NFsim: /home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFinput/NFinput.hh Source File

00001 #ifndef NFINPUT_HH_
00002 #define NFINPUT_HH_
00003 
00004 #include <iostream>
00005 #include <map>
00006 #include <vector>
00007 #include <stdio.h>
00008 // JUSTIN -- added to resolve problem finding INT_MAX
00009 #include <limits.h>
00010 #include <exception>
00011 
00012 
00013 #include "../NFcore/NFcore.hh"
00014 #include "../NFoutput/NFoutput.hh"
00015 #include "../NFfunction/NFfunction.hh"
00016 #include "../NFreactions/reactions/reaction.hh"
00017 #include "TinyXML/tinyxml.h"
00018 
00019 using namespace NFcore;
00020 
00021 
00022 
00024 
00032 namespace NFinput {
00033 
00035 
00038         class component {
00039                 public:
00040                         component(TemplateMolecule *t, string name);
00041                         component(MoleculeType *mt, string name);
00042                         ~component();
00043 
00044                         TemplateMolecule * t;
00045                         MoleculeType *mt;
00046                         string name;
00047                         string uniqueId;
00048 
00049                         string symPermutationName;
00050 
00051 
00052                         string numOfBondsLabel;
00053                         string stateConstraintLabel;
00054         };
00055 
00056 
00057 
00059 
00062         System * initializeFromXML(
00063                         string filename,
00064                         bool blockSameComplexBinding,
00065                         int globalMoleculeLimit,
00066                         bool verbose,
00067                         int &suggestedTraversalLimit);
00068 
00070 
00073         bool initParameters(
00074                         TiXmlElement *pListOfParameters,
00075                         System *s,
00076                         map <string,double> &parameter,
00077                         bool verbose);
00078 
00079 
00081 
00084         bool initFunctions(
00085                 TiXmlElement * pListOfFunctions,
00086                 System * system,
00087                 map <string,double> &parameter,
00088                 TiXmlElement * pListOfObservables,
00089                 map<string,int> &allowedStates,
00090                 bool verbose);
00091 
00093 
00096         bool initMoleculeTypes(
00097                         TiXmlElement * pListOfMoleculeTypes,
00098                         System * system,
00099                         map<string,int> &allowedStates,
00100                         bool verbose);
00101 
00102 
00103 
00104 
00105 
00106         bool FindReactionRuleSymmetry(
00107                         TiXmlElement * pRxnRule,
00108                         System * s,
00109                         map <string,double> &parameter,
00110                         map<string,int> &allowedStates,
00111                         map <string, component> &symComps,
00112                         map <string, component> &symRxnCenter,
00113                         bool verbose);
00114 
00115         bool readPatternForSymmetry(
00116                         TiXmlElement * pListOfMol,
00117                         System * s,
00118                         string patternName,
00119                         map <string, component> &comps,
00120                         map <string, component> &symComps,
00121                         bool verbose);
00122 
00123         bool generateRxnPermutations(vector<map<string,component> > &permutations,
00124                         map<string,component> &symComps,
00125                         map<string,component> &symRxnCenter,
00126                         bool verbose);
00127 
00128 
00129         bool readObservableForTemplateMolecules(
00130                         TiXmlElement *pObs,
00131                         string observableName,
00132                         vector <TemplateMolecule *> &tmList,
00133                         vector <string> &stochRelation,
00134                         vector <int> &stochQuantity,
00135                         System *s,
00136                         map <string,double> &parameter,
00137                         map<string,int> &allowedStates,
00138                         int obsType,
00139                         bool verbose,
00140                         int &suggestedTraversalLimit);
00141 
00142 
00143 
00144 
00145 
00147 
00150         bool initStartSpecies(
00151                         TiXmlElement * pListOfSpecies,
00152                         System * system,
00153                         map <string,double> &parameter,
00154                         map<string,int> &allowedStates,
00155                         bool verbose);
00156 
00158 
00161         bool initReactionRules(
00162                         TiXmlElement * pListOfReactionRules,
00163                         System * system,
00164                         map <string,double> &parameter,
00165                         map<string,int> &allowedStates,
00166                         bool blockSameComplexBinding,
00167                         bool verbose,
00168                         int &suggestedTraversalLimit);
00169 
00171 
00174         bool initObservables(
00175                         TiXmlElement * pListOfObservables,
00176                         System * system,
00177                         map <string,double> &parameter,
00178                         map<string,int> &allowedStates,
00179                         bool verbose,
00180                         int &suggestedTraversalLimit);
00181 
00182 
00184 
00187         TemplateMolecule *readPattern(
00188                         TiXmlElement * pListOfMol,
00189                         System * s, map <string,double> &parameter,
00190                         map<string,int> &allowedStates,
00191                         string patternName,
00192                         map <string, TemplateMolecule *> &templates,
00193                         map <string, component> &comps,
00194                         map <string, component> &symMap,
00195                         bool verbose,
00196                         int &suggestedTraversalLimit);
00197 
00199 
00203                 bool readProductPattern(
00204                         TiXmlElement * pListOfMol,
00205                         System * s, map <string,double> &parameter,
00206                         map<string,int> &allowedStates,
00207                         string patternName,
00208                         vector <MoleculeType *> &productMoleculeTypes,
00209                         vector < vector <int> > &stateInformation,
00210                         vector < vector <int> > &bindingSiteInformation,
00211                         bool verbose);
00212 
00213 
00214         bool lookup(component *&c, string id, map<string,component> &comps, map<string,component> &symMap);
00215 
00216 
00217 
00219 
00222         bool parseArguments(int argc, const char *argv[], map<string,string> &argMap);
00223 
00224 
00226 
00229         int parseAsInt(map<string,string> &argMap, string argName, int defaultValue);
00230 
00232 
00235         double parseAsDouble(map<string,string> &argMap, string argName, double defaultValue);
00236 
00237 
00239 
00242         void parseAsCommaSeparatedSequence(map<string,string> &argMap,string argName,vector<int> &sequence);
00243 
00244 
00245 
00247 
00250         void walk(System *s);
00251 
00252 
00253 
00255 
00260         bool createSystemDumper(string paramStr, System *s, bool verbose);
00261 
00262 
00263 
00265 
00268         bool parseSequence(string numString, vector <double> &outputTimes);
00269 
00270 
00271 
00272 
00273 
00275 
00276         bool readRNFfile(map<string,string> &argMap, vector<string> &commands, bool verbose);
00277         bool runRNFcommands(System *s, map<string,string> &argMap, vector<string> &commands, bool verbose);
00278 
00279 
00280         //bool runRNFscript(map<string,string> argMap) {};
00281    // bool runRNFscript(System *s, string filename);
00282 }
00283 
00284 
00285 
00286 #endif /*NFINPUT_HH_*/