X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getlineagecommand.h;h=4cee8b6459e3089b4d69e015b2bb4b2edb22c9eb;hp=45b51a89398af8fbd3551560ae425b28520706b6;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=8f89a92f4ada82a2b3bf51b23b6a977770f2b9e2

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 45b51a8..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 {
 	
@@ -18,29 +20,43 @@ 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 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;
-		map<string, vector<string> > outputTypes;
+        vector<SharedRAbundVector*> lookup;
+        ListVector* list;
 		
 		int readFasta();
 		int readName();
+        int readCount();
 		int readGroup();
 		int readAlign();
 		int readList();
-		int readTax();	
-		string removeConfidences(string);
-		vector< map<string, int> > getTaxons(string);
+		int readTax();
+        int readShared();
+        int readConsTax();
+        int readConsList();
+        int getShared();
+        int getListVector();
+		vector< map<string, float> > getTaxons(string);
 };
 
 #endif