X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.h;h=8bfa5f15be3502e93e878d7ddfadc1870628be39;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=f644972c2672aa19509059c78d631ef0618eba28;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git

diff --git a/removelineagecommand.h b/removelineagecommand.h
index f644972..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 {
 	
@@ -35,8 +38,10 @@ class RemoveLineageCommand : public Command {
 	private:
 		set<string> names;
 		vector<string> outputNames, listOfTaxons;
-		string fastafile, namefile, groupfile, alignfile, listfile, countfile, 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();
@@ -44,7 +49,12 @@ class RemoveLineageCommand : public Command {
         int readCount();
 		int readAlign();
 		int readList();
-		int readTax();	
+		int readTax();
+        int readShared();
+        int readConsTax();
+        int readConsList();
+        int getShared();
+        int getListVector();
 		vector< map<string, float> > getTaxons(string);
 };