Search Toolkit Book for CSeq_interval
#include <objects/seqloc/Seq_interval.hpp>
Inheritance diagram for CSeq_interval:
Collaboration diagram for CSeq_interval:
Public Member Functions | |
| CSeq_interval (void) | |
| CSeq_interval (TId &id, TFrom from, TTo to, TStrand strand=eNa_strand_unknown) | |
| ~CSeq_interval (void) | |
| TSeqPos | GetLength (void) const |
| bool | IsPartialStart (ESeqLocExtremes ext) const |
| bool | IsPartialStop (ESeqLocExtremes ext) const |
| void | SetPartialStart (bool val, ESeqLocExtremes ext) |
| void | SetPartialStop (bool val, ESeqLocExtremes ext) |
| bool | IsTruncatedStart (ESeqLocExtremes ext) const |
| check if parts of the seq-loc are missing More... | |
| bool | IsTruncatedStop (ESeqLocExtremes ext) const |
| void | SetTruncatedStart (bool val, ESeqLocExtremes ext) |
| set / remove e_Lim fuzz on start or stop (tl/tr - indicating removed parts of the seq-loc) More... | |
| void | SetTruncatedStop (bool val, ESeqLocExtremes ext) |
| TSeqPos | GetStart (ESeqLocExtremes ext) const |
| TSeqPos | GetStop (ESeqLocExtremes ext) const |
| void | FlipStrand (void) |
| Public Member Functions inherited from CSeq_interval_Base | |
| CSeq_interval_Base (void) | |
| virtual | ~CSeq_interval_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetFrom (void) const |
| Check if a value has been assigned to From data member. More... | |
| bool | CanGetFrom (void) const |
| Check if it is safe to call GetFrom method. More... | |
| void | ResetFrom (void) |
| Reset From data member. More... | |
| TFrom | GetFrom (void) const |
| Get the From member data. More... | |
| void | SetFrom (TFrom value) |
| Assign a value to From data member. More... | |
| TFrom & | SetFrom (void) |
| Assign a value to From data member. More... | |
| bool | IsSetTo (void) const |
| Check if a value has been assigned to To data member. More... | |
| bool | CanGetTo (void) const |
| Check if it is safe to call GetTo method. More... | |
| void | ResetTo (void) |
| Reset To data member. More... | |
| TTo | GetTo (void) const |
| Get the To member data. More... | |
| void | SetTo (TTo value) |
| Assign a value to To data member. More... | |
| TTo & | SetTo (void) |
| Assign a value to To data member. More... | |
| bool | IsSetStrand (void) const |
| Check if a value has been assigned to Strand data member. More... | |
| bool | CanGetStrand (void) const |
| Check if it is safe to call GetStrand method. More... | |
| void | ResetStrand (void) |
| Reset Strand data member. More... | |
| TStrand | GetStrand (void) const |
| Get the Strand member data. More... | |
| void | SetStrand (TStrand value) |
| Assign a value to Strand data member. More... | |
| TStrand & | SetStrand (void) |
| Assign a value to Strand data member. More... | |
| bool | IsSetId (void) const |
| WARNING: this used to be optional Check if a value has been assigned to Id data member. More... | |
| bool | CanGetId (void) const |
| Check if it is safe to call GetId method. More... | |
| void | ResetId (void) |
| Reset Id data member. More... | |
| const TId & | GetId (void) const |
| Get the Id member data. More... | |
| void | SetId (TId &value) |
| Assign a value to Id data member. More... | |
| TId & | SetId (void) |
| Assign a value to Id data member. More... | |
| bool | IsSetFuzz_from (void) const |
| Check if a value has been assigned to Fuzz_from data member. More... | |
| bool | CanGetFuzz_from (void) const |
| Check if it is safe to call GetFuzz_from method. More... | |
| void | ResetFuzz_from (void) |
| Reset Fuzz_from data member. More... | |
| const TFuzz_from & | GetFuzz_from (void) const |
| Get the Fuzz_from member data. More... | |
| void | SetFuzz_from (TFuzz_from &value) |
| Assign a value to Fuzz_from data member. More... | |
| TFuzz_from & | SetFuzz_from (void) |
| Assign a value to Fuzz_from data member. More... | |
| bool | IsSetFuzz_to (void) const |
| Check if a value has been assigned to Fuzz_to data member. More... | |
| bool | CanGetFuzz_to (void) const |
| Check if it is safe to call GetFuzz_to method. More... | |
| void | ResetFuzz_to (void) |
| Reset Fuzz_to data member. More... | |
| const TFuzz_to & | GetFuzz_to (void) const |
| Get the Fuzz_to member data. More... | |
| void | SetFuzz_to (TFuzz_to &value) |
| Assign a value to Fuzz_to data member. More... | |
| TFuzz_to & | SetFuzz_to (void) |
