X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapsimcommand.h;h=f421fdc5bf2c3ff8aed22a197afc3309a86b4e34;hp=dbaa6840b4513ca085da696c485e5b73e74f37b9;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index dbaa684..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()); }	
 	
@@ -40,8 +44,9 @@ private:
 	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();