CSeq_loc_Mapper Class Reference

Search Toolkit Book for CSeq_loc_Mapper

CSeq_loc_Mapper –. More...

#include <objmgr/seq_loc_mapper.hpp>

Inheritance diagram for CSeq_loc_Mapper:

Collaboration diagram for CSeq_loc_Mapper:

Public Types
enum	ESeqMapDirection { eSeqMap_Up , eSeqMap_Down }
enum	EGCAssemblyAlias {   eGCA_Genbank , eGCA_GenbankAcc , eGCA_Refseq , eGCA_RefseqAcc ,   eGCA_UCSC , eGCA_Other }
	Destination of seq-id mapping through a GC-Assembly. More...
enum	EScopeFlag { eOriginalScope , eCopyScope }
	Using CScope for virtual bioseqs created from GC-Assemblies. More...
Public Types inherited from CSeq_loc_Mapper_Base
enum	EFeatMapDirection { eLocationToProduct , eProductToLocation }
	Mapping direction used when initializing the mapper with a feature. More...
enum	EMapOptions {   fAlign_Dense_seg_TotalRange = 1 << 0 , fAlign_Sparse_ToFirst = 0 , fAlign_Sparse_ToSecond = 1 << 1 , fMapSingleLevel = 1 << 2 ,   fTrimMappedLocation = 1 << 3 }
	Options for interpretations of locations. More...
enum	ESplicedRow { eSplicedRow_Prod = 0 , eSplicedRow_Gen = 1 }
	Spliced-seg row indexing constants. More...
enum	FFuzzOption { fFuzzOption_CStyle = 1 << 0 , fFuzzOption_RemoveLimTlOrTr = 1 << 1 }
enum	FAnnotMapFlag {   fAnnotMap_Location = 1 << 0 , fAnnotMap_Product = 1 << 1 , fAnnotMap_Both = fAnnotMap_Location | fAnnotMap_Product , fAnnotMap_RemoveNonMapping = 1 << 2 ,   fAnnotMap_ThrowOnFailure = 1 << 3 , fAnnotMap_Default = fAnnotMap_Both }
	Flags defining seq-annot mapping options. More...
enum	EMapResult { eMapped_None = 0 , eMapped_Some , eMapped_All }
	Result of seq-annot mapping. More...
enum	ESeqType { eSeq_unknown = 0 , eSeq_nuc = 1 , eSeq_prot = 3 }
typedef int	TMapOptions
typedef int	TFuzzOption
typedef int	TAnnotMapFlags
typedef set< CSeq_id_Handle >	TSynonyms
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
	CSeq_loc_Mapper (CMappingRanges *mapping_ranges, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through a pre-filled CMappipngRanges. More...
	CSeq_loc_Mapper (const CSeq_feat &map_feat, EFeatMapDirection dir, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through a feature, both location and product must be set. More...
	CSeq_loc_Mapper (const CSeq_loc &source, const CSeq_loc &target, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping between two seq_locs. More...
	CSeq_loc_Mapper (const CSeq_align &map_align, const CSeq_id &to_id, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through an alignment. More...
	CSeq_loc_Mapper (const CSeq_align &map_align, size_t to_row, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	CSeq_loc_Mapper (const CSeq_id &from_id, const CSeq_id &to_id, const CSeq_align &map_align, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through an alignment using specific source and target ids. More...
	CSeq_loc_Mapper (size_t from_row, size_t to_row, const CSeq_align &map_align, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through an alignment using specific source and target row numbers. More...
	CSeq_loc_Mapper (CBioseq_Handle target_seq, ESeqMapDirection direction, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping between segments and the top level sequence. More...
	CSeq_loc_Mapper (CBioseq_Handle target_seq, ESeqMapDirection direction, SSeqMapSelector selector, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping between segments and the top level sequence. More...
	CSeq_loc_Mapper (const CSeqMap &seq_map, ESeqMapDirection direction, const CSeq_id *top_level_id=0, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through a seq-map. More...
	CSeq_loc_Mapper (const CSeqMap &seq_map, ESeqMapDirection direction, SSeqMapSelector selector, const CSeq_id *top_level_id=0, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through a seq-map. More...
	CSeq_loc_Mapper (size_t depth, const CBioseq_Handle &top_level_seq, ESeqMapDirection direction, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping between segments and the top level sequence limited by depth. More...
	CSeq_loc_Mapper (size_t depth, const CSeqMap &top_level_seq, ESeqMapDirection direction, const CSeq_id *top_level_id=0, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Depth-limited mapping through a seq-map. More...
	CSeq_loc_Mapper (const CGC_Assembly &gc_assembly, EGCAssemblyAlias to_alias, CScope *scope=0, EScopeFlag scope_flag=eCopyScope)
	Initialize the mapper to map through a GC-Assembly to the selected alias type. More...
	CSeq_loc_Mapper (const CGC_Assembly &gc_assembly, ESeqMapDirection direction, SSeqMapSelector selector, CScope *scope=0, EScopeFlag scope_flag=eCopyScope, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Initialize the mapper to map through deltas from a GC-Assembly. More...
	~CSeq_loc_Mapper (void)
Public Member Functions inherited from CSeq_loc_Mapper_Base
	CSeq_loc_Mapper_Base (CMappingRanges *mapping_ranges, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through a pre-filled CMappipngRanges. More...
