Iterators

Collaboration diagram for Iterators:

Classes
class	CAlign_CI
	CAlign_CI –. More...
class	CAnnot_CI
	CAnnot_CI –. More...
struct	IFeatComparator
	IFeatComparator. More...
struct	SAnnotSelector
	SAnnotSelector –. More...
class	CBioseq_CI
	CBioseq_CI –. More...
class	CFeat_CI
	CFeat_CI –. More...
class	CMappedGraph
	CMappedGraph –. More...
class	CGraph_CI
	CGraph_CI –. More...
class	CMappedFeat
	CMappedFeat –. More...
class	CSeq_annot_CI
	CSeq_annot_CI –. More...
class	CSeq_descr_CI
	CSeq_descr_CI –. More...
class	CSeq_entry_CI
	CSeq_entry_CI –. More...
class	CSeq_entry_I
	CSeq_entry_I –. More...
class	CSeqMap_CI_SegmentInfo
struct	SSeqMapSelector
	Selector used in CSeqMap methods returning iterators. More...
class	CSeqMap_CI
	Iterator over CSeqMap. More...
class	CSeqMap_I
	Non-const iterator over CSeqMap (allows to edit the sequence). More...
class	CSeq_table_CI
	CSeq_table_CI –. More...
class	CSeqVectorTypes
class	INcbi2naRandomizer
class	CSeqVector_CI
class	CSeqVector_CI::CTempValue
	special temporary holder for return value from postfix operators More...
class	CSeqdesc_CI
	CSeqdesc_CI –. More...

Typedefs
typedef set< CSeq_annot_Handle >	CAnnot_CI::TSeqAnnotSet
typedef TSeqAnnotSet::const_iterator	CAnnot_CI::TIterator
typedef vector< SAnnotTypeSelector >	SAnnotSelector::TAdaptiveTriggers
typedef Uint1	SAnnotSelector::TAdaptiveDepthFlags
typedef size_t	SAnnotSelector::TMaxSize
typedef unsigned	SAnnotSelector::TMaxSearchSegments
typedef float	SAnnotSelector::TMaxSearchTime
typedef vector< CAnnotName >	SAnnotSelector::TAnnotsNames
	Object manager recognizes several fields of Seq-annot as annot name. More...
typedef map< string, int >	SAnnotSelector::TNamedAnnotAccessions
typedef Uint8	SAnnotSelector::TBitFilter
	Set bit filter for annotations that support it (SNP) If filter is set then collect only annotations that have masked (filter_mask) bits equal to the filter_bits. More...
typedef CSeq_id::ESNPScaleLimit	SAnnotSelector::TSNPScaleLimit
typedef bitset< CSeqFeatData::eSubtype_max+3 >	SAnnotSelector::TAnnotTypesBitset
typedef vector< CTSE_Handle >	SAnnotSelector::TTSE_Limits
typedef vector< CSeq_entry_CI >	CBioseq_CI::TEntryStack
typedef CObject_id	CFeat_CI::TFeatureId
	Search features with specified id. More...
typedef int	CFeat_CI::TFeatureIdInt
typedef string	CFeat_CI::TFeatureIdStr
typedef vector< CSeq_feat_Handle >	CFeat_CI::TSeq_feat_Handles
typedef CGraphRanges::TRange	CMappedGraph::TRange
typedef CGraphRanges::TGraphRanges	CMappedGraph::TGraphRanges
typedef vector< CRef< CSeq_annot_Info > >	CSeq_annot_CI::TAnnots
typedef TAnnots::const_iterator	CSeq_annot_CI::TAnnot_CI
typedef stack< CSeq_entry_CI >	CSeq_annot_CI::TEntryStack
typedef int	CSeq_entry_CI::TFlags
	bitwise OR of "EFlags" More...
typedef EFlags	CSeq_entry_CI::ERecursionMode
	backward compatibility synonym More...
typedef CSeqMap::TFlags	SSeqMapSelector::TFlags
typedef CRange< TSeqPos >	SSeqMapSelector::TRange
typedef SSeqMapSelector::TFlags	CSeqMap_CI::TFlags
typedef CSeqMap_CI_SegmentInfo	CSeqMap_CI::TSegmentInfo
typedef vector< TSegmentInfo >	CSeqMap_CI::TStack
typedef unsigned char	CSeqVectorTypes::TResidue
typedef CSeq_data::E_Choice	CSeqVectorTypes::TCoding
typedef TResidue	CSeqVectorTypes::value_type
typedef TSeqPos	CSeqVectorTypes::size_type
typedef TSignedSeqPos	CSeqVectorTypes::difference_type
typedef std::random_access_iterator_tag	CSeqVectorTypes::iterator_category
typedef const TResidue *	CSeqVectorTypes::pointer
typedef const TResidue &	CSeqVectorTypes::reference
typedef AutoArray< char >	CSeqVector_CI::TCacheData
typedef char *	CSeqVector_CI::TCache_I
typedef vector< CSeqdesc::E_Choice >	CSeqdesc_CI::TDescChoices
typedef unsigned	CSeqdesc_CI::TDescTypeMask
typedef list< CRef< CSeqdesc > >	CSeqdesc_CI::TDescList
typedef TDescList::const_iterator	CSeqdesc_CI::TDescList_CI

Enumerations
enum	SAnnotSelector::EOverlapType { SAnnotSelector::eOverlap_Intervals , SAnnotSelector::eOverlap_TotalRange }
	Flag to indicate location overlapping method. More...
enum	SAnnotSelector::EResolveMethod { SAnnotSelector::eResolve_None , SAnnotSelector::eResolve_TSE , SAnnotSelector::eResolve_All }
	Flag to indicate references resolution method. More...
enum	SAnnotSelector::ESortOrder { SAnnotSelector::eSortOrder_None , SAnnotSelector::eSortOrder_Normal , SAnnotSelector::eSortOrder_Reverse }
	Flag to indicate sorting method. More...
enum	SAnnotSelector::EUnresolvedFlag { SAnnotSelector::eIgnoreUnresolved , SAnnotSelector::eSearchUnresolved , SAnnotSelector::eFailUnresolved }
	Flag to indicate handling of unresolved seq-ids. More...
enum	SAnnotSelector::EAdaptiveDepthFlags {   SAnnotSelector::kAdaptive_None = 0 , SAnnotSelector::fAdaptive_Default = 1 , SAnnotSelector::kAdaptive_Default = fAdaptive_Default , SAnnotSelector::fAdaptive_ByTriggers = 1<<1 ,   SAnnotSelector::fAdaptive_BySubtypes = 1<<2 , SAnnotSelector::fAdaptive_ByPolicy = 1<<3 , SAnnotSelector::fAdaptive_BySeqClass = 1<<4 , SAnnotSelector::fAdaptive_ByNamedAcc = 1<<5 ,   SAnnotSelector::kAdaptive_All , SAnnotSelector::kAdaptive_DefaultBits }
enum	SAnnotSelector::EMaxSearchSegmentsAction { SAnnotSelector::eMaxSearchSegmentsThrow , SAnnotSelector::eMaxSearchSegmentsLog , SAnnotSelector::eMaxSearchSegmentsSilent }
enum	SAnnotSelector::ELimitObject { SAnnotSelector::eLimit_None , SAnnotSelector::eLimit_TSE_Info , SAnnotSelector::eLimit_Seq_entry_Info , SAnnotSelector::eLimit_Seq_annot_Info }
enum	CBioseq_CI::EBioseqLevelFlag { CBioseq_CI::eLevel_All , CBioseq_CI::eLevel_Mains , CBioseq_CI::eLevel_Parts , CBioseq_CI::eLevel_IgnoreClass }
	Class of bioseqs to iterate. More...
enum	CSeq_annot_CI::EFlags { CSeq_annot_CI::eSearch_entry , CSeq_annot_CI::eSearch_recursive }
enum	CSeq_entry_CI::EFlags { CSeq_entry_CI::fRecursive = (1 << 0) , CSeq_entry_CI::fIncludeGivenEntry = (1 << 1) , CSeq_entry_CI::eNonRecursive = 0 , CSeq_entry_CI::eRecursive = fRecursive }
	Flags that affect iteration. More...
enum	CSeqVectorTypes::ECaseConversion { CSeqVectorTypes::eCaseConversion_none , CSeqVectorTypes::eCaseConversion_upper , CSeqVectorTypes::eCaseConversion_lower }

