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