changing command name classify.shared to classifyrf.shared

[mothur.git] / getlineagecommand.h

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 68f974f21461933b8feed0657bc07f86c17b4e20..4cee8b6459e3089b4d69e015b2bb4b2edb22c9eb 100644 (file)
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -11,6 +11,8 @@
  */
  
 #include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
 
 class GetLineageCommand : public Command {
        
@@ -37,8 +39,10 @@ class GetLineageCommand : public Command {
        private:
                set<string> names;
                vector<string> outputNames, listOfTaxons;
-               string fastafile, namefile, groupfile, alignfile, countfile, listfile, taxfile, outputDir, taxons;
+               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();
@@ -46,7 +50,12 @@ class GetLineageCommand : public Command {
                int readGroup();
                int readAlign();
                int readList();
-               int readTax();  
+               int readTax();
+        int readShared();
+        int readConsTax();
+        int readConsList();
+        int getShared();
+        int getListVector();
                vector< map<string, float> > getTaxons(string);
 };