| Assign a value to Fuzz_to data member. More... | |
| virtual void | Reset (void) |
| Reset the whole object. More... | |
| Public Member Functions inherited from CSerialObject | |
| CSerialObject (void) | |
| virtual | ~CSerialObject (void) |
| virtual const CTypeInfo * | GetThisTypeInfo (void) const =0 |
| virtual void | Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) |
| Set object to copy of another one. More... | |
| virtual bool | Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const |
| Check if both objects contain the same values. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| void | ThrowUnassigned (TMemberIndex index) const |
| void | ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const |
| bool | HasNamespaceName (void) const |
| Check if object data type has namespace name. More... | |
| const string & | GetNamespaceName (void) const |
| Get namespace name. More... | |
| bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More... | |
| const string & | GetNamespacePrefix (void) const |
| Get namespace prefix. More... | |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const |
| Remove reference to object. More... | |
| void | ReleaseReference (void) const |
| Remove reference without deleting object. More... | |
| virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More... | |
| virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More... | |
| void * | operator new (size_t size) |
| Define new operator for memory allocation. More... | |
| void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More... | |
| void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More... | |
| void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More... | |
| void * | operator new (size_t size, void *place) |
| Define new operator. More... | |
| void | operator delete (void *ptr, void *place) |
| Define delete operator. More... | |
| void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More... | |
| void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More... | |
| Public Member Functions inherited from CDebugDumpable | |
| CDebugDumpable (void) | |
| virtual | ~CDebugDumpable (void) |
| void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
| void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
| void | DumpToConsole (void) const |
Private Types | |
| typedef CSeq_interval_Base | Tparent |
Private Member Functions | |
| CSeq_interval (const CSeq_interval &) | |
| CSeq_interval & | operator= (const CSeq_interval &) |
| bool | x_IsMinusStrand (void) const |
Additional Inherited Members | |
| Public Types inherited from CSeq_interval_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_from , e_to , e_strand , e_id , e_fuzz_from , e_fuzz_to } |
| typedef TSeqPos | TFrom |
| typedef TSeqPos | TTo |
| typedef ENa_strand | TStrand |
| typedef CSeq_id | TId |
| typedef CInt_fuzz | TFuzz_from |
| typedef CInt_fuzz | TFuzz_to |
| typedef Tparent::CMemberIndex< E_memberIndex, 7 > | TmemberIndex |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
| Static Public Member Functions inherited from CSerialObject | |
| static void | SetVerifyDataThread (ESerialVerifyData verify) |
| static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
| static string | UnassignedString (void) |
| static CStringUTF8 | UnassignedStringUTF8 (void) |
| static char | UnassignedByte (void) |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
| Static Public Attributes inherited from CSerialObject | |
| static const char * | ms_UnassignedStr = "<*unassigned*>" |
| static const char | ms_UnassignedByte = char(0xcd) |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Detailed Description
Definition at line 50 of file Seq_interval.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 52 of file Seq_interval.hpp.
Constructor & Destructor Documentation
◆ CSeq_interval() [1/3]
|
inline |
Definition at line 106 of file Seq_interval.hpp.
◆ CSeq_interval() [2/3]
|
inline |
Definition at line 112 of file Seq_interval.hpp.
References eNa_strand_unknown, CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().
◆ ~CSeq_interval()
| CSeq_interval::~CSeq_interval | ( | void | ) |
Definition at line 51 of file Seq_interval.cpp.
◆ CSeq_interval() [3/3]
|
private |
Member Function Documentation
◆ FlipStrand()
| void CSeq_interval::FlipStrand | ( | void | ) |
Definition at line 244 of file Seq_interval.cpp.
