X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapsimcommand.h;h=cd12c176f44994e4ea1da4128737dabe2931b6ac;hb=3a13eff5c26d6fc156a299c9fa7f5497bded94a0;hp=091da26af7db4cf4e9302c0e9a9d0e8a4587f5de;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 091da26..cd12c17 100644
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -22,7 +22,12 @@ 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();
 	
@@ -38,10 +43,13 @@ private:
 	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, line, label, calc;
-	vector<string> Estimators, Groups;
+	string format, groups, label, calc, phylipfile, columnfile, namefile, outputDir;
+	vector<string> Estimators, Groups, outputNames;
+	map<string, vector<string> > outputTypes;
+	
+	int runCommandShared();
+	int runCommandDist();
 
 
 };