	CSeq_loc_Mapper_Base (const CSeq_feat &map_feat, EFeatMapDirection dir, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through a feature, both location and product must be set. More...
	CSeq_loc_Mapper_Base (const CSeq_loc &source, const CSeq_loc &target, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping between two seq_locs. More...
	CSeq_loc_Mapper_Base (const CSeq_align &map_align, const CSeq_id &to_id, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through an alignment. More...
	CSeq_loc_Mapper_Base (const CSeq_id &from_id, const CSeq_id &to_id, const CSeq_align &map_align, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through an alignment using specific source and target ids. More...
	CSeq_loc_Mapper_Base (const CSeq_align &map_align, const CSeq_id &to_id, TMapOptions opts, IMapper_Sequence_Info *seq_info)
	CSeq_loc_Mapper_Base (const CSeq_align &map_align, size_t to_row, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Sparse alignments require special row indexing since each row contains two seq-ids. More...
	CSeq_loc_Mapper_Base (size_t from_row, size_t to_row, const CSeq_align &map_align, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
	Mapping through an alignment using specific source and target row numbers. More...
	CSeq_loc_Mapper_Base (const CSeq_align &map_align, size_t to_row, TMapOptions opts, IMapper_Sequence_Info *seq_info)
	~CSeq_loc_Mapper_Base (void)
void	SetFuzzOption (TFuzzOption newOption)
CSeq_loc_Mapper_Base &	SetMergeNone (void)
	Intervals' merging mode MergeNone and MergeAbutting do not change the order of ranges in the destination seq-loc. More...
CSeq_loc_Mapper_Base &	SetMergeAbutting (void)
	Merge only abutting intervals, keep overlapping. More...
CSeq_loc_Mapper_Base &	SetMergeBySeg (void)
	Merge only intervals from the same group. More...
CSeq_loc_Mapper_Base &	SetMergeContained (void)
	Merge intervals only if one is completely covered by another. More...
CSeq_loc_Mapper_Base &	SetMergeAll (void)
	Merge any abutting or overlapping intervals. More...
CSeq_loc_Mapper_Base &	SetGapPreserve (void)
	Whether to preserve or remove NULL sub-locations (usually indicating gaps) from the result. More...
CSeq_loc_Mapper_Base &	SetGapRemove (void)
CSeq_loc_Mapper_Base &	SetTrimSplicedSeg (bool trim)
	For mapping spliced-segs only: preserve or trim starting/ending indels. More...
CSeq_loc_Mapper_Base &	KeepNonmappingRanges (void)
	Keep ranges which can not be mapped. More...
CSeq_loc_Mapper_Base &	TruncateNonmappingRanges (void)
CSeq_loc_Mapper_Base &	SetCheckStrand (bool value=true)
	Check strands before mapping a range. More...
CSeq_loc_Mapper_Base &	MixedAlignsAsSpliced (bool value=true)
	When set to 'true' if mapped alignment has exactly one genomic and one protein row, convert it to spliced-seg. More...
CSeq_loc_Mapper_Base &	IncludeSourceLocs (bool value=true)
	Include source ranges in the mapped location. More...
CSeq_loc_Mapper_Base &	SetErrorOnPartial (bool value=true)
	Report source range trimming as an error. More...
CRef< CSeq_loc >	Map (const CSeq_loc &src_loc)
	Map seq-loc. More...
CRef< CSeq_loc >	MapTotalRange (const CSeq_loc &seq_loc)
	Take the total range from the location and run it through the mapper. More...
CRef< CSeq_align >	Map (const CSeq_align &src_align)
	Map the whole alignment. More...
CRef< CSeq_align >	Map (const CSeq_align &src_align, size_t row)
	Map a single row of the alignment. More...
CRef< CSeq_graph >	Map (const CSeq_graph &src_graph)
	Map seq-graph. More...
EMapResult	Map (CSeq_annot &annot, TAnnotMapFlags flags=fAnnotMap_Default)
	Map each object from the Seq-annot and replace the original with the mapped one. More...
bool	LastIsPartial (void)
	Check if the last mapping resulted in partial location (not all ranges from the original location could be mapped to the target). More...
const CSeq_id_Handle &	CollectSynonyms (const CSeq_id_Handle &id) const
	CSeq_loc_Mapper_Base (CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
ESeqType	GetSeqTypeById (const CSeq_id_Handle &idh) const
	Methods for getting sequence types, use cached types (m_SeqTypes) if possible. More...
ESeqType	GetSeqTypeById (const CSeq_id &id) const
void	SetSeqTypeById (const CSeq_id_Handle &idh, ESeqType seqtype) const
	Methods for setting sequence types. More...
void	SetSeqTypeById (const CSeq_id &id, ESeqType seqtype) const
int	GetWidthById (const CSeq_id_Handle &idh) const
	Get sequence width. More...
int	GetWidthById (const CSeq_id &id) const
const CMappingRanges &	GetMappingRanges (void) const
	Get mapping ranges. More...
void	CollectSynonyms (const CSeq_id_Handle &id, TSynonyms &synonyms) const
	NOTE: In most cases CollectSynonyms(const CSeq_id_Handle& id) should be used instead, since it takes care of synonym storage and mapping. 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...
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

