X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.h;h=4cee8b6459e3089b4d69e015b2bb4b2edb22c9eb;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=0d07ac6193f37807a25247df864f762e67369d58;hpb=ca0785e447ca7aa7e2f0ab8bb1155db126b551ea;p=mothur.git

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 0d07ac6..4cee8b6 100644
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -11,29 +11,52 @@
  */
  
 #include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
 
 class GetLineageCommand : public Command {
 	
 	public:
 	
 		GetLineageCommand(string);
-		~GetLineageCommand(){};
-		int execute();
-		void help();	
+		GetLineageCommand();
+		~GetLineageCommand(){}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "get.lineage";				}
+		string getCommandCategory()		{ return "Phylotype Analysis";		}
 		
+	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()); }	
+	
+	
 	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);
 };
 
 #endif