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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 "ArrayOfReads.h"
#include <stdlib.h>
#include <assert.h>
#include <iostream>
using namespace std;
void ArrayOfReads::constructor(MyAllocator*allocator){
#ifdef CONFIG_ASSERT
assert(allocator!=NULL);
#endif
m_allocator=allocator;
m_CHUNK_SIZE=100000;
m_maxNumberOfChunks=100000;
/* increased the maximum number of chunks... */
m_chunks=(Read**)m_allocator->allocate(m_maxNumberOfChunks*sizeof(Read*));
for(int i=0;i<m_maxNumberOfChunks;i++)
m_chunks[i]=NULL;
#ifdef CONFIG_ASSERT
assert(m_chunks!=NULL);
#endif
m_elements=0;
m_numberOfChunks=0;
m_maxSize=0;
}
void ArrayOfReads::push_back(Read*a){
#ifdef CONFIG_ASSERT
assert(a!=NULL);
#endif
if(m_elements==m_maxSize){
#ifdef CONFIG_ASSERT
assert(m_numberOfChunks!=m_maxNumberOfChunks);
#endif
m_maxSize+=m_CHUNK_SIZE;
m_numberOfChunks++;
#ifdef CONFIG_ASSERT
assert(m_numberOfChunks!=0);
#endif
#ifdef CONFIG_ASSERT
assert(m_chunks!=NULL);
#endif
m_chunks[m_numberOfChunks-1]=(Read*)m_allocator->allocate(m_CHUNK_SIZE*sizeof(Read));
#ifdef CONFIG_ASSERT
assert(m_chunks[m_numberOfChunks-1]!=NULL);
assert(m_elements<m_maxSize);
assert(m_numberOfChunks!=0);
assert(m_maxSize!=0);
#endif
}
#ifdef CONFIG_ASSERT
assert(m_elements!=m_maxSize);
assert(m_maxSize!=0);
if(m_numberOfChunks==0){
cout<<"ChunkSize="<<m_CHUNK_SIZE<<" ChunksPointer="<<m_chunks<<" NumberOfChunks="<<m_numberOfChunks<<" NumberOfElements="<<m_elements<<" MaxNumberOfElements="<<m_maxSize<<endl;
}
assert(m_numberOfChunks!=0);
#endif
m_elements++;
Read*b=at(m_elements-1);
*b=*a;
#ifdef CONFIG_ASSERT
assert(m_elements<=m_maxSize);
assert(m_elements!=0);
assert(m_maxSize!=0);
assert(m_chunks!=0);
assert(m_numberOfChunks!=0);
#endif
}
LargeCount ArrayOfReads::size(){
return m_elements;
}
Read*ArrayOfReads::at(LargeIndex i){
#ifdef CONFIG_ASSERT
assert(m_maxSize!=0);
assert(m_numberOfChunks!=0);
assert(m_elements!=0);
assert(m_chunks!=NULL);
assert(i<m_elements);
#endif
int chunkNumber=i/m_CHUNK_SIZE;
#ifdef CONFIG_ASSERT
if(chunkNumber>=m_numberOfChunks){
cout<<"ElementIdentifier="<<i<<" ChunkIdentifier="<<chunkNumber<<" NumberOfChunks="<<m_numberOfChunks<<" NumberOfElements="<<m_elements<<" MaxNumberOfElements="<<m_maxSize<<endl;
}
assert(chunkNumber<m_numberOfChunks);
#endif
int positionInSaidChunk=i%m_CHUNK_SIZE;
#ifdef CONFIG_ASSERT
assert(positionInSaidChunk<m_CHUNK_SIZE);
#endif
Read*theRead=m_chunks[chunkNumber]+positionInSaidChunk;
return theRead;
}
Read*ArrayOfReads::operator[](LargeIndex i){
return at(i);
}
void ArrayOfReads::clear(){
if(m_chunks!=NULL){
m_chunks=NULL;
m_elements=0;
m_numberOfChunks=0;
m_maxSize=0;
}
#ifdef CONFIG_ASSERT
assert(m_chunks==NULL);
assert(m_elements==0);
assert(m_numberOfChunks==0);
assert(m_maxSize==0);
#endif
}
void ArrayOfReads::reset(){
m_elements=0;
m_numberOfChunks=0;
m_maxSize=0;
m_chunks=(Read**)m_allocator->allocate(m_maxNumberOfChunks*sizeof(Read*));
}
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