fixed metastats, added resize to cluster.classic, added code to kill children if...

[mothur.git] / subsamplecommand.h

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 98085ee9d02cd163e8d9ed76022f5a0c2ee59fea..f068ac32eb975f6fa246fe654d84f56db0e33c3a 100644 (file)
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -11,11 +11,12 @@
  */
  
 #include "command.hpp"
-#include "inputdata.h"
-#include "readotu.h"
+#include "globaldata.hpp"
 #include "sharedrabundvector.h"
+#include "listvector.hpp"
+#include "rabundvector.hpp"
+#include "inputdata.h"
 
-class GlobalData;
 
 class SubSampleCommand : public Command {
 
@@ -32,21 +33,19 @@ public:
        
 private:
        GlobalData* globaldata;
-       ReadOTUFile* read;
-       InputData* input;
-       vector<SharedRAbundVector*> lookup;
-       ListVector* list;
-       RAbundVector* rabund;
-       SAbundVector* sabund;
        
-       bool abort, allLines, pickedGroups;
+       bool abort, pickedGroups, allLines;
+       string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
        set<string> labels; //holds labels to be used
        string groups, label, outputDir;
        vector<string> Groups, outputNames;
        map<string, vector<string> > outputTypes;
+       int size;
        
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
-       int getSubSampleShared(vector<SharedRAbundVector*>&, ofstream&);
+       int getSubSampleShared();
+       int processShared(vector<SharedRAbundVector*>&, ofstream&);
+       
 };
 
 #endif