pat's differences before v.1.8

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 56c9d82f1625a2a9481a203b7b217a9bc3b66bc4..5b44091dbd07d044f0de288490ff0d4633495008 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,25 +11,23 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
 
 class ScreenSeqsCommand : public Command {
        
 public:
-       ScreenSeqsCommand();
+       ScreenSeqsCommand(string);
        ~ScreenSeqsCommand();
        int execute();
+       void help();
+       
 private:
        void screenNameGroupFile(set<string>);
        void screenGroupFile(set<string>);
-
-       GlobalData* globaldata; 
+       void screenAlignReport(set<string>);
+       
+       bool abort;
+       string fastafile, namefile, groupfile, alignreport, outputDir;
+       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
 };
 
 #endif