Search Toolkit Book for CRef_ext
#include <objects/seq/Ref_ext.hpp>
Inheritance diagram for CRef_ext:
Collaboration diagram for CRef_ext:
Public Member Functions | |
| CRef_ext (void) | |
| Public Member Functions inherited from CRef_ext_Base | |
| CRef_ext_Base (void) | |
| DECLARE_INTERNAL_TYPE_INFO () | |
| const CSeq_loc & | Get (void) const |
| CSeq_loc & | Set (void) |
| Public Member Functions inherited from CSeq_loc | |
| 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 |
| Public Member Functions inherited from CSeq_loc_Base | |
| 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... | |
| Public Member Functions inherited from CSerialObject | |
| 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... | |
| 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 CRef_ext_Base | Tparent |
Additional Inherited Members | |
| Public Types inherited from CSeq_loc | |
| 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... | |
| Public Types inherited from CSeq_loc_Base | |
| 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 |
| 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 CSeq_loc_Base | |
| static string | SelectionName (E_Choice index) |
| Retrieve selection name (for diagnostic purposes). 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
CRef_ext –.
Definition at line 65 of file Ref_ext.hpp.
The documentation for this class was generated from the following file:
- include/objects/seq/Ref_ext.hpp
