X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapsimcommand.h;h=f421fdc5bf2c3ff8aed22a197afc3309a86b4e34;hp=2a2c3676b31610b32dcb4b3996dc7134aa6078ed;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 2a2c367..f421fdc 100644
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -26,8 +26,12 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "heatmap.sim";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getHelpString();	
 	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; }
+	string getDescription()		{ return "generate a heatmap indicating the pairwise distance between multiple samples using a variety of calculators"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
@@ -36,13 +40,13 @@ private:
 	InputData* input;
 	vector<SharedRAbundVector*> lookup;
 	vector<Calculator*> heatCalculators;
-	ValidCalculators* validCalculator;
 	HeatMapSim* heatmap;
 	OptionParser* parser;
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
-	string format, groups, label, calc, sharedfile, phylipfile, columnfile, namefile, outputDir, inputfile;
+	string format, groups, label, calc, sharedfile, phylipfile, columnfile, countfile, namefile, outputDir, inputfile;
 	vector<string> Estimators, Groups, outputNames;
+	int fontsize;
 	
 	int runCommandShared();
 	int runCommandDist();