added cluster.classic command

[mothur.git] / heatmapcommand.h

diff --git a/heatmapcommand.h b/heatmapcommand.h
index fc50554c601c3c897f949775de7743c94cf33c9a..a85d510074c55a73adc25b07f16a8a81bdd4a30c 100644 (file)
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -23,9 +23,15 @@ class GlobalData;
 class HeatMapCommand : public Command {
 
 public:
+       HeatMapCommand(string);
        HeatMapCommand();
        ~HeatMapCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -34,8 +40,16 @@ private:
        SharedListVector* SharedList;
        RAbundVector* rabund;
        vector<SharedRAbundVector*> lookup;
+       vector<SharedRAbundFloatVector*> lookupFloat;
        HeatMap* heatmap;
-       string format;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string format, groups, sorted, scale, label, outputDir;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
+       int numOTU, fontSize;
+
 
 };