broke up globaldata and moved error checking and help into commands

[mothur.git] / heatmapsimcommand.h

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 33696a33ac87b34bedea636810b32e4daa09be8c..091da26af7db4cf4e9302c0e9a9d0e8a4587f5de 100644 (file)
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -21,9 +21,10 @@ class GlobalData;
 class HeatMapSimCommand : public Command {
 
 public:
-       HeatMapSimCommand();
+       HeatMapSimCommand(string);
        ~HeatMapSimCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -33,6 +34,15 @@ private:
        vector<Calculator*> heatCalculators;
        ValidCalculators* validCalculator;
        HeatMapSim* heatmap;
+       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 format, groups, line, label, calc;
+       vector<string> Estimators, Groups;
+
 
 };