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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCRefextBase.html below:

NCBI C++ ToolKit: CRef_ext_Base Class Reference

CRef_ext_Base (void) DECLARE_INTERNAL_TYPE_INFO () const CSeq_loc & Get (void) const CSeq_loc & Set (void) CSeq_loc (void) constructors More...
CSeq_loc (E_Choice index) CSeq_loc (TId &id, TPoint point, TStrand strand=eNa_strand_unknown) CSeq_loc (TId &id, const TPoints &points, TStrand strand=eNa_strand_unknown) CSeq_loc (TId &id, TPoint from, TPoint to, TStrand strand=eNa_strand_unknown) CSeq_loc (TId &id, TRanges ivals, TStrand strand=eNa_strand_unknown) virtual ~CSeq_loc (void) TRange GetTotalRange (void) const void InvalidateTotalRangeCache (void) const bool IsSetStrand (EIsSetStrand flag=eIsSetStrand_Any) const Check if strand is set for any/all part(s) of the seq-loc depending on the flag. More...
ENa_strand GetStrand (void) const Get the location's strand. More...
bool IsReverseStrand (void) const Return true if all ranges have reverse strand. More...
void FlipStrand (void) Flip the strand (e.g. plus to minus) More...
void SetStrand (ENa_strand strand) Set the strand for all of the location's ranges. More...
void ResetStrand (void) Reset the strand on this location. More...
TSeqPos GetStart (ESeqLocExtremes ext) const Return start and stop positions of the seq-loc. More...
TSeqPos GetStop (ESeqLocExtremes ext) const TSeqPos GetCircularLength (TSeqPos seq_len) const Special case for circular sequences. More...
void GetLabel (string *label) const Appends a label suitable for display (e.g., error messages) label must point to an existing string object Method just returns if label is null. More...
bool IsPartialStart (ESeqLocExtremes ext) const check start or stop of location for e_Lim fuzz More...
bool IsPartialStop (ESeqLocExtremes ext) const void SetPartialStart (bool val, ESeqLocExtremes ext) set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval) More...
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) const CSeq_id * GetId (void) const Get the id of the location return NULL if has multiple ids or no id at all. More...
bool CheckId (const CSeq_id *&id, bool may_throw=true) const check that the 'id' field in all parts of the location is the same as the specifies id. More...
void InvalidateIdCache (void) const void SetId (CSeq_id &id) set the 'id' field in all parts of this location More...
void SetId (const CSeq_id &id) void InvalidateCache (void) const Combine invalidation of all cached values. More...
virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) Override Assign() to incorporate cache invalidation. More...
void SetNull (void) Override all setters to incorporate cache invalidation. More...
void SetEmpty (TEmpty &v) TEmpty & SetEmpty (void) void SetWhole (TWhole &v) TWhole & SetWhole (void) void SetInt (TInt &v) TInt & SetInt (void) void SetPacked_int (TPacked_int &v) TPacked_int & SetPacked_int (void) void SetPnt (TPnt &v) TPnt & SetPnt (void) void SetPacked_pnt (TPacked_pnt &v) TPacked_pnt & SetPacked_pnt (void) void SetMix (TMix &v) TMix & SetMix (void) void SetEquiv (TEquiv &v) TEquiv & SetEquiv (void) void SetBond (TBond &v) TBond & SetBond (void) void SetFeat (TFeat &v) TFeat & SetFeat (void) void PostRead (void) const Invalidate id/range cache after deserialization. More...
int Compare (const CSeq_loc &loc) const int Compare (const CSeq_loc &loc, TCompareFlags flags) const Compare locations by total range for each seq-id. More...
int CompareSubLoc (const CSeq_loc &loc, ENa_strand strand, const ISubLocFilter *filter=NULL) const Compare first-level sub-locations sequentially to order them by biological "complexity". More...
void Add (const CSeq_loc &other) Simple adding of seq-locs. More...
void ChangeToMix (void) void ChangeToPackedInt (void) Works only if location is currently an interval, point, packed-int (handled trivially), or a mix built recursively from these. More...
CRef< CSeq_loc > Merge (TOpFlags flags, ISynonymMapper *syn_mapper) const All functions create and return a new seq-loc object. More...
CRef< CSeq_loc > Add (const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper) const Add seq-loc, merge/sort resulting ranges depending on flags. More...
CRef< CSeq_loc > Subtract (const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper, ILengthGetter *len_getter) const Subtract seq-loc from this, merge/sort resulting ranges depending on flags. More...
CRef< CSeq_loc > Intersect (const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper) const Find the intersection with the seq-loc, merge/sort resulting ranges depending on flags. More...
const_iterator begin (void) const const_iterator end (void) const CSeq_loc_Base (void) virtual ~CSeq_loc_Base (void) DECLARE_INTERNAL_TYPE_INFO () virtual void Reset (void) Reset the whole object. More...
virtual void ResetSelection (void) Reset the selection (set it to e_not_set). More...
E_Choice Which (void) const Which variant is currently selected. More...
void CheckSelected (E_Choice index) const Verify selection, throw exception if it differs from the expected. More...
void ThrowInvalidSelection (E_Choice index) const Throw 'InvalidSelection' exception. More...
void Select (E_Choice index, EResetVariant reset=eDoResetVariant) Select the requested variant if needed. More...
void Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool) Select the requested variant if needed, allocating CObject variants from memory pool. More...
