finishing the container classes, combining read.otu and read.list commands. some...

[mothur.git] / sharedlistvector.h

diff --git a/sharedlistvector.h b/sharedlistvector.h
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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 <Carbon/Carbon.h>
+#include "datavector.hpp"
+#include "groupmap.h"
+#include "globaldata.hpp"
+#include "sharedrabundvector.h"
+#include "sharedsabundvector.h"
+#include <iostream>
+#include <map>
+
+/* 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(int);
+       SharedListVector(ifstream&);
+       SharedListVector(const SharedListVector& lv) : DataVector(lv.label), data(lv.data), maxRank(lv.maxRank), numBins(lv.numBins), numSeqs(lv.numSeqs){};
+       ~SharedListVector(){};
+       
+       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
+       
+private:
+       vector<string> data;  //data[i] is a list of names of sequences in the ith OTU.
+       GlobalData* globaldata;
+       GroupMap* groupmap;
+       int maxRank;
+       int numBins;
+       int numSeqs;
+
+};
+
+#endif
+