X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.h;h=0ab042bac365b64840e32212a6705f62d46d5ff1;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=5b7c43ed65808f7038b3c46cb96f3b7a32b8849a;hpb=a4f05f09c250323132a4b9427f41a3ededaec634;p=mothur.git

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 5b7c43e..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();
@@ -39,7 +45,6 @@ class GetLineageCommand : public Command {
 		int readAlign();
 		int readList();
 		int readTax();	
-		string removeConfidences(string);
 		vector< map<string, float> > getTaxons(string);
 };