X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedordervector.h;h=7d383ac84f431830e2324cd51d4777d80a3390e0;hp=a530ad65289a67a9c92cbeeb55c0ce661ef1ac8c;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=eb1c88346fb246e95a6b38935b103f95e38b82ca

diff --git a/sharedordervector.h b/sharedordervector.h
index a530ad6..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.
@@ -15,8 +15,6 @@
 	the group it is in and the abundance is equal to the OTU number.  */
 
 
-using namespace std;
-
 #include "datavector.hpp"
 
 struct individual {
@@ -26,13 +24,24 @@ struct individual {
 		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 "globaldata.hpp"
 #include "groupmap.h"
 
 class SharedOrderVector : public DataVector {
@@ -46,15 +55,16 @@ public:
 	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();
@@ -66,9 +76,9 @@ 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:
-	GlobalData* globaldata;
 	GroupMap* groupmap;
 	vector<individual>  data; 
 	map< int, vector<individual> >::iterator it;
@@ -76,7 +86,8 @@ private:
 	int numBins;
 	int numSeqs;
 	bool needToUpdate;
-	void updateStats();
+	void set(int, int, int, string);	//index, OTU, abundance, group
+	
 };
 
 #endif