added groups option to read.otu, added qtrim option to trim.seqs, fixed bug in get...

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index f88fe2c442cf1d8ea6b0457a45390383c0c45698..269275d38409c251ef3f9b0b1c2552602367f348 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,27 +11,23 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-#include <set>
-
-using namespace std;
 
 class ScreenSeqsCommand : public Command {
        
 public:
-       ScreenSeqsCommand();
+       ScreenSeqsCommand(string);
        ~ScreenSeqsCommand();
        int execute();
+       void help();
+       
 private:
        void screenNameGroupFile(set<string>);
-       int numSeqs;    
-       GlobalData* globaldata; 
-       ReadSeqs* readSeqs;
-       SequenceDB* db;
+       void screenGroupFile(set<string>);
+       void screenAlignReport(set<string>);
+       
+       bool abort;
+       string fastafile, namefile, groupfile, alignreport;
+       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
 };
 
 #endif