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CFlatSeqLoc Class Reference

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#include <objtools/format/items/flat_seqloc.hpp>

+ Inheritance diagram for CFlatSeqLoc:
+ Collaboration diagram for CFlatSeqLoc:

Classes

class  CGuardedToAccessionMap
 

Public Types

enum  EType { eType_location , eType_assembly }
 
typedef EType TType
 
- 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...
 

Public Member Functions

 CFlatSeqLoc (const CSeq_loc &loc, CBioseqContext &ctx, TType type=eType_location, bool show_all_accns=false, bool add_join=false, bool suppress_accession=false)
 
const string & GetString (void) const
 
- 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...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. 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

enum  EHTML { eHTML_None = 0 , eHTML_Yes }
 
enum  EForce { eForce_None = 0 , eForce_ToRange }
 
enum  ESource { eSource_Other = 0 , eSource_Point }
 
typedef std::map< CSeq_id_Handle, CSeq_id_Handle > TToAccessionMap
 

Private Member Functions

bool x_Add (const CSeq_loc &loc, CNcbiOstrstream &oss, CBioseqContext &ctx, TType type, bool show_comp, bool show_all_accns=false, bool join_whole_loc=false, bool suppress_accession=false)
 
bool x_Add (const CSeq_interval &si, CNcbiOstrstream &oss, CBioseqContext &ctx, TType type, bool show_comp, bool show_all_accns=false, bool suppress_accession=false)
 
bool x_Add (const CSeq_point &pnt, CNcbiOstrstream &oss, CBioseqContext &ctx, TType type, bool show_comp, bool show_all_accns=false, bool suppress_accession=false)
 
bool x_Add (TSeqPos pnt, const CInt_fuzz *fuzz, CNcbiOstrstream &oss, EHTML html, EForce force=eForce_None, ESource source=eSource_Other, bool show_all_accns=false, bool suppress_accession=false)
 
void x_AddID (const CSeq_id &id, CNcbiOstrstream &oss, CBioseqContext &ctx, TType type, bool show_all_accns=false, bool suppress_accession=false)
 
bool x_IsAccessionVersion (CSeq_id_Handle id)
 
bool x_FuzzToDisplayed (const CSeq_interval &si) const
 

Private Attributes

string m_String
 

Static Private Attributes

static CGuardedToAccessionMap m_ToAccessionMap
 

Additional Inherited Members

- 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 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 71 of file flat_seqloc.hpp.

Member Typedef Documentation

◆ TToAccessionMap

typedef std::map<CSeq_id_Handle, CSeq_id_Handle> CFlatSeqLoc::TToAccessionMap
private

Definition at line 131 of file flat_seqloc.hpp.

◆ TType

typedef EType CFlatSeqLoc::TType

Definition at line 79 of file flat_seqloc.hpp.

Member Enumeration Documentation

◆ EForce

enum CFlatSeqLoc::EForce
private
Enumerator
eForce_None 
eForce_ToRange 

Definition at line 97 of file flat_seqloc.hpp.

◆ EHTML

enum CFlatSeqLoc::EHTML
private
Enumerator
eHTML_None 
eHTML_Yes 

Definition at line 92 of file flat_seqloc.hpp.

◆ ESource

enum CFlatSeqLoc::ESource
private
Enumerator
eSource_Other 
eSource_Point 

Definition at line 102 of file flat_seqloc.hpp.

◆ EType

enum CFlatSeqLoc::EType ( void  )
Enumerator
eType_location 
eType_assembly 

Definition at line 74 of file flat_seqloc.hpp.

Constructor & Destructor Documentation

◆ CFlatSeqLoc()

CFlatSeqLoc::CFlatSeqLoc ( const CSeq_loc &  loc,
CBioseqContext &  ctx,
TType  type = eType_location,
bool  show_all_accns = false,
bool  add_join = false,
bool  suppress_accession = false 
)

Definition at line 148 of file flat_seqloc.cpp.

References _ASSERT, set< Key, Compare >::begin(), copy(), ctx, set< Key, Compare >::empty(), set< Key, Compare >::end(), CFlatSeqLoc::CGuardedToAccessionMap::Get(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSeq_id_Handle(), set< Key, Compare >::insert(), CFlatSeqLoc::CGuardedToAccessionMap::Insert(), m_String, m_ToAccessionMap, results, s_FlattenLoc(), s_NeedsFlattening(), string, swap(), x_Add(), and x_IsAccessionVersion().

Member Function Documentation

◆ GetString()

const string& CFlatSeqLoc::GetString ( void  ) const
inline

Definition at line 88 of file flat_seqloc.hpp.

References m_String.

Referenced by CFlatAnticodonQVal::Format(), CFlatCodeBreakQVal::Format(), CGenbankFormatter::FormatAccession(), CGBSeqFormatter::FormatContig(), CGenbankFormatter::FormatContig(), CFeatureItem::x_AddFTableAnticodon(), CFeatureItem::x_AddFTableCdregionQuals(), and CFastaOstreamEx::x_AddLocationAttribute().

◆ x_Add() [1/4]

bool CFlatSeqLoc::x_Add ( const CSeq_interval &  si,
CNcbiOstrstream &  oss,
CBioseqContext &  ctx,
TType  type,
bool  show_comp,
bool  show_all_accns = false,
bool  suppress_accession = false 
)
private

Definition at line 508 of file flat_seqloc.cpp.

References ctx, eHTML_None, eHTML_Yes, eNa_strand_minus, eNa_strand_unknown, eType_assembly, eType_location, CSeq_id_Handle::GetHandle(), s_IsVirtualId(), si, x_Add(), x_AddID(), and x_FuzzToDisplayed().

