broke up globaldata and moved error checking and help into commands

[mothur.git] / heatmapcommand.h

diff --git a/heatmapcommand.h b/heatmapcommand.h
index 5eeae265471785c8d582e7b250c76046554711e7..2ae9882db4ff0c5390293cdfd6ea0e2b2c496c11 100644 (file)
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -13,32 +13,38 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "sharedlistvector.h"
 #include "heatmap.h"
-
+#include "rabundvector.hpp"
 
 class GlobalData;
 
-
 class HeatMapCommand : public Command {
 
 public:
-       HeatMapCommand();
+       HeatMapCommand(string);
        ~HeatMapCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        InputData* input;
        SharedListVector* SharedList;
-       SharedOrderVector* order;
-       OrderVector* ordersingle;
+       RAbundVector* rabund;
+       vector<SharedRAbundVector*> lookup;
        HeatMap* heatmap;
-       string format;
-       
-       void setGroups();
+       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;
+
 
 };