broke up globaldata and moved error checking and help into commands

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index a21167e3d07e2064c6e9a1dae736b0b1aeccf3a8..586e6ef36e5ca3ab015db96b493c191612a9330a 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -33,9 +33,10 @@ class GlobalData;
 
 class ReadOtuCommand : public Command {
 public:
-       ReadOtuCommand();
+       ReadOtuCommand(string);
        ~ReadOtuCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -44,7 +45,14 @@ private:
        Command* shared;
        Command* parselist;
        GroupMap* groupMap;
-       string filename;
+       string filename, listfile, orderfile, sharedfile, line, label, groupfile, sabundfile, rabundfile, format;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+
 };
 
 #endif