::ruleID

protected

Definition at line 242 of file Rule_GML_grammar.hh.

std::string& ggl::Rule_GML_grammar::wildcard

protected

Definition at line 251 of file Rule_GML_grammar.hh.

The documentation for this class was generated from the following file:

src/ggl/Rule_GML_grammar.hh

Data Structures

Public Member Functions

Static Public Member Functions

Protected Types

Static Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation