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//
// constaxonomy.cpp
// Mothur
//
// Created by Sarah Westcott on 1/13/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#include "taxonomy.hpp"
/***********************************************************************/
Taxonomy::Taxonomy(){
m = MothurOut::getInstance();
containsConfidence = false;
}
/***********************************************************************/
Taxonomy::Taxonomy(string otuname, string consensusTax, int num) {
try {
m = MothurOut::getInstance();
containsConfidence = false;
name = otuname;
numReps = num;
taxonomy = parseTax(consensusTax);
}
catch(exception& e) {
m->errorOut(e, "Taxonomy", "Taxonomy");
exit(1);
}
}
/***********************************************************************/
Taxonomy::Taxonomy(string otuname, string consensusTax) {
try {
m = MothurOut::getInstance();
containsConfidence = false;
name = otuname;
numReps = 1;
taxonomy = parseTax(consensusTax);
}
catch(exception& e) {
m->errorOut(e, "Taxonomy", "Taxonomy");
exit(1);
}
}
/***********************************************************************/
Taxonomy::Taxonomy(ifstream& in) {
try {
m = MothurOut::getInstance();
containsConfidence = false;
string otu = ""; string consensusTax = "unknown";
int size = 0;
in >> otu; gobble(in);
in >> size; gobble(in);
consensusTax = util.getline(in); gobble(in);
name = otu;
numReps = size;
taxonomy = parseTax(consensusTax);
}
catch(exception& e) {
m->errorOut(e, "Taxonomy", "Taxonomy");
exit(1);
}
}
/***********************************************************************/
void Taxonomy::setTaxons(string consensusTax){
try {
taxonomy = parseTax(consensusTax);
}catch(exception& e) {
m->errorOut(e, "Taxonomy", "setTaxons");
exit(1);
}
}
/***********************************************************************/
string Taxonomy::getInlineConsTaxonomy(){
try {
string otuConsensus = "";
otuConsensus += name + '\t' + toString(numReps) + '\t' + getConsTaxString(true);
return otuConsensus;
}catch(exception& e) {
m->errorOut(e, "Taxonomy", "getInlineConsTaxonomy");
exit(1);
}
}
/***********************************************************************/
vector<string> Taxonomy::getSimpleTaxons(bool includeConfidence) { //pass in true to include confidences
try {
if (!containsConfidence) { includeConfidence = false; }
vector<string> items;
for (int i = 0; i < taxonomy.size(); i++) {
if (m->getControl_pressed()) { break; }
string conTax = taxonomy[i].name;
if (includeConfidence) { conTax += "(" + toString(taxonomy[i].confidence) + ")"; }
items.push_back(conTax);
}
return items;
}catch(exception& e) {
m->errorOut(e, "Taxonomy", "getSimpleTaxons");
exit(1);
}
}
/***********************************************************************/
string Taxonomy::getConsTaxString(bool includeConfidence) { //pass in true to include confidences
try {
string conTax = "";
if (!containsConfidence) { includeConfidence = false; }
for (int i = 0; i < taxonomy.size(); i++) {
if (m->getControl_pressed()) { break; }
conTax += taxonomy[i].name;
if (includeConfidence) { conTax += "(" + toString(taxonomy[i].confidence) + ")"; }
conTax += ";";
}
return conTax;
}catch(exception& e) {
m->errorOut(e, "Taxonomy", "getConsTaxString");
exit(1);
}
}
/***********************************************************************/
vector<Taxon> Taxonomy::parseTax(string tax){
try {
string taxon = "";
vector<Taxon> consTaxs;
for(int i=0;i<tax.length();i++){
if (m->getControl_pressed()) { break; }
if(tax[i] == ';'){
string newtaxon = taxon; float confidence = 0;
containsConfidence = util.hasConfidenceScore(newtaxon, confidence);
Taxon thisTax(newtaxon, confidence);
consTaxs.push_back(thisTax);
taxon = "";
}
else{ taxon += tax[i]; }
}
return consTaxs;
}catch(exception& e) {
m->errorOut(e, "Taxonomy", "parseTax");
exit(1);
}
}
/***********************************************************************/
void Taxonomy::printConsTax(ostream& out){
try {
out << getInlineConsTaxonomy() << endl;
}catch(exception& e) {
m->errorOut(e, "Taxonomy", "printConsTax");
exit(1);
}
}
/***********************************************************************/
void Taxonomy::printConsTax(OutputWriter* out){
try {
out->write(getInlineConsTaxonomy()+"\n");
}catch(exception& e) {
m->errorOut(e, "Taxonomy", "printConsTax");
exit(1);
}
}
/***********************************************************************/
void Taxonomy::printConsTaxNoConfidence(ostream& out){
try {
string otuConsensus = name + '\t' + toString(numReps) + '\t' + getConsTaxString(false);
out << otuConsensus << endl;
}catch(exception& e) {
m->errorOut(e, "Taxonomy", "printConsTaxNoConfidence");
exit(1);
}
}
/***********************************************************************/
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