X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=269275d38409c251ef3f9b0b1c2552602367f348;hb=e7729bb337cfefcaba24549092cc89b44002af39;hp=9b987261d10cc62f5296d1717752eb5d7c587dae;hpb=faf4e99552d6fb4595ff348b1f909ddc74536da2;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 9b98726..269275d 100644
--- 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