#include "mothur.h"
#include "command.hpp"
-#include "globaldata.hpp"
+
class ShhherCommand : public Command {
public:
ShhherCommand(string);
ShhherCommand();
- ~ShhherCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ShhherCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "shhh.seqs"; }
+ string getCommandCategory() { return "Hidden"; }
+ string getHelpString();
+ string getCitation() { return "no citation"; }
+ string getDescription() { return "shhh.seqs"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
int abort;
- map<string, vector<string> > outputTypes;
- string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName;
+ string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName, compositeNamesFileName;
int processors, maxIters;
float cutoff, sigma, minDelta;
+ string flowOrder;
vector<int> nSeqsBreaks;
vector<int> nOTUsBreaks;
vector<int> mapSeqToUnique;
vector<int> mapUniqueToSeq;
vector<int> uniqueLengths;
-
+
+ vector<string> outputNames;
+
int numSeqs, numUniques, numOTUs, numFlowCells;
void getSingleLookUp();