◆ x_Add() [2/4]

bool CFlatSeqLoc::x_Add ( const CSeq_loc &  loc,
CNcbiOstrstream &  oss,
CBioseqContext &  ctx,
TType  type,
bool  show_comp,
bool  show_all_accns = false,
bool  join_whole_loc = false,
bool  suppress_accession = false 
)
private

Definition at line 220 of file flat_seqloc.cpp.

References CSeq_bond_Base::CanGetA(), CSeq_bond_Base::CanGetB(), CPacked_seqpnt_Base::CanGetFuzz(), ctx, CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_CI::eEmpty_Allow, eForce_None, eHTML_None, eHTML_Yes, CInt_fuzz_Base::eLim_unk, eNa_strand_minus, eNa_strand_unknown, eSource_Other, eType_location, CPacked_seqint_Base::Get(), CSeq_loc_equiv_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_bond_Base::GetA(), CSeq_bond_Base::GetB(), CSeq_loc_Base::GetBond(), CSeq_loc_CI::GetEmbeddingSeq_loc(), CSeq_loc_Base::GetEquiv(), CFlatGapLoc::GetFuzz(), CPacked_seqpnt_Base::GetFuzz(), CPacked_seqpnt_Base::GetId(), CSeq_loc_Base::GetInt(), GetLength(), CFlatGapLoc::GetLength(), CInt_fuzz_Base::GetLim(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CPacked_seqpnt_Base::GetPoints(), GetStrand(), CPacked_seqpnt_Base::GetStrand(), CSeq_loc_Base::GetWhole(), CSeq_loc_Base::IsInt(), CInt_fuzz_Base::IsLim(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsNull(), CSeq_loc_Base::IsPacked_int(), CSeq_loc_Base::IsPnt(), CPacked_seqpnt_Base::IsSetStrand(), ITERATE, len, next(), CSeq_loc_CI::Rewind(), s_IsVirtualLocation(), s_IsVirtualSeqInt(), SeqLocRevCmpl(), CSeq_loc_Base::Which(), and x_AddID().

Referenced by CFlatSeqLoc(), and x_Add().

◆ x_Add() [3/4]

bool CFlatSeqLoc::x_Add ( const CSeq_point &  pnt,
CNcbiOstrstream &  oss,
CBioseqContext &  ctx,
TType  type,
bool  show_comp,
bool  show_all_accns = false,
bool  suppress_accession = false 
)
private

Definition at line 554 of file flat_seqloc.cpp.

References CSeq_point_Base::CanGetPoint(), ctx, eForce_None, eForce_ToRange, eHTML_None, eHTML_Yes, eSource_Point, eType_assembly, CSeq_point_Base::GetFuzz(), CSeq_point_Base::GetId(), CSeq_point_Base::GetPoint(), CSeq_point_Base::GetStrand(), IsReverse(), CSeq_point_Base::IsSetFuzz(), CSeq_point_Base::IsSetStrand(), x_Add(), and x_AddID().

◆ x_Add() [4/4]

bool CFlatSeqLoc::x_Add ( TSeqPos  pnt,
const CInt_fuzz *  fuzz,
CNcbiOstrstream &  oss,
EHTML  html,
EForce  force = eForce_None,
ESource  source = eSource_Other,
bool  show_all_accns = false,
bool  suppress_accession = false 
)
private

Definition at line 588 of file flat_seqloc.cpp.

References delta(), CInt_fuzz_Base::e_Lim, CInt_fuzz_Base::e_P_m, CInt_fuzz_Base::e_Pct, CInt_fuzz_Base::e_Range, eForce_ToRange, eHTML_Yes, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, eSource_Point, CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::C_Range::GetMax(), CInt_fuzz_Base::C_Range::GetMin(), CInt_fuzz_Base::GetP_m(), CInt_fuzz_Base::GetPct(), CInt_fuzz_Base::GetRange(), rapidjson::source, and CInt_fuzz_Base::Which().

◆ x_AddID()

void CFlatSeqLoc::x_AddID ( const CSeq_id &  id,
CNcbiOstrstream &  oss,
CBioseqContext &  ctx,
TType  type,
bool  show_all_accns = false,
bool  suppress_accession = false 
)
private

Definition at line 686 of file flat_seqloc.cpp.

References ctx, CSeq_id_Base::e_Gi, eType_assembly, CFlatSeqLoc::CGuardedToAccessionMap::Get(), CSeq_id_Handle::GetHandle(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetSeqIdString(), m_ToAccessionMap, CConstRef< C, Locker >::Reset(), strLinkBaseEntrezViewer, and CSeq_id_Base::Which().

Referenced by x_Add().

◆ x_FuzzToDisplayed()

bool CFlatSeqLoc::x_FuzzToDisplayed ( const CSeq_interval &  si) const
private

Definition at line 480 of file flat_seqloc.cpp.

References CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::IsLim(), and si.

Referenced by x_Add().

◆ x_IsAccessionVersion()

bool CFlatSeqLoc::x_IsAccessionVersion ( CSeq_id_Handle  id)
private

Definition at line 737 of file flat_seqloc.cpp.

References CSeq_id::GetTextseq_Id().

Referenced by CFlatSeqLoc().

Member Data Documentation

◆ m_String

string CFlatSeqLoc::m_String
private

Definition at line 129 of file flat_seqloc.hpp.

Referenced by CFlatSeqLoc(), and GetString().

◆ m_ToAccessionMap

CFlatSeqLoc::CGuardedToAccessionMap CFlatSeqLoc::m_ToAccessionMap
staticprivate

Definition at line 145 of file flat_seqloc.hpp.

Referenced by CFlatSeqLoc(), and x_AddID().

The documentation for this class was generated from the following files:
Generated by doxygen 1.9.0
Modified on Fri Sep 20 14:57:35 2024 by modify_doxy.py rev. 669887