added shared, constaxonomy and label parameter to get.lineage and remove.lineage...

[mothur.git] / removelineagecommand.h

diff --git a/removelineagecommand.h b/removelineagecommand.h
index f644972c2672aa19509059c78d631ef0618eba28..8bfa5f15be3502e93e878d7ddfadc1870628be39 100644 (file)
--- 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);
 };