public:
SeqSummaryCommand(string);
SeqSummaryCommand();
- ~SeqSummaryCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~SeqSummaryCommand(){}
+ vector<string> setParameters();
+ string getCommandName() { return "summary.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
string fastafile, outputDir, namefile;
int processors;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
map<string, int> nameMap;
struct linePair {
int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);
- int readNames();
#ifdef USE_MPI
int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&);