Functions
	CAlign_CI::CAlign_CI (void)
	Create an empty iterator. More...
	CAlign_CI::CAlign_CI (const CBioseq_Handle &bioseq)
	Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
	CAlign_CI::CAlign_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand=eNa_strand_unknown)
	Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
	CAlign_CI::CAlign_CI (const CBioseq_Handle &bioseq, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
	CAlign_CI::CAlign_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
	CAlign_CI::CAlign_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
	CAlign_CI::CAlign_CI (CScope &scope, const CSeq_loc &loc, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_align objects related to the given seq-loc. More...
	CAlign_CI::CAlign_CI (CScope &scope, const CSeq_loc &loc)
	Create an iterator that enumerates CSeq_align objects related to the given seq-loc. More...
	CAlign_CI::CAlign_CI (const CSeq_annot_Handle &annot)
	Create an iterator that enumerates CSeq_align objects from the annotation regardless of their location. More...
	CAlign_CI::CAlign_CI (const CSeq_annot_Handle &annot, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_align objects from the annotation regardless of their location based on selection. More...
	CAlign_CI::CAlign_CI (const CSeq_loc &loc, const CSeq_annot_Handle &annot)
	Iterate all alignments from the seq-annot that annotate the location. More...
	CAlign_CI::CAlign_CI (const CSeq_loc &loc, const CSeq_annot_Handle &annot, const SAnnotSelector &sel)
	Iterate all alignments from the seq-annot that annotate the location. More...
	CAlign_CI::CAlign_CI (const CSeq_entry_Handle &entry)
	Create an iterator that enumerates CSeq_align objects from the seq-entry regardless of their location. More...
	CAlign_CI::CAlign_CI (const CSeq_entry_Handle &entry, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_align objects from the seq-entry regardless of their location based on selection. More...
	CAlign_CI::CAlign_CI (const CAlign_CI &iter)
CAlign_CI &	CAlign_CI::operator= (const CAlign_CI &iter)
virtual	CAlign_CI::~CAlign_CI (void)
CAlign_CI &	CAlign_CI::operator++ (void)
	Move to the next object in iterated sequence. More...
CAlign_CI &	CAlign_CI::operator-- (void)
	Move to the pervious object in iterated sequence. More...
void	CAlign_CI::Rewind (void)
	Move to the first object in iterated sequence. More...
	CAlign_CI::DECLARE_OPERATOR_BOOL (IsValid())
	Check if iterator points to an object. More...
const CAlign_CI &	CAlign_CI::begin () const
CAlign_CI	CAlign_CI::end () const
bool	CAlign_CI::operator!= (const CAlign_CI &it) const
const CSeq_align &	CAlign_CI::operator* (void) const
	Mapped alignment, not the original one. More...
const CSeq_align *	CAlign_CI::operator-> (void) const
	Mapped alignment, not the original one. More...
const CSeq_align &	CAlign_CI::GetOriginalSeq_align (void) const
	Get original alignment. More...
CSeq_align_Handle	CAlign_CI::GetSeq_align_Handle (void) const
	Get original alignment handle. More...
CAlign_CI	CAlign_CI::operator++ (int)
CAlign_CI	CAlign_CI::operator-- (int)
	CAlign_CI::CAlign_CI (const CAlign_CI &it, EAtEnd)
	CAnnot_CI::CAnnot_CI (void)
	Create an empty iterator. More...
	CAnnot_CI::CAnnot_CI (const CBioseq_Handle &bioseq)
	Create an iterator that enumerates CSeq_annot objects related to the given bioseq. More...
	CAnnot_CI::CAnnot_CI (const CBioseq_Handle &bioseq, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_annot objects related to the given bioseq. More...
	CAnnot_CI::CAnnot_CI (CScope &scope, const CSeq_loc &loc)
	Create an iterator that enumerates CSeq_annot objects related to the given seq-loc based on selection. More...
	CAnnot_CI::CAnnot_CI (CScope &scope, const CSeq_loc &loc, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_annot objects related to the given seq-loc based on selection. More...
	CAnnot_CI::CAnnot_CI (const CSeq_entry_Handle &entry, const SAnnotSelector &sel)
	Iterate all Seq-annot objects from the seq-entry regardless of their location, using SAnnotSelector for filtering. More...
	CAnnot_CI::CAnnot_CI (const CAnnot_CI &iter)
	Copy constructor. More...
	CAnnot_CI::CAnnot_CI (const CAnnotTypes_CI &iter)
	Create an iterator that enumerates all CSeq_annot objects collected by another iterator CFeat_CI, CGraph_CI, or CAlign_CI. More...
virtual	CAnnot_CI::~CAnnot_CI (void)
CAnnot_CI &	CAnnot_CI::operator= (const CAnnot_CI &iter)
CAnnot_CI &	CAnnot_CI::operator++ (void)
	Move to the next object in iterated sequence. More...
CAnnot_CI &	CAnnot_CI::operator-- (void)
	Move to the pervious object in iterated sequence. More...
void	CAnnot_CI::Rewind (void)
	CAnnot_CI::DECLARE_OPERATOR_BOOL (x_IsValid())
	Check if iterator points to an object. More...
bool	CAnnot_CI::empty (void) const
	Check if iterator is empty. More...
size_t	CAnnot_CI::size (void) const
	Get number of collected Seq-annots. More...
const CSeq_annot_Handle &	CAnnot_CI::operator* (void) const
const CSeq_annot_Handle *	CAnnot_CI::operator-> (void) const
void	CAnnot_CI::x_Initialize (const CAnnotTypes_CI &iter)
bool	CAnnot_CI::x_IsValid (void) const
CAnnot_CI	CAnnot_CI::operator++ (int)
CAnnot_CI	CAnnot_CI::operator-- (int)
virtual	IFeatComparator::~IFeatComparator ()
virtual bool	IFeatComparator::Less (const CSeq_feat &f1, const CSeq_feat &f2, CScope *scope)=0
	SAnnotSelector::SAnnotSelector (TAnnotType annot=CSeq_annot::C_Data::e_not_set, TFeatType feat=CSeqFeatData::e_not_set, bool feat_product=false)
	SAnnotSelector::SAnnotSelector (TFeatType feat, bool feat_product=false)
	SAnnotSelector::SAnnotSelector (TFeatSubtype feat_subtype)
	SAnnotSelector::SAnnotSelector (const SAnnotSelector &sel)
SAnnotSelector &	SAnnotSelector::operator= (const SAnnotSelector &sel)
	SAnnotSelector::~SAnnotSelector (void)
SAnnotSelector &	SAnnotSelector::SetAnnotType (TAnnotType type)
	Set annotation type (feat, align, graph) More...
SAnnotSelector &	SAnnotSelector::SetFeatType (TFeatType type)
	Set feature type (also set annotation type to feat) More...
SAnnotSelector &	SAnnotSelector::SetFeatSubtype (TFeatSubtype subtype)
	Set feature subtype (also set annotation and feat type) More...
SAnnotSelector &	SAnnotSelector::IncludeAnnotType (TAnnotType type)
	Include annotation type in the search. More...
SAnnotSelector &	SAnnotSelector::ExcludeAnnotType (TAnnotType type)
	Exclude annotation type from the search. More...
SAnnotSelector &	SAnnotSelector::IncludeFeatType (TFeatType type)
	Include feature type in the search. More...
SAnnotSelector &	SAnnotSelector::ExcludeFeatType (TFeatType type)
	Exclude feature type from the search. More...
SAnnotSelector &	SAnnotSelector::IncludeFeatSubtype (TFeatSubtype subtype)
	Include feature subtype in the search. More...
SAnnotSelector &	SAnnotSelector::ExcludeFeatSubtype (TFeatSubtype subtype)
	Exclude feature subtype from the search. More...
bool	SAnnotSelector::CheckAnnotType (TAnnotType type) const
	Check annot type (ignore subtypes). More...
SAnnotSelector &	SAnnotSelector::ForceAnnotType (TAnnotType type)
	Set annot type, include all subtypes. More...
bool	SAnnotSelector::IncludedAnnotType (TAnnotType type) const
	Return true if at least one subtype of the type is included or selected type is not set (any). More...
bool	SAnnotSelector::IncludedFeatType (TFeatType type) const
bool	SAnnotSelector::IncludedFeatSubtype (TFeatSubtype subtype) const
bool	SAnnotSelector::MatchType (const CAnnotObject_Info &annot_info) const
	Check if type of the annotation matches the selector. More...
bool	SAnnotSelector::GetFeatProduct (void) const
	Return true if the features should be searched using their product rather than location. More...
SAnnotSelector &	SAnnotSelector::SetByProduct (bool byProduct=true)
	Set flag indicating if the features should be searched by their product rather than location. More...
EOverlapType	SAnnotSelector::GetOverlapType (void) const
	Get the selected overlap type. More...
SAnnotSelector &	SAnnotSelector::SetOverlapType (EOverlapType overlap_type)
	Set overlap type. More...
SAnnotSelector &	SAnnotSelector::SetOverlapIntervals (void)
	Check overlapping of individual intervals. More...
SAnnotSelector &	SAnnotSelector::SetOverlapTotalRange (void)
	Check overlapping only of total ranges. More...
ESortOrder	SAnnotSelector::GetSortOrder (void) const
	Get the selected sort order. More...
SAnnotSelector &	SAnnotSelector::SetSortOrder (ESortOrder sort_order)
	Set sort order of annotations. More...
SAnnotSelector &	SAnnotSelector::SetFeatComparator (IFeatComparator *comparator)
SAnnotSelector &	SAnnotSelector::ResetFeatComparator (void)
bool	SAnnotSelector::IsSetFeatComparator (void) const
IFeatComparator *	SAnnotSelector::GetFeatComparator (void) const
EResolveMethod	SAnnotSelector::GetResolveMethod (void) const
	GetResolveMethod() returns current value of resolve_method. More...
SAnnotSelector &	SAnnotSelector::SetResolveMethod (EResolveMethod resolve_method)
	SetResolveMethod() controls visibility of subsegments depending on whether it's packaged together with master sequence. More...
SAnnotSelector &	SAnnotSelector::SetResolveNone (void)
	SetResolveNone() is equivalent to SetResolveMethod(eResolve_None). More...
SAnnotSelector &	SAnnotSelector::SetResolveTSE (void)
	SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE). More...
SAnnotSelector &	SAnnotSelector::SetResolveAll (void)
	SetResolveAll() is equivalent to SetResolveMethod(eResolve_All). More...
int	SAnnotSelector::GetResolveDepth (void) const
	GetResolveDepth() returns current limit of subsegment resolution in searching annotations. More...
SAnnotSelector &	SAnnotSelector::SetResolveDepth (int depth)
	SetResolveDepth sets the limit of subsegment resolution in searching annotations. More...
bool	SAnnotSelector::GetAdaptiveDepth (void) const
	GetAdaptiveDepth() returns current value of 'adaptive depth' flag. More...
SAnnotSelector &	SAnnotSelector::SetAdaptiveDepth (bool value=true)
	SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower level of segments. More...
SAnnotSelector &	SAnnotSelector::SetAdaptiveDepthFlags (TAdaptiveDepthFlags flags)
	SetAdaptiveDepthFlags() sets flags for adaptive depth heuristics. More...
TAdaptiveDepthFlags	SAnnotSelector::GetAdaptiveDepthFlags (void) const
	GetAdaptiveDepthFlags() returns current set of adaptive depth heuristics flags. More...
static TAdaptiveDepthFlags	SAnnotSelector::GetDefaultAdaptiveDepthFlags ()
	Get default set of adaptive depth flags. More...
static void	SAnnotSelector::SetDefaultAdaptiveDepthFlags (TAdaptiveDepthFlags flags)
	Set default set of adaptive depth flags. More...
SAnnotSelector &	SAnnotSelector::SetAdaptiveTrigger (const SAnnotTypeSelector &sel)
	SetAdaptiveTrigger() allows to change default set of adaptive trigger annotations. More...
SAnnotSelector &	SAnnotSelector::SetExactDepth (bool value=true)
	SetExactDepth() specifies that annotations will be searched on the segment level specified by SetResolveDepth() only. More...
bool	SAnnotSelector::GetExactDepth (void) const
	GetExactDepth() returns current value of 'exact depth' flag. More...
TMaxSize	SAnnotSelector::GetMaxSize (void) const
	Get maximum allowed number of annotations to find. More...
SAnnotSelector &	SAnnotSelector::SetMaxSize (TMaxSize max_size)
	Set maximum number of annotations to find. More...
TMaxSearchSegments	SAnnotSelector::GetMaxSearchSegments (void) const
	Get maximum number of empty segments to search before giving up. More...
SAnnotSelector &	SAnnotSelector::SetMaxSearchSegments (TMaxSearchSegments max_segments)
	Set maximum number of empty segments to search before giving up. More...
EMaxSearchSegmentsAction	SAnnotSelector::GetMaxSearchSegmentsAction (void) const
SAnnotSelector &	SAnnotSelector::SetMaxSearchSegmentsAction (EMaxSearchSegmentsAction action)
TMaxSearchTime	SAnnotSelector::GetMaxSearchTime (void) const
	Get maximum time (in seconds) to search before giving up. More...
SAnnotSelector &	SAnnotSelector::SetMaxSearchTime (TMaxSearchTime max_time)
	Set maximum time (in seconds) to search before giving up. More...
bool	SAnnotSelector::HasLimit (void)
	Check if the parent object of annotations is set. More...
SAnnotSelector &	SAnnotSelector::SetLimitNone (void)
	Remove restrictions on the parent object of annotations. More...
SAnnotSelector &	SAnnotSelector::SetLimitTSE (const CTSE_Handle &limit)
	Limit annotations to those from the TSE only. More...
SAnnotSelector &	SAnnotSelector::SetLimitTSE (const CSeq_entry_Handle &limit)
SAnnotSelector &	SAnnotSelector::SetLimitSeqEntry (const CSeq_entry_Handle &limit)
	Limit annotations to those from the seq-entry only. More...
SAnnotSelector &	SAnnotSelector::SetLimitSeqAnnot (const CSeq_annot_Handle &limit)
	Limit annotations to those from the seq-annot only. More...
EUnresolvedFlag	SAnnotSelector::GetUnresolvedFlag (void) const
	Get current method of handling unresolved seq-ids. More...
SAnnotSelector &	SAnnotSelector::SetUnresolvedFlag (EUnresolvedFlag flag)
	Set method of handling unresolved seq-ids. More...
SAnnotSelector &	SAnnotSelector::SetIgnoreUnresolved (void)
SAnnotSelector &	SAnnotSelector::SetSearchUnresolved (void)
SAnnotSelector &	SAnnotSelector::SetFailUnresolved (void)
SAnnotSelector &	SAnnotSelector::SetExcludeExternal (bool exclude=true)
	External annotations for the Object Manger are annotations located in top level Seq-entry different from TSE with the sequence they annotate. More...
SAnnotSelector &	SAnnotSelector::SetSearchExternal (const CTSE_Handle &tse)
	Set all flags for searching standard GenBank external annotations. More...
SAnnotSelector &	SAnnotSelector::SetSearchExternal (const CSeq_entry_Handle &tse)
SAnnotSelector &	SAnnotSelector::SetSearchExternal (const CBioseq_Handle &seq)
SAnnotSelector &	SAnnotSelector::ResetAnnotsNames (void)
	Select annotations from all Seq-annots. More...
SAnnotSelector &	SAnnotSelector::ResetUnnamedAnnots (void)
	Reset special processing of unnamed annots (added or excluded) More...
SAnnotSelector &	SAnnotSelector::ResetNamedAnnots (const CAnnotName &name)
	Reset special processing of named annots (added or excluded) More...
SAnnotSelector &	SAnnotSelector::ResetNamedAnnots (const char *name)
SAnnotSelector &	SAnnotSelector::AddUnnamedAnnots (void)
	Add unnamed annots to set of annots names to look for. More...
SAnnotSelector &	SAnnotSelector::AddNamedAnnots (const CAnnotName &name)
	Add named annot to set of annots names to look for. More...
SAnnotSelector &	SAnnotSelector::AddNamedAnnots (const char *name)
SAnnotSelector &	SAnnotSelector::ExcludeUnnamedAnnots (void)
	Add unnamed annots to set of annots names to exclude. More...
SAnnotSelector &	SAnnotSelector::ExcludeNamedAnnots (const CAnnotName &name)
	Add named annot to set of annots names to exclude. More...
SAnnotSelector &	SAnnotSelector::ExcludeNamedAnnots (const char *name)
SAnnotSelector &	SAnnotSelector::SetAllNamedAnnots (void)
	Look for all named Seq-annots Resets the filter, and then excludes unnamed annots. More...
SAnnotSelector &	SAnnotSelector::SetDataSource (const string &name)
	Look for named annot. More...
const TAnnotsNames &	SAnnotSelector::GetIncludedAnnotsNames (void) const
const TAnnotsNames &	SAnnotSelector::GetExcludedAnnotsNames (void) const
bool	SAnnotSelector::IsSetAnnotsNames (void) const
bool	SAnnotSelector::IsSetIncludedAnnotsNames (void) const
bool	SAnnotSelector::HasWildcardInAnnotsNames () const
bool	SAnnotSelector::HasExplicitAnnotsNames () const
bool	SAnnotSelector::IncludedAnnotName (const CAnnotName &name) const
bool	SAnnotSelector::ExcludedAnnotName (const CAnnotName &name) const
bool	SAnnotSelector::HasIncludedOnlyNamedAnnotAccessions () const
SAnnotSelector &	SAnnotSelector::ResetNamedAnnotAccessions (void)
	Add named annot accession (NA*) in the search. More...
SAnnotSelector &	SAnnotSelector::IncludeNamedAnnotAccession (const string &acc, int zoom_level=0)
SAnnotSelector &	SAnnotSelector::ExcludeNamedAnnotAccession (const string &acc)
const TNamedAnnotAccessions &	SAnnotSelector::GetNamedAnnotAccessions (void) const
bool	SAnnotSelector::IsIncludedAnyNamedAnnotAccession (void) const
	check if any named annot accession is included in the search More...
bool	SAnnotSelector::IsIncludedNamedAnnotAccession (const string &acc) const
	check if named annot accession is included in the search More...
SAnnotSelector &	SAnnotSelector::ExcludeTSE (const CTSE_Handle &tse)
SAnnotSelector &	SAnnotSelector::ExcludeTSE (const CSeq_entry_Handle &tse)
SAnnotSelector &	SAnnotSelector::ResetExcludedTSE (void)
bool	SAnnotSelector::ExcludedTSE (const CTSE_Handle &tse) const
bool	SAnnotSelector::ExcludedTSE (const CSeq_entry_Handle &tse) const
bool	SAnnotSelector::GetNoMapping (void) const
SAnnotSelector &	SAnnotSelector::SetNoMapping (bool value=true)
SAnnotSelector &	SAnnotSelector::SetCollectSeq_annots (bool value=true)
	Try to avoid collecting multiple objects from the same seq-annot. More...
SAnnotSelector &	SAnnotSelector::SetCollectTypes (bool value=true)
	Collect available annot types rather than annots. More...
SAnnotSelector &	SAnnotSelector::SetCollectNames (bool value=true)
	Collect available annot names rather than annots. More...
SAnnotSelector &	SAnnotSelector::SetCollectCostOfLoading (bool value=true)
	Collect cost of loading requested data. More...
SAnnotSelector &	SAnnotSelector::SetIgnoreStrand (bool value=true)
	Ignore strand when testing for range overlap. More...
SAnnotSelector &	SAnnotSelector::SetSourceLoc (const CSeq_loc &loc)
	Set filter for source location of annotations. More...
SAnnotSelector &	SAnnotSelector::ResetSourceLoc (void)
	Reset filter for source location of annotations. More...
SAnnotSelector &	SAnnotSelector::SetIgnoreFarLocationsForSorting (const CBioseq_Handle &handle)
	Set handle used for determining what locations are "near". More...
const CBioseq_Handle &	SAnnotSelector::GetIgnoreFarLocationsForSorting (void) const
SAnnotSelector &	SAnnotSelector::SetBitFilter (TBitFilter filter_bits, TBitFilter filter_mask=TBitFilter(-1))
SAnnotSelector &	SAnnotSelector::ResetBitFilter (void)
bool	SAnnotSelector::HasBitFilter (void) const
TBitFilter	SAnnotSelector::GetFilterMask (void) const
TBitFilter	SAnnotSelector::GetFilterBits (void) const
SAnnotSelector &	SAnnotSelector::SetExcludeIfGeneIsSuppressed (bool exclude=true)
	Exclude features with empty gene xref: xref { { data gene { } } }. More...
bool	SAnnotSelector::GetExcludeIfGeneIsSuppressed (void) const
TSNPScaleLimit	SAnnotSelector::GetSNPScaleLimit (void) const
SAnnotSelector &	SAnnotSelector::SetSNPScaleLimit (TSNPScaleLimit value)
SAnnotSelector &	SAnnotSelector::ResetSNPScaleLimit (void)
void	SAnnotSelector::CheckLimitObjectType (void) const
void	SAnnotSelector::x_InitializeAnnotTypesSet (bool default_value)
void	SAnnotSelector::x_ClearAnnotTypesSet (void)
bool	ExtractZoomLevel (const string &full_name, string *acc_ptr, int *zoom_level_ptr)
	Extract optional zoom level suffix from named annotation string. More...
string	CombineWithZoomLevel (const string &acc, int zoom_level)
