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/*
Ray
Copyright (C) 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 "ExtensionData.h"
#include <RayPlatform/structures/SplayTreeIterator.h>
#include <RayPlatform/cryptography/crypto.h>
#include <string.h>
#include <sstream>
using namespace std;
void ExtensionData::constructor(Parameters*parameters){
m_parameters=parameters;
m_numberOfBins=1;
m_database=(SplayTree<ReadHandle,ExtensionElement>*)__Malloc(m_numberOfBins*sizeof(SplayTree<ReadHandle,ExtensionElement>),
"RAY_MALLOC_TYPE_EXTENSION_DATA_TREES",m_parameters->showMemoryAllocations());
createStructures();
ostringstream prefixFull;
prefixFull<<m_parameters->getMemoryPrefix()<<"_ExtensionData";
m_allocator.constructor(4194304,"RAY_MALLOC_TYPE_EXTENSION_DATA_ALLOCATOR",m_parameters->showMemoryAllocations());
}
void ExtensionData::createStructures(){
m_EXTENSION_extension.clear();
m_repeatedValues.clear();
m_extensionCoverageValues.clear();
m_EXTENSION_coverages.clear();
m_EXTENSION_readsInRange.clear();
m_expirations.clear();
m_pairedReadsWithoutMate.clear();
for(int i=0;i<m_numberOfBins;i++){
m_database[i].constructor();
}
}
void ExtensionData::destroyStructures(Profiler*m_profiler){
MACRO_COLLECT_PROFILING_INFORMATION();
m_EXTENSION_extension.clear();
m_extensionCoverageValues.clear();
m_repeatedValues.clear();
MACRO_COLLECT_PROFILING_INFORMATION();
m_EXTENSION_coverages.clear();
m_EXTENSION_readsInRange.clear();
MACRO_COLLECT_PROFILING_INFORMATION();
m_pairedReadsWithoutMate.clear();
MACRO_COLLECT_PROFILING_INFORMATION();
m_expirations.clear();
MACRO_COLLECT_PROFILING_INFORMATION();
for(int i=0;i<m_numberOfBins;i++){
m_database[i].clear();
}
MACRO_COLLECT_PROFILING_INFORMATION();
}
void ExtensionData::resetStructures(Profiler*m_profiler){
MACRO_COLLECT_PROFILING_INFORMATION();
m_allocator.reset();
MACRO_COLLECT_PROFILING_INFORMATION();
destroyStructures(m_profiler);
MACRO_COLLECT_PROFILING_INFORMATION();
}
void ExtensionData::destructor(){
destroyStructures(NULL);
__Free(m_database,"RAY_MALLOC_TYPE_EXTENSION_DATA_TREES",m_parameters->showMemoryAllocations());
}
ExtensionElement*ExtensionData::getUsedRead(ReadHandle a){
int bin=0;
SplayNode<ReadHandle,ExtensionElement>*node=m_database[bin].find(a,false);
if(node!=NULL && node->getValue()->isActive()){
return node->getValue();
}
return NULL;
}
ExtensionElement*ExtensionData::addUsedRead(ReadHandle a){
bool val;
int bin=0;
SplayNode<ReadHandle,ExtensionElement>*node=m_database[bin].find(a,false);
if(node!=NULL){
ExtensionElement*element=node->getValue();
element->activate();
element->increaseNumberOfTries();
return element;
}
ExtensionElement*element=m_database[bin].insert(a,&m_allocator,&val)->getValue();
element->constructor();
element->activate();
element->increaseNumberOfTries();
return element;
}
void ExtensionData::removeSequence(ReadHandle a){
int bin=0;
SplayNode<ReadHandle,ExtensionElement>*node=m_database[bin].find(a,false);
if(node!=NULL){
node->getValue()->deactivate();
return;
}
// the line below is useless
m_database[bin].remove(a,false,&m_allocator);
}
MyAllocator*ExtensionData::getAllocator(){
return &m_allocator;
}
void ExtensionData::lazyDestructor(){
SplayTreeIterator<ReadHandle,ExtensionElement> i;
i.constructor(&(m_database[0]));
while(i.hasNext()){
ExtensionElement*element=i.next()->getValue();
element->deactivate();
}
}
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