X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.h;h=68f974f21461933b8feed0657bc07f86c17b4e20;hb=c48d91112209b841444923670dca5454da0e2a4d;hp=6375b9483fb335bafde123f3e99e4620c2614234;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 6375b94..68f974f 100644
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -23,7 +23,12 @@ class GetLineageCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "get.lineage";				}
 		string getCommandCategory()		{ return "Phylotype Analysis";		}
-		string getHelpString();	
+		
+	string getHelpString();	
+    string getOutputPattern(string);	
+		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()); }	
@@ -31,17 +36,17 @@ 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);
 };