References eNa_strand_minus, CSeq_interval_Base::GetStrand(), CSeq_interval_Base::IsSetStrand(), Reverse(), and CSeq_interval_Base::SetStrand().
Referenced by CSeq_loc::FlipStrand(), and ReverseComplementLocation().
◆ GetLength()
|
inline |
Definition at line 125 of file Seq_interval.hpp.
References CSeq_interval_Base::GetFrom(), and CSeq_interval_Base::GetTo().
Referenced by NTweakExon::CanCreateNonframeshiftingGap(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), NTweakExon::ConvertOverlapsToGaps(), GetCoverage(), CBlobSplitterImpl::GetLength(), GetLength(), CDDAnnotateDialog::NewOrEditMotif(), SCigarAlignment::operator()(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetIntronsAndSpliceSiteLocs(), s_GetSeq_intervalLabel(), s_GetTrimmedLength(), s_GetUngapLoc(), CClippedScorer::ScoreAlignments(), CBedFeatureRecord::SetBlocks(), NTweakExon::SubsumeMicroIntervals(), sx_AddBits(), CSeqMap::x_Add(), CBioseq_Info::x_CalcBioseqLength(), CCommonComponentScorer::x_GetDeltaExtCompList(), CGencollIdMapper::x_IsLoc_Int_InAGap(), CSeqTableInfo::x_IsSorted(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CUnorderedSplitter::x_SplitSeqData(), CGtfWriter::xAssignFeaturesCds(), and CGff3Writer::xWriteFeatureCds().
◆ GetStart()
| TSeqPos CSeq_interval::GetStart | ( | ESeqLocExtremes | ext | ) | const |
Definition at line 230 of file Seq_interval.cpp.
References eExtreme_Biological, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetTo(), and x_IsMinusStrand().
Referenced by NTweakExon::AdjustBioStart(), CConvertFeatToDescComment::apply(), CConvertFeatToDescSource::apply(), CConvertFeatToDescPub::apply(), ConvertMixToInterval(), NTweakExon::GetBiostartsDelta(), CEditingActionFeatAnticodon::GetIntervalString(), GetIntervalString(), CPacked_seqint::GetStart(), and CSeq_loc::GetStart().
◆ GetStop()
| TSeqPos CSeq_interval::GetStop | ( | ESeqLocExtremes | ext | ) | const |
Definition at line 237 of file Seq_interval.cpp.
References eExtreme_Biological, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetTo(), and x_IsMinusStrand().
Referenced by NTweakExon::AdjustBioStop(), CConvertFeatToDescComment::apply(), CConvertFeatToDescSource::apply(), CConvertFeatToDescPub::apply(), ConvertMixToInterval(), CEditingActionFeatAnticodon::GetIntervalString(), GetIntervalString(), CPacked_seqint::GetStop(), and CSeq_loc::GetStop().
◆ IsPartialStart()
| bool CSeq_interval::IsPartialStart | ( | ESeqLocExtremes | ext | ) | const |
Definition at line 62 of file Seq_interval.cpp.
References eExtreme_Biological, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::IsLim(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), and x_IsMinusStrand().
Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::ConvertPacked_int(), CEditingActionFeatAnticodon::GetIntervalString(), GetIntervalString(), CPacked_seqint::IsPartialStart(), CSeq_loc::IsPartialStart(), and SetPartialStart().
◆ IsPartialStop()
| bool CSeq_interval::IsPartialStop | ( | ESeqLocExtremes | ext | ) | const |
Definition at line 82 of file Seq_interval.cpp.
References eExtreme_Biological, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::IsLim(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), and x_IsMinusStrand().
Referenced by BOOST_AUTO_TEST_CASE(), CEditingActionFeatAnticodon::GetIntervalString(), GetIntervalString(), CPacked_seqint::IsPartialStop(), CSeq_loc::IsPartialStop(), and SetPartialStop().
◆ IsTruncatedStart()
| bool CSeq_interval::IsTruncatedStart | ( | ESeqLocExtremes | ext | ) | const |
check if parts of the seq-loc are missing
Definition at line 146 of file Seq_interval.cpp.
References eExtreme_Biological, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::IsLim(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), and x_IsMinusStrand().
