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#include "stdafx.h"
#include "chromosomeInBits.h"
CChromosomeInBits::CChromosomeInBits(void)
{
}
CChromosomeInBits::~CChromosomeInBits(void)
{
delete [] this->pLowerBits;
delete [] this->pUpperBits;
// don't delete this->caChromosome.
}
CChromosomeInBits::CChromosomeInBits(char* caChromosome, unsigned int uiChrLength)
{
this->caChromosome = caChromosome;
this->uiChrLength = uiChrLength;
this->uiChrLengthInWordSize = (uiChrLength - 1) / wordSize + 1;
this->pLowerBits = new WORD_SIZE[uiChrLengthInWordSize];
this->pUpperBits = new WORD_SIZE[uiChrLengthInWordSize];
memset(pLowerBits, 0x00, uiChrLengthInWordSize);
memset(pUpperBits, 0x00, uiChrLengthInWordSize);
//TODO, find a better way to interpret the non ACGT character
//If there are non-ACGT characters in caChromosome. The memory will still set to A
unsigned int i;
for (i = 0; i + 1 < this->uiChrLengthInWordSize; i++) { //The first this->uiChrLengthInWordSize - 1 word are fully encoded
encodeRead(&caChromosome[i * wordSize], wordSize,
&this->pUpperBits[i], &this->pLowerBits[i]);
}
encodeRead(&caChromosome[i * wordSize], uiChrLength - wordSize * i,
&this->pUpperBits[i], &this->pLowerBits[i]);
}
int CChromosomeInBits::initialization()
{
this->pLowerBits = NULL;
this->pUpperBits = NULL;
this->caChromosome = NULL;
caSubstring[0] = '\0';
return (0);
}
/* Note the chromosome encoding is NOT continuous. The more significant bits of each words encodes
* nucleotides in front of those less significant bits. This encodeing make bits incontinuously mapped
* to chromosome index. Note the first bit of each WORD represent the first base of each section
*/
CReadInBits CChromosomeInBits::getSubstringInBits(unsigned int uiGenomeIndex)
{
CReadInBits r;
unsigned int indexInWords = uiGenomeIndex / wordSize;
unsigned int bitsShits = uiGenomeIndex % wordSize;
if (this->uiChrLengthInWordSize > indexInWords) {
r.UpperBits = this->pUpperBits[indexInWords] >> bitsShits;
r.LowerBits = this->pLowerBits[indexInWords] >> bitsShits;
if (bitsShits != 0) {
r.UpperBits |= (this->pUpperBits[indexInWords + 1] << (wordSize - bitsShits));
r.LowerBits |= (this->pLowerBits[indexInWords + 1] << (wordSize - bitsShits));
}
} else
cout << "Warning, wrong chromosome index " << endl;
return(r);
}
// eliminate the tail bits out of read length range
CReadInBits CChromosomeInBits::getSubstringInBits(unsigned int uiGenomeIndex, unsigned int uiSubstringLength)
{
CReadInBits r;
unsigned int indexInWords = uiGenomeIndex / wordSize;
unsigned int bitsShits = uiGenomeIndex % wordSize;
r.UpperBits = this->pUpperBits[indexInWords] >> bitsShits;
r.LowerBits = this->pLowerBits[indexInWords] >> bitsShits;
if (bitsShits != 0) {
r.UpperBits |= (this->pUpperBits[indexInWords + 1] << (wordSize - bitsShits));
r.LowerBits |= (this->pLowerBits[indexInWords + 1] << (wordSize - bitsShits));
}
unsigned int elimatedBitsNo = wordSize - uiSubstringLength;
r.UpperBits <<= elimatedBitsNo;
r.LowerBits <<= elimatedBitsNo;
r.UpperBits >>= elimatedBitsNo;
r.LowerBits >>= elimatedBitsNo;
return (r);
}
char* CChromosomeInBits::getSubstring(unsigned int uiGenomeIndex)
{
CReadInBits r = getSubstringInBits(uiGenomeIndex);
decodeRead(caSubstring, wordSize, r.UpperBits, r.LowerBits);
return (caSubstring);
}
char* CChromosomeInBits::getSubstring(unsigned int uiGenomeIndex, unsigned int uiSubstringLength)
{
CReadInBits r = getSubstringInBits(uiGenomeIndex);
decodeRead(caSubstring, wordSize, r.UpperBits, r.LowerBits);
if (uiSubstringLength <= wordSize) {
caSubstring[uiSubstringLength] = '\0';
}
if (uiGenomeIndex + uiSubstringLength > uiChrLength) {
if (uiChrLength > uiGenomeIndex)
caSubstring[uiChrLength - uiGenomeIndex] = '\0';
else {
cout << "Warning, Wrong genome index " << endl;
caSubstring[0] = '\0';
}
}
return (caSubstring);
}
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