Search Toolkit Book for TMaskedQueryRegions
Collection of masked regions for a single query sequence. More...
#include <objects/seq/seqlocinfo.hpp>
Inheritance diagram for TMaskedQueryRegions:
Collaboration diagram for TMaskedQueryRegions:
Public Member Functions | |
| TMaskedQueryRegions | RestrictToSeqInt (const objects::CSeq_interval &location) const |
| Return a new instance of this object that is restricted to the location specified. More... | |
| CRef< objects::CPacked_seqint > | ConvertToCPacked_seqint () const |
| Converts this object to a CPacked_seqint (this is the convention used to encode masking locations in the network BLAST 4 protocol) More... | |
| bool | HasNegativeStrandMasks () const |
| Returns true if there are masks on the negative strand. More... | |
Detailed Description
Collection of masked regions for a single query sequence.
Definition at line 112 of file seqlocinfo.hpp.
Member Function Documentation
◆ ConvertToCPacked_seqint()
| CRef< objects::CPacked_seqint > TMaskedQueryRegions::ConvertToCPacked_seqint | ( | ) | const |
Converts this object to a CPacked_seqint (this is the convention used to encode masking locations in the network BLAST 4 protocol)
Definition at line 127 of file seqlocinfo.cpp.
References ITERATE, mask, and CRef< C, Locker >::Reset().
Referenced by CObjMgr_QueryFactory::GetTSeqLocVector(), and MaskedQueryRegionsToPackedSeqLoc().
◆ HasNegativeStrandMasks()
| bool TMaskedQueryRegions::HasNegativeStrandMasks | ( | ) | const |
Returns true if there are masks on the negative strand.
Definition at line 148 of file seqlocinfo.cpp.
References eNa_strand_minus, ITERATE, and mask.
◆ RestrictToSeqInt()
| TMaskedQueryRegions TMaskedQueryRegions::RestrictToSeqInt | ( | const objects::CSeq_interval & | location | ) | const |
Return a new instance of this object that is restricted to the location specified.
- Parameters
-
location location describing the range to restrict. Note that only the provided range is examined, the Seq-id and strand of the location (if assigned and different from unknown) is copied verbatim into the return value of this method [in]
- Returns
- empty TMaskedQueryRegions if this object is empty, otherwise the intersection of location and this object
Definition at line 98 of file seqlocinfo.cpp.
References CSeq_interval_Base::CanGetStrand(), eNa_strand_unknown, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), COpenRange< Position >::IntersectionWith(), ITERATE, NMacroArgs::kStrand, location, mask, compile_time_bits::range(), COpenRange< Position >::SetToOpen(), and si.
Referenced by BOOST_AUTO_TEST_CASE().
The documentation for this class was generated from the following files:
- include/objects/seq/seqlocinfo.hpp
- src/objects/seq/seqlocinfo.cpp
