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#include "stdafx.h"
#include "AlignmentsQ.h"
const unsigned int CAlignmentsQ::NULL_RECORD = std::numeric_limits<unsigned int>::max();
const unsigned short CAlignmentsQ::NULL_EDIT_DIS = std::numeric_limits<unsigned short>::max();
CAlignmentsQ::CAlignmentsQ(unsigned int iMaxCapacity)
{
this->initialization(iMaxCapacity);
}
CAlignmentsQ::CAlignmentsQ(char cFlag_of_Queue_All_Best_One, unsigned int iMaxCapacity)
{
this->initialization(iMaxCapacity);
this->cFlag_of_Queue_All_Best_One = cFlag_of_Queue_All_Best_One;
}
CAlignmentsQ::~CAlignmentsQ(void)
{
delete [] this->aiHitIndex;
this->aiHitIndex = NULL;
delete [] this->asdiff;
this->asdiff = NULL;
}
void CAlignmentsQ::setQueue_All_Best_OneFlag(char cFlag_of_Queue_All_Best_One)
{
//Simply a public function used to set the flag option to queue the best set or all or one alignment
this->cFlag_of_Queue_All_Best_One = cFlag_of_Queue_All_Best_One;
}
char CAlignmentsQ::returnQueue_All_Best_OneFlag()
{
return(this->cFlag_of_Queue_All_Best_One);
}
inline void CAlignmentsQ::pushHits(unsigned int startindex, unsigned short diff)
{
if (this->load < this->iMaxCapacity) {
this->aiHitIndex[this->load] = startindex;
this->asdiff[this->load] = diff;
this->load++;
} else { // if the buffer is overflow.
// cout << "Alignment Queue overflow" << endl;
}
}
// return true if there is a same hit
bool CAlignmentsQ::checkHits(unsigned int startindex)
{
for (unsigned int i = 0; i < this->load && i < this->iMaxCapacity; i++) {
// If the maping is in the record, return(true);
if (this->aiHitIndex[i] == startindex) {
return(true);
}
}
return(false);
}
// replace the record with the largest diff
int CAlignmentsQ::replaceHits(unsigned int startindex, unsigned short diff)
{
int candidateId = -1;
unsigned short candidateDiff = this->MinDiff;
for (unsigned int i = 0; i < this->load && i < this->iMaxCapacity; i++) {
if (diff < this->asdiff[i]) {
if (candidateDiff < asdiff[i]) {
candidateId = i;
}
}
}
if (candidateId >= 0) { // replace the worse record
this->aiHitIndex[candidateId] = startindex;
this->asdiff[candidateId] = diff;
return(candidateId);
}
return(-1);
}
unsigned int CAlignmentsQ::saveHits(unsigned int startindex, unsigned short diff)
{
bool recordIsAsGoodOrBetter = (diff <= this->MinDiff);
bool saveAllMapping = (this->cFlag_of_Queue_All_Best_One == 'A');
if ( recordIsAsGoodOrBetter || saveAllMapping) {
if (diff < this->MinDiff) { // If the new alignment is better
this->MinDiff = diff;
if (this->cFlag_of_Queue_All_Best_One == 'B') {
this->load = 0; //NOT this->clearHits();
this->ForwardAlignmentLoad = 0;
}
// Definition of non-ambiguous is having a unique best mapping.
this->AmbiguousFlag = false;
} else { // linear check if the record has occured. (Buttlenect?)
