X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removeotulabelscommand.h;h=fd03d1018582d04de5efe1c11910610c0186252e;hp=da2441dd32039ee4574df10a8ed8c9493f168f4d;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=e0b6040c7b6ad4ecdad4aa90b4326c0528379178

diff --git a/removeotulabelscommand.h b/removeotulabelscommand.h
index da2441d..fd03d10 100644
--- 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();
 };
 
 /**************************************************************************************************/