X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedordervector.h;fp=sharedordervector.h;h=7d383ac84f431830e2324cd51d4777d80a3390e0;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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+#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
+