X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.h;h=99bc0fa347313bb023e8bd1b41a5c3e2be5c93ed;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=d62c50f55d253b7e3fd15790e2a6d4b21cb35b8f;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/getlineagecommand.h b/getlineagecommand.h
index d62c50f..99bc0fa 100644
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -23,8 +23,11 @@ class GetLineageCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "get.lineage";				}
 		string getCommandCategory()		{ return "Phylotype Analysis";		}
-		string getHelpString();	
+		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()); }	
@@ -32,17 +35,17 @@ class GetLineageCommand : public Command {
 	
 	private:
 		set<string> names;
-		vector<string> outputNames;
-		string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+		vector<string> outputNames, listOfTaxons;
+		string fastafile, namefile, groupfile, alignfile, countfile, listfile, taxfile, outputDir, taxons;
 		bool abort, dups;
 		
 		int readFasta();
 		int readName();
+        int readCount();
 		int readGroup();
 		int readAlign();
 		int readList();
 		int readTax();	
-		string removeConfidences(string);
 		vector< map<string, float> > getTaxons(string);
 };