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