added modify names parameter to set.dir

[mothur.git] / inputdata.h

diff --git a/inputdata.h b/inputdata.h
index 46d1655cdd62f4578b5bf82a114143a31454a689..658b21d8cdfe649d8434e883655ecd18922f2554 100644 (file)
--- a/inputdata.h
+++ b/inputdata.h
@@ -1,16 +1,14 @@
 #ifndef INPUTDATA_H
 #define INPUTDATA_H
 
-#include <iostream>
-#include <iomanip>
-#include <string>
-#include <fstream>
+#include "mothur.h"
 #include "ordervector.hpp"
+#include "sharedlistvector.h"
+#include "sharedordervector.h"
 #include "listvector.hpp"
+#include "sharedrabundfloatvector.h"
 
 
-using namespace std;
-
 class InputData {
        
 public:
@@ -18,18 +16,37 @@ public:
        InputData(string, string, string);
        ~InputData();
        ListVector* getListVector();
-       OrderVector* getOrderVector();
+       ListVector* getListVector(string);  //pass the label you want
+       ListVector* getListVector(string, bool);  //pass the label you want, reset filepointer
+       SharedListVector* getSharedListVector();
+       SharedListVector* getSharedListVector(string);  //pass the label you want
+       OrderVector* getOrderVector(); 
+       OrderVector* getOrderVector(string); //pass the label you want
+       SharedOrderVector* getSharedOrderVector();
+       SharedOrderVector* getSharedOrderVector(string);  //pass the label you want
        SAbundVector* getSAbundVector();
+       SAbundVector* getSAbundVector(string);  //pass the label you want
+       RAbundVector* getRAbundVector();
+       RAbundVector* getRAbundVector(string);  //pass the label you want
+       vector<SharedRAbundVector*> getSharedRAbundVectors();
+       vector<SharedRAbundVector*> getSharedRAbundVectors(string);  //pass the label you want
+       vector<SharedRAbundFloatVector*> getSharedRAbundFloatVectors();
+       vector<SharedRAbundFloatVector*> getSharedRAbundFloatVectors(string);  //pass the label you want
        
 private:
        string format;
        ifstream fileHandle;
        DataVector* input;
        ListVector* list;
+       SharedListVector* SharedList;
        OrderVector* output;
+       SharedOrderVector* SharedOrder;
        SAbundVector* sabund;
+       RAbundVector* rabund;
        map<string,int> orderMap;
+       string filename;
+       MothurOut* m;
 };
 
 
-#endif
\ No newline at end of file
+#endif