C++ Data::AddSpecies方法代码示例

void ProcessWebInterfaceModels() {
	string Filename(GetParameter("web interface model directory"));
	Filename.append("ModelList.txt");
	vector<string> Lines = ReadStringsFromFile(Filename,false);

	//this database will hold a combination of all of the model compounds and reactions
	Data* CompleteDatabase = new Data(0);

	//the following structures will hold the data for the various models as they are read in
	vector<Data*> Models;
	vector< map<string, Identity*, std::less<string> > > ModelGenes;
	map<string, vector<string>, std::less<string> > ReactionGenes;
	map<string, vector<string>, std::less<string> > ReactionModels;
	map<string, vector<string>, std::less<string> > CompoundModels;
	//Reading in the models and storing the data in the above structures
	for (int i=1; i < int(Lines.size()); i++) {
		cout << i << endl;
		//Parsing the model list line
		vector<string>* Strings = StringToStrings(Lines[i], "\t");
		
		if (Strings->size() >= 4) {
			Filename.assign(GetParameter("web interface model directory"));
			Filename.append((*Strings)[3]);
		}

		//Loading each model from the combined model file
		if (FileExists(Filename)) {
			map<string, Identity*, std::less<string> > CurrentGeneData;
			ModelGenes.push_back(CurrentGeneData);
			Data* NewData = new Data(0);
			Models.push_back(NewData);
			NewData->AddData("NAME",(*Strings)[0].data(),STRING);
			NewData->AddData("AUTHORS",(*Strings)[1].data(),STRING);
			NewData->AddData("ORGANISMS NAME",(*Strings)[2].data(),STRING);
			NewData->AddData("FILENAME",(*Strings)[3].data(),STRING);
			NewData->LoadSystem(Filename);
			//Loading additional data on compounds and reactions from the centralized database
			int TotalTransported = 0;
			for (int j=0; j < NewData->FNumSpecies(); j++) {
				if (NewData->GetSpecies(j)->FExtracellular()) {
					TotalTransported++;
				}
				NewData->GetSpecies(j)->LoadSpecies(NewData->GetSpecies(j)->GetData("DATABASE",STRING));
				CompoundModels[NewData->GetSpecies(j)->Query("CGI_ID")].push_back((*Strings)[0]);
				if (CompleteDatabase->FindSpecies("DATABASE;CGI_ID",NewData->GetSpecies(j)->Query("CGI_ID").data()) == NULL && CompleteDatabase->FindSpecies("DATABASE;CGI_ID",NewData->GetSpecies(j)->GetData("DATABASE",STRING).data()) == NULL) {
					CompleteDatabase->AddSpecies(NewData->GetSpecies(j));
				}
			}
			//Note that the reaction equation that was read in was cleared in favor of the database equation... this could lead to problems
			int TotalReactionsWithGenes = 0;
			for (int j=0; j < NewData->FNumReactions(); j++) {
				NewData->GetReaction(j)->LoadReaction(NewData->GetReaction(j)->GetData("DATABASE",STRING));
				ReactionModels[NewData->GetReaction(j)->Query("CGI_ID")].push_back((*Strings)[0]);
				//Capturing the gene data for entry into the gene hash
				vector<string> GeneData = NewData->GetReaction(j)->GetAllData("ASSOCIATED PEG",DATABASE_LINK);
				if (GeneData.size() > 0) {
					TotalReactionsWithGenes++;
				}
				for (int k=0; k < int(GeneData.size()); k++) {
					//Adding the gene to the reaction gene hash
					string GeneName((*Strings)[2]);
					GeneName.append(":");
					GeneName.append(GeneData[k]);
					ReactionGenes[NewData->GetReaction(j)->Query("CGI_ID")].push_back(GeneName);
					//Finding the gene and creating a new gene if the gene does not currently exist
					Identity* CurrentGene = ModelGenes[ModelGenes.size()-1][GeneData[k]];
					if (CurrentGene == NULL) {
						CurrentGene = new Identity;
						ModelGenes[ModelGenes.size()-1][GeneData[k]] = CurrentGene;
					}
					//Adding the reaction data to the gene data
					CurrentGene->AddData("REACTIONS",NewData->GetReaction(j)->Query("CGI_ID").data(),STRING);
					vector<string> EnzymeData = NewData->GetReaction(j)->GetAllData("ENZYME",DATABASE_LINK);
					for (int l=0; l < int(EnzymeData.size()); l++) {
						CurrentGene->AddData("ENZYME",EnzymeData[l].data(),STRING);
					}
					EnzymeData = NewData->GetReaction(j)->GetAllData("PATHWAYS",STRING);
					for (int l=0; l < int(EnzymeData.size()); l++) {
						CurrentGene->AddData("PATHWAY",EnzymeData[l].data(),STRING);
					}

				}
				//Adding all unique reactions to the complete database
				if (CompleteDatabase->FindReaction("DATABASE;CGI_ID",NewData->GetReaction(j)->Query("CGI_ID").data()) == NULL && CompleteDatabase->FindReaction("DATABASE;CGI_ID",NewData->GetReaction(j)->GetData("DATABASE",STRING).data()) == NULL) {
					CompleteDatabase->AddReaction(NewData->GetReaction(j));
				}
			}
			//Searching the model for dead compounds and reactions
			NewData->FindDeadEnds();
			NewData->AddData("TRANSPORTED COMPOUNDS",double(TotalTransported));
			NewData->AddData("REACTION WITH GENES",double(TotalReactionsWithGenes));
		}

		delete Strings;
	}

	//Printing the combined compounds table
	Filename.assign(GetParameter("web interface model directory"));
	Filename.append("AllCompoundsTable.txt");
	ofstream CompleteOutput;
//.........这里部分代码省略.........