broke up globaldata and moved error checking and help into commands

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index 135c4025ec15d0097c6bee83f239039bf22c83f4..895f9d7429deac952eab6a0bd29ee9fb07dd95a3 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -33,9 +33,10 @@ class GlobalData;
 class SummaryCommand : public Command {
 
 public:
-       SummaryCommand();
+       SummaryCommand(string);
        ~SummaryCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -47,5 +48,14 @@ private:
        string outputFileName;
        ofstream outputFileHandle;
        int abund, size;
+       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
+       string line, label, calc;
+       vector<string>  Estimators;
+
 };
 #endif