broke up globaldata and moved error checking and help into commands

[mothur.git] / heatmapcommand.h

diff --git a/heatmapcommand.h b/heatmapcommand.h
index fc50554c601c3c897f949775de7743c94cf33c9a..2ae9882db4ff0c5390293cdfd6ea0e2b2c496c11 100644 (file)
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -23,9 +23,10 @@ class GlobalData;
 class HeatMapCommand : public Command {
 
 public:
-       HeatMapCommand();
+       HeatMapCommand(string);
        ~HeatMapCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -35,7 +36,15 @@ private:
        RAbundVector* rabund;
        vector<SharedRAbundVector*> lookup;
        HeatMap* heatmap;
-       string 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
+       string format, groups, sorted, scale, line, label;
+       vector<string> Groups;
+
 
 };