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);
}
