*/
#include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
+#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 doSoft(Sequence);
- void doVertical(Sequence);
- string filter;
+ string vertical, filter, fastafile, hard, outputDir;
int alignmentLength;
char trump;
- bool vertical;
-
- GlobalData* globaldata;
-// ReadSeqs* readSeqs;
-// SequenceDB* db;
+ bool abort;
+ float soft;
+ int numSeqs;
+ Filters F;
+
+ vector<int> a, t, g, c, gap;
};