--- /dev/null
+/*
+ * sabund.cpp
+ *
+ *
+ * Created by Pat Schloss on 8/8/08.
+ * Copyright 2008 Patrick D. Schloss. All rights resesaved.
+ *
+ */
+using namespace std;
+
+#include "sabundvector.hpp"
+#include "datavector.hpp"
+#include "utilities.hpp"
+#include <exception>
+
+/***********************************************************************/
+
+SAbundVector::SAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
+
+/***********************************************************************/
+
+SAbundVector::SAbundVector(int size) : DataVector(), data(size, 0), maxRank(0), numBins(0), numSeqs(0) {};
+
+/***********************************************************************/
+
+SAbundVector::SAbundVector(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 SAbundVector class Function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SAbundVector class function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+SAbundVector::SAbundVector(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 SAbundVector class Function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SAbundVector class function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void SAbundVector::set(int sabund, int abundance){
+ try {
+
+ int initSize = data[sabund];
+ data[sabund] = abundance;
+
+ if(sabund != 0){
+ numBins += (abundance - initSize);
+ }
+
+ numSeqs += sabund * (abundance - initSize);
+
+ if(sabund > maxRank) { maxRank = sabund; }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+int SAbundVector::get(int index){
+ return data[index];
+}
+
+/***********************************************************************/
+
+void SAbundVector::push_back(int abundance){
+ try {
+ data.push_back(abundance);
+
+ maxRank++;
+
+ numBins += abundance;
+
+ numSeqs += (maxRank * abundance);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector 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 SAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void SAbundVector::resize(int size){
+ data.resize(size);
+}
+
+/***********************************************************************/
+
+int SAbundVector::size(){
+ return data.size();
+}
+
+/***********************************************************************/
+void SAbundVector::print(string prefix, ostream& output){
+
+ output << prefix << '\t' << maxRank << '\t';
+
+ for(int i=1;i<=maxRank;i++){
+ output << data[i] << '\t';
+ }
+ output << endl;
+}
+
+/***********************************************************************/
+void SAbundVector::print(ostream& output){
+ try {
+ output << label << '\t' << maxRank << '\t';
+
+ for(int i=1;i<=maxRank;i++){
+ output << data[i] << '\t';
+ }
+ output << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/**********************************************************************/
+int SAbundVector::getNumBins(){
+// if(needToUpdate == 1){ updateStats(); }
+ return numBins;
+}
+
+/***********************************************************************/
+
+int SAbundVector::getNumSeqs(){
+// if(needToUpdate == 1){ updateStats(); }
+ return numSeqs;
+}
+
+/***********************************************************************/
+
+int SAbundVector::getMaxRank(){
+// if(needToUpdate == 1){ updateStats(); }
+ return maxRank;
+}
+/***********************************************************************/
+RAbundVector SAbundVector::getRAbundVector(){
+ try {
+ RAbundVector rav;
+
+ for(int i=1;i<=data.size();i++){
+ for(int j=0;j<data[i];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 SAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+SAbundVector SAbundVector::getSAbundVector(){
+ return *this;
+}
+
+/***********************************************************************/
+
+OrderVector SAbundVector::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];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 SAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
projects / mothur.git / blobdiff