added an alignreport option to screen seqs

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 9b987261d10cc62f5296d1717752eb5d7c587dae..269275d38409c251ef3f9b0b1c2552602367f348 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,19 +11,23 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 
 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;
+       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
 };
 
 #endif