X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedordervector.h;h=7d383ac84f431830e2324cd51d4777d80a3390e0;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=b1b4a653dd51fb0280a5ea1189d690cf090614a4;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/sharedordervector.h b/sharedordervector.h
index b1b4a65..7d383ac 100644
--- a/sharedordervector.h
+++ b/sharedordervector.h
@@ -2,7 +2,7 @@
 #define SHAREDORDER_H
 /*
  *  sharedorder.h
- *  Dotur
+ *  Mothur
  *
  *  Created by Sarah Westcott on 12/9/08.
  *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
@@ -15,20 +15,34 @@
 	the group it is in and the abundance is equal to the OTU number.  */
 
 
-using namespace std;
-
 #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 {
 	
@@ -38,18 +52,19 @@ public:
 	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(ifstream&);
 	~SharedOrderVector(){};
 	
-	void set(int, int, int, string);	//index, OTU, abundance, group
+	
 	individual get(int);
-	void push_back(int, int, string);  //OTU, abundance, group
 	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();
@@ -61,15 +76,18 @@ public:
 	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 updateStats();
+	void set(int, int, int, string);	//index, OTU, abundance, group
+	
 };
 
 #endif