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