moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / sharedrabundvector.h

diff --git a/sharedrabundvector.h b/sharedrabundvector.h
deleted file mode 100644 (file)
index 792543e..0000000
--- a/sharedrabundvector.h
+++ /dev/null
@@ -1,95 +0,0 @@
-#ifndef SHAREDRABUNDVECTOR_H
-#define SHAREDRABUNDVECTOR_H
-
-/*
- *  sharedrabundvector.h
- *  Dotur
- *
- *  Created by Sarah Westcott on 12/5/08.
- *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "datavector.hpp"
-#include "sharedordervector.h"
-#include "sharedsabundvector.h"
-#include "sharedrabundfloatvector.h"
-#include "rabundvector.hpp"
-//#include "groupmap.h"
-
-/*  DataStructure for a shared file.
-       This class is a child to datavector.  It represents OTU information at a certain distance. 
-       It is similiar to an rabundvector 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 GlobalData;
-
-class SharedRAbundVector : public DataVector {
-       
-public:
-       SharedRAbundVector();
-       SharedRAbundVector(int);
-       //SharedRAbundVector(string, vector<int>);
-       SharedRAbundVector(const SharedRAbundVector& bv) : DataVector(bv), data(bv.data), maxRank(bv.maxRank), numBins(bv.numBins), numSeqs(bv.numSeqs), group(bv.group), index(bv.index){};
-    SharedRAbundVector(ifstream&);
-       ~SharedRAbundVector();
-
-       int getNumBins();               
-       int getNumSeqs();                                                       
-       int getMaxRank();
-       string getGroup();
-       void setGroup(string);
-       string getBinLabel();
-       void setBinLabel(string);
-       int getGroupIndex();
-       void setGroupIndex(int);                                                                
-
-       void set(int, int, string);                     //OTU, abundance, groupname
-       void setData(vector <individual>);
-       individual get(int);
-       vector <individual> getData();
-       int getAbundance(int);
-       int numNZ();
-       void sortD();  //Sorts the data in descending order.
-       void push_front(int, int, string); //abundance, otu, groupname
-       void insert(int, int, string); //abundance, otu, groupname
-       void push_back(int, string);  //abundance, groupname
-       void pop_back();
-       void resize(int);
-       int size();
-       void clear();
-       vector<individual>::reverse_iterator rbegin();
-       vector<individual>::reverse_iterator rend();
-       
-       void print(ostream&);
-       void printHeaders(ostream&);
-               
-       RAbundVector getRAbundVector();
-       RAbundVector getRAbundVector2();
-       SAbundVector getSAbundVector();
-       OrderVector getOrderVector(map<string,int>*);
-       SharedOrderVector getSharedOrderVector();
-       SharedSAbundVector getSharedSAbundVector();
-       SharedRAbundVector getSharedRAbundVector();
-       vector<SharedRAbundVector*> getSharedRAbundVectors();
-       vector<SharedRAbundFloatVector*> getSharedRAbundFloatVectors(vector<SharedRAbundVector*>);
-       
-private:
-       vector<individual>  data; 
-       vector<SharedRAbundVector*> lookup;
-       //GlobalData* globaldata;
-       //GroupMap* groupmap;
-       int maxRank;
-       int numBins;
-       int numSeqs;
-       string group;
-       int index;      
-       
-       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
-};
-
-
-#endif
-