X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedsabundvector.cpp;h=efd14bcc249207ac4181fc552b8a918d57144083;hp=5175f5ee23b6a24b881eef09deb7272bee3ee6b2;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/sharedsabundvector.cpp b/sharedsabundvector.cpp
index 5175f5e..efd14bc 100644
--- a/sharedsabundvector.cpp
+++ b/sharedsabundvector.cpp
@@ -3,22 +3,17 @@
  *  Dotur
  *
  *  Created by Sarah Westcott on 12/10/08.
- *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "sharedsabundvector.h"
 #include "sabundvector.hpp"
-#include "datavector.hpp"
-#include "utilities.hpp"
-#include <exception>
-
-using namespace std;
 
 
 /***********************************************************************/
 
-SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
+SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){  }
 
 /***********************************************************************/
 
@@ -30,58 +25,6 @@ SharedSAbundVector::SharedSAbundVector(int size) :	DataVector(), maxRank(0), num
 			newGuy.abundance = 0;
 			data.push_back(newGuy);
 		}
-	//	for(int i=0;i<data.size();i++){
-	//		if(data[i].abundance != 0){	maxRank = i;	}
-	//		numSeqs += i*data[i].abundance;
-	//		numBins += data[i].abundance;
-	//	}
-
-};
-
-/***********************************************************************
-
-SharedSAbundVector::SharedSAbundVector(string id, vector<int> sav) : DataVector(id), data(sav) {
-	try {
-		
-		for(int i=0;i<sav.size();i++){
-			if(data[i] != 0){	maxRank = i;	}
-			numSeqs += i*data[i];
-			numBins += data[i];
-		}
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSAbundVector class function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-}
-
-/***********************************************************************
-
-SharedSAbundVector::SharedSAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), numSeqs(0) {
-	try {
-		int hold;
-		f >> label >> hold;
-	
-		data.assign(hold+1, 0);
-		int inputData;
-	
-		for(int i=1;i<=hold;i++){
-			f >> inputData;
-			set(i, inputData);
-		}
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSAbundVector class function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
 }
 
 /***********************************************************************/
@@ -102,13 +45,9 @@ void SharedSAbundVector::set(int bin, int abundance, string groupName){
 		if(bin > maxRank)	{	maxRank = bin;		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedSAbundVector", "set");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -140,13 +79,9 @@ void SharedSAbundVector::push_back(int abundance, int bin, string groupName){
 		numSeqs += (maxRank * abundance);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedSAbundVector", "push_back");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /***********************************************************************/
@@ -172,13 +107,9 @@ void SharedSAbundVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedSAbundVector", "print");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 /***********************************************************************/
 string SharedSAbundVector::getGroup(){
@@ -212,7 +143,7 @@ RAbundVector SharedSAbundVector::getRAbundVector(){
 	try {
 		RAbundVector rav;
 	
-		for(int i=1;i<=data.size();i++){		
+		for(int i=1;i<data.size();i++){		
 			for(int j=0;j<data[i].abundance;j++){
 				rav.push_back(i);
 			}
@@ -223,13 +154,9 @@ RAbundVector SharedSAbundVector::getRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedSAbundVector", "getRAbundVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 /***********************************************************************/
 SAbundVector SharedSAbundVector::getSAbundVector(){
@@ -243,13 +170,9 @@ SAbundVector SharedSAbundVector::getSAbundVector(){
 	
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedSAbundVector", "getSAbundVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSAbundVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /***********************************************************************/
@@ -264,15 +187,13 @@ bool compareMembers (individual member, individual member2){
 }
 
 /***********************************************************************/
-SharedRAbundVector SharedSAbundVector::getSharedVector(){
+SharedRAbundVector SharedSAbundVector::getSharedRAbundVector(){
 	try {
 		SharedRAbundVector rav;
 		
-		int binNumber = 0;
-		for(int i=1;i<=data.size();i++){		
+		for(int i=1;i<data.size();i++){		
 			for(int j=0;j<data[i].abundance;j++){
-				rav.push_back(i, binNumber, data[i].group);
-				binNumber++;
+				rav.push_back(i, data[i].group);
 			}
 		}
 		sort(rav.rbegin(), rav.rend(), compareMembers);
@@ -283,13 +204,9 @@ SharedRAbundVector SharedSAbundVector::getSharedVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getSharedVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedSAbundVector", "getSharedRAbundVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSAbundVector class function getSharedVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 
@@ -300,7 +217,33 @@ SharedSAbundVector SharedSAbundVector::getSharedSAbundVector(){
 }
 
 /***********************************************************************/
+SharedOrderVector SharedSAbundVector::getSharedOrderVector() {
+	try {
+		SharedRAbundVector rav;
+		SharedOrderVector ov;
+		
+		rav = this->getSharedRAbundVector();
+		ov = rav.getSharedOrderVector();
+		
+		ov.updateStats();
+		
+		return ov;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedSAbundVector", "getSharedOrderVector");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+void SharedSAbundVector::clear(){
+	numBins = 0;
+	maxRank = 0;
+	numSeqs = 0;
+	data.clear();
+}
 
+/***********************************************************************/
 OrderVector SharedSAbundVector::getOrderVector(map<string,int>* hold = NULL){
 	try {
 		OrderVector ov;
@@ -323,13 +266,9 @@ OrderVector SharedSAbundVector::getOrderVector(map<string,int>* hold = NULL){
 		return ov;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedSAbundVector", "getOrderVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /***********************************************************************/