	Combine accession string and zoom level into a string with separator. More...
void	AddZoomLevel (string &acc, int zoom_level)
	CBioseq_CI::CBioseq_CI (void)
	CBioseq_CI::CBioseq_CI (const CSeq_entry_Handle &entry, CSeq_inst::EMol filter=CSeq_inst::eMol_not_set, EBioseqLevelFlag level=eLevel_All)
	Create an iterator that enumerates bioseqs from the entry taken from the scope. More...
	CBioseq_CI::CBioseq_CI (const CBioseq_set_Handle &bioseq_set, CSeq_inst::EMol filter=CSeq_inst::eMol_not_set, EBioseqLevelFlag level=eLevel_All)
	CBioseq_CI::CBioseq_CI (CScope &scope, const CSeq_entry &entry, CSeq_inst::EMol filter=CSeq_inst::eMol_not_set, EBioseqLevelFlag level=eLevel_All)
	Create an iterator that enumerates bioseqs from the entry taken from the given scope. More...
	CBioseq_CI::CBioseq_CI (const CBioseq_CI &bioseq_ci)
	CBioseq_CI::~CBioseq_CI (void)
CScope &	CBioseq_CI::GetScope (void) const
	Get the current scope for the iterator. More...
CBioseq_CI &	CBioseq_CI::operator= (const CBioseq_CI &bioseq_ci)
CBioseq_CI &	CBioseq_CI::operator++ (void)
	Move to the next object in iterated sequence. More...
	CBioseq_CI::DECLARE_OPERATOR_BOOL (m_CurrentBioseq)
	Check if iterator points to an object. More...
const CBioseq_Handle &	CBioseq_CI::operator* (void) const
const CBioseq_Handle *	CBioseq_CI::operator-> (void) const
void	CBioseq_CI::x_Initialize (const CSeq_entry_Handle &entry)
void	CBioseq_CI::x_PushEntry (const CSeq_entry_Handle &entry)
void	CBioseq_CI::x_PopEntry (bool next=true)
void	CBioseq_CI::x_NextEntry (void)
void	CBioseq_CI::x_Settle (void)
bool	CBioseq_CI::x_IsValidMolType (const CBioseq_Info &seq) const
bool	CBioseq_CI::x_SkipClass (CBioseq_set::TClass set_class)
	CFeat_CI::CFeat_CI (void)
	CFeat_CI::CFeat_CI (const CBioseq_Handle &bioseq)
	Search features on the whole bioseq. More...
	CFeat_CI::CFeat_CI (const CBioseq_Handle &bioseq, const SAnnotSelector &sel)
	Search features on the whole bioseq. More...
	CFeat_CI::CFeat_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand=eNa_strand_unknown)
	Search features on part of the bioseq. More...
	CFeat_CI::CFeat_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, const SAnnotSelector &sel)
	Search features on part of the bioseq. More...
	CFeat_CI::CFeat_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &sel)
	Search features on part of the bioseq. More...
	CFeat_CI::CFeat_CI (CScope &scope, const CSeq_loc &loc)
	Search features related to the location. More...
	CFeat_CI::CFeat_CI (CScope &scope, const CSeq_loc &loc, const SAnnotSelector &sel)
	Search features related to the location. More...
	CFeat_CI::CFeat_CI (const CSeq_annot_Handle &annot)
	Iterate all features from the seq-annot regardless of their location. More...
	CFeat_CI::CFeat_CI (const CSeq_annot_Handle &annot, const SAnnotSelector &sel)
	Iterate all features from the seq-annot regardless of their location. More...
	CFeat_CI::CFeat_CI (const CSeq_loc &loc, const CSeq_annot_Handle &annot)
	Iterate all features from the seq-annot that annotate the location. More...
	CFeat_CI::CFeat_CI (const CSeq_loc &loc, const CSeq_annot_Handle &annot, const SAnnotSelector &sel)
	Iterate all features from the seq-annot that annotate the location. More...
	CFeat_CI::CFeat_CI (const CSeq_entry_Handle &entry)
	Iterate all features from the seq-entry regardless of their location. More...
	CFeat_CI::CFeat_CI (const CSeq_entry_Handle &entry, const SAnnotSelector &sel)
	Iterate all features from the seq-entry regardless of their location. More...
	CFeat_CI::CFeat_CI (const CTSE_Handle &tse, const SAnnotSelector &sel, const TFeatureId &id)
	CFeat_CI::CFeat_CI (const CTSE_Handle &tse, const SAnnotSelector &sel, const TFeatureIdInt &int_id)
	CFeat_CI::CFeat_CI (const CTSE_Handle &tse, const SAnnotSelector &sel, const TFeatureIdStr &str_id)
	CFeat_CI::CFeat_CI (const CFeat_CI &iter)
virtual	CFeat_CI::~CFeat_CI (void)
CFeat_CI &	CFeat_CI::operator= (const CFeat_CI &iter)
CFeat_CI &	CFeat_CI::operator++ (void)
	Move to the next object in iterated sequence. More...
CFeat_CI &	CFeat_CI::operator-- (void)
	Move to the pervious object in iterated sequence. More...
	CFeat_CI::DECLARE_OPERATOR_BOOL (IsValid())
	Check if iterator points to an object. More...
void	CFeat_CI::Update (void)
void	CFeat_CI::Rewind (void)
const CFeat_CI &	CFeat_CI::begin () const
CFeat_CI	CFeat_CI::end () const
bool	CFeat_CI::operator!= (const CFeat_CI &it) const
const CMappedFeat &	CFeat_CI::operator* (void) const
const CMappedFeat *	CFeat_CI::operator-> (void) const
CFeat_CI &	CFeat_CI::operator++ (int)
CFeat_CI &	CFeat_CI::operator-- (int)
	CFeat_CI::CFeat_CI (const CFeat_CI &it, EAtEnd)
void	CFeat_CI::x_AddFeaturesWithId (const CTSE_Handle &tse, const SAnnotSelector &sel, const TFeatureId &feat_id)
void	CFeat_CI::x_AddFeatures (const SAnnotSelector &sel, const TSeq_feat_Handles &feats)
	CMappedGraph::CMappedGraph ()
	empty CMappedGraph More...
const CSeq_graph &	CMappedGraph::GetOriginalGraph (void) const
	Get original graph with unmapped location/product. More...
CSeq_annot_Handle	CMappedGraph::GetAnnot (void) const
	Get containing annot handle. More...
CSeq_graph_Handle	CMappedGraph::GetSeq_graph_Handle (void) const
	Get original graph handle. More...
bool	CMappedGraph::operator== (const CMappedGraph &graph) const
	Check if it's the same graph. More...
bool	CMappedGraph::operator!= (const CMappedGraph &graph) const
bool	CMappedGraph::operator< (const CMappedGraph &graph) const
const CSeq_graph &	CMappedGraph::GetMappedGraph (void) const
	Graph mapped to the master sequence. More...
bool	CMappedGraph::IsSetTitle (void) const
const string &	CMappedGraph::GetTitle (void) const
bool	CMappedGraph::IsSetComment (void) const
const string &	CMappedGraph::GetComment (void) const
const CSeq_loc &	CMappedGraph::GetLoc (void) const
bool	CMappedGraph::IsSetTitle_x (void) const
const string &	CMappedGraph::GetTitle_x (void) const
bool	CMappedGraph::IsSetTitle_y (void) const
const string &	CMappedGraph::GetTitle_y (void) const
bool	CMappedGraph::IsSetComp (void) const
TSeqPos	CMappedGraph::GetComp (void) const
bool	CMappedGraph::IsSetA (void) const
double	CMappedGraph::GetA (void) const
bool	CMappedGraph::IsSetB (void) const
double	CMappedGraph::GetB (void) const
TSeqPos	CMappedGraph::GetNumval (void) const
const CSeq_graph::C_Graph &	CMappedGraph::GetGraph (void) const
const TRange &	CMappedGraph::GetMappedGraphTotalRange (void) const
	Get the range of graph data used in the mapped graph. More...
const TGraphRanges &	CMappedGraph::GetMappedGraphRanges (void) const
	Get all mapped graph ranges. More...
void	CMappedGraph::Set (CAnnot_Collector &collector, const CAnnotObject_Ref &annot_ref)
void	CMappedGraph::Reset (void)
void	CMappedGraph::MakeMappedGraph (void) const
void	CMappedGraph::MakeMappedLoc (void) const
void	CMappedGraph::MakeMappedGraphData (CSeq_graph &dst) const
	CGraph_CI::CGraph_CI (void)
	Create an empty iterator. More...
	CGraph_CI::CGraph_CI (const CBioseq_Handle &bioseq)
	Create an iterator that enumerates CSeq_graph objects related to the given bioseq. More...
	CGraph_CI::CGraph_CI (const CBioseq_Handle &bioseq, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_graph objects related to the given bioseq. More...
	CGraph_CI::CGraph_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand=eNa_strand_unknown)
	Create an iterator that enumerates CSeq_graph objects related to the given bioseq. More...
	CGraph_CI::CGraph_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_graph objects related to the given bioseq. More...
	CGraph_CI::CGraph_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_graph objects related to the given bioseq. More...
	CGraph_CI::CGraph_CI (CScope &scope, const CSeq_loc &loc)
	Create an iterator that enumerates CSeq_graph objects related to the given seq-loc. More...
	CGraph_CI::CGraph_CI (CScope &scope, const CSeq_loc &loc, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_graph objects related to the given seq-loc. More...
	CGraph_CI::CGraph_CI (const CSeq_annot_Handle &annot)
	Iterate all graphs from the seq-annot regardless of their location. More...
	CGraph_CI::CGraph_CI (const CSeq_annot_Handle &annot, const SAnnotSelector &sel)
	Iterate all graphs from the seq-annot regardless of their location. More...
	CGraph_CI::CGraph_CI (const CSeq_loc &loc, const CSeq_annot_Handle &annot)
	Iterate all graphs from the seq-annot that annotate the location. More...
	CGraph_CI::CGraph_CI (const CSeq_loc &loc, const CSeq_annot_Handle &annot, const SAnnotSelector &sel)
	Iterate all graphs from the seq-annot that annotate the location. More...
	CGraph_CI::CGraph_CI (const CSeq_entry_Handle &entry)
	Iterate all graphs from the seq-entry regardless of their location. More...
	CGraph_CI::CGraph_CI (const CSeq_entry_Handle &entry, const SAnnotSelector &sel)
	Iterate all graphs from the seq-entry regardless of their location. More...
	CGraph_CI::CGraph_CI (const CGraph_CI &iter)
CGraph_CI &	CGraph_CI::operator= (const CGraph_CI &iter)
virtual	CGraph_CI::~CGraph_CI (void)
CGraph_CI &	CGraph_CI::operator++ (void)
CGraph_CI &	CGraph_CI::operator-- (void)
void	CGraph_CI::Rewind (void)
	CGraph_CI::DECLARE_OPERATOR_BOOL (IsValid())
const CGraph_CI &	CGraph_CI::begin () const
CGraph_CI	CGraph_CI::end () const
bool	CGraph_CI::operator!= (const CGraph_CI &it) const
const CMappedGraph &	CGraph_CI::operator* (void) const
const CMappedGraph *	CGraph_CI::operator-> (void) const
void	CGraph_CI::x_Update (void)
CGraph_CI	CGraph_CI::operator++ (int)
CGraph_CI	CGraph_CI::operator-- (int)
	CGraph_CI::CGraph_CI (const CGraph_CI &it, EAtEnd)
	CMappedFeat::CMappedFeat (void)
	CMappedFeat::CMappedFeat (const CSeq_feat_Handle &feat)
	CMappedFeat::CMappedFeat (const CMappedFeat &feat)
CMappedFeat &	CMappedFeat::operator= (const CMappedFeat &feat)
	CMappedFeat::~CMappedFeat (void)
const CSeq_feat &	CMappedFeat::GetOriginalFeature (void) const
	Get original feature with unmapped location/product. More...
const CSeq_feat_Handle &	CMappedFeat::GetSeq_feat_Handle (void) const
	Get original feature handle. More...
bool	CMappedFeat::IsMapped (void) const
	Fast way to check if mapped feature is different from the original one. More...
const CSeq_feat &	CMappedFeat::GetMappedFeature (void) const
	Feature mapped to the master sequence. More...
bool	CMappedFeat::IsSetPartial (void) const
bool	CMappedFeat::GetPartial (void) const
const CSeq_loc &	CMappedFeat::GetProduct (void) const
const CSeq_loc &	CMappedFeat::GetLocation (void) const
CConstRef< CSeq_feat >	CMappedFeat::GetSeq_feat (void) const
	Get current seq-feat. More...
TRange	CMappedFeat::GetRange (void) const
	Get range for mapped seq-feat's location. More...
TRange	CMappedFeat::GetTotalRange (void) const
CSeq_id_Handle	CMappedFeat::GetLocationId (void) const
TRange	CMappedFeat::GetLocationTotalRange (void) const
CSeq_id_Handle	CMappedFeat::GetProductId (void) const
TRange	CMappedFeat::GetProductTotalRange (void) const
CMappedFeat &	CMappedFeat::Set (CAnnot_Collector &collector, const CAnnotObject_Ref &feat_ref)
void	CMappedFeat::Reset (void)
CConstRef< CSeq_loc >	CMappedFeat::GetMappedLocation (void) const
	CSeq_annot_CI::CSeq_annot_CI (void)
	Create an empty iterator. More...
	CSeq_annot_CI::CSeq_annot_CI (const CSeq_entry_Handle &entry, EFlags flags=eSearch_recursive)
	Create an iterator that enumerates CSeq_annot objects related to the given seq-entry. More...
	CSeq_annot_CI::CSeq_annot_CI (const CBioseq_set_Handle &bioseq_set, EFlags flags=eSearch_recursive)
	Create an iterator that enumerates CSeq_annot objects related to the given seq-set. More...
	CSeq_annot_CI::CSeq_annot_CI (CScope &scope, const CSeq_entry &entry, EFlags flags=eSearch_recursive)
	Create an iterator that enumerates CSeq_annot objects related to the given seq-entry from different scope. More...
	CSeq_annot_CI::CSeq_annot_CI (const CBioseq_Handle &bioseq)
	Create an iterator that enumerates CSeq_aannot objects related to the given bioseq up to the TSE. More...
	CSeq_annot_CI::CSeq_annot_CI (const CSeq_annot_CI &iter)
	CSeq_annot_CI::~CSeq_annot_CI (void)
CSeq_annot_CI &	CSeq_annot_CI::operator= (const CSeq_annot_CI &iter)
	CSeq_annot_CI::DECLARE_OPERATOR_BOOL (m_CurrentAnnot)
	Check if iterator points to an object. More...
CSeq_annot_CI &	CSeq_annot_CI::operator++ (void)
	Move to the next object in iterated sequence. More...
CScope &	CSeq_annot_CI::GetScope (void) const
	Get the current scope of the iterator. More...
const CSeq_annot_Handle &	CSeq_annot_CI::operator* (void) const
const CSeq_annot_Handle *	CSeq_annot_CI::operator-> (void) const
void	CSeq_annot_CI::x_Initialize (const CSeq_entry_Handle &entry_handle, EFlags flags)
void	CSeq_annot_CI::x_SetEntry (const CSeq_entry_Handle &entry)
void	CSeq_annot_CI::x_Push (void)
void	CSeq_annot_CI::x_Settle (void)
const TAnnots &	CSeq_annot_CI::x_GetAnnots (void) const
	CSeq_descr_CI::CSeq_descr_CI (void)
	Create an empty iterator. More...
	CSeq_descr_CI::CSeq_descr_CI (const CBioseq_Handle &handle, size_t search_depth=0)
	Create an iterator that enumerates CSeq_descr objects from a bioseq with limit number of seq-entries to "search_depth" (0 = unlimited). More...
	CSeq_descr_CI::CSeq_descr_CI (const CBioseq_set_Handle &handle, size_t search_depth=0)
	Create an iterator that enumerates CSeq_descr objects from a bioseq with limit number of seq-entries to "search_depth" (0 = unlimited). More...
	CSeq_descr_CI::CSeq_descr_CI (const CSeq_entry_Handle &entry, size_t search_depth=0)
	Create an iterator that enumerates CSeq_descr objects from a seq-entry, limit number of seq-entries to "search_depth" (0 = unlimited). More...
	CSeq_descr_CI::CSeq_descr_CI (const CSeq_descr_CI &iter)
	CSeq_descr_CI::~CSeq_descr_CI (void)
CSeq_descr_CI &	CSeq_descr_CI::operator= (const CSeq_descr_CI &iter)
CSeq_descr_CI &	CSeq_descr_CI::operator++ (void)
	Move to the next object in iterated sequence. More...
	CSeq_descr_CI::DECLARE_OPERATOR_BOOL_REF (m_CurrentBase)
	Check if iterator points to an object. More...
const CSeq_descr &	CSeq_descr_CI::operator* (void) const
const CSeq_descr *	CSeq_descr_CI::operator-> (void) const
CSeq_entry_Handle	CSeq_descr_CI::GetSeq_entry_Handle (void) const
void	CSeq_descr_CI::x_Next (void)
void	CSeq_descr_CI::x_Step (void)
void	CSeq_descr_CI::x_Settle (void)
const CBioseq_Base_Info &	CSeq_descr_CI::x_GetBaseInfo (void) const
	CSeq_entry_CI::CSeq_entry_CI (void)
	Create an empty iterator. More...
	CSeq_entry_CI::CSeq_entry_CI (const CSeq_entry_Handle &entry, TFlags flags=0, CSeq_entry::E_Choice type_filter=CSeq_entry::e_not_set)
	Create an iterator that enumerates Seq-entries inside the given Seq-entry. More...
	CSeq_entry_CI::CSeq_entry_CI (const CBioseq_set_Handle &set, TFlags flags=0, CSeq_entry::E_Choice type_filter=CSeq_entry::e_not_set)
	Create an iterator that enumerates Seq-entries inside the given Bioseq-set. More...
	CSeq_entry_CI::CSeq_entry_CI (const CSeq_entry_CI &iter)
CSeq_entry_CI &	CSeq_entry_CI::operator= (const CSeq_entry_CI &iter)
	CSeq_entry_CI::DECLARE_OPERATOR_BOOL (IsValid())
	Check if iterator points to an object. More...
bool	CSeq_entry_CI::operator== (const CSeq_entry_CI &iter) const
bool	CSeq_entry_CI::operator!= (const CSeq_entry_CI &iter) const
CSeq_entry_CI &	CSeq_entry_CI::operator++ (void)
	Move to the next object in iterated sequence. More...
const CSeq_entry_Handle &	CSeq_entry_CI::operator* (void) const
const CSeq_entry_Handle *	CSeq_entry_CI::operator-> (void) const
const CBioseq_set_Handle &	CSeq_entry_CI::GetParentBioseq_set (void) const
int	CSeq_entry_CI::GetDepth (void) const
	Returns the current depth, which may vary depending on flags. More...
bool	CSeq_entry_CI::IsValid (void) const
void	CSeq_entry_CI::x_Initialize (const CBioseq_set_Handle &set)
void	CSeq_entry_CI::x_SetCurrentEntry (void)
CSeq_entry_CI &	CSeq_entry_CI::operator++ (int)
bool	CSeq_entry_CI::x_ValidType (void) const
void	CSeq_entry_CI::x_Next (void)
	CSeq_entry_I::CSeq_entry_I (void)
	Create an empty iterator. More...
	CSeq_entry_I::CSeq_entry_I (const CSeq_entry_EditHandle &entry, TFlags flags=0, CSeq_entry::E_Choice type_filter=CSeq_entry::e_not_set)
	Create an iterator that enumerates seq-entries related to the given seq-entry. More...
	CSeq_entry_I::CSeq_entry_I (const CBioseq_set_EditHandle &set, TFlags flags=0, CSeq_entry::E_Choice type_filter=CSeq_entry::e_not_set)
	Create an iterator that enumerates seq-entries related to the given seq-set. More...
	CSeq_entry_I::CSeq_entry_I (const CSeq_entry_I &iter)
CSeq_entry_I &	CSeq_entry_I::operator= (const CSeq_entry_I &iter)
	CSeq_entry_I::OVERRIDE_OPERATOR_BOOL (CSeq_entry_CI, CSeq_entry_CI::IsValid())
	Check if iterator points to an object. More...
bool	CSeq_entry_I::operator== (const CSeq_entry_I &iter) const
bool	CSeq_entry_I::operator!= (const CSeq_entry_I &iter) const
CSeq_entry_I &	CSeq_entry_I::operator++ (void)
const CSeq_entry_EditHandle	CSeq_entry_I::operator* (void) const
unique_ptr< const CSeq_entry_EditHandle >	CSeq_entry_I::operator-> (void) const
CBioseq_set_EditHandle	CSeq_entry_I::GetParentBioseq_set (void) const
CSeq_entry_I &	CSeq_entry_I::operator++ (int)
	Move to the next object in iterated sequence. More...
	CSeqMap_CI_SegmentInfo::CSeqMap_CI_SegmentInfo (void)
TSeqPos	CSeqMap_CI_SegmentInfo::GetRefPosition (void) const
bool	CSeqMap_CI_SegmentInfo::GetRefMinusStrand (void) const
const CSeqMap &	CSeqMap_CI_SegmentInfo::x_GetSeqMap (void) const
size_t	CSeqMap_CI_SegmentInfo::x_GetIndex (void) const
const CSeqMap::CSegment &	CSeqMap_CI_SegmentInfo::x_GetSegment (void) const
const CSeqMap::CSegment &	CSeqMap_CI_SegmentInfo::x_GetNextSegment (void) const
bool	CSeqMap_CI_SegmentInfo::InRange (void) const
CSeqMap::ESegmentType	CSeqMap_CI_SegmentInfo::GetType (void) const
bool	CSeqMap_CI_SegmentInfo::IsSetData (void) const
bool	CSeqMap_CI_SegmentInfo::x_Move (bool minusStrand, CScope *scope)
TSeqPos	CSeqMap_CI_SegmentInfo::x_GetLevelRealPos (void) const
TSeqPos	CSeqMap_CI_SegmentInfo::x_GetLevelRealEnd (void) const
TSeqPos	CSeqMap_CI_SegmentInfo::x_GetLevelPos (void) const
TSeqPos	CSeqMap_CI_SegmentInfo::x_GetLevelEnd (void) const
TSeqPos	CSeqMap_CI_SegmentInfo::x_GetSkipBefore (void) const
TSeqPos	CSeqMap_CI_SegmentInfo::x_GetSkipAfter (void) const
TSeqPos	CSeqMap_CI_SegmentInfo::x_CalcLength (void) const
TSeqPos	CSeqMap_CI_SegmentInfo::x_GetTopOffset (void) const
int	CSeqMap_CI_SegmentInfo::x_GetSequenceClass (void) const
	SSeqMapSelector::SSeqMapSelector (void)
	SSeqMapSelector::SSeqMapSelector (TFlags flags, size_t resolve_count=0)
SSeqMapSelector &	SSeqMapSelector::SetPosition (TSeqPos pos)
	Find segment containing the position. More...
SSeqMapSelector &	SSeqMapSelector::SetRange (TSeqPos start, TSeqPos length)
	Set range for iterator. More...
SSeqMapSelector &	SSeqMapSelector::SetRange (const TRange &range)
	Set range for iterator - CRange<> version. More...
SSeqMapSelector &	SSeqMapSelector::SetStrand (ENa_strand strand)
	Set strand to iterate over. More...
SSeqMapSelector &	SSeqMapSelector::SetResolveCount (size_t res_cnt)
