X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getlineagecommand.h;h=4cee8b6459e3089b4d69e015b2bb4b2edb22c9eb;hp=d62c50f55d253b7e3fd15790e2a6d4b21cb35b8f;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/getlineagecommand.h b/getlineagecommand.h
index d62c50f..4cee8b6 100644
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -11,6 +11,8 @@
  */
  
 #include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
 
 class GetLineageCommand : public Command {
 	
@@ -23,8 +25,12 @@ 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()); }	
@@ -32,17 +38,24 @@ 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, sharedfile, constaxonomy, label;
 		bool abort, dups;
+        vector<SharedRAbundVector*> lookup;
+        ListVector* list;
 		
 		int readFasta();
 		int readName();
+        int readCount();
 		int readGroup();
 		int readAlign();
 		int readList();
-		int readTax();	
-		string removeConfidences(string);
+		int readTax();
+        int readShared();
+        int readConsTax();
+        int readConsList();
+        int getShared();
+        int getListVector();
 		vector< map<string, float> > getTaxons(string);
 };