Revert to previous commit

[mothur.git] / heatmapcommand.h

diff --git a/heatmapcommand.h b/heatmapcommand.h
new file mode 100644 (file)
index 0000000..ccd5f48
--- /dev/null
+++ b/heatmapcommand.h
@@ -0,0 +1,57 @@
+#ifndef HEATMAPCOMMAND_H
+#define HEATMAPCOMMAND_H
+
+/*
+ *  heatmapcommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/25/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedlistvector.h"
+#include "heatmap.h"
+#include "rabundvector.hpp"
+
+
+class HeatMapCommand : public Command {
+
+public:
+       HeatMapCommand(string);
+       HeatMapCommand();
+       ~HeatMapCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "heatmap.bin";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Heatmap.bin"; }
+       string getDescription()         { return "generate a heatmap where the color represents the relative abundanceof an OTU"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       InputData* input;
+       RAbundVector* rabund;
+       vector<SharedRAbundVector*> lookup;
+       vector<SharedRAbundFloatVector*> lookupFloat;
+       HeatMap* heatmap;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string format, groups, sorted, scale, label, outputDir, sharedfile, relabundfile, listfile, rabundfile, sabundfile, inputfile;
+       vector<string> Groups, outputNames;
+       int numOTU, fontSize;
+
+
+};
+
+#endif
+