*/
#include "command.hpp"
-#include "mothur.h"
#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
+#include "sequence.hpp"
class FilterSeqsCommand : public Command {
public:
- FilterSeqsCommand() {};
+ FilterSeqsCommand();
~FilterSeqsCommand() {};
int execute();
private:
- void doTrump();
+ void doHard();
+ void doTrump(Sequence);
+ void doVertical();
void doSoft();
- void doFilter();
-
- GlobalData* globaldata;
- string filename, trump, filter;
-
- ReadFasta* readFasta;
- ReadNexus* readNexus;
- ReadClustal* readClustal;
- ReadPhylip* readPhylip;
+ void getFreqs(Sequence);
+ string filter;
+ int alignmentLength;
+
+ char trump;
+ bool vertical;
+ float soft;
+ int numSeqs;
- vector<bool> columnsToRemove;
- SequenceDB* db;
- double soft;
+ GlobalData* globaldata;
+ vector<int> a, t, g, c, gap;
+
};
-#endif
\ No newline at end of file
+#endif