bool CBioseq_Handle::ContainsSegment(CSeq_id_Handle id,
size_t resolve_depth,
EFindSegment limit_flag) const
{
CBioseq_Handle h = GetScope().GetBioseqHandle(id);
CConstRef<CSynonymsSet> syns;
if ( h ) {
syns = h.GetSynonyms();
}
SSeqMapSelector sel;
sel.SetFlags(CSeqMap::fFindRef);
if ( limit_flag == eFindSegment_LimitTSE ) {
sel.SetLimitTSE(GetTopLevelEntry());
}
sel.SetResolveCount(resolve_depth);
CSeqMap_CI it = GetSeqMap().BeginResolved(&GetScope(), sel);
for ( ; it; ++it) {
if ( syns ) {
if ( syns->ContainsSynonym(it.GetRefSeqid()) ) {
return true;
}
}
else {
if (it.GetRefSeqid() == id) {
return true;
}
}
}
return false;
}
void CGapAnalysis::AddBioseqGaps(
const CBioseq_Handle & bioseq_h,
TAddFlag add_flags,
TFlag fFlags,
size_t max_resolve_count)
{
// get CSeq_id of CBioseq
TSeqIdConstRef pSeqId = bioseq_h.GetSeqId();
const TSeqPos bioseq_len = bioseq_h.GetBioseqLength();
// fFlags control what we look at
CSeqMap::TFlags seq_map_flags = 0;
if( add_flags & fAddFlag_IncludeSeqGaps ) {
seq_map_flags |= CSeqMap::fFindGap;
}
if( add_flags & fAddFlag_IncludeUnknownBases ) {
seq_map_flags |= CSeqMap::fFindData;
}
TSeqPos end_of_last_segment = 0; // exclusive
bool all_segments_and_in_order = true;
SSeqMapSelector selector;
selector.SetFlags(seq_map_flags).SetResolveCount(max_resolve_count);
CSeqMap_CI seqmap_ci(bioseq_h, selector);
for( ; seqmap_ci; ++seqmap_ci ) {
if( seqmap_ci.GetPosition() != end_of_last_segment ) {
all_segments_and_in_order = false;
}
end_of_last_segment = seqmap_ci.GetEndPosition();
CSeqMap::ESegmentType seg_type = seqmap_ci.GetType();
switch(seg_type) {
case CSeqMap::eSeqGap:
_ASSERT(add_flags & fAddFlag_IncludeSeqGaps);
AddGap(
eGapType_SeqGap, pSeqId,
seqmap_ci.GetLength(),
bioseq_len,
seqmap_ci.GetPosition(), seqmap_ci.GetEndPosition(),
fFlags);
break;
case CSeqMap::eSeqData:
_ASSERT(add_flags & fAddFlag_IncludeUnknownBases);
x_AddGapsFromBases(
seqmap_ci, pSeqId,
bioseq_len, fFlags);
break;
default:
NCBI_USER_THROW_FMT(
"This segment type is not supported at this time: " <<
static_cast<int>(seg_type) );
}
}
if( end_of_last_segment != bioseq_len ) {
all_segments_and_in_order = false;
}
if( ! all_segments_and_in_order ) {
ERR_POST(
Warning << "Not all segments on bioseq '"
<< pSeqId->AsFastaString() << "' were in order "
"or some positions appear to have been skipped. "
"One possible reason is that there were far references for "
"which no attempt was made to resolve due to max resolve count "
"being reached.");
}
}
