--- /dev/null
+/*
+ * rabundvector.cpp
+ *
+ *
+ * Created by Pat Schloss on 8/8/08.
+ * Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+using namespace std;
+
+#include "datavector.hpp"
+#include "utilities.hpp"
+#include <exception>
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "ordervector.hpp"
+
+
+/***********************************************************************/
+
+RAbundVector::RAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {};
+
+/***********************************************************************/
+
+RAbundVector::RAbundVector(int n) : DataVector(), data(n,0) , maxRank(0), numBins(0), numSeqs(0) {};
+
+/***********************************************************************/
+
+//RAbundVector::RAbundVector(const RAbundVector& rav) : DataVector(rav), data(rav.data), (rav.label), (rav.maxRank), (rav.numBins), (rav.numSeqs){};
+
+
+/***********************************************************************/
+
+RAbundVector::RAbundVector(string id, vector<int> rav) : DataVector(id), data(rav) {
+ try {
+ numBins = 0;
+ maxRank = 0;
+ numSeqs = 0;
+
+ for(int i=0;i<data.size();i++){
+ if(data[i] != 0) { numBins = i+1; }
+ if(data[i] > maxRank) { maxRank = data[i]; }
+ numSeqs += data[i];
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the RAbundVector class function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
+/***********************************************************************/
+
+
+RAbundVector::RAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
+ try {
+ int hold;
+ f >> label >> hold;
+
+ data.assign(hold, 0);
+ int inputData;
+
+ for(int i=0;i<hold;i++){
+ f >> inputData;
+ set(i, inputData);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the RAbundVector class function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+RAbundVector::~RAbundVector() {
+
+}
+
+/***********************************************************************/
+
+void RAbundVector::set(int binNumber, int newBinSize){
+ try {
+ int oldBinSize = data[binNumber];
+ data[binNumber] = newBinSize;
+
+ if(oldBinSize == 0) { numBins++; }
+ if(newBinSize == 0) { numBins--; }
+ if(newBinSize > maxRank) { maxRank = newBinSize; }
+
+ numSeqs += (newBinSize - oldBinSize);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the RAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+int RAbundVector::get(int index){
+ return data[index];
+
+}
+
+/***********************************************************************/
+
+void RAbundVector::push_back(int binSize){
+ try {
+ data.push_back(binSize);
+ numBins++;
+
+ if(binSize > maxRank){
+ maxRank = binSize;
+ }
+
+ numSeqs += binSize;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector 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 RAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void RAbundVector::pop_back(){
+
+ return data.pop_back();
+}
+
+/***********************************************************************/
+
+void RAbundVector::resize(int size){
+
+ data.resize(size);
+}
+
+/***********************************************************************/
+
+int RAbundVector::size(){
+ return data.size();
+}
+
+/***********************************************************************/
+
+vector<int>::reverse_iterator RAbundVector::rbegin(){
+ return data.rbegin();
+}
+
+/***********************************************************************/
+
+vector<int>::reverse_iterator RAbundVector::rend(){
+ return data.rend();
+}
+
+/***********************************************************************/
+void RAbundVector::print(string prefix, ostream& output){
+ try {
+ output << prefix << '\t' << numBins << '\t';
+
+ vector<int> hold = data;
+ sort(hold.rbegin(), hold.rend());
+
+ for(int i=0;i<numBins;i++){ output << hold[i] << '\t'; }
+ output << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the RAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+void RAbundVector::print(ostream& output){
+ try {
+ output << label << '\t' << numBins << '\t';
+
+ vector<int> hold = data;
+ sort(hold.rbegin(), hold.rend());
+
+ for(int i=0;i<numBins;i++){ output << hold[i] << '\t'; }
+ output << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the RAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+int RAbundVector::getNumBins(){
+ return numBins;
+}
+
+/***********************************************************************/
+
+int RAbundVector::getNumSeqs(){
+ return numSeqs;
+}
+
+/***********************************************************************/
+
+int RAbundVector::getMaxRank(){
+ return maxRank;
+}
+
+/***********************************************************************/
+
+RAbundVector RAbundVector::getRAbundVector(){
+ return *this;
+}
+
+/***********************************************************************/
+
+SAbundVector RAbundVector::getSAbundVector() {
+ try {
+ SAbundVector sav(maxRank+1);
+
+ for(int i=0;i<data.size();i++){
+ int abund = data[i];
+ sav.set(abund, sav.get(abund) + 1);
+ }
+ sav.set(0, 0);
+ sav.setLabel(label);
+ return sav;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the RAbundVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+OrderVector RAbundVector::getOrderVector(map<string,int>* nameMap = NULL) {
+ try {
+ OrderVector ov;
+
+ for(int i=0;i<data.size();i++){
+ for(int j=0;j<data[i];j++){
+ ov.push_back(i);
+ }
+ }
+ random_shuffle(ov.begin(), ov.end());
+
+ ov.setLabel(label);
+ return ov;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the RAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
projects / mothur.git / blobdiff