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| CSeq_loc (void) |
| constructors More...
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| CSeq_loc (E_Choice index) |
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| CSeq_loc (TId &id, TPoint point, TStrand strand=eNa_strand_unknown) |
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| CSeq_loc (TId &id, const TPoints &points, TStrand strand=eNa_strand_unknown) |
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| CSeq_loc (TId &id, TPoint from, TPoint to, TStrand strand=eNa_strand_unknown) |
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| CSeq_loc (TId &id, TRanges ivals, TStrand strand=eNa_strand_unknown) |
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virtual | ~CSeq_loc (void) |
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TRange | GetTotalRange (void) const |
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void | InvalidateTotalRangeCache (void) const |
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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...
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ENa_strand | GetStrand (void) const |
| Get the location's strand. More...
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bool | IsReverseStrand (void) const |
| Return true if all ranges have reverse strand. More...
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void | FlipStrand (void) |
| Flip the strand (e.g. plus to minus) More...
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void | SetStrand (ENa_strand strand) |
| Set the strand for all of the location's ranges. More...
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void | ResetStrand (void) |
| Reset the strand on this location. More...
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TSeqPos | GetStart (ESeqLocExtremes ext) const |
| Return start and stop positions of the seq-loc. More...
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TSeqPos | GetStop (ESeqLocExtremes ext) const |
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TSeqPos | GetCircularLength (TSeqPos seq_len) const |
| Special case for circular sequences. More...
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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...
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bool | IsPartialStart (ESeqLocExtremes ext) const |
| check start or stop of location for e_Lim fuzz More...
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bool | IsPartialStop (ESeqLocExtremes ext) const |
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void | SetPartialStart (bool val, ESeqLocExtremes ext) |
| set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval) More...
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void | SetPartialStop (bool val, ESeqLocExtremes ext) |
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bool | IsTruncatedStart (ESeqLocExtremes ext) const |
| check if parts of the seq-loc are missing More...
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bool | IsTruncatedStop (ESeqLocExtremes ext) const |
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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...
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void | SetTruncatedStop (bool val, ESeqLocExtremes ext) |
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const CSeq_id * | GetId (void) const |
| Get the id of the location return NULL if has multiple ids or no id at all. More...
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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...
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void | InvalidateIdCache (void) const |
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void | SetId (CSeq_id &id) |
| set the 'id' field in all parts of this location More...
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void | SetId (const CSeq_id &id) |
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void | InvalidateCache (void) const |
| Combine invalidation of all cached values. More...
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virtual void | Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) |
| Override Assign() to incorporate cache invalidation. More...
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void | SetNull (void) |
| Override all setters to incorporate cache invalidation. More...
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void | SetEmpty (TEmpty &v) |
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TEmpty & | SetEmpty (void) |
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void | SetWhole (TWhole &v) |
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TWhole & | SetWhole (void) |
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void | SetInt (TInt &v) |
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TInt & | SetInt (void) |
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void | SetPacked_int (TPacked_int &v) |
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TPacked_int & | SetPacked_int (void) |
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void | SetPnt (TPnt &v) |
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TPnt & | SetPnt (void) |
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void | SetPacked_pnt (TPacked_pnt &v) |
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TPacked_pnt & | SetPacked_pnt (void) |
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void | SetMix (TMix &v) |
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TMix & | SetMix (void) |
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void | SetEquiv (TEquiv &v) |
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TEquiv & | SetEquiv (void) |
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void | SetBond (TBond &v) |
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TBond & | SetBond (void) |
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void | SetFeat (TFeat &v) |
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TFeat & | SetFeat (void) |
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void | PostRead (void) const |
| Invalidate id/range cache after deserialization. More...
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int | Compare (const CSeq_loc &loc) const |
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int | Compare (const CSeq_loc &loc, TCompareFlags flags) const |
| Compare locations by total range for each seq-id. More...
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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...
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void | Add (const CSeq_loc &other) |
| Simple adding of seq-locs. More...
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void | ChangeToMix (void) |
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void | ChangeToPackedInt (void) |
| Works only if location is currently an interval, point, packed-int (handled trivially), or a mix built recursively from these. More...
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CRef< CSeq_loc > | Merge (TOpFlags flags, ISynonymMapper *syn_mapper) const |
| All functions create and return a new seq-loc object. More...
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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...
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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...
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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...
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const_iterator | begin (void) const |
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const_iterator | end (void) const |
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| CSeq_loc_Base (void) |
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virtual | ~CSeq_loc_Base (void) |
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| DECLARE_INTERNAL_TYPE_INFO () |
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virtual void | Reset (void) |
| Reset the whole object. More...
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virtual void | ResetSelection (void) |
| Reset the selection (set it to e_not_set). More...
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E_Choice | Which (void) const |
| Which variant is currently selected. More...
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void | CheckSelected (E_Choice index) const |
| Verify selection, throw exception if it differs from the expected. More...
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void | ThrowInvalidSelection (E_Choice index) const |
| Throw 'InvalidSelection' exception. More...
