added cluster.classic command

[mothur.git] / heatmapcommand.h

diff --git a/heatmapcommand.h b/heatmapcommand.h
index 2ae9882db4ff0c5390293cdfd6ea0e2b2c496c11..a85d510074c55a73adc25b07f16a8a81bdd4a30c 100644 (file)
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -24,7 +24,12 @@ 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();
        
@@ -35,15 +40,15 @@ private:
        SharedListVector* SharedList;
        RAbundVector* rabund;
        vector<SharedRAbundVector*> lookup;
+       vector<SharedRAbundFloatVector*> lookupFloat;
        HeatMap* heatmap;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
+
        bool abort, allLines;
-       set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
-       string format, groups, sorted, scale, line, label;
-       vector<string> Groups;
+       string format, groups, sorted, scale, label, outputDir;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
+       int numOTU, fontSize;
 
 
 };