get.oturep change and trim.seqs fix

[mothur.git] / heatmapsimcommand.h

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 33696a33ac87b34bedea636810b32e4daa09be8c..cd12c176f44994e4ea1da4128737dabe2931b6ac 100644 (file)
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -21,9 +21,15 @@ class GlobalData;
 class HeatMapSimCommand : public Command {
 
 public:
+       HeatMapSimCommand(string);
        HeatMapSimCommand();
        ~HeatMapSimCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -33,6 +39,18 @@ private:
        vector<Calculator*> heatCalculators;
        ValidCalculators* validCalculator;
        HeatMapSim* heatmap;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string format, groups, label, calc, phylipfile, columnfile, namefile, outputDir;
+       vector<string> Estimators, Groups, outputNames;
+       map<string, vector<string> > outputTypes;
+       
+       int runCommandShared();
+       int runCommandDist();
+
 
 };