+++ /dev/null
-/*
- * rabundvector.cpp
- *
- *
- * Created by Pat Schloss on 8/8/08.
- * Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "ordervector.hpp"
-#include "calculator.h"
-
-
-/***********************************************************************/
-
-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) {
- m->errorOut(e, "RAbundVector", "RAbundVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-RAbundVector::RAbundVector(vector<int> rav, int mr, int nb, int ns) {
- try {
- numBins = nb;
- maxRank = mr;
- numSeqs = ns;
- data = rav;
- }
- catch(exception& e) {
- m->errorOut(e, "RAbundVector", "RAbundVector");
- 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) {
- m->errorOut(e, "RAbundVector", "RAbundVector");
- 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) {
- m->errorOut(e, "RAbundVector", "set");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-int RAbundVector::get(int index){
- return data[index];
-
-}
-/***********************************************************************/
-
-void RAbundVector::clear(){
- numBins = 0;
- maxRank = 0;
- numSeqs = 0;
- data.clear();
-
-}
-/***********************************************************************/
-
-void RAbundVector::push_back(int binSize){
- try {
- data.push_back(binSize);
- numBins++;
-
- if(binSize > maxRank){
- maxRank = binSize;
- }
-
- numSeqs += binSize;
- }
- catch(exception& e) {
- m->errorOut(e, "RAbundVector", "push_back");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void RAbundVector::pop_back(){
-
- return data.pop_back();
-}
-
-/***********************************************************************/
-
-void RAbundVector::resize(int size){
-
- data.resize(size);
-}
-
-/***********************************************************************/
-
-int RAbundVector::size(){
- return data.size();
-}
-
-/***********************************************************************/
-
-void RAbundVector::quicksort(){
- sort(data.rbegin(), data.rend());
-}
-
-/***********************************************************************/
-
-int RAbundVector::sum(){
- VecCalc vecCalc;
- return vecCalc.sumElements(data);
-}
-
-/***********************************************************************/
-
-int RAbundVector::sum(int index){
- VecCalc vecCalc;
- return vecCalc.sumElements(data, index);
-}
-
-/***********************************************************************/
-
-int RAbundVector::numNZ(){
- VecCalc vecCalc;
- return vecCalc.numNZ(data);
-}
-
-/***********************************************************************/
-
-vector<int>::reverse_iterator RAbundVector::rbegin(){
- return data.rbegin();
-}
-
-/***********************************************************************/
-
-vector<int>::reverse_iterator RAbundVector::rend(){
- return data.rend();
-}
-
-/***********************************************************************/
-void RAbundVector::nonSortedPrint(ostream& output){
- try {
- output << label << '\t' << numBins << '\t';
-
- for(int i=0;i<numBins;i++){ output << data[i] << '\t'; }
- output << endl;
- }
- catch(exception& e) {
- m->errorOut(e, "RAbundVector", "nonSortedPrint");
- exit(1);
- }
-}
-/***********************************************************************/
-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) {
- m->errorOut(e, "RAbundVector", "print");
- 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) {
- m->errorOut(e, "RAbundVector", "print");
- 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) {
- m->errorOut(e, "RAbundVector", "getSAbundVector");
- 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);
- ov.getNumBins();
-
- return ov;
- }
- catch(exception& e) {
- m->errorOut(e, "RAbundVector", "getOrderVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
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