X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getotulabelscommand.h;h=06ad27162535bb2aacf2ddbba48c1df2201cbf34;hp=bad0f55beb921acc8907016e0d27b180271a716b;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=e0b6040c7b6ad4ecdad4aa90b4326c0528379178

diff --git a/getotulabelscommand.h b/getotulabelscommand.h
index bad0f55..06ad271 100644
--- a/getotulabelscommand.h
+++ b/getotulabelscommand.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 "get.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 select 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();
 };
 
 /**************************************************************************************************/