bool CellTrack::tracking()
{
assert(m_numFrames >= 2);
/*
* 0. reset containers
*/
cout<<endl<<"start tracking ..."<<endl;
m_frames.clear();
m_frames.resize(m_numFrames);
if(! m_tracks.empty())
{
vector<Track>::iterator it = m_tracks.begin();
while(it != m_tracks.end())
{
Cell* p = (*it).entry;
assert(p!=NULL);
Cell* next = p;
while(p->next)
{
next = p->next;
delete p;
p = next;
}
delete p;
it++;
}
m_tracks.clear();
m_numTracks = 0;
}
/*
* 1. local variables and member vaiable getParams
*/
vector<Frame> t_frames;
Alignment alg;
t_frames.resize(2*m_numFrames - 2);
double * row = NULL; // the delete operation of row is done by alg
/*
* 2. the first round of comparison
*/
// 2.1 load the first tree
int i = 0; // the entry of t_frames
int t = 1; // the entry of time
// 2.2 go to the loop of m_numFrames - 1 times comparison
// and m_numFrames -1 matches will bed set
m_matches.resize(m_numFrames - 1);
cout<<"\tThe first round alignment "<<endl;
for(int t = 1; t < m_numFrames; t++)
{
cout<<"\talign tree"<<t<<" and tree"<<(t+1)<<endl;
alg.align(m_trees[t-1], m_trees[t]);
row = alg.result();
create_match(row, m_trees[t-1].nodeCount(), m_trees[t].nodeCount(), m_matches[t-1]);
create_frames(m_matches[t-1],t_frames[i],t_frames[i+1]);
alg.clear();
i = i + 2;
}
/*
* 3. the second round of alignment to merge nodes from tim 1 ~ m_numFrames -2
*/
cout<<endl<<"\tThe second round alignment "<<endl;
i = 0;
t = 0;
m_frames[t++] = t_frames[i++];
while( t <= m_numFrames - 2)
{
cout<<"\talign tree"<<(t+1)<<endl;
alg.align(m_trees[t],t_frames[i], t_frames[i+1]);
row = alg.result();
m_frames[t++] = merge_frames(m_trees[t], row , t_frames[i], t_frames[i+1]);
alg.clear();
i = i+2;
}
// now t = m_numFrames - 1, i+1 = 2*m_numFrames -2
m_frames[t] = t_frames[i];
t_frames.clear();
/*
* 4. set tracks and trackId for each cell
*/
t = 0;
int trackId = 1; //the cell id starts from 1, the cell id = 0 is the background
while(t < m_numFrames)
{
Frame& f = m_frames[t];
Frame::iterator it = f.begin();
while(it != f.end())
{
if((*it)->prev == NULL)
{
Track tk;
tk.trackId = trackId;
tk.start = t;
tk.end = t; // to be set later
tk.altitude = 0.00;
tk.entry = (*it);
//set the cell's cell id
Cell* p = *it;
while(p)
{
ComponentTree::Node* node = m_trees[(tk.end)++].getNode(p->label);
tk.altitude += node->mean - node->level;
p->trackId = trackId;
p = p->next;
}
tk.altitude = tk.altitude/(tk.end - tk.start);
m_tracks.push_back(tk);
trackId++;
}
it++;
}
t++;
}
m_numTracks = m_tracks.size();
cout<<"number of tracks : "<<m_numTracks<<endl;
//out put tracks
for(int i=0; i< m_numTracks; i++)
{
Cell* entry = m_tracks[i].entry;
Cell* p = entry;
while(p)
{
p=p->next;
}
}
cout<<endl;
/*
* 5. save results according to the trackId and labels
*/
time(&end);
timeElapsed(start,end);
saveImages();
saveGraph();
saveGraph2();
saveTracking();
return true;
}
/********************************************************************/
TrimOligos::~TrimOligos() {}
//*******************************************************************/
int TrimOligos::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
try {
string rawSequence = seq.getUnaligned();
int success = bdiffs + 1; //guilty until proven innocent
//can you find the barcode
for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
string oligo = it->first;
if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
break;
}
if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
group = it->second;
seq.setUnaligned(rawSequence.substr(oligo.length()));
if(qual.getName() != ""){
qual.trimQScores(oligo.length(), -1);
}
success = 0;
break;
}
}
//if you found the barcode or if you don't want to allow for diffs
if ((bdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
int maxLength = 0;
Alignment* alignment;
if (barcodes.size() > 0) {
map<string,int>::iterator it=barcodes.begin();
for(it;it!=barcodes.end();it++){
if(it->first.length() > maxLength){
maxLength = it->first.length();
}
}
alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
}else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
int minCount = 1;
int minGroup = -1;
int minPos = 0;
for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
string oligo = it->first;
// int length = oligo.length();
if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
success = bdiffs + 10;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
int alnLength = oligo.length();
for(int i=oligo.length()-1;i>=0;i--){
if(oligo[i] != '-'){ alnLength = i+1; break; }
}
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;
minGroup = it->second;
minPos = 0;
for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
minPos++;
}
}
}
else if(numDiff == minDiff){
minCount++;
}
}
if(minDiff > bdiffs) { success = minDiff; } //no good matches
else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
else{ //use the best match
group = minGroup;
seq.setUnaligned(rawSequence.substr(minPos));
if(qual.getName() != ""){
qual.trimQScores(minPos, -1);
}
success = minDiff;
}
if (alignment != NULL) { delete alignment; }
}
return success;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "stripBarcode");
exit(1);
}
}
//*******************************************************************/
int TrimOligos::stripBarcode(Sequence& seq, int& group){
try {
string rawSequence = seq.getUnaligned();
int success = bdiffs + 1; //guilty until proven innocent
//can you find the barcode
for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
string oligo = it->first;
if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
break;
}
if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
group = it->second;
seq.setUnaligned(rawSequence.substr(oligo.length()));
success = 0;
break;
}
}
//if you found the barcode or if you don't want to allow for diffs
