X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapsimcommand.h;h=cd12c176f44994e4ea1da4128737dabe2931b6ac;hb=662c0b60d65f79f672ab199300b7ee4975233465;hp=33696a33ac87b34bedea636810b32e4daa09be8c;hpb=f15f7092c97277337d4fdd9ef674015c15a13220;p=mothur.git

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 33696a3..cd12c17 100644
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -21,9 +21,15 @@ class GlobalData;
 class HeatMapSimCommand : public Command {
 
 public:
+	HeatMapSimCommand(string);
 	HeatMapSimCommand();
 	~HeatMapSimCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
@@ -33,6 +39,18 @@ private:
 	vector<Calculator*> heatCalculators;
 	ValidCalculators* validCalculator;
 	HeatMapSim* heatmap;
+	OptionParser* parser;
+	map<string, string> parameters;
+	map<string, string>::iterator it;
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string format, groups, label, calc, phylipfile, columnfile, namefile, outputDir;
+	vector<string> Estimators, Groups, outputNames;
+	map<string, vector<string> > outputTypes;
+	
+	int runCommandShared();
+	int runCommandDist();
+
 
 };