X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.h;h=6375b9483fb335bafde123f3e99e4620c2614234;hb=2405cc589aaaf0c44809a48fe98d3b96863dac0b;hp=45b51a89398af8fbd3551560ae425b28520706b6;hpb=8f89a92f4ada82a2b3bf51b23b6a977770f2b9e2;p=mothur.git

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 45b51a8..6375b94 100644
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -18,20 +18,22 @@ class GetLineageCommand : public Command {
 	
 		GetLineageCommand(string);
 		GetLineageCommand();
-		~GetLineageCommand(){};
-		vector<string> getRequiredParameters();
-		vector<string> getValidParameters();
-		vector<string> getRequiredFiles();
-		map<string, vector<string> > getOutputFiles() { return outputTypes; }
-		int execute();
-		void help();	
-		
+		~GetLineageCommand(){}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "get.lineage";				}
+		string getCommandCategory()		{ return "Phylotype Analysis";		}
+		string getHelpString();	
+	
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
+	
 	private:
 		set<string> names;
 		vector<string> outputNames;
 		string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
 		bool abort, dups;
-		map<string, vector<string> > outputTypes;
 		
 		int readFasta();
 		int readName();
@@ -40,7 +42,7 @@ class GetLineageCommand : public Command {
 		int readList();
 		int readTax();	
 		string removeConfidences(string);
-		vector< map<string, int> > getTaxons(string);
+		vector< map<string, float> > getTaxons(string);
 };
 
 #endif