	Set max depth of resolving seq-map. More...
SSeqMapSelector &	SSeqMapSelector::SetLinkUsedTSE (bool link=true)
SSeqMapSelector &	SSeqMapSelector::SetLinkUsedTSE (const CTSE_Handle &top_tse)
SSeqMapSelector &	SSeqMapSelector::SetLinkUsedTSE (vector< CTSE_Handle > &used_tses)
SSeqMapSelector &	SSeqMapSelector::SetLimitTSE (const CSeq_entry_Handle &tse)
	Limit TSE to resolve references. More...
SSeqMapSelector &	SSeqMapSelector::SetFlags (TFlags flags)
	Select segment type(s) More...
SSeqMapSelector &	SSeqMapSelector::SetByFeaturePolicy (void)
SSeqMapSelector &	SSeqMapSelector::SetBySequenceClass (void)
size_t	SSeqMapSelector::GetResolveCount (void) const
bool	SSeqMapSelector::CanResolve (void) const
void	SSeqMapSelector::PushResolve (void)
void	SSeqMapSelector::PopResolve (void)
void	SSeqMapSelector::AddUsedTSE (const CTSE_Handle &tse) const
bool	SSeqMapSelector::x_HasLimitTSE (void) const
const CTSE_Handle &	SSeqMapSelector::x_GetLimitTSE (CScope *scope=0) const
	CSeqMap_CI::CSeqMap_CI (void)
	CSeqMap_CI::CSeqMap_CI (const CBioseq_Handle &bioseq, const SSeqMapSelector &selector, TSeqPos pos=0)
	CSeqMap_CI::CSeqMap_CI (const CBioseq_Handle &bioseq, const SSeqMapSelector &selector, const CRange< TSeqPos > &range)
	CSeqMap_CI::CSeqMap_CI (const CConstRef< CSeqMap > &seqmap, CScope *scope, const SSeqMapSelector &selector, TSeqPos pos=0)
	CSeqMap_CI::CSeqMap_CI (const CConstRef< CSeqMap > &seqmap, CScope *scope, const SSeqMapSelector &selector, const CRange< TSeqPos > &range)
	CSeqMap_CI::~CSeqMap_CI (void)
bool	CSeqMap_CI::IsInvalid (void) const
bool	CSeqMap_CI::IsValid (void) const
	CSeqMap_CI::DECLARE_OPERATOR_BOOL (IsValid())
bool	CSeqMap_CI::operator== (const CSeqMap_CI &seg) const
bool	CSeqMap_CI::operator!= (const CSeqMap_CI &seg) const
bool	CSeqMap_CI::operator< (const CSeqMap_CI &seg) const
bool	CSeqMap_CI::operator> (const CSeqMap_CI &seg) const
bool	CSeqMap_CI::operator<= (const CSeqMap_CI &seg) const
bool	CSeqMap_CI::operator>= (const CSeqMap_CI &seg) const
bool	CSeqMap_CI::Next (bool resolveExternal=true)
	go to next/next segment, return false if no more segments if no_resolve_current == true, do not resolve current segment More...
bool	CSeqMap_CI::Prev (void)
TFlags	CSeqMap_CI::GetFlags (void) const
void	CSeqMap_CI::SetFlags (TFlags flags)
CSeqMap_CI &	CSeqMap_CI::operator++ (void)
CSeqMap_CI &	CSeqMap_CI::operator-- (void)
size_t	CSeqMap_CI::GetDepth (void) const
	return the depth of current segment More...
TSeqPos	CSeqMap_CI::GetPosition (void) const
	return position of current segment in sequence More...
TSeqPos	CSeqMap_CI::GetLength (void) const
	return length of current segment More...
bool	CSeqMap_CI::IsUnknownLength (void) const
	return true if current segment is a gap of unknown length More...
TSeqPos	CSeqMap_CI::GetEndPosition (void) const
	return end position of current segment in sequence (exclusive) More...
CSeqMap::ESegmentType	CSeqMap_CI::GetType (void) const
bool	CSeqMap_CI::IsSetData (void) const
const CSeq_data &	CSeqMap_CI::GetData (void) const
	will allow only regular data segments (whole, plus strand) More...
const CSeq_data &	CSeqMap_CI::GetRefData (void) const
	will allow any data segments, user should check for position and strand More...
CConstRef< CSeq_literal >	CSeqMap_CI::GetRefGapLiteral (void) const
	return CSeq_literal with gap data, or null if either the segment is not a gap, or an unspecified gap More...
CSeq_id_Handle	CSeqMap_CI::GetRefSeqid (void) const
	The following function makes sense only when the segment is a reference to another seq. More...
TSeqPos	CSeqMap_CI::GetRefPosition (void) const
TSeqPos	CSeqMap_CI::GetRefEndPosition (void) const
bool	CSeqMap_CI::GetRefMinusStrand (void) const
CScope *	CSeqMap_CI::GetScope (void) const
const CTSE_Handle &	CSeqMap_CI::GetUsingTSE (void) const
bool	CSeqMap_CI::FeaturePolicyWasApplied (void) const
	CSeqMap_CI::CSeqMap_CI (const CSeqMap_CI &base, const CSeqMap &seqmap, size_t index, TSeqPos pos)
const TSegmentInfo &	CSeqMap_CI::x_GetSegmentInfo (void) const
TSegmentInfo &	CSeqMap_CI::x_GetSegmentInfo (void)
bool	CSeqMap_CI::x_RefTSEMatch (const CSeqMap::CSegment &seg) const
bool	CSeqMap_CI::x_CanResolve (const CSeqMap::CSegment &seg) const
const CSeqMap &	CSeqMap_CI::x_GetSeqMap (void) const
size_t	CSeqMap_CI::x_GetIndex (void) const
const CSeqMap::CSegment &	CSeqMap_CI::x_GetSegment (void) const
TSeqPos	CSeqMap_CI::x_GetTopOffset (void) const
void	CSeqMap_CI::x_Resolve (TSeqPos pos)
CBioseq_Handle	CSeqMap_CI::x_GetBioseq (const CSeq_id &seq_id) const
bool	CSeqMap_CI::x_Found (void) const
bool	CSeqMap_CI::x_Push (TSeqPos offset, bool resolveExternal)
bool	CSeqMap_CI::x_Push (TSeqPos offset)
void	CSeqMap_CI::x_Push (const CConstRef< CSeqMap > &seqMap, const CTSE_Handle &tse, TSeqPos from, TSeqPos length, bool minusStrand, TSeqPos pos)
bool	CSeqMap_CI::x_Pop (void)
bool	CSeqMap_CI::x_Next (bool resolveExternal)
bool	CSeqMap_CI::x_Next (void)
bool	CSeqMap_CI::x_Prev (void)
bool	CSeqMap_CI::x_TopNext (void)
bool	CSeqMap_CI::x_TopPrev (void)
bool	CSeqMap_CI::x_SettleNext (void)
bool	CSeqMap_CI::x_SettlePrev (void)
void	CSeqMap_CI::x_Select (const CConstRef< CSeqMap > &seqMap, const SSeqMapSelector &selector, TSeqPos pos)
int	CSeqMap_CI::x_GetSequenceClass (void) const
void	CSeqMap_CI::x_UpdateLength (void)
	CSeqMap_I::CSeqMap_I (void)
	CSeqMap_I::CSeqMap_I (const CBioseq_EditHandle &bioseq, const SSeqMapSelector &selector, TSeqPos pos=0)
	CSeqMap_I::CSeqMap_I (const CBioseq_EditHandle &bioseq, const SSeqMapSelector &selector, const CRange< TSeqPos > &range)
	CSeqMap_I::CSeqMap_I (CRef< CSeqMap > &seqmap, CScope *scope, const SSeqMapSelector &selector, TSeqPos pos=0)
	CSeqMap_I::CSeqMap_I (CRef< CSeqMap > &seqmap, CScope *scope, const SSeqMapSelector &selector, const CRange< TSeqPos > &range)
	CSeqMap_I::~CSeqMap_I (void)
void	CSeqMap_I::SetGap (TSeqPos length, CSeq_data *gap_data=0)
	Change current segment to gap. More...
void	CSeqMap_I::SetRef (const CSeq_id_Handle &ref_id, TSeqPos ref_pos, TSeqPos ref_length, bool ref_minus_strand=false)
	Change current segment to reference. More...
void	CSeqMap_I::SetSeq_data (TSeqPos length, CSeq_data &data)
	Change current segment to data. More...
CSeqMap_I &	CSeqMap_I::InsertGap (TSeqPos length, CSeq_data *gap_data=0)
	Insert gap. On return the iterator points to the new segment. More...
CSeqMap_I &	CSeqMap_I::InsertRef (const CSeq_id_Handle &ref_id, TSeqPos ref_pos, TSeqPos ref_length, bool ref_minus_strand=false)
	Insert reference. On return the iterator points to the new segment. More...
CSeqMap_I &	CSeqMap_I::InsertData (TSeqPos length, CSeq_data &data)
	Insert data. On return the iterator points to the new segment. More...
CSeqMap_I &	CSeqMap_I::InsertData (const string &buffer, CSeqUtil::ECoding buffer_coding, CSeq_data::E_Choice seq_data_coding)
	Insert data segment using the sequence string and the selected coding. More...
CSeqMap_I &	CSeqMap_I::Remove (void)
	Remove current segment. More...
void	CSeqMap_I::GetSequence (string &buffer, CSeqUtil::ECoding buffer_coding) const
	Get current sequence as a string with the selected encoding. More...
void	CSeqMap_I::SetSequence (const string &buffer, CSeqUtil::ECoding buffer_coding, CSeq_data::E_Choice seq_data_coding)
	Set sequence data. More...
static SSeqMapSelector	CSeqMap_I::sx_AdjustSelector (const SSeqMapSelector &selector)
	CSeq_table_CI::CSeq_table_CI (void)
	Create an empty iterator. More...
	CSeq_table_CI::CSeq_table_CI (const CBioseq_Handle &bioseq)
	Create an iterator that enumerates CSeq_table objects related to the given bioseq. More...
	CSeq_table_CI::CSeq_table_CI (const CBioseq_Handle &bioseq, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_table objects related to the given bioseq. More...
	CSeq_table_CI::CSeq_table_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand=eNa_strand_unknown)
	Create an iterator that enumerates CSeq_table objects related to the given bioseq. More...
	CSeq_table_CI::CSeq_table_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_table objects related to the given bioseq. More...
	CSeq_table_CI::CSeq_table_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_table objects related to the given bioseq. More...
	CSeq_table_CI::CSeq_table_CI (CScope &scope, const CSeq_loc &loc)
	Create an iterator that enumerates CSeq_table objects related to the given seq-loc. More...
	CSeq_table_CI::CSeq_table_CI (CScope &scope, const CSeq_loc &loc, const SAnnotSelector &sel)
	Create an iterator that enumerates CSeq_table objects related to the given seq-loc. More...
	CSeq_table_CI::CSeq_table_CI (const CSeq_annot_Handle &annot)
	Iterate all Seq-tables from the seq-annot regardless of their location. More...
	CSeq_table_CI::CSeq_table_CI (const CSeq_annot_Handle &annot, const SAnnotSelector &sel)
	Iterate all Seq-tables from the seq-annot regardless of their location. More...
	CSeq_table_CI::CSeq_table_CI (const CSeq_entry_Handle &entry)
	Iterate all Seq-tables from the seq-entry regardless of their location. More...
	CSeq_table_CI::CSeq_table_CI (const CSeq_entry_Handle &entry, const SAnnotSelector &sel)
	Iterate all Seq-tables from the seq-entry regardless of their location. More...
bool	CSeq_table_CI::IsMapped (void) const
const CSeq_loc &	CSeq_table_CI::GetMappedLocation (void) const
const CSeq_loc &	CSeq_table_CI::GetOriginalLocation (void) const
	CSeq_table_CI::CSeq_table_CI (const CSeq_table_CI &iter)
CSeq_table_CI &	CSeq_table_CI::operator= (const CSeq_table_CI &iter)
virtual	CSeq_table_CI::~CSeq_table_CI (void)
CSeq_table_CI &	CSeq_table_CI::operator++ (void)
CSeq_table_CI &	CSeq_table_CI::operator-- (void)
	CSeq_table_CI::DECLARE_OPERATOR_BOOL (IsValid())
const CSeq_table_CI &	CSeq_table_CI::begin () const
CSeq_table_CI	CSeq_table_CI::end () const
bool	CSeq_table_CI::operator!= (const CSeq_table_CI &it) const
const CSeq_annot_Handle &	CSeq_table_CI::operator* (void) const
const CSeq_annot_Handle *	CSeq_table_CI::operator-> (void) const
CSeq_table_CI	CSeq_table_CI::operator++ (int)
CSeq_table_CI	CSeq_table_CI::operator-- (int)
	CSeq_table_CI::CSeq_table_CI (const CSeq_table_CI &it, EAtEnd)
static TResidue	CSeqVectorTypes::sx_GetGapChar (TCoding coding, ECaseConversion case_cvt)
static const char *	CSeqVectorTypes::sx_GetConvertTable (TCoding src, TCoding dst, bool reverse, ECaseConversion case_cvt)
virtual	INcbi2naRandomizer::~INcbi2naRandomizer (void)
virtual void	INcbi2naRandomizer::RandomizeData (char *buffer, size_t count, TSeqPos pos)=0
	Convert count unpacked bases in buffer 4na -> 2na with randomization. More...
	CSeqVector_CI::CSeqVector_CI (void)
	CSeqVector_CI::~CSeqVector_CI (void)
	CSeqVector_CI::CSeqVector_CI (const CSeqVector &seq_vector, TSeqPos pos=0)
	CSeqVector_CI::CSeqVector_CI (const CSeqVector &seq_vector, TSeqPos pos, ECaseConversion case_cvt)
	CSeqVector_CI::CSeqVector_CI (const CSeqVector &seq_vector, ENa_strand strand, TSeqPos pos=0, ECaseConversion=eCaseConversion_none)
	CSeqVector_CI::CSeqVector_CI (const CSeqVector_CI &sv_it)
CSeqVector_CI &	CSeqVector_CI::operator= (const CSeqVector_CI &sv_it)
bool	CSeqVector_CI::operator== (const CSeqVector_CI &iter) const
bool	CSeqVector_CI::operator!= (const CSeqVector_CI &iter) const
bool	CSeqVector_CI::operator< (const CSeqVector_CI &iter) const
bool	CSeqVector_CI::operator> (const CSeqVector_CI &iter) const
bool	CSeqVector_CI::operator>= (const CSeqVector_CI &iter) const
bool	CSeqVector_CI::operator<= (const CSeqVector_CI &iter) const
bool	CSeqVector_CI::CanGetRange (TSeqPos start, TSeqPos stop)
	Check if the sequence can be obtained for the interval [start, stop) More...
void	CSeqVector_CI::GetSeqData (TSeqPos start, TSeqPos stop, string &buffer)
	Fill the buffer string with the sequence data for the interval [start, stop). More...
void	CSeqVector_CI::GetSeqData (string &buffer, TSeqPos count)
	Fill the buffer string with the count bytes of sequence data starting with current iterator position. More...
TSeqPos	CSeqVector_CI::GetBufferSize (void) const
	Get number of chars from current position to the current buffer end. More...
const char *	CSeqVector_CI::GetBufferPtr (void) const
	Get pointer to current char in the buffer. More...
const char *	CSeqVector_CI::GetBufferEnd (size_t size) const
	Get pointer to current position+size. More...
CSeqVector_CI &	CSeqVector_CI::operator++ (void)
CSeqVector_CI &	CSeqVector_CI::operator-- (void)
	CSeqVector_CI::CTempValue::CTempValue (value_type value)
value_type	CSeqVector_CI::CTempValue::operator* (void) const
CTempValue	CSeqVector_CI::operator++ (int)
	Restricted postfix operators. More...
CTempValue	CSeqVector_CI::operator-- (int)
TSeqPos	CSeqVector_CI::GetPos (void) const
CSeqVector_CI &	CSeqVector_CI::SetPos (TSeqPos pos)
TCoding	CSeqVector_CI::GetCoding (void) const
void	CSeqVector_CI::SetCoding (TCoding coding)
ENa_strand	CSeqVector_CI::GetStrand (void) const
void	CSeqVector_CI::SetStrand (ENa_strand strand)
void	CSeqVector_CI::SetRandomizeAmbiguities (void)
void	CSeqVector_CI::SetRandomizeAmbiguities (Uint4 seed)
void	CSeqVector_CI::SetRandomizeAmbiguities (CRandom &random_gen)
void	CSeqVector_CI::SetRandomizeAmbiguities (CRef< INcbi2naRandomizer > randomizer)
void	CSeqVector_CI::SetNoAmbiguities (void)
TResidue	CSeqVector_CI::operator* (void) const
bool	CSeqVector_CI::IsValid (void) const
	CSeqVector_CI::DECLARE_OPERATOR_BOOL (IsValid())
const CSeqMap_CI &	CSeqVector_CI::GetCurrentSeqMap_CI () const
bool	CSeqVector_CI::IsInGap (void) const
	true if current position of CSeqVector_CI is inside of sequence gap More...
CConstRef< CSeq_literal >	CSeqVector_CI::GetGapSeq_literal (void) const
	returns gap Seq-data object ref returns null if it's not a gap or an unspecified gap More...
TResidue	CSeqVector_CI::GetGapChar (void) const
	returns character representation of gap in sequence More...
TSeqPos	CSeqVector_CI::GetGapSizeForward (void) const
	returns number of gap symbols ahead including current symbol returns 0 if current position is not in gap More...
TSeqPos	CSeqVector_CI::GetGapSizeBackward (void) const
	returns number of gap symbols before current symbol returns 0 if current position is not in gap More...
TSeqPos	CSeqVector_CI::SkipGap (void)
	skip current gap forward returns number of skipped gap symbols does nothing and returns 0 if current position is not in gap More...
TSeqPos	CSeqVector_CI::SkipGapBackward (void)
	skip current gap backward returns number of skipped gap symbols does nothing and returns 0 if current position is not in gap More...
bool	CSeqVector_CI::HasZeroGapBefore (void)
	true if there is zero-length gap before current position More...
CSeqVector_CI &	CSeqVector_CI::operator+= (TSeqPos value)
CSeqVector_CI &	CSeqVector_CI::operator-= (TSeqPos value)
TSeqPos	CSeqVector_CI::x_GetSize (void) const
TCoding	CSeqVector_CI::x_GetCoding (TCoding cacheCoding, TCoding dataCoding) const
void	CSeqVector_CI::x_SetPos (TSeqPos pos)
void	CSeqVector_CI::x_InitializeCache (void)
void	CSeqVector_CI::x_ClearCache (void)
void	CSeqVector_CI::x_ResizeCache (size_t size)
void	CSeqVector_CI::x_SwapCache (void)
void	CSeqVector_CI::x_UpdateCacheUp (TSeqPos pos)
void	CSeqVector_CI::x_UpdateCacheDown (TSeqPos pos)
void	CSeqVector_CI::x_FillCache (TSeqPos start, TSeqPos count)
void	CSeqVector_CI::x_UpdateSeg (TSeqPos pos)
void	CSeqVector_CI::x_InitSeg (TSeqPos pos)
void	CSeqVector_CI::x_IncSeg (void)
void	CSeqVector_CI::x_DecSeg (void)
void	CSeqVector_CI::x_CheckForward (void)
void	CSeqVector_CI::x_CheckBackward (void)
void	CSeqVector_CI::x_InitRandomizer (CRandom &random_gen)
void	CSeqVector_CI::x_NextCacheSeg (void)
void	CSeqVector_CI::x_PrevCacheSeg (void)
TSeqPos	CSeqVector_CI::x_CachePos (void) const
TSeqPos	CSeqVector_CI::x_CacheSize (void) const
TSeqPos	CSeqVector_CI::x_CacheEndPos (void) const
TSeqPos	CSeqVector_CI::x_BackupPos (void) const
TSeqPos	CSeqVector_CI::x_BackupSize (void) const
TSeqPos	CSeqVector_CI::x_BackupEndPos (void) const
TSeqPos	CSeqVector_CI::x_CacheOffset (void) const
void	CSeqVector_CI::x_ResetCache (void)
void	CSeqVector_CI::x_ResetBackup (void)
void	CSeqVector_CI::x_ThrowOutOfRange (void) const
void	CSeqVector_CI::x_SetVector (CSeqVector &seq_vector)
CSeqVector_CI	operator+ (const CSeqVector_CI &iter, TSeqPos value)
CSeqVector_CI	operator- (const CSeqVector_CI &iter, TSeqPos value)
CSeqVector_CI	operator+ (const CSeqVector_CI &iter, TSignedSeqPos value)
CSeqVector_CI	operator- (const CSeqVector_CI &iter, TSignedSeqPos value)
TSignedSeqPos	operator- (const CSeqVector_CI &iter1, const CSeqVector_CI &iter2)
	CSeqdesc_CI::CSeqdesc_CI (void)
	CSeqdesc_CI::CSeqdesc_CI (const CSeq_descr_CI &desc_it, CSeqdesc::E_Choice choice=CSeqdesc::e_not_set)
	CSeqdesc_CI::CSeqdesc_CI (const CBioseq_Handle &handle, CSeqdesc::E_Choice choice=CSeqdesc::e_not_set, size_t search_depth=0)
	Create an iterator that enumerates CSeqdesc objects from a bioseq with limit number of seq-entries to "search_depth" (0 = unlimited) for specific type. More...
	CSeqdesc_CI::CSeqdesc_CI (const CSeq_entry_Handle &entry, CSeqdesc::E_Choice choice=CSeqdesc::e_not_set, size_t search_depth=0)
	Create an iterator that enumerates CSeqdesc objects from a seq-entry, limit number of seq-entries to "search_depth" (0 = unlimited) for specific type. More...
	CSeqdesc_CI::CSeqdesc_CI (const CBioseq_Handle &handle, const TDescChoices &choices, size_t search_depth=0)
	Create an iterator that enumerates CSeqdesc objects from a bioseq with limit number of seq-entries to "search_depth" (0 = unlimited) for set of types. More...
	CSeqdesc_CI::CSeqdesc_CI (const CSeq_entry_Handle &entry, const TDescChoices &choices, size_t search_depth=0)
	Create an iterator that enumerates CSeqdesc objects from a seq-entry, limit number of seq-entries to "search_depth" (0 = unlimited) for set of types. More...
	CSeqdesc_CI::CSeqdesc_CI (const CSeqdesc_CI &iter)
	CSeqdesc_CI::~CSeqdesc_CI (void)
CSeqdesc_CI &	CSeqdesc_CI::operator= (const CSeqdesc_CI &iter)
CSeqdesc_CI &	CSeqdesc_CI::operator++ (void)
	Move to the next object in iterated sequence. More...
	CSeqdesc_CI::DECLARE_OPERATOR_BOOL (m_Entry)
	Check if iterator points to an object. More...
const CSeqdesc &	CSeqdesc_CI::operator* (void) const
const CSeqdesc *	CSeqdesc_CI::operator-> (void) const
CSeq_entry_Handle	CSeqdesc_CI::GetSeq_entry_Handle (void) const
CSeqdesc_CI	CSeqdesc_CI::operator++ (int)
void	CSeqdesc_CI::x_AddChoice (CSeqdesc::E_Choice choice)
void	CSeqdesc_CI::x_RemoveChoice (CSeqdesc::E_Choice choice)
void	CSeqdesc_CI::x_SetChoice (CSeqdesc::E_Choice choice)
void	CSeqdesc_CI::x_SetChoices (const TDescChoices &choices)
bool	CSeqdesc_CI::x_RequestedType (void) const
bool	CSeqdesc_CI::x_Valid (void) const
bool	CSeqdesc_CI::x_ValidDesc (void) const
void	CSeqdesc_CI::x_FirstDesc (void)
void	CSeqdesc_CI::x_NextDesc (void)
void	CSeqdesc_CI::x_SetEntry (const CSeq_descr_CI &entry)
void	CSeqdesc_CI::x_Next (void)
void	CSeqdesc_CI::x_Settle (void)
const CBioseq_Base_Info &	CSeqdesc_CI::x_GetBaseInfo (void) const
void	CSeqdesc_CI::x_CheckRef (const CBioseq_Handle &handle)

