X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=4683c59b63050de20e6bb79e2103563478066a71;hb=c5c7502f435e1413c19e373dab1dfebcaa67588d;hp=6bdeed0753e767de6616930a6cdc560c6e0f2610;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 6bdeed0..4683c59 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -11,10 +11,6 @@
 using namespace std;
 
 #include "sharedrabundvector.h" 
-#include "datavector.hpp"
-#include "utilities.hpp"
-#include <exception>
-#include "sharedrabundvector.h"
 #include "sabundvector.hpp"
 #include "ordervector.hpp"
 
@@ -65,10 +61,11 @@ SharedRAbundVector::SharedRAbundVector(string id, vector<individual> rav) : Data
 
 SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
-		int i, hold;
+		int i, num;
+		string holdLabel, group
 		individual newGuy;
 		
-		f >> label >> hold;
+		f >> label >> group >> num;
 		
 		//initialize data
 		for (i=0; i<hold; i++) {
@@ -121,6 +118,11 @@ void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){
 		exit(1);
 	}
 }
+/***********************************************************************/
+
+void SharedRAbundVector::setData(vector <individual> newData){
+	data = newData;
+}
 
 /***********************************************************************/
 
@@ -128,14 +130,32 @@ int SharedRAbundVector::getAbundance(int index){
 	return data[index].abundance;
 	
 }
+/***********************************************************************/
+
+int SharedRAbundVector::numNZ(){
+	int sum = 0;
+	for(int i = 1; i < numBins; i++)
+		if(data[i].abundance > 0)
+			sum++;
+	return sum;
+}
+/***********************************************************************/
 
+void SharedRAbundVector::sortD(){
+	struct individual indObj;
+	sort(data.begin()+1, data.end(), indObj);
+}
 /***********************************************************************/
 
 individual SharedRAbundVector::get(int index){
 	return data[index];
 	
 }
+/***********************************************************************/
 
+vector <individual> SharedRAbundVector::getData(){
+	return data;
+}
 /***********************************************************************/
 
 void SharedRAbundVector::push_back(int binSize, int otu, string groupName){
@@ -166,6 +186,61 @@ void SharedRAbundVector::push_back(int binSize, int otu, string groupName){
 
 /***********************************************************************/
 
+void SharedRAbundVector::insert(int binSize, int otu, string groupName){
+	try {
+		individual newGuy;
+		newGuy.abundance = binSize;
+		newGuy.group = groupName;
+		newGuy.bin = otu;
+		
+		data.insert(data.begin()+otu, newGuy);
+		numBins++;
+	
+		if(binSize > maxRank){
+			maxRank = binSize;
+		}
+	
+		numSeqs += binSize;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedRAbundVector class function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+void SharedRAbundVector::push_front(int binSize, int otu, string groupName){
+	try {
+		individual newGuy;
+		newGuy.abundance = binSize;
+		newGuy.group = groupName;
+		newGuy.bin = otu;
+		
+		data.insert(data.begin(), newGuy);
+		numBins++;
+	
+		if(binSize > maxRank){
+			maxRank = binSize;
+		}
+	
+		numSeqs += binSize;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function push_front. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedRAbundVector class function push_front. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************************/
 void SharedRAbundVector::pop_back(){
 
 	return data.pop_back();
@@ -223,8 +298,10 @@ string SharedRAbundVector::getGroup(){
 void SharedRAbundVector::setGroup(string groupName){
 	group = groupName;
 }
-
-
+/***********************************************************************/
+int SharedRAbundVector::getGroupIndex()  { return index; }
+/***********************************************************************/
+void SharedRAbundVector::setGroupIndex(int vIndex)	{ index = vIndex; }
 /***********************************************************************/
 int SharedRAbundVector::getNumBins(){
 	return numBins;
@@ -241,13 +318,77 @@ int SharedRAbundVector::getNumSeqs(){
 int SharedRAbundVector::getMaxRank(){
 	return maxRank;
 }
-
 /***********************************************************************/
 
 SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){
 	return *this;			
 }
+/***********************************************************************/
+
+RAbundVector SharedRAbundVector::getRAbundVector() {
+	try {
+		RAbundVector rav(data.size());
+		
+		for (int i = 0; i < data.size(); i++) {
+			rav.set(i, data[i].abundance);
+		}
+	
+		return rav;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+RAbundVector SharedRAbundVector::getRAbundVector2() {
+	try {
+		RAbundVector rav;
+		for(int i = 0; i < numBins; i++)
+			if(data[i].abundance != 0)
+				rav.push_back(data[i].abundance-1);
+		return rav;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+/***********************************************************************/
 
+SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
+	try {
+		SharedSAbundVector sav(maxRank+1);
+		
+		for(int i=0;i<data.size();i++){
+			int abund = data[i].abundance;
+			sav.set(abund, sav.getAbundance(abund) + 1, group);
+		}
+		
+		sav.set(0, 0, group);
+		sav.setLabel(label);
+		sav.setGroup(group);
+		
+		return sav;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedRAbundVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
 /***********************************************************************/
 
 SAbundVector SharedRAbundVector::getSAbundVector() {