broke up globaldata and moved error checking and help into commands

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 9b987261d10cc62f5296d1717752eb5d7c587dae..97b36155af670c3d038c882e742356a1c6ee9a03 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -16,14 +16,22 @@
 class ScreenSeqsCommand : public Command {
        
 public:
-       ScreenSeqsCommand();
+       ScreenSeqsCommand(string);
        ~ScreenSeqsCommand();
        int execute();
+       void help();
+       
 private:
        void screenNameGroupFile(set<string>);
        void screenGroupFile(set<string>);
 
        GlobalData* globaldata; 
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort;
+       string fastafile, namefile, groupfile;
+       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
 };
 
 #endif