Variables
CConstRef< CSeq_align >	CAlign_CI::m_MappedAlign
TSeqAnnotSet	CAnnot_CI::m_SeqAnnotSet
TIterator	CAnnot_CI::m_Iterator
bool	SAnnotSelector::m_FeatProduct
int	SAnnotSelector::m_ResolveDepth
EOverlapType	SAnnotSelector::m_OverlapType
EResolveMethod	SAnnotSelector::m_ResolveMethod
ESortOrder	SAnnotSelector::m_SortOrder
CIRef< IFeatComparator >	SAnnotSelector::m_FeatComparator
ELimitObject	SAnnotSelector::m_LimitObjectType
EUnresolvedFlag	SAnnotSelector::m_UnresolvedFlag
CConstRef< CObject >	SAnnotSelector::m_LimitObject
CTSE_Handle	SAnnotSelector::m_LimitTSE
TMaxSize	SAnnotSelector::m_MaxSize
TMaxSearchSegments	SAnnotSelector::m_MaxSearchSegments
TMaxSearchTime	SAnnotSelector::m_MaxSearchTime
TAnnotsNames	SAnnotSelector::m_IncludeAnnotsNames
TAnnotsNames	SAnnotSelector::m_ExcludeAnnotsNames
AutoPtr< TNamedAnnotAccessions >	SAnnotSelector::m_NamedAnnotAccessions
EMaxSearchSegmentsAction	SAnnotSelector::m_MaxSearchSegmentsAction
bool	SAnnotSelector::m_NoMapping
TAdaptiveDepthFlags	SAnnotSelector::m_AdaptiveDepthFlags
bool	SAnnotSelector::m_ExactDepth
bool	SAnnotSelector::m_ExcludeExternal
bool	SAnnotSelector::m_CollectSeq_annots
bool	SAnnotSelector::m_CollectTypes
bool	SAnnotSelector::m_CollectNames
bool	SAnnotSelector::m_CollectCostOfLoading
bool	SAnnotSelector::m_IgnoreStrand
bool	SAnnotSelector::m_HasWildcardInAnnotsNames
TAdaptiveTriggers	SAnnotSelector::m_AdaptiveTriggers
TTSE_Limits	SAnnotSelector::m_ExcludedTSE
TAnnotTypesBitset	SAnnotSelector::m_AnnotTypesBitset
AutoPtr< CHandleRangeMap >	SAnnotSelector::m_SourceLoc
CBioseq_Handle	SAnnotSelector::m_IgnoreFarLocationsForSorting
TBitFilter	SAnnotSelector::m_FilterMask
TBitFilter	SAnnotSelector::m_FilterBits
bool	SAnnotSelector::m_ExcludeIfGeneIsSuppressed
TSNPScaleLimit	SAnnotSelector::m_SNPScaleLimit
CHeapScope	CBioseq_CI::m_Scope
CSeq_inst::EMol	CBioseq_CI::m_Filter
EBioseqLevelFlag	CBioseq_CI::m_Level
CSeq_entry_Handle	CBioseq_CI::m_CurrentEntry
CBioseq_Handle	CBioseq_CI::m_CurrentBioseq
TEntryStack	CBioseq_CI::m_EntryStack
int	CBioseq_CI::m_InParts
CMappedFeat	CFeat_CI::m_MappedFeat
CRef< CAnnot_Collector >	CMappedGraph::m_Collector
const CAnnotObject_Ref *	CMappedGraph::m_GraphRef
CConstRef< CSeq_graph >	CMappedGraph::m_MappedGraph
CConstRef< CSeq_loc >	CMappedGraph::m_MappedLoc
CMappedGraph	CGraph_CI::m_Graph
CAnnotMapping_Info *	CMappedFeat::m_MappingInfoPtr
CAnnotMapping_Info	CMappedFeat::m_MappingInfoObj
CCreatedFeat_Ref	CMappedFeat::m_MappedFeat
CSeq_entry_Handle	CSeq_annot_CI::m_CurrentEntry
TAnnot_CI	CSeq_annot_CI::m_AnnotIter
CSeq_annot_Handle	CSeq_annot_CI::m_CurrentAnnot
TEntryStack	CSeq_annot_CI::m_EntryStack
bool	CSeq_annot_CI::m_UpTree
CConstRef< CBioseq_Base_Info >	CSeq_descr_CI::m_CurrentBase
CBioseq_Handle	CSeq_descr_CI::m_CurrentSeq
CBioseq_set_Handle	CSeq_descr_CI::m_CurrentSet
size_t	CSeq_descr_CI::m_ParentLimit
CBioseq_set_Handle	CSeq_entry_CI::m_Parent
size_t	CSeq_entry_CI::m_Index
CSeq_entry_Handle	CSeq_entry_CI::m_Current
TFlags	CSeq_entry_CI::m_Flags
CSeq_entry::E_Choice	CSeq_entry_CI::m_Filter
unique_ptr< CSeq_entry_CI >	CSeq_entry_CI::m_SubIt
CTSE_Handle	CSeqMap_CI_SegmentInfo::m_TSE
CConstRef< CSeqMap >	CSeqMap_CI_SegmentInfo::m_SeqMap
size_t	CSeqMap_CI_SegmentInfo::m_Index
TSeqPos	CSeqMap_CI_SegmentInfo::m_LevelRangePos
TSeqPos	CSeqMap_CI_SegmentInfo::m_LevelRangeEnd
bool	CSeqMap_CI_SegmentInfo::m_MinusStrand
Int1	CSeqMap_CI_SegmentInfo::m_SequenceClass
TSeqPos	SSeqMapSelector::m_Position
TSeqPos	SSeqMapSelector::m_Length
bool	SSeqMapSelector::m_MinusStrand
bool	SSeqMapSelector::m_LinkUsedTSE
CTSE_Handle	SSeqMapSelector::m_TopTSE
size_t	SSeqMapSelector::m_MaxResolveCount
CTSE_Handle	SSeqMapSelector::m_LimitTSE
TFlags	SSeqMapSelector::m_Flags
vector< CTSE_Handle > *	SSeqMapSelector::m_UsedTSEs
CHeapScope	CSeqMap_CI::m_Scope
TStack	CSeqMap_CI::m_Stack
SSeqMapSelector	CSeqMap_CI::m_Selector
TSeqPos	CSeqMap_CI::m_SearchPos
TSeqPos	CSeqMap_CI::m_SearchEnd
bool	CSeqMap_CI::m_FeaturePolicyWasApplied
CRef< CSeqMap >	CSeqMap_I::m_SeqMap
CConstRef< CSeq_loc >	CSeq_table_CI::m_MappedLoc
static const char	CSeqVectorTypes::sm_TrivialTable [256]
value_type	CSeqVector_CI::CTempValue::m_Value
CHeapScope	CSeqVector_CI::m_Scope
CConstRef< CSeqMap >	CSeqVector_CI::m_SeqMap
CTSE_Handle	CSeqVector_CI::m_TSE
vector< CTSE_Handle >	CSeqVector_CI::m_UsedTSEs
ENa_strand	CSeqVector_CI::m_Strand
TCoding	CSeqVector_CI::m_Coding
ECaseConversion	CSeqVector_CI::m_CaseConversion
CSeqMap_CI	CSeqVector_CI::m_Seg
TCache_I	CSeqVector_CI::m_Cache
TSeqPos	CSeqVector_CI::m_CachePos
TCacheData	CSeqVector_CI::m_CacheData
TCache_I	CSeqVector_CI::m_CacheEnd
TSeqPos	CSeqVector_CI::m_BackupPos
TCacheData	CSeqVector_CI::m_BackupData
TCache_I	CSeqVector_CI::m_BackupEnd
CRef< INcbi2naRandomizer >	CSeqVector_CI::m_Randomizer
TSeqPos	CSeqVector_CI::m_ScannedStart
TSeqPos	CSeqVector_CI::m_ScannedEnd
TDescTypeMask	CSeqdesc_CI::m_Choice
CSeq_descr_CI	CSeqdesc_CI::m_Entry
TDescList_CI	CSeqdesc_CI::m_Desc_CI
CBioseq_Handle	CSeqdesc_CI::m_Ref
bool	CSeqdesc_CI::m_HaveTitle
size_t	CSeqdesc_CI::m_Depth