Protected Member Functions
virtual CSeq_align_Mapper_Base *	InitAlignMapper (const CSeq_align &src_align)
Protected Member Functions inherited from CSeq_loc_Mapper_Base
ESeqType	GetSeqType (const CSeq_id_Handle &idh) const
TSeqPos	GetSequenceLength (const CSeq_id &id)
void	x_InitializeFeat (const CSeq_feat &map_feat, EFeatMapDirection dir)
void	x_InitializeLocs (const CSeq_loc &source, const CSeq_loc &target, int src_frame=0, int dst_frame=0)
void	x_InitializeAlign (const CSeq_align &map_align, const CSeq_id &to_id, const CSeq_id *from_id=nullptr)
void	x_InitializeAlign (const CSeq_align &map_align, const TSynonyms &to_ids, const TSynonyms *from_ids=nullptr)
void	x_InitializeAlign (const CSeq_align &map_align, size_t to_row, size_t from_row=size_t(-1))
void	x_PreserveDestinationLocs (void)
void	x_NextMappingRange (const CSeq_id &src_id, TSeqPos &src_start, TSeqPos &src_len, ENa_strand src_strand, const CSeq_id &dst_id, TSeqPos &dst_start, TSeqPos &dst_len, ENa_strand dst_strand, const CInt_fuzz *fuzz_from=0, const CInt_fuzz *fuzz_to=0, int frame=0, TSeqPos src_bioseq_len=kInvalidSeqPos)
void	x_AddConversion (const CSeq_id &src_id, TSeqPos src_start, ENa_strand src_strand, const CSeq_id &dst_id, TSeqPos dst_start, ENa_strand dst_strand, TSeqPos length, bool ext_right, int frame, TSeqPos src_bioseq_len, TSeqPos dst_length)
void	x_MapSeq_loc (const CSeq_loc &src_loc)
void	x_PushRangesToDstMix (void)
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Member Functions
	CSeq_loc_Mapper (const CSeq_loc_Mapper &)
CSeq_loc_Mapper &	operator= (const CSeq_loc_Mapper &)
void	x_InitializeSeqMap (const CSeqMap &seq_map, const CSeq_id *top_id, ESeqMapDirection direction)
void	x_InitializeSeqMap (const CSeqMap &seq_map, size_t depth, const CSeq_id *top_id, ESeqMapDirection direction)
void	x_InitializeSeqMap (const CSeqMap &seq_map, SSeqMapSelector selector, const CSeq_id *top_id, ESeqMapDirection direction)
void	x_InitializeSeqMap (CSeqMap_CI seg_it, const CSeq_id *top_id, ESeqMapDirection direction)
void	x_InitializeSeqMapUp (CSeqMap_CI seg_it, const CSeq_id *top_id)
void	x_InitializeSeqMapDown (CSeqMap_CI seg_it, const CSeq_id *top_id)
void	x_InitializeSeqMapSingleLevel (CSeqMap_CI seg_it, const CSeq_id *top_id, ESeqMapDirection direction)
void	x_InitGCAssembly (const CGC_Assembly &gc_assembly, EGCAssemblyAlias to_alias)
void	x_InitGCSequence (const CGC_Sequence &gc_seq, EGCAssemblyAlias to_alias)
CBioseq_Handle	x_AddVirtualBioseq (const TSynonyms &synonyms, const CGC_Sequence &gc_seq)
bool	x_IsUCSCRandomChr (const CGC_Sequence &gc_seq, CConstRef< CSeq_id > &chr_id, TSynonyms &synonyms) const

