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();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
+
+ struct linePair {
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ };
+
+ vector<int> processIDS; //processid
+ vector<linePair*> lines;
+
int screenNameGroupFile(set<string>);
int screenGroupFile(set<string>);
int screenAlignReport(set<string>);
+ int screenQual(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&, vector<unsigned long int>&, set<string>&);
+ #endif
+
bool abort;
- string fastafile, namefile, groupfile, alignreport, outputDir;
- int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
+ 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