X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedsabundvector.cpp;fp=sharedsabundvector.cpp;h=0000000000000000000000000000000000000000;hp=efd14bcc249207ac4181fc552b8a918d57144083;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76

diff --git a/sharedsabundvector.cpp b/sharedsabundvector.cpp
deleted file mode 100644
index efd14bc..0000000
--- a/sharedsabundvector.cpp
+++ /dev/null
@@ -1,275 +0,0 @@
-/*
- *  sharedSharedSAbundVector.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 12/10/08.
- *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedsabundvector.h"
-#include "sabundvector.hpp"
-
-
-/***********************************************************************/
-
-SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){  }
-
-/***********************************************************************/
-
-SharedSAbundVector::SharedSAbundVector(int size) :	DataVector(), maxRank(0), numBins(0), numSeqs(0) {
-		individual newGuy;
-		//initialize data
-		for (int i=0; i< size; i++) {
-			newGuy.bin = i;
-			newGuy.abundance = 0;
-			data.push_back(newGuy);
-		}
-}
-
-/***********************************************************************/
-
-void SharedSAbundVector::set(int bin, int abundance, string groupName){
-	try {
-
-		int initSize = data[bin].abundance;
-		data[bin].abundance = abundance;
-		data[bin].group = groupName;
-	
-		if(bin != 0){
-			numBins += (abundance - initSize);
-		}
-	
-		numSeqs += bin * (abundance - initSize);
-	
-		if(bin > maxRank)	{	maxRank = bin;		}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SharedSAbundVector", "set");
-		exit(1);
-	}
-}
-
-/***********************************************************************/
-
-individual SharedSAbundVector::get(int index){
-	return data[index];
-}
-/***********************************************************************/
-
-int SharedSAbundVector::getAbundance(int index){
-	return data[index].abundance;
-}
-
-/***********************************************************************/
-
-void SharedSAbundVector::push_back(int abundance, int bin, string groupName){
-	try {
-		individual newGuy;
-		newGuy.abundance = abundance;
-		newGuy.bin = bin;
-		newGuy.group = groupName;
-		
-		data.push_back(newGuy);
-	
-		maxRank++;	
-	
-		numBins += abundance;
-	
-		numSeqs += (maxRank * abundance);
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SharedSAbundVector", "push_back");
-		exit(1);
-	}
-}
-
-/***********************************************************************/
-
-void SharedSAbundVector::resize(int size){
-	data.resize(size);
-}
-
-/***********************************************************************/
-
-int SharedSAbundVector::size(){
-	return data.size();		
-}
-
-/***********************************************************************/
-void SharedSAbundVector::print(ostream& output){
-	try {
-		output << label << '\t' << maxRank << '\t';
-	
-		for(int i=1;i<=maxRank;i++){
-			output << data[i].abundance << '\t';
-		}
-		output << endl;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SharedSAbundVector", "print");
-		exit(1);
-	}
-}
-/***********************************************************************/
-string SharedSAbundVector::getGroup(){
-	return group;
-}
-
-/***********************************************************************/
-
-void SharedSAbundVector::setGroup(string groupName){
-	group = groupName;
-}
-
-/**********************************************************************/
-int SharedSAbundVector::getNumBins(){
-	return numBins;
-}
-
-/***********************************************************************/
-
-int SharedSAbundVector::getNumSeqs(){
-	return numSeqs;
-}
-
-/***********************************************************************/
-
-int SharedSAbundVector::getMaxRank(){
-	return maxRank;
-}
-/***********************************************************************/
-RAbundVector SharedSAbundVector::getRAbundVector(){
-	try {
-		RAbundVector rav;
-	
-		for(int i=1;i<data.size();i++){		
-			for(int j=0;j<data[i].abundance;j++){
-				rav.push_back(i);
-			}
-		}
-		sort(rav.rbegin(), rav.rend());
-	
-		rav.setLabel(label);
-		return rav;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SharedSAbundVector", "getRAbundVector");
-		exit(1);
-	}
-}
-/***********************************************************************/
-SAbundVector SharedSAbundVector::getSAbundVector(){
-	try {
-		RAbundVector rav;
-		SAbundVector sav;
-		
-		rav = getRAbundVector();
-		sav = rav.getSAbundVector();
-		return sav;
-	
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SharedSAbundVector", "getSAbundVector");
-		exit(1);
-	}
-}
-
-/***********************************************************************/
-
-bool compareMembers (individual member, individual member2){
-
-  if(member.abundance < member2.abundance){
-    return true;   }   
-  else{
-	return false; 
-  }
-}
-
-/***********************************************************************/
-SharedRAbundVector SharedSAbundVector::getSharedRAbundVector(){
-	try {
-		SharedRAbundVector rav;
-		
-		for(int i=1;i<data.size();i++){		
-			for(int j=0;j<data[i].abundance;j++){
-				rav.push_back(i, data[i].group);
-			}
-		}
-		sort(rav.rbegin(), rav.rend(), compareMembers);
-	
-		rav.setLabel(label);
-		rav.setGroup(group);
-		
-		return rav;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SharedSAbundVector", "getSharedRAbundVector");
-		exit(1);
-	}
-}
-
-
-/***********************************************************************/
-
-SharedSAbundVector SharedSAbundVector::getSharedSAbundVector(){
-	return *this;			
-}
-
-/***********************************************************************/
-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;
-	
-		int binIndex = 0;
-	
-		for(int i=1;i<data.size();i++){
-			for(int j=0;j<data[i].abundance;j++){
-				for(int k=0;k<i;k++){
-					ov.push_back(binIndex);
-				}
-				binIndex++;
-			}
-		}
-	
-		random_shuffle(ov.begin(), ov.end());
-
-		ov.setLabel(label);
-		ov.getNumBins();
-		return ov;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SharedSAbundVector", "getOrderVector");
-		exit(1);
-	}
-}
-
-/***********************************************************************/
-