Friends
class	SAnnotSelector::CAnnot_Collector
class	CMappedGraph::CGraph_CI
class	CMappedGraph::CAnnot_CI
class	CMappedGraph::CAnnot_Collector
class	CMappedFeat::CFeat_CI
class	CMappedFeat::CAnnot_CI
class	CMappedFeat::CAnnot_Collector
class	CSeq_descr_CI::CSeqdesc_CI
class	CSeq_entry_CI::CBioseq_set_Handle
class	CSeq_entry_I::CBioseq_set_Handle
class	CSeqMap_CI_SegmentInfo::CSeqMap_CI
class	CSeqMap_CI_SegmentInfo::CSeqMap
class	SSeqMapSelector::CSeqMap
class	SSeqMapSelector::CSeqMap_CI
class	CSeqMap_CI::CSeqMap
class	CSeqMap_CI::CSeqMap_I
class	CSeqVector_CI::CSeqVector

Detailed Description

Typedef Documentation

difference_type

typedef TSignedSeqPos CSeqVectorTypes::difference_type

Definition at line 61 of file seq_vector_ci.hpp.

ERecursionMode

typedef EFlags CSeq_entry_CI::ERecursionMode

backward compatibility synonym

Deprecated:

Use EFlags instead.

Definition at line 87 of file seq_entry_ci.hpp.

iterator_category

typedef std::random_access_iterator_tag CSeqVectorTypes::iterator_category

Definition at line 62 of file seq_vector_ci.hpp.

pointer

typedef const TResidue* CSeqVectorTypes::pointer

Definition at line 63 of file seq_vector_ci.hpp.

reference

typedef const TResidue& CSeqVectorTypes::reference

Definition at line 64 of file seq_vector_ci.hpp.

size_type

typedef TSeqPos CSeqVectorTypes::size_type

Definition at line 60 of file seq_vector_ci.hpp.

TAdaptiveDepthFlags

typedef Uint1 SAnnotSelector::TAdaptiveDepthFlags

Definition at line 349 of file annot_selector.hpp.

TAdaptiveTriggers

typedef vector<SAnnotTypeSelector> SAnnotSelector::TAdaptiveTriggers

Definition at line 333 of file annot_selector.hpp.

TAnnot_CI

typedef TAnnots::const_iterator CSeq_annot_CI::TAnnot_CI

private

Definition at line 127 of file seq_annot_ci.hpp.

TAnnots

typedef vector< CRef<CSeq_annot_Info> > CSeq_annot_CI::TAnnots

private

Definition at line 126 of file seq_annot_ci.hpp.

TAnnotsNames

typedef vector<CAnnotName> SAnnotSelector::TAnnotsNames

Object manager recognizes several fields of Seq-annot as annot name.

The fields are: 1. Seq-annot.id.other.accession with optional version. 2. Seq-annot.desc.name This annot name applies to all contained annotations, and it's possible to filter annotations by their name. By default, or after ResetAnnotsNames() is called, no filter is set. You can set add annot names to the filter, so only annotations with added names are visilble. Otherwise, or you can exclude annot names, so that matching annot names are excluded from search. Relevant methods are: ResetAnnotsNames() ResetUnnamedAnnots() ResetNamedAnnots() AddUnnamedAnnots() AddNamedAnnots() ExcludeUnnamedAnnots() ExcludeNamedAnnots() SetAllNamedAnnots()

Definition at line 609 of file annot_selector.hpp.

TAnnotTypesBitset

typedef bitset<CSeqFeatData::eSubtype_max+3> SAnnotSelector::TAnnotTypesBitset

protected

Definition at line 841 of file annot_selector.hpp.

TBitFilter

typedef Uint8 SAnnotSelector::TBitFilter

Set bit filter for annotations that support it (SNP) If filter is set then collect only annotations that have masked (filter_mask) bits equal to the filter_bits.

Definition at line 790 of file annot_selector.hpp.

TCache_I

typedef char* CSeqVector_CI::TCache_I

private

Definition at line 274 of file seq_vector_ci.hpp.

TCacheData

typedef AutoArray<char> CSeqVector_CI::TCacheData

private

Definition at line 273 of file seq_vector_ci.hpp.

TCoding

typedef CSeq_data::E_Choice CSeqVectorTypes::TCoding

Definition at line 58 of file seq_vector_ci.hpp.

TDescChoices

typedef vector<CSeqdesc::E_Choice> CSeqdesc_CI::TDescChoices

Definition at line 67 of file seqdesc_ci.hpp.

TDescList

typedef list< CRef<CSeqdesc> > CSeqdesc_CI::TDescList

private

Definition at line 126 of file seqdesc_ci.hpp.

TDescList_CI

typedef TDescList::const_iterator CSeqdesc_CI::TDescList_CI

private

Definition at line 127 of file seqdesc_ci.hpp.

TDescTypeMask

typedef unsigned CSeqdesc_CI::TDescTypeMask

private

Definition at line 124 of file seqdesc_ci.hpp.

TEntryStack [1/2]

typedef vector<CSeq_entry_CI> CBioseq_CI::TEntryStack

private

Definition at line 136 of file bioseq_ci.hpp.

TEntryStack [2/2]

typedef stack<CSeq_entry_CI> CSeq_annot_CI::TEntryStack

private

Definition at line 128 of file seq_annot_ci.hpp.

TFeatureId

typedef CObject_id CFeat_CI::TFeatureId

Search features with specified id.

Definition at line 142 of file feat_ci.hpp.

TFeatureIdInt

typedef int CFeat_CI::TFeatureIdInt

Definition at line 143 of file feat_ci.hpp.

TFeatureIdStr

typedef string CFeat_CI::TFeatureIdStr

Definition at line 144 of file feat_ci.hpp.

TFlags [1/3]

typedef int CSeq_entry_CI::TFlags

bitwise OR of "EFlags"

Definition at line 82 of file seq_entry_ci.hpp.

TFlags [2/3]

typedef CSeqMap::TFlags SSeqMapSelector::TFlags

Definition at line 114 of file seq_map_ci.hpp.

TFlags [3/3]

typedef SSeqMapSelector::TFlags CSeqMap_CI::TFlags

Definition at line 254 of file seq_map_ci.hpp.

TGraphRanges

typedef CGraphRanges::TGraphRanges CMappedGraph::TGraphRanges

Definition at line 197 of file graph_ci.hpp.

TIterator

typedef TSeqAnnotSet::const_iterator CAnnot_CI::TIterator

private

Definition at line 138 of file annot_ci.hpp.

TMaxSearchSegments

typedef unsigned SAnnotSelector::TMaxSearchSegments

Definition at line 462 of file annot_selector.hpp.

TMaxSearchTime

typedef float SAnnotSelector::TMaxSearchTime

Definition at line 492 of file annot_selector.hpp.

TMaxSize

typedef size_t SAnnotSelector::TMaxSize

Definition at line 448 of file annot_selector.hpp.

TNamedAnnotAccessions

typedef map<string, int> SAnnotSelector::TNamedAnnotAccessions

Definition at line 610 of file annot_selector.hpp.

TRange [1/2]

typedef CGraphRanges::TRange CMappedGraph::TRange

Definition at line 196 of file graph_ci.hpp.

TRange [2/2]

typedef CRange<TSeqPos> SSeqMapSelector::TRange

Definition at line 134 of file seq_map_ci.hpp.

TResidue

typedef unsigned char CSeqVectorTypes::TResidue

Definition at line 57 of file seq_vector_ci.hpp.

TSegmentInfo

typedef CSeqMap_CI_SegmentInfo CSeqMap_CI::TSegmentInfo

private

Definition at line 337 of file seq_map_ci.hpp.

TSeq_feat_Handles

typedef vector<CSeq_feat_Handle> CFeat_CI::TSeq_feat_Handles

private

Definition at line 199 of file feat_ci.hpp.

TSeqAnnotSet

typedef set<CSeq_annot_Handle> CAnnot_CI::TSeqAnnotSet

private

Definition at line 137 of file annot_ci.hpp.

TSNPScaleLimit

typedef CSeq_id::ESNPScaleLimit SAnnotSelector::TSNPScaleLimit

Definition at line 828 of file annot_selector.hpp.

TStack

typedef vector<TSegmentInfo> CSeqMap_CI::TStack

private

Definition at line 384 of file seq_map_ci.hpp.

TTSE_Limits

typedef vector<CTSE_Handle> SAnnotSelector::TTSE_Limits

protected

Definition at line 842 of file annot_selector.hpp.

value_type

typedef TResidue CSeqVectorTypes::value_type

Definition at line 59 of file seq_vector_ci.hpp.

Enumeration Type Documentation

EAdaptiveDepthFlags

enum SAnnotSelector::EAdaptiveDepthFlags

Enumerator
kAdaptive_None
fAdaptive_Default
kAdaptive_Default
fAdaptive_ByTriggers
fAdaptive_BySubtypes
fAdaptive_ByPolicy
fAdaptive_BySeqClass
fAdaptive_ByNamedAcc
kAdaptive_All
kAdaptive_DefaultBits

Definition at line 334 of file annot_selector.hpp.

EBioseqLevelFlag

enum CBioseq_CI::EBioseqLevelFlag

Class of bioseqs to iterate.

Enumerator
eLevel_All	Any bioseq.
eLevel_Mains	Main bioseq only.
eLevel_Parts	Parts only.
eLevel_IgnoreClass	Search for bioseqs in any bioseq-set regardless of types and classes.

Definition at line 72 of file bioseq_ci.hpp.

ECaseConversion

enum CSeqVectorTypes::ECaseConversion

Enumerator
eCaseConversion_none
eCaseConversion_upper
eCaseConversion_lower

Definition at line 66 of file seq_vector_ci.hpp.

EFlags [1/2]

enum CSeq_annot_CI::EFlags

Enumerator
eSearch_entry
eSearch_recursive

Definition at line 75 of file seq_annot_ci.hpp.

EFlags [2/2]

enum CSeq_entry_CI::EFlags

Flags that affect iteration.

Flags that are irrelevant are ignored. For example, passing fIncludeGivenEntry into the constructor that takes a CBioseq_set_Handle is ignored because there is no "given entry" because only a CBioseq_set_Handle has been given.

Enumerator
fRecursive	Iterate recursively.
fIncludeGivenEntry	Include the top (given) entry.
eNonRecursive	Deprecated. Deprecated: No need to use.
eRecursive	Deprecated. Deprecated: Use fRecursive instead.

Definition at line 74 of file seq_entry_ci.hpp.

ELimitObject

enum SAnnotSelector::ELimitObject

protected

Enumerator
eLimit_None
eLimit_TSE_Info
eLimit_Seq_entry_Info
eLimit_Seq_annot_Info

Definition at line 851 of file annot_selector.hpp.

EMaxSearchSegmentsAction

enum SAnnotSelector::EMaxSearchSegmentsAction

Enumerator
eMaxSearchSegmentsThrow
eMaxSearchSegmentsLog
eMaxSearchSegmentsSilent

Definition at line 477 of file annot_selector.hpp.

EOverlapType

enum SAnnotSelector::EOverlapType

Flag to indicate location overlapping method.

Enumerator
eOverlap_Intervals	default - overlapping of individual intervals
eOverlap_TotalRange	overlapping of total ranges only

Definition at line 92 of file annot_selector.hpp.

EResolveMethod

enum SAnnotSelector::EResolveMethod

Flag to indicate references resolution method.

Enumerator
eResolve_None	Do not search annotations on segments.
eResolve_TSE	default - search only on segments in the same TSE
eResolve_All	Search annotations for all referenced sequences.

Definition at line 97 of file annot_selector.hpp.

ESortOrder

enum SAnnotSelector::ESortOrder

Flag to indicate sorting method.

Enumerator
eSortOrder_None	do not sort annotations for faster retrieval
eSortOrder_Normal	default - increasing start, decreasing length
eSortOrder_Reverse	decresing end, decreasing length

Definition at line 103 of file annot_selector.hpp.

EUnresolvedFlag

enum SAnnotSelector::EUnresolvedFlag

Flag to indicate handling of unresolved seq-ids.

Enumerator
eIgnoreUnresolved	Ignore unresolved ids (default)
eSearchUnresolved	Search annotations for unresolvable IDs.
eFailUnresolved	Throw exception for unresolved ids.

Definition at line 109 of file annot_selector.hpp.

Function Documentation

AddNamedAnnots() [1/2]

SAnnotSelector & SAnnotSelector::AddNamedAnnots

(

const CAnnotName &

name

)

Add named annot to set of annots names to look for.

Definition at line 476 of file annot_selector.cpp.

References SAnnotSelector::HasWildcardInAnnotsNames(), SAnnotSelector::m_ExcludeAnnotsNames, SAnnotSelector::m_HasWildcardInAnnotsNames, and SAnnotSelector::m_IncludeAnnotsNames.

Referenced by SAnnotSelector::AddNamedAnnots(), SAnnotSelector::AddUnnamedAnnots(), CGraphUtils::CalcGraphLevels(), CGBObjectLoader::Execute(), NSearchFeatPanel::GatherFeatures(), CSeqUtils::GetAnnotSelector(), NSnpBins::GetBinSelector(), CDataLoader::GetCDDAnnots(), NSnpAnnot::GetFeat_CI(), NSnpAnnot::GetGraph_CI(), CNAUtils::GetNATrackInfo(), NSnp::IsSnpKnown(), CDemoApp::Run(), CTestBMApp::Run(), s_GetAnnotSelector(), s_GetRnaMappingLocs(), SAnnotSelector::SetDataSource(), CSnpJob::x_FetchFtable(), CBinsJob::x_FetchGraphs(), CSnpJob::x_FetchGraphs(), CMacroBioData::x_GetAnnotSelector(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CLDBlockJob::x_Load(), CSGAnnotJob::x_LoadCoverageGraph(), CFeatureGenerator::x_SetAnnotName(), and CFeatureGraph::x_StartJob().

AddNamedAnnots() [2/2]

SAnnotSelector & SAnnotSelector::AddNamedAnnots

(

const char *

name

)

Definition at line 487 of file annot_selector.cpp.

References SAnnotSelector::AddNamedAnnots().

AddUnnamedAnnots()

SAnnotSelector & SAnnotSelector::AddUnnamedAnnots

(

void

)

Add unnamed annots to set of annots names to look for.

Definition at line 493 of file annot_selector.cpp.

References SAnnotSelector::AddNamedAnnots().

Referenced by NSearchFeatPanel::GatherFeatures(), CSGAlignmentJob::GetAlignType(), CSeqUtils::GetAnnotSelector(), NSnpAnnot::GetFeat_CI(), CDemoApp::Run(), SAnnotSelector::SetDataSource(), CSnpJob::x_FetchFtable(), CSnpJob::x_FetchGraphs(), CSGAlnQualityScore::x_RetrieveQualityMap(), and CFeatureGenerator::x_SetAnnotName().

AddUsedTSE()

void SSeqMapSelector::AddUsedTSE

(

const CTSE_Handle &

tse

)

const

Definition at line 94 of file seq_map_ci.cpp.

References SSeqMapSelector::m_UsedTSEs.

Referenced by CSeqMap::CanResolveRange(), and CSeqMap_CI::x_Push().

AddZoomLevel()

void AddZoomLevel	(	string &	acc,
		int	zoom_level
	)

Definition at line 983 of file annot_selector.cpp.

References CSeq_annot::AddZoomLevel(), CException::GetMsg(), and NCBI_THROW_FMT.

begin() [1/4]

const CAlign_CI& CAlign_CI::begin ( void  ) const

inline

Definition at line 179 of file align_ci.hpp.

begin() [2/4]

const CFeat_CI& CFeat_CI::begin ( void  ) const

inline

Definition at line 171 of file feat_ci.hpp.

begin() [3/4]

const CGraph_CI& CGraph_CI::begin ( void  ) const

inline

Definition at line 337 of file graph_ci.hpp.

begin() [4/4]

const CSeq_table_CI& CSeq_table_CI::begin ( void  ) const

inline

Definition at line 151 of file seq_table_ci.hpp.

CAlign_CI() [1/16]

CAlign_CI::CAlign_CI ( const CAlign_CI &  it, EAtEnd    )

inlineprivate

Definition at line 208 of file align_ci.hpp.

CAlign_CI() [2/16]

CAlign_CI::CAlign_CI ( const CAlign_CI &  iter )

inline

Definition at line 224 of file align_ci.hpp.

CAlign_CI() [3/16]

CAlign_CI::CAlign_CI ( const CBioseq_Handle &  bioseq )

explicit

Create an iterator that enumerates CSeq_align objects related to the given bioseq.

Definition at line 47 of file align_ci.cpp.

CAlign_CI() [4/16]

CAlign_CI::CAlign_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_align objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 78 of file align_ci.cpp.

CAlign_CI() [5/16]

CAlign_CI::CAlign_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		ENa_strand	strand,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_align objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 90 of file align_ci.cpp.

CAlign_CI() [6/16]

CAlign_CI::CAlign_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		ENa_strand	strand = eNa_strand_unknown
	)

Create an iterator that enumerates CSeq_align objects related to the given bioseq.

Definition at line 56 of file align_ci.cpp.

CAlign_CI() [7/16]

CAlign_CI::CAlign_CI	(	const CBioseq_Handle &	bioseq,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_align objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 67 of file align_ci.cpp.

CAlign_CI() [8/16]

CAlign_CI::CAlign_CI ( const CSeq_annot_Handle &  annot )

explicit

Create an iterator that enumerates CSeq_align objects from the annotation regardless of their location.

