void CSplignTrim::AdjustGaps(TSegs& segments)
{
TSegs new_segments;
int gap_start_idx (-1);
if(segments.size() && segments[0].m_exon == false) {
gap_start_idx = 0;
}
for(size_t k (0); k < segments.size(); ++k) {
TSeg& s (segments[k]);
if(!s.m_exon) {
if(gap_start_idx == -1) {
gap_start_idx = int(k);
if(k > 0) {
s.m_box[0] = segments[k-1].m_box[1] + 1;
s.m_box[2] = segments[k-1].m_box[3] + 1;
}
}
}
else {
if(gap_start_idx >= 0) {
TSeg& g = segments[gap_start_idx];
g.m_box[1] = s.m_box[0] - 1;
g.m_box[3] = s.m_box[2] - 1;
g.m_len = g.m_box[1] - g.m_box[0] + 1;
g.m_details.resize(0);
new_segments.push_back(g);
gap_start_idx = -1;
}
new_segments.push_back(s);
}
}
if(gap_start_idx >= 0) {
TSeg& g (segments[gap_start_idx]);
g.m_box[1] = segments[segments.size()-1].m_box[1];
g.m_box[3] = segments[segments.size()-1].m_box[3];
g.m_len = g.m_box[1] - g.m_box[0] + 1;
g.m_details.resize(0);
new_segments.push_back(g);
}
segments.swap(new_segments);
}
// aka stich holes
//joins exons segments[p1] and segments[p1] into a singe exon
//everithing in between becomes a regular gap in query adjacent to a regular gap in subject
void CSplignTrim::JoinExons(TSegs& segments, TSeqPos p1, TSeqPos p2)
{
//sanity check
if( p1 >= segments.size() ) return;
if( p2 >= segments.size() ) return;
if( !segments[p1].m_exon ) return;
if( !segments[p2].m_exon ) return;
size_t pos1 = min( p1, p2);
size_t pos2 = max( p1, p2);
if( segments[pos1].m_box[1] >= segments[pos2].m_box[0] ||
segments[pos1].m_box[3] >= segments[pos2].m_box[2] ) {
return; // segments intersect
}
//join
TSegs new_segments;
for( size_t pos = 0; pos < pos1; ++pos) {
new_segments.push_back(segments[pos]);
}
//joint exon
TSeg s(segments[pos1]);
s.m_box[1] = segments[pos2].m_box[1];
s.m_box[3] = segments[pos2].m_box[3];
if( segments[pos1].m_box[1] + 1 < segments[pos2].m_box[0]) {
s.m_details.append(segments[pos2].m_box[0] - segments[pos1].m_box[1] - 1, 'D');
}
if( segments[pos1].m_box[3] + 1 < segments[pos2].m_box[2]) {
s.m_details.append(segments[pos2].m_box[2] - segments[pos1].m_box[3] - 1, 'I');
}
s.m_details += segments[pos2].m_details;
Update(s);
new_segments.push_back(s);
//write the rest
for( size_t pos = ++pos2; pos < segments.size(); ++pos) {
new_segments.push_back(segments[pos]);
}
segments.swap(new_segments);
}
//check if the exon segments[p] abuts another exon in genomic coordinates, right side
bool CSplignTrim::HasAbuttingExonOnRight(TSegs segments, TSeqPos p)
{
TSeqPos len = segments.size();
TSeqPos np = p+1;
for( ; np < len; ++np) {
if( segments[np].m_exon ) break;
}
if(np == len) {// no exons on the right found
return false;
}
if( segments[p].m_box[3] + 1 == segments[np].m_box[2] ) { //abutting
return true;
}
return false;
}
BEGIN_NCBI_SCOPE
//check if the exon segments[p] abuts another exon in genomic coordinates, right side
bool CSplignTrim::HasAbuttingExonOnRight(TSegs segments, TSeqPos p)
{
TSeqPos len = segments.size();
TSeqPos np = p+1;
for( ; np < len; ++np) {
if( segments[np].m_exon ) break;
}
if(np == len) {// no exons on the right found
return false;
}
if( segments[p].m_box[3] + 1 == segments[np].m_box[2] ) { //abutting
return true;
}
return false;
}
//trims exons around internal alignment gaps to complete codons
//if CDS can be retrieved from bioseq
void CSplignTrim::TrimHolesToCodons(TSegs& segments, CBioseq_Handle& mrna_bio_handle, bool mrna_strand, size_t mrna_len)
{
if( mrna_bio_handle ) {
//collect CDS intervals (could be more than one in a case of ribosomal slippage)
vector<TSeqRange> tr;
for(CFeat_CI ci(mrna_bio_handle, SAnnotSelector(CSeqFeatData::e_Cdregion)); ci; ++ci) {
for(CSeq_loc_CI slit(ci->GetLocation()); slit; ++slit) {
TSeqRange r, ori;
ori = slit.GetRange();
if( mrna_strand ) {
r = ori;
} else {//reverse
r.SetFrom(mrna_len - ori.GetTo() - 1);
r.SetTo(mrna_len - ori.GetFrom() - 1);
}
tr.push_back(r);
}
}
if(tr.empty()) return;// CDS not found
//trim
AdjustGaps(segments);//make sure there is no adjacent gaps
size_t pos1 = 0, pos2 = 2;
for(; pos2 < segments.size(); ++pos1, ++pos2) {
if( segments[pos1].m_exon && !segments[pos1+1].m_exon && segments[pos2].m_exon ) {//candidate for trimming
//trim left exon
TSeqPos p1 = segments[pos1].m_box[1];
ITERATE(vector<TSeqRange>, it, tr) {
if( p1 >= it->GetFrom() && p1 <= it->GetTo() ) {
TSeqPos cut_mrna_len = (p1 + 1 - it->GetFrom()) % 3, cnt = 0;
string transcript = segments[pos1].m_details;
int i = (int)transcript.size() - 1;
for(; i>=0; --i) {
if( cnt%3 == cut_mrna_len && transcript[i] == 'M' ) { //cut point
CutFromRight(transcript.size() - i - 1, segments[pos1]);
break;
}
if( transcript[i] != 'I' ) ++cnt;
}
if( i < 0 ) {// exon should not be so bad
NCBI_THROW(CAlgoAlignException, eInternal, g_msg_InvalidRange);
}
break;
}
}
//trim right exon
TSeqPos p2 = segments[pos2].m_box[0];
ITERATE(vector<TSeqRange>, it, tr) {
if( p2 >= it->GetFrom() && p2 <= it->GetTo() ) {
TSeqPos cut_mrna_len = ( 3 - ( p2 - it->GetFrom()) % 3 ) %3, cnt = 0;
string transcript = segments[pos2].m_details;
int i = 0;
for( ; i < (int)transcript.size(); ++i) {
if( cnt%3 == cut_mrna_len && transcript[i] == 'M' ) { //cut point
CutFromLeft(i, segments[pos2]);
break;
}
if( transcript[i] != 'I' ) ++cnt;
}
if( i == (int)transcript.size() ) {// exon should not be so bad
NCBI_THROW(CAlgoAlignException, eInternal, g_msg_InvalidRange);
}
break;
}
}
}
}
AdjustGaps(segments);
}
