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