added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / heatmapsimcommand.h

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index ba5a240c8ade230de7433413cefe1dcfdf930402..2c3a470761d719af0bff13bc4d194e5164bd42e0 100644 (file)
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -26,9 +26,11 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "heatmap.sim";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        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()); }  
        
@@ -41,8 +43,9 @@ 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();