pat's mods to morisitahorn and pre.cluster

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index b3b3e6f5d0381d2354d8113012b13251cdbec7e7..5b922b6d6255eb993f8607fedc9696d4054f7caa 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -9,14 +9,10 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <map>
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "shared.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 
 /* The shared() command:
        The shared command can only be executed after a successful read.shared command.  
@@ -33,17 +29,25 @@ public:
        SharedCommand();        
        ~SharedCommand();
        int execute();  
+       void help() {}
        
 private:
-       void printSharedData();
+       void printSharedData(vector<SharedRAbundVector*>);
+       void createMisMatchFile();
+       bool isValidGroup(string, vector<string>);
+       void eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        SharedListVector* SharedList;
        InputData* input;
-       Shared* shared;
-       map<string, SharedRAbundVector*>::iterator it;
+       GroupMap* groupMap;
+       vector<string> groups;
        ofstream out;
-       string filename;
+       string filename, fileroot;
+       bool firsttime, pickedGroups;
+       map<string, ofstream*> filehandles;
+       map<string, ofstream*>::iterator it3;
 
 };