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//
// sharedrabundvector.cpp
// Mothur
//
// Created by Sarah Westcott on 7/24/17.
// Copyright © 2017 Schloss Lab. All rights reserved.
//
#include "sharedrabundvector.hpp"
/***********************************************************************/
SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0), group("") {}
/***********************************************************************/
SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), data(n,0) , maxRank(0), numBins(n), numSeqs(0), group("") {}
/***********************************************************************/
SharedRAbundVector::SharedRAbundVector(vector<int> rav) : DataVector(), maxRank(0), numBins(rav.size()), numSeqs(0), group("") {
try {
data.assign(numBins, 0);
for(int i=0;i<rav.size();i++){ set(i, rav[i]); }
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
exit(1);
}
}
/***********************************************************************/
SharedRAbundVector::SharedRAbundVector(vector<int> rav, int mr, int nb, int ns) : DataVector(), group(""){
try {
numBins = nb;
maxRank = mr;
numSeqs = ns;
data = rav;
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
exit(1);
}
}
/***********************************************************************/
SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
try {
f >> label >> group >> numBins;
data.assign(numBins, 0);
int inputData;
for(int i=0;i<numBins;i++){
f >> inputData;
set(i, inputData);
}
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
exit(1);
}
}
/***********************************************************************/
SharedRAbundVector::SharedRAbundVector(ifstream& f, string l, string g, int n) : DataVector(), maxRank(0), numBins(n), numSeqs(0) {
try {
label = l;
group = g;
data.assign(numBins, 0);
string otuCountsData = util.getline(f);
vector<string> o = util.splitWhiteSpace(otuCountsData);
if (o.size() != n) { m->mothurOut("[ERROR] : group " + group + " contains otu data for " + toString(o.size()) + " otus, but your sharedfile indicates you have " + toString(n) + " otus. Please correct.\n"); m->setControl_pressed(true); }
else {
int inputData;
for(int i=0;i<o.size();i++){
util.mothurConvert(o[i], inputData);
set(i, inputData);
}
}
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
exit(1);
}
}
/***********************************************************************/
SharedRAbundVector::~SharedRAbundVector() { }
/***********************************************************************/
void SharedRAbundVector::set(int binNumber, int newBinSize){
try {
int oldBinSize = data[binNumber];
data[binNumber] = newBinSize;
if(newBinSize > maxRank) { maxRank = newBinSize; }
numSeqs += (newBinSize - oldBinSize);
}
catch(exception& e) {
m->errorOut(e, "RAbundVector", "set");
exit(1);
}
}
/***********************************************************************/
int SharedRAbundVector::increment(int binNumber){
try {
data[binNumber]++;
int newBinSize = data[binNumber];
if(newBinSize > maxRank) { maxRank = newBinSize; }
numSeqs++;
return newBinSize;
}
catch(exception& e) {
m->errorOut(e, "RAbundVector", "increment");
exit(1);
}
}
/***********************************************************************/
int SharedRAbundVector::get(int index){ return data[index]; }
/***********************************************************************/
void SharedRAbundVector::clear(){
numBins = 0;
maxRank = 0;
numSeqs = 0;
group = "";
data.clear();
}
/***********************************************************************/
void SharedRAbundVector::push_back(int binSize){
try {
data.push_back(binSize);
numBins++;
if(binSize > maxRank){ maxRank = binSize; }
numSeqs += binSize;
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "push_back");
exit(1);
}
}
/***********************************************************************/
int SharedRAbundVector::remove(int bin){
try {
int abund = data[bin];
data.erase(data.begin()+bin);
numBins--;
if(abund == maxRank){
vector<int>::iterator it = max_element(data.begin(), data.end());
maxRank = *it;
}
numSeqs -= abund;
return abund;
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "remove");
exit(1);
}
}
/***********************************************************************/
int SharedRAbundVector::remove(vector<int> bins){
try {
if (bins.size() == 0) { return 0; }
int numRemoved = 0;
vector<int> newData; int binIndex = 0;
for (int i = 0; i < data.size(); i++) {
if (m->getControl_pressed()) { break; }
if (i != bins[binIndex]) {
newData.push_back(data[i]);
}else if (i == bins[binIndex]) {
binIndex++;
numRemoved += data[i];
if (binIndex > bins.size()) { //removed all bins
newData.insert(newData.end(), data.begin()+i, data.end()); //add rest of good bins
break;
}
}
}
data = newData;
numBins = data.size();
vector<int>::iterator it = max_element(data.begin(), data.end());
maxRank = *it;
numSeqs -= numRemoved;
return numRemoved;
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "remove");
exit(1);
}
}
/***********************************************************************/
void SharedRAbundVector::resize(int size){
data.resize(size);
vector<int>::iterator it = max_element(data.begin(), data.end());
maxRank = *it;
numSeqs = util.sum(data);
numBins = size;
}
/***********************************************************************/
int SharedRAbundVector::size(){ return data.size(); }
/***********************************************************************/
void SharedRAbundVector::print(ostream& output){
try {
output << label;
output << '\t' << group << '\t' << numBins;
for(int i=0;i<numBins;i++){ output << '\t' << int(data[i]); }
output << endl;
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "nonSortedPrint");
exit(1);
}
}
/***********************************************************************/
int SharedRAbundVector::getNumBins(){
return numBins;
}
/***********************************************************************/
int SharedRAbundVector::getNumSeqs(){
return numSeqs;
}
/***********************************************************************/
int SharedRAbundVector::getMaxRank(){
return maxRank;
}
/***********************************************************************/
RAbundVector SharedRAbundVector::getRAbundVector(){
RAbundVector rav;
for(int i = 0; i < data.size(); i++) { if (data[i] != 0) { rav.push_back(int(data[i])); } }
rav.setLabel(label);
return rav;
}
/***********************************************************************/
RAbundFloatVector SharedRAbundVector::getRAbundFloatVector(){
RAbundFloatVector rav;
for(int i = 0; i < data.size(); i++) { if (data[i] != 0) { rav.push_back(float(data[i])); } }
rav.setLabel(label);
rav.setGroup(group);
return rav;
}
/***********************************************************************/
SAbundVector SharedRAbundVector::getSAbundVector() {
try {
SAbundVector sav(int(maxRank+1));
for(int i=0;i<data.size();i++){
int abund = data[i];
sav.set(abund, int(sav.get(abund)) + 1);
}
sav.set(0, 0);
sav.setLabel(label);
return sav;
}
catch(exception& e) {
m->errorOut(e, "RAbundVector", "getSAbundVector");
exit(1);
}
}
/***********************************************************************/
OrderVector SharedRAbundVector::getOrderVector(map<string,int>* nameMap = nullptr) {
try {
m->mothurOut("[ERROR]: can not convert SharedRAbundVectors to an ordervector, ordervectors assume no zero OTUS.\n"); m->setControl_pressed(true);
OrderVector o; return o;
}
catch(exception& e) {
m->errorOut(e, "RAbundVector", "getOrderVector");
exit(1);
}
}
/***********************************************************************/
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