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

[mothur.git] / sharedordervector.h

diff --git a/sharedordervector.h b/sharedordervector.h
deleted file mode 100644 (file)
index 7d383ac..0000000
--- a/sharedordervector.h
+++ /dev/null
@@ -1,94 +0,0 @@
-#ifndef SHAREDORDER_H
-#define SHAREDORDER_H
-/*
- *  sharedorder.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 12/9/08.
- *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
- 
- /* This class is a child to datavector.  It represents OTU information at a certain distance. 
-       It is similiar to an order vector except each member of data knows which group it belongs to.
-       Each member of the internal container "data" represents is an individual which knows the OTU from which it came, 
-       the group it is in and the abundance is equal to the OTU number.  */
-
-
-#include "datavector.hpp"
-
-struct individual {
-               string group;
-               int bin;
-               int abundance;
-               bool operator()(const individual& i1, const individual& i2) {
-               return (i1.abundance > i2.abundance);
-               }
-       individual() {  group = ""; bin = 0; abundance = 0; }
-};
-
-struct individualFloat {
-               string group;
-               int bin;
-               float abundance;
-               bool operator()(const individual& i1, const individual& i2) {
-               return (i1.abundance > i2.abundance);
-               }
-       individualFloat() { group = ""; bin = 0; abundance = 0.0; }
-};
-
-
-#include "sabundvector.hpp"
-#include "rabundvector.hpp"
-#include "sharedrabundvector.h"
-#include "sharedsabundvector.h"
-#include "groupmap.h"
-
-class SharedOrderVector : public DataVector {
-       
-public:
-       SharedOrderVector();
-//     SharedOrderVector(int ns, int nb=0, int mr=0)   : DataVector(), data(ns, -1), maxRank(0), numBins(0), numSeqs(0) {};
-       SharedOrderVector(const SharedOrderVector& ov)  : DataVector(ov.label), data(ov.data), maxRank(ov.maxRank), numBins(ov.numBins), numSeqs(ov.numSeqs), needToUpdate(ov.needToUpdate) {if(needToUpdate == 1){     updateStats();}};
-
-       SharedOrderVector(string, vector<individual>);
-       SharedOrderVector(ifstream&);
-       ~SharedOrderVector(){};
-       
-       
-       individual get(int);
-       void resize(int);
-       int size();
-       void print(ostream&);
-       vector<individual>::iterator begin();
-       vector<individual>::iterator end();
-       void push_back(int, int, string);  //OTU, abundance, group  MUST CALL UPDATE STATS AFTER PUSHBACK!!!
-       void updateStats();
-       void clear();
-
-       int getNumBins();
-       int getNumSeqs();
-       int getMaxRank();
-               
-       RAbundVector getRAbundVector();
-       SAbundVector getSAbundVector();
-       OrderVector getOrderVector(map<string,int>*);
-       SharedOrderVector getSharedOrderVector();
-       SharedRAbundVector getSharedRAbundVector(string);  //get the sharedRabundvector for a sepecific group
-       SharedSAbundVector getSharedSAbundVector(string);       //get the sharedSabundvector for a sepecific group
-       vector<SharedRAbundVector*> getSharedRAbundVector(); //returns sharedRabundVectors for all the users groups
-       
-private:
-       GroupMap* groupmap;
-       vector<individual>  data; 
-       map< int, vector<individual> >::iterator it;
-       int maxRank;
-       int numBins;
-       int numSeqs;
-       bool needToUpdate;
-       void set(int, int, int, string);        //index, OTU, abundance, group
-       
-};
-
-#endif
-