bool IsNull (void) const Check if variant Null is selected. More...
void SetNull (void) Select the variant. More...
bool IsEmpty (void) const Check if variant Empty is selected. More...
const TEmpty & GetEmpty (void) const Get the variant data. More...
TEmpty & SetEmpty (void) Select the variant. More...
void SetEmpty (TEmpty &value) Select the variant and set its data. More...
bool IsWhole (void) const Check if variant Whole is selected. More...
const TWhole & GetWhole (void) const Get the variant data. More...
TWhole & SetWhole (void) Select the variant. More...
void SetWhole (TWhole &value) Select the variant and set its data. More...
bool IsInt (void) const Check if variant Int is selected. More...
const TInt & GetInt (void) const Get the variant data. More...
TInt & SetInt (void) Select the variant. More...
void SetInt (TInt &value) Select the variant and set its data. More...
bool IsPacked_int (void) const Check if variant Packed_int is selected. More...
const TPacked_int & GetPacked_int (void) const Get the variant data. More...
TPacked_int & SetPacked_int (void) Select the variant. More...
void SetPacked_int (TPacked_int &value) Select the variant and set its data. More...
bool IsPnt (void) const Check if variant Pnt is selected. More...
const TPnt & GetPnt (void) const Get the variant data. More...
TPnt & SetPnt (void) Select the variant. More...
void SetPnt (TPnt &value) Select the variant and set its data. More...
bool IsPacked_pnt (void) const Check if variant Packed_pnt is selected. More...
const TPacked_pnt & GetPacked_pnt (void) const Get the variant data. More...
TPacked_pnt & SetPacked_pnt (void) Select the variant. More...
void SetPacked_pnt (TPacked_pnt &value) Select the variant and set its data. More...
bool IsMix (void) const Check if variant Mix is selected. More...
const TMix & GetMix (void) const Get the variant data. More...
TMix & SetMix (void) Select the variant. More...
void SetMix (TMix &value) Select the variant and set its data. More...
bool IsEquiv (void) const Check if variant Equiv is selected. More...
const TEquiv & GetEquiv (void) const Get the variant data. More...
TEquiv & SetEquiv (void) Select the variant. More...
void SetEquiv (TEquiv &value) Select the variant and set its data. More...
bool IsBond (void) const Check if variant Bond is selected. More...
const TBond & GetBond (void) const Get the variant data. More...
TBond & SetBond (void) Select the variant. More...
void SetBond (TBond &value) Select the variant and set its data. More...
bool IsFeat (void) const Check if variant Feat is selected. More...
const TFeat & GetFeat (void) const Get the variant data. More...
TFeat & SetFeat (void) Select the variant. More...
void SetFeat (TFeat &value) Select the variant and set its data. More...
CSerialObject (void) virtual ~CSerialObject (void) virtual const CTypeInfo * GetThisTypeInfo (void) const =0 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...
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...
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 enum ECompareFlags { fCompare_Default = 0 , fCompare_Strand = 1 } Flags for location comparison. More...
enum EOpFlags {
  fStrand_Ignore = 1<<0 , fMerge_Contained = 1<<1 , fMerge_AbuttingOnly = 1<<2 , fMerge_Abutting = fMerge_AbuttingOnly | fMerge_Contained ,
  fMerge_OverlappingOnly = 1<<3 , fMerge_Overlapping = fMerge_OverlappingOnly | fMerge_Contained , fMerge_All = fMerge_Abutting | fMerge_Overlapping , fMerge_SingleRange = 1<<4 ,
  fSort = 1<<5 , fSortAndMerge_All = fSort | fMerge_All
} CSeq_loc operations. More...
typedef CSeq_loc_Base Tparent typedef CPacked_seqpnt_Base::TPoints TPoints typedef CPacked_seqint_Base::Tdata TIntervals typedef CSeq_loc_mix_Base::Tdata TLocations typedef CSeq_id TId typedef ENa_strand TStrand typedef TSeqPos TPoint typedef CPacked_seqint::TRanges TRanges typedef CRange< TSeqPos > TRange See related functions in objmgr/util/seq_loc_util.hpp: More...
typedef int TCompareFlags typedef int TOpFlags typedef CSeq_loc_CI const_iterator Make CSeq_loc look like an STL container. More...
enum E_Choice {
  e_not_set = 0 , e_Null , e_Empty , e_Whole ,
  e_Int , e_Packed_int , e_Pnt , e_Packed_pnt ,
  e_Mix , e_Equiv , e_Bond , e_Feat
} Choice variants. More...
enum E_ChoiceStopper { e_MaxChoice = 12 } Maximum+1 value of the choice variant enumerator. More...
typedef CSeq_id TEmpty typedef CSeq_id TWhole typedef CSeq_interval TInt typedef CPacked_seqint TPacked_int typedef CSeq_point TPnt typedef CPacked_seqpnt TPacked_pnt typedef CSeq_loc_mix TMix typedef CSeq_loc_equiv TEquiv typedef CSeq_bond TBond typedef CFeat_id TFeat 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 string SelectionName (E_Choice index) Retrieve selection name (for diagnostic purposes). More...
static void SetVerifyDataThread (ESerialVerifyData verify) static void SetVerifyDataGlobal (ESerialVerifyData verify) static string UnassignedString (void) static CStringUTF8 UnassignedStringUTF8 (void) static char UnassignedByte (void) 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 void EnableDebugDump (bool on) static const char * ms_UnassignedStr = "<*unassigned*>" static const char ms_UnassignedByte = char(0xcd) 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...
virtual void DeleteThis (void) Virtual method "deleting" this object. More...

CRef_ext_Base –.

Definition at line 72 of file Ref_ext_.hpp.

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