worked on hcluster. made .single command run using a sharedfile. and various other...

[mothur.git] / sharedsabundvector.h

diff --git a/sharedsabundvector.h b/sharedsabundvector.h
index 7010968f53ce641bd9f6396e4213ecb2dd5fb361..29b374523bf975653ff3b8943f2d967685a4644b 100644 (file)
--- a/sharedsabundvector.h
+++ b/sharedsabundvector.h
@@ -7,19 +7,22 @@
  *  Dotur
  *
  *  Created by Sarah Westcott on 12/10/08.
- *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
-
-#include <Carbon/Carbon.h>
 #include "datavector.hpp"
 #include "rabundvector.hpp"
 #include "ordervector.hpp"
 #include "sharedordervector.h"
 #include "sharedrabundvector.h"
 
-using namespace std;
+/* This class is a child to datavector.  It represents OTU information at a certain distance. 
+       It is similiar to an sabundvector except each member of data knows which group it belongs to.
+       Each member of the internal container "data" is a struct of type individual. 
+       An individual which knows the OTU from which it came, 
+       the group it is in and its abundance.  */
+
 
 class SharedSAbundVector : public DataVector {
        
@@ -35,10 +38,10 @@ public:
        string getGroup();
        void setGroup(string);  
        
-       void set(int, int, string);     
+       void set(int, int, string);      //OTU, abundance, group
        individual get(int);
        int getAbundance(int);
-       void push_back(int, int, string);
+       void push_back(int, int, string);       //abundance, OTU, group
        void pop_back();
        void resize(int);
        int size();
@@ -47,9 +50,10 @@ public:
                
        RAbundVector getRAbundVector(); 
        SAbundVector getSAbundVector();
-       SharedSAbundVector getSharedSAbundVector();
-       SharedRAbundVector getSharedVector();
        OrderVector getOrderVector(map<string,int>*);
+       SharedSAbundVector getSharedSAbundVector();
+       SharedRAbundVector getSharedRAbundVector();
+       SharedOrderVector getSharedOrderVector();
        
 private:
        vector<individual> data;