X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.h;h=0ab042bac365b64840e32212a6705f62d46d5ff1;hb=c7e8c2d15bd7cedcfdf18675cb0ea1a0dcd0e3c0;hp=45b51a89398af8fbd3551560ae425b28520706b6;hpb=8f89a92f4ada82a2b3bf51b23b6a977770f2b9e2;p=mothur.git

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 45b51a8..0ab042b 100644
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -18,20 +18,26 @@ 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 getOutputFileNameTag(string, string);
+	string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
+		string getDescription()		{ return "gets sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
+
+	
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
+	
 	private:
 		set<string> names;
-		vector<string> outputNames;
+		vector<string> outputNames, listOfTaxons;
 		string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
 		bool abort, dups;
-		map<string, vector<string> > outputTypes;
 		
 		int readFasta();
 		int readName();
@@ -39,8 +45,7 @@ class GetLineageCommand : public Command {
 		int readAlign();
 		int readList();
 		int readTax();	
-		string removeConfidences(string);
-		vector< map<string, int> > getTaxons(string);
+		vector< map<string, float> > getTaxons(string);
 };
 
 #endif