Private Attributes
CHeapScope	m_Scope

Additional Inherited Members
Static Public Member Functions inherited from CSeq_loc_Mapper_Base
static bool	GetNonMappingAsNull (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 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 Types inherited from CSeq_loc_Mapper_Base
typedef CMappingRange::TRange	TRange
typedef CMappingRanges::TRangeMap	TRangeMap
typedef CMappingRanges::TRangeIterator	TRangeIterator
typedef CMappingRanges::TSortedMappings	TSortedMappings
typedef list< TRange >	TDstRanges
typedef map< CSeq_id_Handle, TDstRanges >	TDstIdMap
typedef vector< TDstIdMap >	TDstStrandMap
typedef CRef< CInt_fuzz >	TFuzz
typedef pair< TFuzz, TFuzz >	TRangeFuzz
typedef list< SMappedRange >	TMappedRanges
typedef vector< TMappedRanges >	TRangesByStrand
typedef map< CSeq_id_Handle, TRangesByStrand >	TRangesById
typedef map< CSeq_id_Handle, ESeqType >	TSeqTypeById
typedef CSeq_align::C_Segs::TDendiag	TDendiag
typedef CSeq_align::C_Segs::TStd	TStd
Protected Attributes inherited from CSeq_loc_Mapper_Base
TSeqTypeById	m_SeqTypes
bool	m_Partial
bool	m_LastTruncated
CRef< CMappingRanges >	m_Mappings
CRef< CSeq_loc >	m_Dst_loc
TDstStrandMap	m_DstRanges
int	m_CurrentGroup
TFuzzOption	m_FuzzOption
CSeq_loc_Mapper_Options	m_MapOptions

Detailed Description

CSeq_loc_Mapper –.

Mapping locations and alignments between bioseqs through seq-locs, features, alignments or between parts of segmented bioseqs.

Definition at line 75 of file seq_loc_mapper.hpp.

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The documentation for this class was generated from the following files:

• include/objmgr/seq_loc_mapper.hpp
• src/objmgr/seq_loc_mapper.cpp