X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.h;h=8bfa5f15be3502e93e878d7ddfadc1870628be39;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=310a66a5a90ea24acf34d7a94d8f7ff7df5a154d;hpb=f06fdb807822f8e06db003ed809c87250905cfc8;p=mothur.git

diff --git a/removelineagecommand.h b/removelineagecommand.h
index 310a66a..8bfa5f1 100644
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -11,6 +11,9 @@
  */
  
 #include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
+
 
 class RemoveLineageCommand : public Command {
 	
@@ -23,25 +26,35 @@ class RemoveLineageCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "remove.lineage";			}
 		string getCommandCategory()		{ return "Phylotype Analysis";		}
-		string getHelpString();	
+		
+	string getHelpString();	
+    string getOutputPattern(string);	
 		string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
-	
+		string getDescription()		{ return "removes 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, listOfTaxons;
-		string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+		string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
 		bool abort, dups;
+        vector<SharedRAbundVector*> lookup;
+        ListVector* list;
 		
 		int readFasta();
 		int readName();
 		int readGroup();
+        int readCount();
 		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);
 };