Lines Matching refs:seq2
149 CAlnMixSeq * refseq = 0, * seq1 = 0, * seq2 = 0; in x_Merge() local
249 seq2 = match->m_AlnSeq2; in x_Merge()
251 if ( seq2 ) in x_Merge()
258 seq2 = match->m_AlnSeq1; in x_Merge()
260 if ( seq2 ) in x_Merge()
264 seq2 = match->m_AlnSeq2; in x_Merge()
270 if (seq2) { in x_Merge()
272 seq2->m_MatchList.insert(seq2->m_MatchList.end(), match); in x_Merge()
295 match->m_AlnSeq2 = seq2; in x_Merge()
298 if ( seq2 ) in x_Merge()
301 if (m_MergeFlags & fTruncateOverlaps && seq2) { in x_Merge()
310 if ((plane_it = m_Planes.find(make_pair(seq1, seq2))) != in x_Merge()
316 plane = &(m_Planes[make_pair(seq1, seq2)] = new_plane); in x_Merge()
334 if (seq2) { in x_Merge()
335 width2 = seq2->m_Width; in x_Merge()
347 seq2 = match->m_AlnSeq2; in x_Merge()
349 if ( seq2 ) in x_Merge()
380 if (seq2) { in x_Merge()
382 seq2->m_RefBy = refseq; in x_Merge()
386 if ( !seq2->m_MatchList.empty() ) { in x_Merge()
387 seq2->m_MatchList.erase(match_list_iter2); in x_Merge()
388 match_list_iter2 = seq2->m_MatchList.end(); in x_Merge()
406 if (seq2) { in x_Merge()
425 seq2 = match->m_AlnSeq2; in x_Merge()
427 if ( seq2 ) in x_Merge()
432 if (!seq2->m_ExtraRow) { in x_Merge()
435 row->m_BioseqHandle = seq2->m_BioseqHandle; in x_Merge()
436 row->m_SeqId = seq2->m_SeqId; in x_Merge()
437 row->m_Width = seq2->m_Width; in x_Merge()
439 row->m_SeqIdx = seq2->m_SeqIdx; in x_Merge()
440 row->m_ChildIdx = seq2->m_ChildIdx + 1; in x_Merge()
445 row->m_ExtraRowIdx = seq2->m_ExtraRowIdx + 1; in x_Merge()
446 seq2 = match->m_AlnSeq2 = seq2->m_ExtraRow = row; in x_Merge()
449 seq2 = match->m_AlnSeq2 = seq2->m_ExtraRow; in x_Merge()
458 seq2 = match->m_AlnSeq2; in x_Merge()
460 if ( seq2 ) in x_Merge()
500 seq2->m_DsIdx = match->m_DsIdx; in x_Merge()
688 if (seq2) { in x_Merge()
692 if (!seq2->m_ExtraRow) { in x_Merge()
695 row->m_BioseqHandle = seq2->m_BioseqHandle; in x_Merge()
696 row->m_SeqId = seq2->m_SeqId; in x_Merge()
697 row->m_Width = seq2->m_Width; in x_Merge()
699 row->m_SeqIdx = seq2->m_SeqIdx; in x_Merge()
700 row->m_ChildIdx = seq2->m_ChildIdx + 1; in x_Merge()
705 row->m_ExtraRowIdx = seq2->m_ExtraRowIdx + 1; in x_Merge()
706 seq2 = match->m_AlnSeq2 = seq2->m_ExtraRow = row; in x_Merge()
709 seq2 = match->m_AlnSeq2 = seq2->m_ExtraRow; in x_Merge()
718 seq2 = match->m_AlnSeq2; in x_Merge()
720 if ( seq2 ) in x_Merge()
738 if (seq2->GetStarts().empty()) { in x_Merge()
739 seq2->m_PositiveStrand = in x_Merge()
773 start_i->second->StartItsConsistencyCheck(*seq2, in x_Merge()
780 seq2->SetStarts()[start] = start_i->second; in x_Merge()
787 if (start_i->second->m_StartIts.find(seq2) != in x_Merge()
795 start_i->second->SetStartIterator(seq2, start2_i); in x_Merge()
797 start_i->second->StartItsConsistencyCheck(*seq2, in x_Merge()
838 CAlnMixSeq*& seq2 = match->m_AlnSeq2; in x_SecondRowFits() local
843 const int& width2 = seq2->m_Width; in x_SecondRowFits()
850 if (seq2->m_DsIdx) { in x_SecondRowFits()
852 if (seq2->m_DsIdx == match->m_DsIdx) { in x_SecondRowFits()
859 seq2->m_DsIdx = match->m_DsIdx; in x_SecondRowFits()
866 if ( !seq2->GetStarts().empty() ) { in x_SecondRowFits()
870 if (seq2->m_PositiveStrand != in x_SecondRowFits()
874 if (seq2->m_ExtraRow) { in x_SecondRowFits()
875 seq2 = seq2->m_ExtraRow; in x_SecondRowFits()
885 if (seq2->m_Width == 3 && seq2->m_Frame != (int)(start2 % 3)) { in x_SecondRowFits()
889 starts2_i = seq2->GetStarts().lower_bound(start2); in x_SecondRowFits()
892 if (starts2_i != seq2->GetStarts().begin()) { in x_SecondRowFits()
1003 if (starts2_i != seq2->GetStarts().end()) { in x_SecondRowFits()
1009 while (starts2_i != seq2->GetStarts().end() && in x_SecondRowFits()
1050 if (starts2_i != seq2->GetStarts().end()) { in x_SecondRowFits()
1127 if ((seq2_start_it_i = seg_start_its.find(seq2)) != in x_SecondRowFits()
1145 if (seq2->m_DsIdx == match->m_DsIdx) { in x_SecondRowFits()