Definition at line 118 of file align_ci.cpp.

CAlign_CI() [9/16]

CAlign_CI::CAlign_CI	(	const CSeq_annot_Handle &	annot,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_align objects from the annotation regardless of their location based on selection.

See also

SAnnotSelector

Definition at line 124 of file align_ci.cpp.

CAlign_CI() [10/16]

CAlign_CI::CAlign_CI ( const CSeq_entry_Handle &  entry )

explicit

Create an iterator that enumerates CSeq_align objects from the seq-entry regardless of their location.

Definition at line 151 of file align_ci.cpp.

CAlign_CI() [11/16]

CAlign_CI::CAlign_CI	(	const CSeq_entry_Handle &	entry,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_align objects from the seq-entry regardless of their location based on selection.

See also

SAnnotSelector

Definition at line 157 of file align_ci.cpp.

CAlign_CI() [12/16]

CAlign_CI::CAlign_CI	(	const CSeq_loc &	loc,
		const CSeq_annot_Handle &	annot
	)

Iterate all alignments from the seq-annot that annotate the location.

Definition at line 131 of file align_ci.cpp.

CAlign_CI() [13/16]

CAlign_CI::CAlign_CI	(	const CSeq_loc &	loc,
		const CSeq_annot_Handle &	annot,
		const SAnnotSelector &	sel
	)

Iterate all alignments from the seq-annot that annotate the location.

See also

SAnnotSelector

Definition at line 140 of file align_ci.cpp.

CAlign_CI() [14/16]

CAlign_CI::CAlign_CI	(	CScope &	scope,
		const CSeq_loc &	loc
	)

Create an iterator that enumerates CSeq_align objects related to the given seq-loc.

Definition at line 103 of file align_ci.cpp.

CAlign_CI() [15/16]

CAlign_CI::CAlign_CI	(	CScope &	scope,
		const CSeq_loc &	loc,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_align objects related to the given seq-loc.

See also

SAnnotSelector

Definition at line 110 of file align_ci.cpp.

CAlign_CI() [16/16]

CAlign_CI::CAlign_CI ( void  )

inline

Create an empty iterator.

Definition at line 218 of file align_ci.hpp.

CanGetRange()

bool CSeqVector_CI::CanGetRange	(	TSeqPos	start,
		TSeqPos	stop
	)

Check if the sequence can be obtained for the interval [start, stop)

Definition at line 206 of file seq_vector_ci.cpp.

References CSeqMap::CanResolveRange(), CSeqMap::fDefaultFlags, CHeapScope::GetScopeOrNull(), kMax_UInt, CSeqVector_CI::m_ScannedEnd, CSeqVector_CI::m_ScannedStart, CSeqVector_CI::m_Scope, CSeqVector_CI::m_SeqMap, CSeqVector_CI::m_Strand, CSeqVector_CI::m_TSE, CSeqVector_CI::m_UsedTSEs, max(), min(), SSeqMapSelector::SetLinkUsedTSE(), SSeqMapSelector::SetRange(), and SSeqMapSelector::SetStrand().

Referenced by CSeqVector::CanGetRange(), CSeqVector_CI::GetSeqData(), CSeqVector_CI::x_CheckBackward(), and CSeqVector_CI::x_CheckForward().

CAnnot_CI() [1/8]

CAnnot_CI::CAnnot_CI

(

const CAnnot_CI &

iter

)

Copy constructor.

Definition at line 49 of file annot_ci.cpp.

CAnnot_CI() [2/8]

CAnnot_CI::CAnnot_CI ( const CAnnotTypes_CI &  iter )

explicit

Create an iterator that enumerates all CSeq_annot objects collected by another iterator CFeat_CI, CGraph_CI, or CAlign_CI.

Definition at line 123 of file annot_ci.cpp.

References CAnnot_CI::x_Initialize().

CAnnot_CI() [3/8]

CAnnot_CI::CAnnot_CI ( const CBioseq_Handle &  bioseq )

explicit

Create an iterator that enumerates CSeq_annot objects related to the given bioseq.

Definition at line 81 of file annot_ci.cpp.

References CSeq_annot_Base::C_Data::e_not_set, eNa_strand_unknown, SAnnotSelector::eSortOrder_None, and CAnnot_CI::x_Initialize().

CAnnot_CI() [4/8]

CAnnot_CI::CAnnot_CI	(	const CBioseq_Handle &	bioseq,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_annot objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 95 of file annot_ci.cpp.

References CSeq_annot_Base::C_Data::e_not_set, eNa_strand_unknown, SAnnotSelector::eSortOrder_None, and CAnnot_CI::x_Initialize().

CAnnot_CI() [5/8]

CAnnot_CI::CAnnot_CI	(	const CSeq_entry_Handle &	entry,
		const SAnnotSelector &	sel
	)

Iterate all Seq-annot objects from the seq-entry regardless of their location, using SAnnotSelector for filtering.

See also

SAnnotSelector

Definition at line 110 of file annot_ci.cpp.

References CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::eSortOrder_None, and CAnnot_CI::x_Initialize().

CAnnot_CI() [6/8]

CAnnot_CI::CAnnot_CI	(	CScope &	scope,
		const CSeq_loc &	loc
	)

Create an iterator that enumerates CSeq_annot objects related to the given seq-loc based on selection.

Definition at line 56 of file annot_ci.cpp.

References CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::eSortOrder_None, and CAnnot_CI::x_Initialize().

CAnnot_CI() [7/8]

CAnnot_CI::CAnnot_CI	(	CScope &	scope,
		const CSeq_loc &	loc,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_annot objects related to the given seq-loc based on selection.

See also

SAnnotSelector

Definition at line 68 of file annot_ci.cpp.

References CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::eSortOrder_None, and CAnnot_CI::x_Initialize().

CAnnot_CI() [8/8]

CAnnot_CI::CAnnot_CI

(

void

)

Create an empty iterator.

Definition at line 44 of file annot_ci.cpp.

CanResolve()

bool SSeqMapSelector::CanResolve ( void  ) const

inline

Definition at line 201 of file seq_map_ci.hpp.

References SSeqMapSelector::GetResolveCount().

Referenced by CSeqMap_CI::Next(), SSeqMapSelector::PopResolve(), SSeqMapSelector::PushResolve(), CSeqMap_CI::x_CanResolve(), CSeqMap_CI::x_Next(), and CSeqMap_CI::x_Push().

CBioseq_CI() [1/5]

CBioseq_CI::CBioseq_CI

(

const CBioseq_CI &

bioseq_ci

)

Definition at line 223 of file bioseq_ci.cpp.

CBioseq_CI() [2/5]

CBioseq_CI::CBioseq_CI ( const CBioseq_set_Handle &  bioseq_set, CSeq_inst::EMol  filter = CSeq_inst::eMol_not_set, EBioseqLevelFlag  level = eLevel_All  )

explicit

Definition at line 246 of file bioseq_ci.cpp.

References CBioseq_set_Handle::GetParentEntry(), and CBioseq_CI::x_Initialize().

CBioseq_CI() [3/5]

CBioseq_CI::CBioseq_CI ( const CSeq_entry_Handle &  entry, CSeq_inst::EMol  filter = CSeq_inst::eMol_not_set, EBioseqLevelFlag  level = eLevel_All  )

explicit

Create an iterator that enumerates bioseqs from the entry taken from the scope.

Use optional filter to iterate over selected bioseq types only. Filter value eMol_na may be used to include both dna and rna bioseqs.

Definition at line 234 of file bioseq_ci.cpp.

References CBioseq_CI::x_Initialize().

CBioseq_CI() [4/5]

CBioseq_CI::CBioseq_CI	(	CScope &	scope,
		const CSeq_entry &	entry,
		CSeq_inst::EMol	filter = CSeq_inst::eMol_not_set,
		EBioseqLevelFlag	level = eLevel_All
	)

Create an iterator that enumerates bioseqs from the entry taken from the given scope.

Use optional filter to iterate over selected bioseq types only. Filter value eMol_na may be used to include both dna and rna bioseqs.

Definition at line 258 of file bioseq_ci.cpp.

References CScope::GetSeq_entryHandle(), and CBioseq_CI::x_Initialize().

CBioseq_CI() [5/5]

CBioseq_CI::CBioseq_CI

(

void

)

Definition at line 215 of file bioseq_ci.cpp.

CFeat_CI() [1/19]

CFeat_CI::CFeat_CI ( const CBioseq_Handle &  bioseq )

explicit

Search features on the whole bioseq.

Definition at line 84 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [2/19]

CFeat_CI::CFeat_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		const SAnnotSelector &	sel
	)

Search features on part of the bioseq.

Definition at line 118 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [3/19]

CFeat_CI::CFeat_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		ENa_strand	strand,
		const SAnnotSelector &	sel
	)

Search features on part of the bioseq.

Definition at line 131 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [4/19]

CFeat_CI::CFeat_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		ENa_strand	strand = eNa_strand_unknown
	)

Search features on part of the bioseq.

Definition at line 106 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [5/19]

CFeat_CI::CFeat_CI	(	const CBioseq_Handle &	bioseq,
		const SAnnotSelector &	sel
	)

Search features on the whole bioseq.

See also

SAnnotSelector

Definition at line 94 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [6/19]

CFeat_CI::CFeat_CI ( const CFeat_CI &  it, EAtEnd    )

inlineprivate

Definition at line 191 of file feat_ci.hpp.

CFeat_CI() [7/19]

CFeat_CI::CFeat_CI

(

const CFeat_CI &

iter

)

Definition at line 62 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [8/19]

CFeat_CI::CFeat_CI ( const CSeq_annot_Handle &  annot )

explicit

Iterate all features from the seq-annot regardless of their location.

Definition at line 167 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [9/19]

CFeat_CI::CFeat_CI	(	const CSeq_annot_Handle &	annot,
		const SAnnotSelector &	sel
	)

Iterate all features from the seq-annot regardless of their location.

See also

SAnnotSelector

Definition at line 175 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [10/19]

CFeat_CI::CFeat_CI ( const CSeq_entry_Handle &  entry )

explicit

Iterate all features from the seq-entry regardless of their location.

Definition at line 207 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [11/19]

CFeat_CI::CFeat_CI	(	const CSeq_entry_Handle &	entry,
		const SAnnotSelector &	sel
	)

Iterate all features from the seq-entry regardless of their location.

See also

SAnnotSelector

Definition at line 215 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [12/19]

CFeat_CI::CFeat_CI	(	const CSeq_loc &	loc,
		const CSeq_annot_Handle &	annot
	)

Iterate all features from the seq-annot that annotate the location.

Definition at line 185 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [13/19]

CFeat_CI::CFeat_CI	(	const CSeq_loc &	loc,
		const CSeq_annot_Handle &	annot,
		const SAnnotSelector &	sel
	)

Iterate all features from the seq-annot that annotate the location.

See also

SAnnotSelector

Definition at line 195 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [14/19]

CFeat_CI::CFeat_CI	(	const CTSE_Handle &	tse,
		const SAnnotSelector &	sel,
		const TFeatureId &	id
	)

Definition at line 225 of file feat_ci.cpp.

References CFeat_CI::x_AddFeaturesWithId().

CFeat_CI() [15/19]

CFeat_CI::CFeat_CI	(	const CTSE_Handle &	tse,
		const SAnnotSelector &	sel,
		const TFeatureIdInt &	int_id
	)

Definition at line 234 of file feat_ci.cpp.

References CObject_id_Base::SetId(), and CFeat_CI::x_AddFeaturesWithId().

CFeat_CI() [16/19]

CFeat_CI::CFeat_CI	(	const CTSE_Handle &	tse,
		const SAnnotSelector &	sel,
		const TFeatureIdStr &	str_id
	)

Definition at line 245 of file feat_ci.cpp.

References CObject_id_Base::SetStr(), and CFeat_CI::x_AddFeaturesWithId().

CFeat_CI() [17/19]

CFeat_CI::CFeat_CI	(	CScope &	scope,
		const CSeq_loc &	loc
	)

Search features related to the location.

Definition at line 145 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [18/19]

CFeat_CI::CFeat_CI	(	CScope &	scope,
		const CSeq_loc &	loc,
		const SAnnotSelector &	sel
	)

Search features related to the location.

See also

SAnnotSelector

Definition at line 155 of file feat_ci.cpp.

References CFeat_CI::Update().

CFeat_CI() [19/19]

CFeat_CI::CFeat_CI

(

void

)

Definition at line 57 of file feat_ci.cpp.

Referenced by CFeat_CI::end().

CGraph_CI() [1/16]

CGraph_CI::CGraph_CI ( const CBioseq_Handle &  bioseq )

explicit

Create an iterator that enumerates CSeq_graph objects related to the given bioseq.

Definition at line 235 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [2/16]

CGraph_CI::CGraph_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_graph objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 269 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [3/16]

CGraph_CI::CGraph_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		ENa_strand	strand,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_graph objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 282 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [4/16]

CGraph_CI::CGraph_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		ENa_strand	strand = eNa_strand_unknown
	)

Create an iterator that enumerates CSeq_graph objects related to the given bioseq.

Definition at line 245 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [5/16]

CGraph_CI::CGraph_CI	(	const CBioseq_Handle &	bioseq,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_graph objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 257 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [6/16]

CGraph_CI::CGraph_CI ( const CGraph_CI &  it, EAtEnd    )

inlineprivate

Definition at line 358 of file graph_ci.hpp.

CGraph_CI() [7/16]

CGraph_CI::CGraph_CI ( const CGraph_CI &  iter )

inline

Definition at line 374 of file graph_ci.hpp.

References CGraph_CI::x_Update().

CGraph_CI() [8/16]

CGraph_CI::CGraph_CI ( const CSeq_annot_Handle &  annot )

explicit

Iterate all graphs from the seq-annot regardless of their location.

Definition at line 296 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [9/16]

CGraph_CI::CGraph_CI	(	const CSeq_annot_Handle &	annot,
		const SAnnotSelector &	sel
	)

Iterate all graphs from the seq-annot regardless of their location.

See also

SAnnotSelector

Definition at line 303 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [10/16]

CGraph_CI::CGraph_CI ( const CSeq_entry_Handle &  entry )

explicit

Iterate all graphs from the seq-entry regardless of their location.

Definition at line 333 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [11/16]

CGraph_CI::CGraph_CI	(	const CSeq_entry_Handle &	entry,
		const SAnnotSelector &	sel
	)

Iterate all graphs from the seq-entry regardless of their location.

See also

SAnnotSelector

Definition at line 340 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [12/16]

CGraph_CI::CGraph_CI	(	const CSeq_loc &	loc,
		const CSeq_annot_Handle &	annot
	)

Iterate all graphs from the seq-annot that annotate the location.

Definition at line 311 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [13/16]

CGraph_CI::CGraph_CI	(	const CSeq_loc &	loc,
		const CSeq_annot_Handle &	annot,
		const SAnnotSelector &	sel
	)

Iterate all graphs from the seq-annot that annotate the location.

See also

SAnnotSelector

Definition at line 321 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [14/16]

CGraph_CI::CGraph_CI	(	CScope &	scope,
		const CSeq_loc &	loc
	)

Create an iterator that enumerates CSeq_graph objects related to the given seq-loc.

Definition at line 220 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [15/16]

CGraph_CI::CGraph_CI	(	CScope &	scope,
		const CSeq_loc &	loc,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_graph objects related to the given seq-loc.

See also

SAnnotSelector

Definition at line 227 of file graph_ci.cpp.

References CGraph_CI::x_Update().

CGraph_CI() [16/16]

CGraph_CI::CGraph_CI ( void  )

inline

Create an empty iterator.

Definition at line 368 of file graph_ci.hpp.

Referenced by CGraph_CI::end().

CheckAnnotType()

bool SAnnotSelector::CheckAnnotType ( TAnnotType  type ) const

inline

Check annot type (ignore subtypes).

Definition at line 166 of file annot_selector.hpp.

References SAnnotTypeSelector::GetAnnotType(), and type.

Referenced by CAnnotTypes_CI::CAnnotTypes_CI().

CheckLimitObjectType()

void SAnnotSelector::CheckLimitObjectType ( void  ) const

protected

Definition at line 932 of file annot_selector.cpp.

References SAnnotSelector::eLimit_None, SAnnotSelector::m_LimitObject, and SAnnotSelector::m_LimitObjectType.

Referenced by CAnnot_Collector::x_Initialize0().

CMappedFeat() [1/3]

CMappedFeat::CMappedFeat

(

const CMappedFeat &

feat

)

Definition at line 54 of file mapped_feat.cpp.

CMappedFeat() [2/3]

CMappedFeat::CMappedFeat

(

const CSeq_feat_Handle &

feat

)

Definition at line 47 of file mapped_feat.cpp.

References CMappedFeat::m_MappingInfoObj, and CMappedFeat::m_MappingInfoPtr.

CMappedFeat() [3/3]

CMappedFeat::CMappedFeat

(

void

)

Definition at line 41 of file mapped_feat.cpp.

References CMappedFeat::m_MappingInfoObj, and CMappedFeat::m_MappingInfoPtr.

CMappedGraph()

CMappedGraph::CMappedGraph ( )

inline

empty CMappedGraph

Definition at line 64 of file graph_ci.hpp.