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void | Select (E_Choice index, EResetVariant reset=eDoResetVariant) |
| Select the requested variant if needed. More...
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void | Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool) |
| Select the requested variant if needed, allocating CObject variants from memory pool. More...
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bool | IsNull (void) const |
| Check if variant Null is selected. More...
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void | SetNull (void) |
| Select the variant. More...
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bool | IsEmpty (void) const |
| Check if variant Empty is selected. More...
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const TEmpty & | GetEmpty (void) const |
| Get the variant data. More...
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TEmpty & | SetEmpty (void) |
| Select the variant. More...
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void | SetEmpty (TEmpty &value) |
| Select the variant and set its data. More...
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bool | IsWhole (void) const |
| Check if variant Whole is selected. More...
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const TWhole & | GetWhole (void) const |
| Get the variant data. More...
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TWhole & | SetWhole (void) |
| Select the variant. More...
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void | SetWhole (TWhole &value) |
| Select the variant and set its data. More...
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bool | IsInt (void) const |
| Check if variant Int is selected. More...
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const TInt & | GetInt (void) const |
| Get the variant data. More...
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TInt & | SetInt (void) |
| Select the variant. More...
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void | SetInt (TInt &value) |
| Select the variant and set its data. More...
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bool | IsPacked_int (void) const |
| Check if variant Packed_int is selected. More...
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const TPacked_int & | GetPacked_int (void) const |
| Get the variant data. More...
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TPacked_int & | SetPacked_int (void) |
| Select the variant. More...
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void | SetPacked_int (TPacked_int &value) |
| Select the variant and set its data. More...
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bool | IsPnt (void) const |
| Check if variant Pnt is selected. More...
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const TPnt & | GetPnt (void) const |
| Get the variant data. More...
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TPnt & | SetPnt (void) |
| Select the variant. More...
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void | SetPnt (TPnt &value) |
| Select the variant and set its data. More...
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bool | IsPacked_pnt (void) const |
| Check if variant Packed_pnt is selected. More...
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const TPacked_pnt & | GetPacked_pnt (void) const |
| Get the variant data. More...
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TPacked_pnt & | SetPacked_pnt (void) |
| Select the variant. More...
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void | SetPacked_pnt (TPacked_pnt &value) |
| Select the variant and set its data. More...
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bool | IsMix (void) const |
| Check if variant Mix is selected. More...
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const TMix & | GetMix (void) const |
| Get the variant data. More...
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TMix & | SetMix (void) |
| Select the variant. More...
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void | SetMix (TMix &value) |
| Select the variant and set its data. More...
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bool | IsEquiv (void) const |
| Check if variant Equiv is selected. More...
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const TEquiv & | GetEquiv (void) const |
| Get the variant data. More...
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TEquiv & | SetEquiv (void) |
| Select the variant. More...
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void | SetEquiv (TEquiv &value) |
| Select the variant and set its data. More...
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bool | IsBond (void) const |
| Check if variant Bond is selected. More...
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const TBond & | GetBond (void) const |
| Get the variant data. More...
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TBond & | SetBond (void) |
| Select the variant. More...
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void | SetBond (TBond &value) |
| Select the variant and set its data. More...
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bool | IsFeat (void) const |
| Check if variant Feat is selected. More...
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const TFeat & | GetFeat (void) const |
| Get the variant data. More...
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TFeat & | SetFeat (void) |
| Select the variant. More...
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void | SetFeat (TFeat &value) |
| Select the variant and set its data. More...
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| CSerialObject (void) |
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virtual | ~CSerialObject (void) |
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virtual const CTypeInfo * | GetThisTypeInfo (void) const =0 |
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virtual bool | Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const |
| Check if both objects contain the same values. More...
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virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More...
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void | ThrowUnassigned (TMemberIndex index) const |
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void | ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const |
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bool | HasNamespaceName (void) const |
| Check if object data type has namespace name. More...
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const string & | GetNamespaceName (void) const |
| Get namespace name. More...
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bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More...
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const string & | GetNamespacePrefix (void) const |
| Get namespace prefix. More...
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| CObject (void) |
| Constructor. More...
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| CObject (const CObject &src) |
| Copy constructor. More...
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virtual | ~CObject (void) |
| Destructor. More...
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CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More...
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bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More...
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bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More...
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bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More...
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bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More...
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void | AddReference (void) const |
| Add reference to object. More...
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void | RemoveReference (void) const |
| Remove reference to object. More...
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void | ReleaseReference (void) const |
| Remove reference without deleting object. More...
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virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More...
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virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More...
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void * | operator new (size_t size) |
| Define new operator for memory allocation. More...
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void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More...
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void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More...
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void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More...
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void * | operator new (size_t size, void *place) |
| Define new operator. More...
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void | operator delete (void *ptr, void *place) |
| Define delete operator. More...
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void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More...
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void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More...
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| CDebugDumpable (void) |
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virtual | ~CDebugDumpable (void) |
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void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
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void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
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void | DumpToConsole (void) const |
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