*/
#include "mothur.h"
#include "command.hpp"
-#include "globaldata.hpp"
class ScreenSeqsCommand : public Command {
void help();
private:
- void screenNameGroupFile(set<string>);
- void screenGroupFile(set<string>);
-
- GlobalData* globaldata;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
+ int screenNameGroupFile(set<string>);
+ int screenGroupFile(set<string>);
+ int screenAlignReport(set<string>);
+
bool abort;
- string fastafile, namefile, groupfile;
+ string fastafile, namefile, groupfile, alignreport, outputDir;
int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
+ vector<string> outputNames;
};
#endif