*/
#include "command.hpp"
-#include "globaldata.hpp"
-#include "sequence.hpp"
+#include "filters.h"
+class Sequence;
class FilterSeqsCommand : public Command {
public:
- FilterSeqsCommand();
+ FilterSeqsCommand(string);
~FilterSeqsCommand() {};
int execute();
+ void help();
private:
- void doHard();
- void doTrump(Sequence);
- void doVertical();
- void doSoft();
- void getFreqs(Sequence);
- string filter;
+ string vertical, filter, fastafile, hard;
int alignmentLength;
char trump;
- bool vertical;
+ bool abort;
float soft;
int numSeqs;
- GlobalData* globaldata;
+ Filters F;
+
vector<int> a, t, g, c, gap;
};