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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "VirtualKmerColor.h"
#include <iostream>
using namespace std;
#ifdef CONFIG_ASSERT
#include <assert.h>
#endif
VirtualKmerColor::VirtualKmerColor(){
clear();
}
void VirtualKmerColor::clear(){
m_references=0;
m_colors.clear();
m_hash=0;
#ifdef CONFIG_ASSERT
assert(getNumberOfReferences()==0);
#endif
#ifdef CONFIG_ASSERT
assert(getNumberOfPhysicalColors()==0);
#endif
}
void VirtualKmerColor::incrementReferences(){
m_references++;
}
void VirtualKmerColor::decrementReferences(){
m_references--;
#ifdef CONFIG_ASSERT
assert(m_references>=0);
#endif
}
void VirtualKmerColor::addPhysicalColor(PhysicalKmerColor color){
#ifdef CONFIG_ASSERT
assert(!hasPhysicalColor(color));
#endif
m_colors.insert(color);
}
LargeCount VirtualKmerColor::getNumberOfReferences(){
return m_references;
}
set<PhysicalKmerColor>*VirtualKmerColor::getPhysicalColors(){
return & m_colors;
}
bool VirtualKmerColor::hasPhysicalColor(PhysicalKmerColor color){
return m_colors.count(color)>0;
}
bool VirtualKmerColor::hasPhysicalColors(set<PhysicalKmerColor>*colors){
// verify the colors
for(set<PhysicalKmerColor>::iterator i=colors->begin();
i!=colors->end();i++){
PhysicalKmerColor physicalColor=*i;
if(!hasPhysicalColor(physicalColor)){
return false;
}
}
return true;
}
void VirtualKmerColor::setHash(uint64_t hash){
m_hash=hash;
}
uint64_t VirtualKmerColor::getCachedHashValue(){
return m_hash;
}
int VirtualKmerColor::getNumberOfPhysicalColors(){
return getPhysicalColors()->size();
}
bool VirtualKmerColor::virtualColorHasAllPhysicalColorsOf(VirtualKmerColor*a,PhysicalKmerColor color){
// we are searching for a virtual color with only the physical color <color> and
// the physical colors of VirtualKmerColor <a>
// this don't have the physical color <color>
if(!hasPhysicalColor(color)){
//cout<<"bah don't have color "<<color<<endl;
//
return false;
}
// this does not have the correct number of physical colors
if((a->getNumberOfPhysicalColors()+1) != getNumberOfPhysicalColors()){
/*
cout<<" mew wrong count"<<endl;
cout<<"Expected: "<<(a->getNumberOfPhysicalColors()+1)<<" Actual: "<<getNumberOfPhysicalColors()<<endl;
cout<<"a->getNumberOfPhysicalColors()-> "<<a->getNumberOfPhysicalColors()<<endl;
*/
return false;
}
// we don't need to check the hash because it was done
// upstream already, hopefully...
// anyway, the class VirtualKmerColor does not have the methods
// to do hash checking
// the current virtual color does not have all the required
// physical colors
if(!hasPhysicalColors(a->getPhysicalColors())){
//cout<<"ah don't have all physical colors"<<endl;
//
return false;
}
return true;
}
void VirtualKmerColor::copyPhysicalColors(VirtualKmerColor*a){
set<PhysicalKmerColor>*colors=a->getPhysicalColors();
addPhysicalColors(colors);
}
void VirtualKmerColor::addPhysicalColors(set<PhysicalKmerColor>*colors){
for(set<PhysicalKmerColor>::iterator i=colors->begin();
i!=colors->end();i++){
PhysicalKmerColor color=*i;
addPhysicalColor(color);
}
}
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