pat's differences before v.1.8

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 97b36155af670c3d038c882e742356a1c6ee9a03..5b44091dbd07d044f0de288490ff0d4633495008 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,7 +11,6 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 
 class ScreenSeqsCommand : public Command {
        
@@ -24,13 +23,10 @@ public:
 private:
        void screenNameGroupFile(set<string>);
        void screenGroupFile(set<string>);
-
-       GlobalData* globaldata; 
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
+       void screenAlignReport(set<string>);
+       
        bool abort;
-       string fastafile, namefile, groupfile;
+       string fastafile, namefile, groupfile, alignreport, outputDir;
        int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
 };