X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedlistvector.h;fp=sharedlistvector.h;h=56ea802a1b1bca511454f83ddcb9e8f29bd5ed27;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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+#ifndef SHAREDLIST_H
+#define SHAREDLIST_H
+
+/*
+ *  sharedlistvector.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 1/22/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "datavector.hpp"
+#include "groupmap.h"
+#include "sharedrabundvector.h"
+#include "sharedsabundvector.h"
+
+/* This class is a child to datavector.  It represents OTU information at a certain distance. 
+	A sharedlistvector can be converted into a sharedordervector, sharedrabundvector or sharedsabundvectorand 
+	as well as an ordervector, rabundvector or sabundvector.
+	Each member of the internal container "data" represents an individual OTU.
+	Each individual in the OTU belongs to a group.
+	So data[0] = "a,b,c,d,e,f".
+	example: listvector		=	a,b,c,d,e,f		g,h,i		j,k		l		m  
+			 rabundvector	=	6				3			2		1		1
+			 sabundvector	=	2		1		1		0		0		1
+			 ordervector	=	1	1	1	1	1	1	2	2	2	3	3	4	5 */
+
+class SharedListVector : public DataVector {
+	
+public:
+	SharedListVector();
+	SharedListVector(int);
+	SharedListVector(ifstream&);
+	SharedListVector(const SharedListVector& lv) : DataVector(lv.label), data(lv.data), maxRank(lv.maxRank), numBins(lv.numBins), numSeqs(lv.numSeqs){ groupmap = NULL; };
+	~SharedListVector(){ if (groupmap != NULL) { delete groupmap; } };
+	
+	int getNumBins()							{	return numBins;		}
+	int getNumSeqs()							{	return numSeqs;		}
+	int getMaxRank()							{	return maxRank;		}
+
+	void set(int, string);	
+	string get(int);
+	void push_back(string);
+	void resize(int);
+	void clear();
+	int size();
+	void print(ostream&);
+	
+	RAbundVector getRAbundVector();
+	SAbundVector getSAbundVector();
+	OrderVector getOrderVector(map<string,int>*);
+	SharedOrderVector* getSharedOrderVector();
+	SharedRAbundVector getSharedRAbundVector(string);  //get sharedrabundvector for a certain group
+	SharedSAbundVector getSharedSAbundVector(string);			//get sharedsabundvector for a certain group
+	vector<SharedRAbundVector*> getSharedRAbundVector(); //returns sharedRabundVectors for all the users groups
+	
+private:
+	vector<string> data;  //data[i] is a list of names of sequences in the ith OTU.
+	GroupMap* groupmap;
+	int maxRank;
+	int numBins;
+	int numSeqs;
+
+};
+
+#endif