Referenced by CPacked_seqint::IsTruncatedStart(), CSeq_loc::IsTruncatedStart(), and SetTruncatedStart().
◆ IsTruncatedStop()
| bool CSeq_interval::IsTruncatedStop | ( | ESeqLocExtremes | ext | ) | const |
Definition at line 167 of file Seq_interval.cpp.
References eExtreme_Biological, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::IsLim(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), and x_IsMinusStrand().
Referenced by CPacked_seqint::IsTruncatedStop(), CSeq_loc::IsTruncatedStop(), and SetTruncatedStop().
◆ operator=()
|
private |
◆ SetPartialStart()
| void CSeq_interval::SetPartialStart | ( | bool | val, |
| ESeqLocExtremes | ext | ||
| ) |
Definition at line 104 of file Seq_interval.cpp.
References _ASSERT, eExtreme_Biological, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, IsPartialStart(), CSeq_interval_Base::ResetFuzz_from(), CSeq_interval_Base::ResetFuzz_to(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CInt_fuzz_Base::SetLim(), val, and x_IsMinusStrand().
Referenced by CConvertCDSToMiscFeat::Convert(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion::ConvertPacked_int(), CPacked_seqint::SetPartialStart(), CSeq_loc::SetPartialStart(), CFeatureTableReader_Imp::x_AddIntervalToFeature(), CSGAlignmentJob::x_CreateFeatGlyph(), and CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons().
◆ SetPartialStop()
| void CSeq_interval::SetPartialStop | ( | bool | val, |
| ESeqLocExtremes | ext | ||
| ) |
Definition at line 125 of file Seq_interval.cpp.
References _ASSERT, eExtreme_Biological, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, IsPartialStop(), CSeq_interval_Base::ResetFuzz_from(), CSeq_interval_Base::ResetFuzz_to(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CInt_fuzz_Base::SetLim(), val, and x_IsMinusStrand().
Referenced by CConvertCDSToMiscFeat::Convert(), CSeq_loc_Conversion_Set::ConvertInterval(), CPacked_seqint::SetPartialStop(), CSeq_loc::SetPartialStop(), CFeatureTableReader_Imp::x_AddIntervalToFeature(), CSGAlignmentJob::x_CreateFeatGlyph(), and CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons().
◆ SetTruncatedStart()
| void CSeq_interval::SetTruncatedStart | ( | bool | val, |
| ESeqLocExtremes | ext | ||
| ) |
set / remove e_Lim fuzz on start or stop (tl/tr - indicating removed parts of the seq-loc)
Definition at line 188 of file Seq_interval.cpp.
References _ASSERT, eExtreme_Biological, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, IsTruncatedStart(), CSeq_interval_Base::ResetFuzz_from(), CSeq_interval_Base::ResetFuzz_to(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CInt_fuzz_Base::SetLim(), val, and x_IsMinusStrand().
Referenced by CPacked_seqint::SetTruncatedStart(), and CSeq_loc::SetTruncatedStart().
◆ SetTruncatedStop()
| void CSeq_interval::SetTruncatedStop | ( | bool | val, |
| ESeqLocExtremes | ext | ||
| ) |
Definition at line 209 of file Seq_interval.cpp.
References _ASSERT, eExtreme_Biological, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, IsTruncatedStop(), CSeq_interval_Base::ResetFuzz_from(), CSeq_interval_Base::ResetFuzz_to(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CInt_fuzz_Base::SetLim(), val, and x_IsMinusStrand().
Referenced by CPacked_seqint::SetTruncatedStop(), and CSeq_loc::SetTruncatedStop().
◆ x_IsMinusStrand()
|
private |
Definition at line 56 of file Seq_interval.cpp.
References CSeq_interval_Base::GetStrand(), IsReverse(), and CSeq_interval_Base::IsSetStrand().
Referenced by GetStart(), GetStop(), IsPartialStart(), IsPartialStop(), IsTruncatedStart(), IsTruncatedStop(), SetPartialStart(), SetPartialStop(), SetTruncatedStart(), and SetTruncatedStop().
The documentation for this class was generated from the following files:
- include/objects/seqloc/Seq_interval.hpp
- src/objects/seqloc/Seq_interval.cpp
