--- /dev/null
+/*
+ * order.cpp
+ *
+ *
+ * Created by Pat Schloss on 8/8/08.
+ * Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+using namespace std;
+
+#include "ordervector.hpp"
+#include "datavector.hpp"
+#include "utilities.hpp"
+#include <exception>
+
+/***********************************************************************/
+
+OrderVector::OrderVector() : DataVector() {}
+
+/***********************************************************************/
+
+//OrderVector::OrderVector(int ns) : DataVector(), data(ns, -1) {};
+
+/***********************************************************************/
+
+OrderVector::OrderVector(string id, vector<int> ov) :
+ DataVector(id), data(ov)
+{
+ updateStats();
+}
+
+/***********************************************************************/
+
+OrderVector::OrderVector(ifstream& f) : DataVector() {
+ try {
+ int hold;
+
+ f >> label;
+ f >> hold;
+
+ data.assign(hold, -1);
+
+ int inputData;
+
+ for(int i=0;i<hold;i++){
+ f >> inputData;
+ set(i, inputData);
+ }
+
+ updateStats();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function OrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OrderVector class function OrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+
+int OrderVector::getNumBins(){
+ if(needToUpdate == 1){ updateStats(); }
+ return numBins;
+}
+
+/***********************************************************************/
+
+int OrderVector::getNumSeqs(){
+ if(needToUpdate == 1){ updateStats(); }
+ return numSeqs;
+}
+
+/***********************************************************************/
+
+int OrderVector::getMaxRank(){
+ if(needToUpdate == 1){ updateStats(); }
+ return maxRank;
+}
+
+/***********************************************************************/
+
+
+
+void OrderVector::set(int index, int binNumber){
+
+ data[index] = binNumber;
+ needToUpdate = 1;
+
+}
+
+/***********************************************************************/
+
+int OrderVector::get(int index){
+ return data[index];
+}
+
+/***********************************************************************/
+
+void OrderVector::push_back(int index){
+
+ data.push_back(index);
+ needToUpdate = 1;
+
+}
+
+/***********************************************************************/
+
+void OrderVector::print(ostream& output){
+ try {
+ output << label << '\t' << numSeqs << '\t';
+
+ for(int i=0;i<data.size();i++){
+ output << data[i] << '\t';
+ }
+ output << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OrderVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void OrderVector::print(string prefix, ostream& output){
+ try {
+ output << prefix << '\t' << numSeqs << '\t';
+
+ for(int i=0;i<numSeqs;i++){
+ output << data[i] << '\t';
+ }
+ output << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OrderVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void OrderVector::resize(int){
+ cout << "resize() did nothing in class OrderVector";
+}
+
+/***********************************************************************/
+
+int OrderVector::size(){
+ return data.size();
+}
+
+/***********************************************************************/
+
+vector<int>::iterator OrderVector::begin(){
+ return data.begin();
+}
+
+/***********************************************************************/
+
+vector<int>::iterator OrderVector::end(){
+ return data.end();
+}
+
+/***********************************************************************/
+
+RAbundVector OrderVector::getRAbundVector(){
+ try {
+ RAbundVector rav(data.size());
+
+ for(int i=0;i<numSeqs;i++){
+ rav.set(data[i], rav.get(data[i]) + 1);
+ }
+ sort(rav.rbegin(), rav.rend());
+ for(int i=numSeqs-1;i>=0;i--){
+ if(rav.get(i) == 0){ rav.pop_back(); }
+ else{
+ break;
+ }
+ }
+ rav.setLabel(label);
+
+ return rav;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OrderVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+SAbundVector OrderVector::getSAbundVector(){
+
+ RAbundVector rav(this->getRAbundVector());
+ return rav.getSAbundVector();
+
+}
+
+/***********************************************************************/
+
+OrderVector OrderVector::getOrderVector(map<string,int>* hold = 0){
+ return *this;
+}
+
+/***********************************************************************/
+
+void OrderVector::updateStats(){
+ try {
+ needToUpdate = 0;
+ // int maxBinVectorLength = 0;
+ numSeqs = 0;
+ numBins = 0;
+ maxRank = 0;
+
+ for(int i=0;i<data.size();i++){
+ if(data[i] != -1){
+ numSeqs++;
+ }
+ }
+
+ vector<int> hold(numSeqs);
+
+ for(int i=0;i<numSeqs;i++){
+ if(data[i] != -1){
+ hold[data[i]] = hold[data[i]]+1;
+ }
+ }
+ for(int i=0;i<numSeqs;i++){
+ if(hold[i] > 0) { numBins++; }
+ if(hold[i] > maxRank) { maxRank = hold[i]; }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OrderVector class function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
projects / mothur.git / blobdiff