public:
TrimFlowsCommand(string);
TrimFlowsCommand();
- ~TrimFlowsCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~TrimFlowsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "trim.flows"; }
+ string getCommandCategory() { return "Hidden"; }
+ string getHelpString();
+ string getCitation() { return "no citation"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >);
int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
- map<string, vector<string> > outputTypes;
vector<string> outputNames;
set<string> filesToRemove;
-
-
void getOligos(vector<vector<string> >&); //a rewrite of what is in trimseqscommand.h
int stripBarcode(Sequence&, int&); //largely redundant with trimseqscommand.h
int stripForward(Sequence&, int&); //largely redundant with trimseqscommand.h