NCBI C++ ToolKit
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TMaskedQueryRegions Class Reference

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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
locationlocation 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:
Modified on Fri Jan 05 07:22:12 2024 by modify_doxy.py rev. 669887