<
typenameTSeq_loc_Set>
389 ITERATE(
typenameTSeq_loc_Set, it, locs) {
ESeqLocExtremes
Used to determine the meaning of a location's Start/Stop positions.
@ eExtreme_Positional
numerical value
Include a standard set of the NCBI C++ Toolkit most basic headers.
unsigned int TSeqPos
Type for sequence locations and lengths.
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
const TSeqPos kInvalidSeqPos
Define special value for invalid sequence position.
void Add(const CSeq_loc &other)
Simple adding of seq-locs.
TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)
If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.
const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)
If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...
bool BadSeqLocSortOrder(const CBioseq_Handle &bsh, const CSeq_loc &loc)
Returns true if the order of Seq_locs is bad, otherwise, false.
TSeqPos GetLength(const CSeq_id &id, CScope *scope)
Get sequence length if scope not null, else return max possible TSeqPos.
ESeqLocCheck
SeqLocCheck results.
ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)
Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...
bool IsValid(const CSeq_point &pt, CScope *scope)
Checks that point >= 0 and point < length of Bioseq.
Int8 TestForOverlapEx(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, CScope *scope=0, TOverlapFlags flags=fOverlap_Default)
Updated version of TestForOverlap64().
TSeqPos LocationOffset(const CSeq_loc &outer, const CSeq_loc &inner, EOffsetType how=eOffset_FromStart, CScope *scope=0)
returns (TSeqPos)-1 if the locations don't overlap
void ChangeSeqLocId(CSeq_loc *loc, bool best, CScope *scope)
Change each of the CSeq_ids embedded in a CSeq_loc to the best or worst CSeq_id accoring to the value...
TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)
If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.
int SeqLocPartialCheck(const CSeq_loc &loc, CScope *scope)
sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)
Returns the sequence::ECompare containment relationship between CSeq_locs.
TSeqPos GetCoverage(const CSeq_loc &loc, CScope *scope)
Get number of unique bases in the location.
CSeq_loc * SeqLocRevCmp(const CSeq_loc &loc, CScope *scope)
Old name for this function.
CRef< CSeq_loc > Seq_loc_Subtract(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)
Subtract the second seq-loc from the first one.
Int8 TestForOverlap64(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSeqPos circular_len=kInvalidSeqPos, CScope *scope=0)
64-bit version of TestForOverlap() Check if the two locations have ovarlap of a given type.
CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)
void ChangeSeqId(CSeq_id *id, bool best, CScope *scope)
Change a CSeq_id to the one for the CBioseq that it represents that has the best rank or worst rank a...
CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)
Merge ranges in the seq-loc.
bool IsOneBioseq(const CSeq_loc &loc, CScope *scope)
Returns true if all embedded CSeq_ids represent the same CBioseq, else false.
CSeq_loc * Seq_locs_Merge(TSeq_loc_Set &locs, CSeq_loc::TOpFlags flags, CScope *scope)
Merge multiple locations.
CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)
Add two seq-locs.
int TestForOverlap(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSeqPos circular_len=kInvalidSeqPos, CScope *scope=0)
Calls TestForOverlap64() and if the result is greater than kMax_Int truncates it to kMax_Int.
bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)
Determines if two CSeq_ids represent the same CBioseq.
EOverlapFlags
Flags, controlling behavior of TestForOverlapEx().
CSeq_loc * SeqLocRevCmpl(const CSeq_loc &loc, CScope *scope)
Get reverse complement of the seq-loc (?)
ESeqLocCheck SeqLocCheck(const CSeq_loc &loc, CScope *scope)
Checks that a CSeq_loc is all on one strand on one CBioseq.
@ eSeqlocPartial_Haderror
@ eSeqlocPartial_Internal
@ eSeqlocPartial_Nointernal
@ eSeqlocPartial_Complete
@ eSeqlocPartial_Limwrong
@ fCompareAbutting
Check if seq-locs are abutting (loc2 follows loc1)
@ fCompareOverlapping
Check if seq-locs are overlapping.
@ fComparePositional
Use positional coordinates (ignore strands) when looking for abutting locations.
@ eOverlap_SubsetRev
1st is a subset of 2nd ranges
@ eOverlap_CheckIntervals
2nd is a subset of 1st with matching boundaries
@ eOverlap_Contains
2nd contains 1st extremes
@ eOverlap_CheckIntRev
1st is a subset of 2nd with matching boundaries
@ eOverlap_Simple
any overlap of extremes
@ eOverlap_Interval
at least one pair of intervals must overlap
@ eOverlap_Contained
2nd contained within 1st extremes
@ eOverlap_Subset
2nd is a subset of 1st ranges
@ eContains
First CSeq_loc contains second.
@ eOverlap
CSeq_locs overlap.
@ eSame
CSeq_locs contain each other.
@ eAbutting
Abutting seq-locs.
@ eContained
First CSeq_loc contained by second.
@ eAbutAndOverlap
Seq-locs do both abut and overlap.
@ eNoOverlap
CSeq_locs do not overlap or abut.
@ fOverlap_NoMultiSeq
Throw if locations reference multiple bioseqs.
@ fOverlap_NoMultiStrand
Throw if locations reference multiple strands.
@ fOverlap_IgnoreTopology
Ignore sequence topology (circularity)
@ fOverlap_Default
Enable multi-id, multi-strand, check topology.
@ eOffset_FromLeft
relative to low-numbered end
@ eOffset_FromRight
relative to high-numbered end
@ eOffset_FromEnd
relative to end of location
@ eOffset_FromStart
For positive-orientation strands, start = left and end = right; for reverse-orientation strands,...
@ eGetBioseq_All
Search bioseq, load if not loaded yet.
int64_t Int8
8-byte (64-bit) signed integer
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.
#define NCBI_XOBJUTIL_EXPORT
ENa_strand
strand of nucleic acid
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.
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