if ((bdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
int maxLength = 0;
Alignment* alignment;
if (barcodes.size() > 0) {
map<string,int>::iterator it=barcodes.begin();
for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
if(it->first.length() > maxLength){
maxLength = it->first.length();
}
}
alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
}else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
int minCount = 1;
int minGroup = -1;
int minPos = 0;
for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
string oligo = it->first;
// int length = oligo.length();
if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
success = bdiffs + 10;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
int alnLength = oligo.length();
for(int i=oligo.length()-1;i>=0;i--){
if(oligo[i] != '-'){ alnLength = i+1; break; }
}
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;
minGroup = it->second;
minPos = 0;
for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
minPos++;
}
}
}
else if(numDiff == minDiff){
minCount++;
}
}
if(minDiff > bdiffs) { success = minDiff; } //no good matches
else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
else{ //use the best match
group = minGroup;
seq.setUnaligned(rawSequence.substr(minPos));
success = minDiff;
}
if (alignment != NULL) { delete alignment; }
}
return success;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "stripBarcode");
exit(1);
}
}
//********************************************************************/
int TrimOligos::stripForward(Sequence& seq, int& group){
try {
string rawSequence = seq.getUnaligned();
int success = pdiffs + 1; //guilty until proven innocent
//can you find the primer
for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
string oligo = it->first;
if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length
success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
break;
}
if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
group = it->second;
seq.setUnaligned(rawSequence.substr(oligo.length()));
success = 0;
break;
}
}
//if you found the barcode or if you don't want to allow for diffs
if ((pdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
int maxLength = 0;
Alignment* alignment;
if (primers.size() > 0) {
map<string,int>::iterator it=primers.begin();
for(it;it!=primers.end();it++){
if(it->first.length() > maxLength){
maxLength = it->first.length();
}
}
alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
}else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
int minCount = 1;
int minGroup = -1;
int minPos = 0;
for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
string oligo = it->first;
// int length = oligo.length();
if(rawSequence.length() < maxLength){
success = pdiffs + 100;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
int alnLength = oligo.length();
for(int i=oligo.length()-1;i>=0;i--){
if(oligo[i] != '-'){ alnLength = i+1; break; }
}
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;
minGroup = it->second;
minPos = 0;
for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
minPos++;
}
}
}
else if(numDiff == minDiff){
minCount++;
}
}
if(minDiff > pdiffs) { success = minDiff; } //no good matches
else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers
else{ //use the best match
group = minGroup;
seq.setUnaligned(rawSequence.substr(minPos));
success = minDiff;
}
if (alignment != NULL) { delete alignment; }
}
return success;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "stripForward");
exit(1);
}
}
//*******************************************************************/
int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group){
try {
string rawSequence = seq.getUnaligned();
int success = pdiffs + 1; //guilty until proven innocent
//can you find the primer
for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
string oligo = it->first;
if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length
success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
break;
}
if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
group = it->second;
seq.setUnaligned(rawSequence.substr(oligo.length()));
if(qual.getName() != ""){
qual.trimQScores(oligo.length(), -1);
}
success = 0;
break;
}
}
//if you found the barcode or if you don't want to allow for diffs
if ((pdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
int maxLength = 0;
Alignment* alignment;
if (primers.size() > 0) {
map<string,int>::iterator it=primers.begin();
for(it;it!=primers.end();it++){
if(it->first.length() > maxLength){
maxLength = it->first.length();
}
}
alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
}else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
int minCount = 1;
int minGroup = -1;
int minPos = 0;
for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
string oligo = it->first;
// int length = oligo.length();
if(rawSequence.length() < maxLength){
success = pdiffs + 100;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
int alnLength = oligo.length();
for(int i=oligo.length()-1;i>=0;i--){
if(oligo[i] != '-'){ alnLength = i+1; break; }
}
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;
minGroup = it->second;
minPos = 0;
for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
minPos++;
}
}
}
else if(numDiff == minDiff){
minCount++;
}
}
if(minDiff > pdiffs) { success = minDiff; } //no good matches
else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers
else{ //use the best match
group = minGroup;
seq.setUnaligned(rawSequence.substr(minPos));
if(qual.getName() != ""){
qual.trimQScores(minPos, -1);
}
success = minDiff;
}
if (alignment != NULL) { delete alignment; }
}
return success;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "stripForward");
exit(1);
}
}
