public:
ScreenSeqsCommand(string);
- ~ScreenSeqsCommand();
- int execute();
- void help();
+ ScreenSeqsCommand();
+ ~ScreenSeqsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "screen.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
+ string getDescription() { return "enables you to keep sequences that fulfill certain user defined criteria"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
int screenNameGroupFile(set<string>);
int screenGroupFile(set<string>);
int screenAlignReport(set<string>);
+ int screenQual(set<string>);
- int driver(linePair*, string, string, string, string, set<string>&);
- int createProcesses(string, string, string, string, set<string>&);
+ int driver(linePair*, string, string, string, set<string>&);
+ int createProcesses(string, string, string, set<string>&);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
#endif
bool abort;
- string fastafile, namefile, groupfile, alignreport, outputDir;
- int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
+ string fastafile, namefile, groupfile, alignreport, outputDir, qualfile;
+ int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
vector<string> outputNames;
+ vector<string> optimize;
+ map<string, int> nameMap;
+ int readNames();
+
+ int getSummary(vector<unsigned long int>&);
+ int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
+ int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair*);
};
#endif