if (checkHits(startindex)) {
return(this->load);
}
// This is put at the end to avoid duplicate record
if (diff == this->MinDiff) {
this->AmbiguousFlag = true;
}
}
//(3) save the alignment in the queue
bool qIsFull = (this->load >= this->iMaxCapacity);
if (saveAllMapping && qIsFull) {
this->replaceHits(startindex, diff);
} else if (!qIsFull) {
this->pushHits(startindex, diff);
}
}
return(load);
}
int CAlignmentsQ::initialization(unsigned int MAX_Q_CAPACITY)
{
this->iMaxCapacity = MAX_Q_CAPACITY;
this->aiHitIndex = new unsigned int [MAX_Q_CAPACITY + 1];
this->asdiff = new unsigned short [MAX_Q_CAPACITY + 1];
this->load = 0;
this->clearHits();
// The default setting is to queue the best set (could be more than one) alignment
this->cFlag_of_Queue_All_Best_One = 'B';
for (unsigned int i = 0; i < this->iMaxCapacity; i++) {
this->aiHitIndex[i] = NULL_RECORD;
this->asdiff[i] = NULL_EDIT_DIS;
}
this->qualityScores = NULL;
this->readID = 0;
this->tag[0] = '\0';
return (0);
}
int CAlignmentsQ::clearHits()
{
for (unsigned int i = 0; i < min(this->load, this->iMaxCapacity); i++) {
this->aiHitIndex[i] = NULL_RECORD;
this->asdiff[i] = NULL_EDIT_DIS;
}
/* Marked this to increase speed */
this->load = 0;
this->ForwardAlignmentLoad = 0;
this->MinDiff = MAX_READ_LENGTH;
this->AmbiguousFlag = false;
this->reverseIsBetter = false;
return(0);
}
int CAlignmentsQ::sortHitsByLocation()
{
// Sort according to distance
vector< pair <int, int> > v;
for (unsigned int i = 0; i < this->ForwardAlignmentLoad; i++) {
v.push_back(pair<unsigned int, unsigned short>(this->aiHitIndex[i], this->asdiff[i]));
}
std::sort(v.begin(), v.end());
for (unsigned int i = 0; i < this->ForwardAlignmentLoad; i++) {
this->aiHitIndex[i] = v.at(i).first;
this->asdiff[i] = (unsigned short)(v.at(i).second);
}
vector< pair <int, int> > w;
for (unsigned int i = this->ForwardAlignmentLoad; i < this->load; i++) {
w.push_back(pair<unsigned int, unsigned short>(this->aiHitIndex[i], this->asdiff[i]));
}
std::sort(w.begin(), w.end());
for (unsigned int i = this->ForwardAlignmentLoad; i < this->load; i++) {
this->aiHitIndex[i] = w.at(i).first;
this->asdiff[i] = (unsigned short)w.at(i).second;
}
return(0);
}
int CAlignmentsQ::filterAlignments(unsigned int mismatchThreshold, bool bKeepAllAlignmentsInThreshold)
{
int noOfMinMisMapping = 0;
if (this->MinDiff > mismatchThreshold) {
this->clearHits();
} else {
unsigned int i, j; // move record from i to j
for (i = 0, j = 0; i < this->load; i++) {
if (i == this->ForwardAlignmentLoad) {
this->ForwardAlignmentLoad = j;
}
bool isMinMisMapping = ((unsigned int)this->asdiff[i] == this->MinDiff);
if (isMinMisMapping) {
noOfMinMisMapping++;
}
if (isMinMisMapping || (bKeepAllAlignmentsInThreshold\
&& (unsigned int) this->asdiff[i] <= mismatchThreshold)) {
this->aiHitIndex[j] = this->aiHitIndex[i];
this->asdiff[j] = this->asdiff[i];
j++;
}
}
this->load = j;
this->AmbiguousFlag = (noOfMinMisMapping > 1);
}
return(this->load);
}
//Simply to a linear search in the queue to find the best alignment and return the genome InDex
unsigned int CAlignmentsQ::topHitsinList(void)
{
unsigned short mindiff = NULL_EDIT_DIS;//Check it again
unsigned int bestHitsIndex = 0;
unsigned int i;
for (i = 0; i < this->load; i++) {
if (mindiff > this->asdiff[i]) {
mindiff = this->asdiff[i];
bestHitsIndex = i;
this->AmbiguousFlag = false;
} else if (mindiff == this->asdiff[i])
this->AmbiguousFlag = true;
}
if (mindiff < MAXTOLERATSUBMIS) {
this->reverseIsBetter = (bestHitsIndex >= this->ForwardAlignmentLoad);
return(this->aiHitIndex[bestHitsIndex]);
} else
return(NULL_RECORD);//(Confuse between bad kmer and not found)
}
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