--- /dev/null
+/*
+ * sharedSharedSAbundVector.cpp
+ * Dotur
+ *
+ * Created by Sarah Westcott on 12/10/08.
+ * Copyright 2008 __MyCompanyName__. 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(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);
+ }
+ // 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);
+ }
+}
+
+/***********************************************************************/
+
+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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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);
+ }
+}
+
+/***********************************************************************/
+
+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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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);
+ }
+}
+
+/***********************************************************************/
+
+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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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(){
+ 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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(){
+ try {
+ RAbundVector rav;
+ SAbundVector sav;
+
+ rav = getRAbundVector();
+ sav = rav.getSAbundVector();
+ return sav;
+
+ }
+ 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";
+ 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);
+ }
+}
+
+/***********************************************************************/
+
+bool compareMembers (individual member, individual member2){
+
+ if(member.abundance < member2.abundance){
+ return true; }
+ else{
+ return false;
+ }
+}
+
+/***********************************************************************/
+SharedRAbundVector SharedSAbundVector::getSharedVector(){
+ try {
+ SharedRAbundVector rav;
+
+ int binNumber = 0;
+ 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++;
+ }
+ }
+ sort(rav.rbegin(), rav.rend(), compareMembers);
+
+ rav.setLabel(label);
+ rav.setGroup(group);
+
+ 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";
+ 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);
+ }
+}
+
+
+/***********************************************************************/
+
+SharedSAbundVector SharedSAbundVector::getSharedSAbundVector(){
+ return *this;
+}
+
+/***********************************************************************/
+
+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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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);
+ }
+}
+
+/***********************************************************************/
+
projects / mothur.git / blobdiff