X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedlistvector.cpp;h=4774180dd6032c0de1b87597360af6d14e7c2a2d;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=2bceace2565f404a08b85e5af59cf18e295bd41a;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf;p=mothur.git

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 2bceace..4774180 100644
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -7,43 +7,41 @@
  *
  */
 
-
-using namespace std;
-
-#include <map>
-#include <exception>
 #include "sabundvector.hpp"
 #include "rabundvector.hpp"
 #include "ordervector.hpp"
-#include "datavector.hpp"
-#include "utilities.hpp"
 #include "sharedlistvector.h"
 #include "sharedordervector.h"
+#include "sharedutilities.h"
+
+/***********************************************************************/
 
+SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){globaldata = GlobalData::getInstance();}
 
 /***********************************************************************/
 
-SharedListVector::SharedListVector(int n):	DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){};
+SharedListVector::SharedListVector(int n):	DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){globaldata = GlobalData::getInstance();}
 
 /***********************************************************************/
 SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
 		globaldata = GlobalData::getInstance();
-		
+
 		//set up groupmap for later.
 		groupmap = new GroupMap(globaldata->getGroupFile());
 		groupmap->readMap();
 
 		int hold;
+		string inputData;
 		f >> label >> hold;
 	
 		data.assign(hold, "");
-		string inputData = "";
 	
 		for(int i=0;i<hold;i++){
 			f >> inputData;
 			set(i, inputData);
 		}
+	
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -232,7 +230,10 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){
 			groupName = groupmap->getGroup(names);
 			order->push_back(i, binSize, groupName);
 		}
+
 		random_shuffle(order->begin(), order->end());
+		order->updateStats();
+		
 		return order;
 	}
 	catch(exception& e) {
@@ -271,6 +272,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
 		
 		rav.setLabel(label);
 		rav.setGroup(groupName);
+
 		return rav;
 		
 	}
@@ -283,6 +285,35 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
 		exit(1);
 	}
 }
+/***********************************************************************/
+vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
+	try {
+		SharedUtil* util;
+		util = new SharedUtil();
+		vector<SharedRAbundVector*> lookup;
+		
+		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
+		
+		delete util;
+
+		for (int i = 0; i < globaldata->Groups.size(); i++) {
+			SharedRAbundVector* temp = new SharedRAbundVector();
+			*temp = getSharedRAbundVector(globaldata->Groups[i]);
+			lookup.push_back(temp);
+		}
+
+		return lookup;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	
+}
 
 /***********************************************************************/
 SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) {