Ejemplos de SequenceParser::getNamesOfGroups en C++ (Cpp)

Ejemplo n.º 1

//**********************************************************************************************************************
int SplitGroupCommand::runNameGroup(){
	try {
        SequenceParser* parser;
		if (namefile == "") {	parser = new SequenceParser(groupfile, fastafile);				}
		else				{	parser = new SequenceParser(groupfile, fastafile, namefile);	}
		
		if (m->control_pressed) { delete parser; return 0; }
        
		vector<string> namesGroups = parser->getNamesOfGroups();
		SharedUtil util;  util.setGroups(Groups, namesGroups);  
		
		string fastafileRoot = outputDir + m->getRootName(m->getSimpleName(fastafile));
		string namefileRoot = outputDir + m->getRootName(m->getSimpleName(namefile));
		
		m->mothurOutEndLine();
		for (int i = 0; i < Groups.size(); i++) {
			
			m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
			
            map<string, string> variables; 
            variables["[filename]"] = fastafileRoot;
            variables["[group]"] = Groups[i];

			string newFasta = getOutputFileName("fasta",variables);
            variables["[filename]"] = namefileRoot;
			string newName = getOutputFileName("name",variables);
			
			parser->getSeqs(Groups[i], newFasta, "/ab=", "/", false);
			outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
			if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0; }
            
			if (namefile != "") { 
				parser->getNameMap(Groups[i], newName); 
				outputNames.push_back(newName); outputTypes["name"].push_back(newName);
			}
			
			if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0; }
		}
		
		delete parser;
        
        return 0;

    }
	catch(exception& e) {
		m->errorOut(e, "SplitGroupCommand", "runNameGroup");
		exit(1);
	}
}