sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / removeotulabelscommand.h

diff --git a/removeotulabelscommand.h b/removeotulabelscommand.h
index da2441dd32039ee4574df10a8ed8c9493f168f4d..fd03d1018582d04de5efe1c11910610c0186252e 100644 (file)
--- a/removeotulabelscommand.h
+++ b/removeotulabelscommand.h
@@ -11,6 +11,9 @@
 //
 
 #include "command.hpp"
+#include "inputdata.h"
+#include "listvector.hpp"
+#include "sharedrabundvector.h"
 
 /**************************************************************************************************/
 
@@ -23,7 +26,9 @@ public:
     vector<string> setParameters();
     string getCommandName()                    { return "remove.otulabels";          }
     string getCommandCategory()                { return "OTU-Based Approaches";        } 
-    string getHelpString();    
+    
+       string getHelpString(); 
+    string getOutputPattern(string);   
     string getCitation() { return "http://www.mothur.org/wiki/Get.otulabels"; }
     string getDescription()            { return "Can be used with output from classify.otu, otu.association, or corr.axes to remove specific otus."; }
     
@@ -32,15 +37,19 @@ public:
     
 private:
     bool abort;
-    string outputDir, accnosfile, constaxonomyfile, otucorrfile, corraxesfile;
+    string outputDir, accnosfile, constaxonomyfile, otucorrfile, corraxesfile, listfile, sharedfile, label;
     vector<string> outputNames;
     set<string> labels;
+    ListVector* list;
+    vector<SharedRAbundVector*> lookup;
     
     int readClassifyOtu();
     int readOtuAssociation();
     int readCorrAxes();
-    int readAccnos();
-    
+    int readList();
+    int readShared();
+    int getListVector();
+    int getShared();
 };
 
 /**************************************************************************************************/