X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.h;h=e45e21b74a9ae58a6beef19a9a484344364c31de;hb=e99751591aa21705e58edda87383457b9738dd9e;hp=b61c03939492fe4147225fadb159e00b9a0ef71e;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/phylotypecommand.h b/phylotypecommand.h
index b61c039..e45e21b 100644
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -20,19 +20,29 @@ class PhylotypeCommand : public Command {
 	
 public:
 	PhylotypeCommand(string);	
+	PhylotypeCommand();
 	~PhylotypeCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute(); 
 	void help();	
 	
 private:
 	bool abort, allLines;
-	string taxonomyFileName, label, outputDir;
+	string taxonomyFileName, label, outputDir, namefile;
 	set<string> labels; //holds labels to be used
 	int cutoff;
+	map<string, string> namemap;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
 	
 	map<int, int> currentNodes;
 	map<int, int> parentNodes;
 	map<int, int>::iterator itCurrent;
+	
+	int readNamesFile();
 
 };