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AlleleRecords.cpp
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AlleleRecords.cpp
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/*
* AlleleRecords
* Date: Mar-28-2013
* Author : Gabriel Renaud gabriel.reno [at sign here ] gmail.com
*
*/
#include "AlleleRecords.h"
AlleleRecords::AlleleRecords(bool glFormat_){
chr="NA";
coordinate=0;
ref='N';
alt='N';
vectorAlleles=0;
vectorGLs=0;
glFormat = glFormat_;
}
AlleleRecords::AlleleRecords(uint32_t sizePops_,bool glFormat_){
chr="NA";
coordinate=0;
ref='N';
alt='N';
vectorAlleles=0;
vectorGLs=0;
glFormat = glFormat_;
sizePops = sizePops_;
// if(glFormat)
// vectorGLs = new vector<SingleGL> (sizePops) ;
// else
// vectorAlleles = new vector<SingleAllele> (sizePops);
}
AlleleRecords::AlleleRecords(const AlleleRecords & other){
//cout<<"copy1#"<<other.glFormat<<"# "<<other.chr<<" "<<other.coordinate<<"#"<<endl;
chr = other.chr;
coordinate = other.coordinate;
ref = other.ref;
alt = other.alt;
glFormat = other.glFormat;
if(other.glFormat){
vectorAlleles = 0;
vectorGLs = new vector<SingleGL> ( *(other.vectorGLs) );
}else{
vectorAlleles = new vector<SingleAllele> ( *(other.vectorAlleles) );
vectorGLs = 0;
}
//cout<<"copy2#"<<other.glFormat<<"# "<<other.chr<<" "<<other.coordinate<<"#"<<endl;
}
AlleleRecords::~AlleleRecords(){
if(vectorAlleles != 0)
delete(vectorAlleles);
if(vectorGLs != 0)
delete(vectorGLs);
}
void AlleleRecords::copyCoreFields(const AlleleRecords & other){
chr = other.chr;
chri = other.chri;
coordinate = other.coordinate;
ref = other.ref;
alt = other.alt;
glFormat = other.glFormat;
sizePops = 0;
if(other.glFormat){
vectorAlleles = 0;
vectorGLs = new vector<SingleGL> ( );
}else{
vectorAlleles = new vector<SingleAllele> ( );
vectorGLs = 0;
}
}
bool AlleleRecords::everyRecordNonNull() const{
bool toReturn=false;
for(unsigned int i=0;i<vectorAlleles->size();i++){
toReturn= toReturn || (vectorAlleles->at(i).getTotalCount() == 0 );
}
return !toReturn;
}
bool AlleleRecords::everyNonChimpAncRecordNonNull() const{
bool toReturn=false;
for(unsigned int i=2;i<vectorAlleles->size();i++){
toReturn= toReturn || (vectorAlleles->at(i).getTotalCount() == 0 );
}
return !toReturn;
}
bool AlleleRecords::isGlFormat() const{
return glFormat;
}
bool operator== (const AlleleRecords & first,const AlleleRecords & second){
bool normalData= ( (first.chr == second.chr) &&
(first.ref == second.ref) &&
(first.alt == second.alt) );
if(!normalData)
return false;
if(first.vectorAlleles->size() != second.vectorAlleles->size()){
return false;
}
if(first.glFormat != second.glFormat)
return false;
if(first.glFormat){
for(unsigned int i=0;i<first.vectorAlleles->size();i++){
if(first.vectorAlleles->at(i) != second.vectorAlleles->at(i) ){
return false;
}
}
}else{
for(unsigned int i=0;i<first.vectorGLs->size();i++){
if(first.vectorGLs->at(i) != second.vectorGLs->at(i) ){
return false;
}
}
}
return true;
}
uint32_t AlleleRecords::getSizePops() const{
return sizePops;
}
void AlleleRecords::writeBinary(char * buffer) const{
}