CombineWithZoomLevel()

string CombineWithZoomLevel	(	const string &	acc,
		int	zoom_level
	)

Combine accession string and zoom level into a string with separator.

If the argument string already contains zoom level verify it's the same as the zoom_level argument. Zoom level value of -1 can be used to add wildcard @*.

Definition at line 972 of file annot_selector.cpp.

References CSeq_annot::CombineWithZoomLevel(), CException::GetMsg(), and NCBI_THROW_FMT.

Referenced by CGraphUtils::CalcGraphLevels(), NSnpAnnot::GetGraph_CI(), CGBDataLoader_Native::GetNamedAnnotAccessions(), CSnpJob::x_FetchGraphs(), CID2SNPProcessor_Impl::x_LoadBlob(), CSGAnnotJob::x_LoadCoverageGraph(), CID2SNPProcessor_Impl::x_ProcessReplyGetBlobId(), and CId2ReaderBase::x_UpdateLoadedSet().

CSeq_annot_CI() [1/6]

CSeq_annot_CI::CSeq_annot_CI ( const CBioseq_Handle &  bioseq )

explicit

Create an iterator that enumerates CSeq_aannot objects related to the given bioseq up to the TSE.

Definition at line 91 of file seq_annot_ci.cpp.

References CSeq_annot_CI::eSearch_entry, CBioseq_Handle::GetParentEntry(), and CSeq_annot_CI::x_Initialize().

CSeq_annot_CI() [2/6]

CSeq_annot_CI::CSeq_annot_CI ( const CBioseq_set_Handle &  bioseq_set, EFlags  flags = eSearch_recursive  )

explicit

Create an iterator that enumerates CSeq_annot objects related to the given seq-set.

Definition at line 98 of file seq_annot_ci.cpp.

References flags, CBioseq_set_Handle::GetParentEntry(), and CSeq_annot_CI::x_Initialize().

CSeq_annot_CI() [3/6]

CSeq_annot_CI::CSeq_annot_CI

(

const CSeq_annot_CI &

iter

)

Definition at line 56 of file seq_annot_ci.cpp.

CSeq_annot_CI() [4/6]

CSeq_annot_CI::CSeq_annot_CI ( const CSeq_entry_Handle &  entry, EFlags  flags = eSearch_recursive  )

explicit

Create an iterator that enumerates CSeq_annot objects related to the given seq-entry.

Definition at line 84 of file seq_annot_ci.cpp.

References flags, and CSeq_annot_CI::x_Initialize().

CSeq_annot_CI() [5/6]

CSeq_annot_CI::CSeq_annot_CI	(	CScope &	scope,
		const CSeq_entry &	entry,
		EFlags	flags = eSearch_recursive
	)

Create an iterator that enumerates CSeq_annot objects related to the given seq-entry from different scope.

Definition at line 76 of file seq_annot_ci.cpp.

References flags, CScope::GetSeq_entryHandle(), and CSeq_annot_CI::x_Initialize().

CSeq_annot_CI() [6/6]

CSeq_annot_CI::CSeq_annot_CI

(

void

)

Create an empty iterator.

Definition at line 45 of file seq_annot_ci.cpp.

CSeq_descr_CI() [1/5]

CSeq_descr_CI::CSeq_descr_CI ( const CBioseq_Handle &  handle, size_t  search_depth = 0  )

explicit

Create an iterator that enumerates CSeq_descr objects from a bioseq with limit number of seq-entries to "search_depth" (0 = unlimited).

Definition at line 52 of file seq_descr_ci.cpp.

References CSeq_descr_CI::x_Settle().

CSeq_descr_CI() [2/5]

CSeq_descr_CI::CSeq_descr_CI ( const CBioseq_set_Handle &  handle, size_t  search_depth = 0  )

explicit

Create an iterator that enumerates CSeq_descr objects from a bioseq with limit number of seq-entries to "search_depth" (0 = unlimited).

Definition at line 62 of file seq_descr_ci.cpp.

References CSeq_descr_CI::x_Settle().

CSeq_descr_CI() [3/5]

CSeq_descr_CI::CSeq_descr_CI

(

const CSeq_descr_CI &

iter

)

Definition at line 89 of file seq_descr_ci.cpp.

References _ASSERT, CBioseq_Base_Info::IsSetDescr(), and CSeq_descr_CI::m_CurrentBase.

CSeq_descr_CI() [4/5]

CSeq_descr_CI::CSeq_descr_CI ( const CSeq_entry_Handle &  entry, size_t  search_depth = 0  )

explicit

Create an iterator that enumerates CSeq_descr objects from a seq-entry, limit number of seq-entries to "search_depth" (0 = unlimited).

Definition at line 72 of file seq_descr_ci.cpp.

References _ASSERT, CSeq_entry_Handle::GetSeq(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSeq(), CBioseq_Base_Info::IsSetDescr(), CSeq_descr_CI::m_CurrentBase, CSeq_descr_CI::m_CurrentSeq, CSeq_descr_CI::m_CurrentSet, CBioseq_Handle::x_GetInfo(), CBioseq_set_Handle::x_GetInfo(), and CSeq_descr_CI::x_Settle().

CSeq_descr_CI() [5/5]

CSeq_descr_CI::CSeq_descr_CI

(

void

)

Create an empty iterator.

Definition at line 46 of file seq_descr_ci.cpp.

CSeq_entry_CI() [1/4]

CSeq_entry_CI::CSeq_entry_CI ( const CBioseq_set_Handle &  set, TFlags  flags = 0, CSeq_entry::E_Choice  type_filter = CSeq_entry::e_not_set  )

explicit

Create an iterator that enumerates Seq-entries inside the given Bioseq-set.

Definition at line 71 of file seq_entry_ci.cpp.

References CSeq_entry_CI::x_Initialize().

CSeq_entry_CI() [2/4]

CSeq_entry_CI::CSeq_entry_CI

(

const CSeq_entry_CI &

iter

)

Definition at line 81 of file seq_entry_ci.cpp.

CSeq_entry_CI() [3/4]

CSeq_entry_CI::CSeq_entry_CI ( const CSeq_entry_Handle &  entry, TFlags  flags = 0, CSeq_entry::E_Choice  type_filter = CSeq_entry::e_not_set  )

explicit

Create an iterator that enumerates Seq-entries inside the given Seq-entry.

Definition at line 52 of file seq_entry_ci.cpp.

CSeq_entry_CI() [4/4]

CSeq_entry_CI::CSeq_entry_CI ( void  )

inline

Create an empty iterator.

Definition at line 223 of file seq_entry_ci.hpp.

Referenced by CSeq_entry_CI::operator=(), and CSeq_entry_CI::x_Next().

CSeq_entry_I() [1/4]

CSeq_entry_I::CSeq_entry_I	(	const CBioseq_set_EditHandle &	set,
		TFlags	flags = 0,
		CSeq_entry::E_Choice	type_filter = CSeq_entry::e_not_set
	)

Create an iterator that enumerates seq-entries related to the given seq-set.

Definition at line 239 of file seq_entry_ci.cpp.

CSeq_entry_I() [2/4]

CSeq_entry_I::CSeq_entry_I	(	const CSeq_entry_EditHandle &	entry,
		TFlags	flags = 0,
		CSeq_entry::E_Choice	type_filter = CSeq_entry::e_not_set
	)

Create an iterator that enumerates seq-entries related to the given seq-entry.

Definition at line 231 of file seq_entry_ci.cpp.

CSeq_entry_I() [3/4]

CSeq_entry_I::CSeq_entry_I

(

const CSeq_entry_I &

iter

)

Definition at line 247 of file seq_entry_ci.cpp.

CSeq_entry_I() [4/4]

CSeq_entry_I::CSeq_entry_I ( void  )

inline

Create an empty iterator.

Definition at line 278 of file seq_entry_ci.hpp.

CSeq_table_CI() [1/14]

CSeq_table_CI::CSeq_table_CI ( const CBioseq_Handle &  bioseq )

explicit

Create an iterator that enumerates CSeq_table objects related to the given bioseq.

Definition at line 57 of file seq_table_ci.cpp.

CSeq_table_CI() [2/14]

CSeq_table_CI::CSeq_table_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_table objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 88 of file seq_table_ci.cpp.

CSeq_table_CI() [3/14]

CSeq_table_CI::CSeq_table_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		ENa_strand	strand,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_table objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 100 of file seq_table_ci.cpp.

CSeq_table_CI() [4/14]

CSeq_table_CI::CSeq_table_CI	(	const CBioseq_Handle &	bioseq,
		const CRange< TSeqPos > &	range,
		ENa_strand	strand = eNa_strand_unknown
	)

Create an iterator that enumerates CSeq_table objects related to the given bioseq.

Definition at line 66 of file seq_table_ci.cpp.

CSeq_table_CI() [5/14]

CSeq_table_CI::CSeq_table_CI	(	const CBioseq_Handle &	bioseq,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_table objects related to the given bioseq.

See also

SAnnotSelector

Definition at line 77 of file seq_table_ci.cpp.

CSeq_table_CI() [6/14]

CSeq_table_CI::CSeq_table_CI ( const CSeq_annot_Handle &  annot )

explicit

Iterate all Seq-tables from the seq-annot regardless of their location.

Definition at line 113 of file seq_table_ci.cpp.

CSeq_table_CI() [7/14]

CSeq_table_CI::CSeq_table_CI	(	const CSeq_annot_Handle &	annot,
		const SAnnotSelector &	sel
	)

Iterate all Seq-tables from the seq-annot regardless of their location.

See also

SAnnotSelector

Definition at line 119 of file seq_table_ci.cpp.

CSeq_table_CI() [8/14]

CSeq_table_CI::CSeq_table_CI ( const CSeq_entry_Handle &  entry )

explicit

Iterate all Seq-tables from the seq-entry regardless of their location.

Definition at line 126 of file seq_table_ci.cpp.

CSeq_table_CI() [9/14]

CSeq_table_CI::CSeq_table_CI	(	const CSeq_entry_Handle &	entry,
		const SAnnotSelector &	sel
	)

Iterate all Seq-tables from the seq-entry regardless of their location.

See also

SAnnotSelector

Definition at line 132 of file seq_table_ci.cpp.

CSeq_table_CI() [10/14]

CSeq_table_CI::CSeq_table_CI ( const CSeq_table_CI &  it, EAtEnd    )

inlineprivate

Definition at line 176 of file seq_table_ci.hpp.

CSeq_table_CI() [11/14]

CSeq_table_CI::CSeq_table_CI ( const CSeq_table_CI &  iter )

inline

Definition at line 192 of file seq_table_ci.hpp.

CSeq_table_CI() [12/14]

CSeq_table_CI::CSeq_table_CI	(	CScope &	scope,
		const CSeq_loc &	loc
	)

Create an iterator that enumerates CSeq_table objects related to the given seq-loc.

Definition at line 44 of file seq_table_ci.cpp.

CSeq_table_CI() [13/14]

CSeq_table_CI::CSeq_table_CI	(	CScope &	scope,
		const CSeq_loc &	loc,
		const SAnnotSelector &	sel
	)

Create an iterator that enumerates CSeq_table objects related to the given seq-loc.

See also

SAnnotSelector

Definition at line 50 of file seq_table_ci.cpp.

CSeq_table_CI() [14/14]

CSeq_table_CI::CSeq_table_CI ( void  )

inline

Create an empty iterator.

Definition at line 186 of file seq_table_ci.hpp.

CSeqdesc_CI() [1/7]

CSeqdesc_CI::CSeqdesc_CI	(	const CBioseq_Handle &	handle,
		const TDescChoices &	choices,
		size_t	search_depth = 0
	)

Create an iterator that enumerates CSeqdesc objects from a bioseq with limit number of seq-entries to "search_depth" (0 = unlimited) for set of types.

CSeqdesc_CI() [2/7]

CSeqdesc_CI::CSeqdesc_CI ( const CBioseq_Handle &  handle, CSeqdesc::E_Choice  choice = CSeqdesc::e_not_set, size_t  search_depth = 0  )

explicit

Create an iterator that enumerates CSeqdesc objects from a bioseq with limit number of seq-entries to "search_depth" (0 = unlimited) for specific type.

Definition at line 121 of file seqdesc_ci.cpp.

References _ASSERT, CSeqdesc_CI::x_CheckRef(), CSeqdesc_CI::x_SetChoice(), CSeqdesc_CI::x_SetEntry(), and CSeqdesc_CI::x_Valid().

CSeqdesc_CI() [3/7]

CSeqdesc_CI::CSeqdesc_CI ( const CSeq_descr_CI &  desc_it, CSeqdesc::E_Choice  choice = CSeqdesc::e_not_set  )

explicit

Definition at line 110 of file seqdesc_ci.cpp.

References _ASSERT, CSeqdesc_CI::x_SetChoice(), CSeqdesc_CI::x_SetEntry(), and CSeqdesc_CI::x_Valid().

CSeqdesc_CI() [4/7]

CSeqdesc_CI::CSeqdesc_CI	(	const CSeq_entry_Handle &	entry,
		const TDescChoices &	choices,
		size_t	search_depth = 0
	)

Create an iterator that enumerates CSeqdesc objects from a seq-entry, limit number of seq-entries to "search_depth" (0 = unlimited) for set of types.

CSeqdesc_CI() [5/7]

CSeqdesc_CI::CSeqdesc_CI ( const CSeq_entry_Handle &  entry, CSeqdesc::E_Choice  choice = CSeqdesc::e_not_set, size_t  search_depth = 0  )

explicit

Create an iterator that enumerates CSeqdesc objects from a seq-entry, limit number of seq-entries to "search_depth" (0 = unlimited) for specific type.

Definition at line 134 of file seqdesc_ci.cpp.

References _ASSERT, CSeqdesc_CI::x_SetChoice(), CSeqdesc_CI::x_SetEntry(), and CSeqdesc_CI::x_Valid().

CSeqdesc_CI() [6/7]

CSeqdesc_CI::CSeqdesc_CI

(

const CSeqdesc_CI &

iter

)

Definition at line 172 of file seqdesc_ci.cpp.

References _ASSERT, and CSeqdesc_CI::x_Valid().

CSeqdesc_CI() [7/7]

CSeqdesc_CI::CSeqdesc_CI

(

void

)

Definition at line 102 of file seqdesc_ci.cpp.

References _ASSERT, and CSeqdesc_CI::x_Valid().

CSeqMap_CI() [1/6]

CSeqMap_CI::CSeqMap_CI	(	const CBioseq_Handle &	bioseq,
		const SSeqMapSelector &	selector,
		const CRange< TSeqPos > &	range
	)

Definition at line 189 of file seq_map_ci.cpp.

References ConstRef(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetTSE_Handle(), compile_time_bits::range(), SSeqMapSelector::SetLinkUsedTSE(), and CSeqMap_CI::x_Select().

CSeqMap_CI() [2/6]

CSeqMap_CI::CSeqMap_CI	(	const CBioseq_Handle &	bioseq,
		const SSeqMapSelector &	selector,
		TSeqPos	pos = 0
	)

Definition at line 175 of file seq_map_ci.cpp.

References ConstRef(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetTSE_Handle(), SSeqMapSelector::SetLinkUsedTSE(), and CSeqMap_CI::x_Select().

CSeqMap_CI() [3/6]

CSeqMap_CI::CSeqMap_CI	(	const CConstRef< CSeqMap > &	seqmap,
		CScope *	scope,
		const SSeqMapSelector &	selector,
		const CRange< TSeqPos > &	range
	)

Definition at line 162 of file seq_map_ci.cpp.

References compile_time_bits::range(), and CSeqMap_CI::x_Select().

CSeqMap_CI() [4/6]

CSeqMap_CI::CSeqMap_CI	(	const CConstRef< CSeqMap > &	seqmap,
		CScope *	scope,
		const SSeqMapSelector &	selector,
		TSeqPos	pos = 0
	)

Definition at line 149 of file seq_map_ci.cpp.

References CSeqMap_CI::x_Select().

CSeqMap_CI() [5/6]

CSeqMap_CI::CSeqMap_CI ( const CSeqMap_CI &  base, const CSeqMap &  seqmap, size_t  index, TSeqPos  pos  )

private

Definition at line 203 of file seq_map_ci.cpp.

References info, kInvalidSeqPos, SSeqMapSelector::m_Length, CSeqMap::CSegment::m_Position, SSeqMapSelector::m_Position, CSeqMap_CI::m_Selector, NCBI_THROW, and CSeqMap_CI::x_GetSegmentInfo().

CSeqMap_CI() [6/6]

CSeqMap_CI::CSeqMap_CI

(

void

)

Definition at line 140 of file seq_map_ci.cpp.

References kInvalidSeqPos, CSeqMap_CI::m_Selector, and SSeqMapSelector::SetPosition().

CSeqMap_CI_SegmentInfo()

CSeqMap_CI_SegmentInfo::CSeqMap_CI_SegmentInfo ( void  )

inline

Definition at line 501 of file seq_map_ci.hpp.

CSeqMap_I() [1/5]

CSeqMap_I::CSeqMap_I	(	const CBioseq_EditHandle &	bioseq,
		const SSeqMapSelector &	selector,
		const CRange< TSeqPos > &	range
	)

Definition at line 766 of file seq_map_ci.cpp.

CSeqMap_I() [2/5]

CSeqMap_I::CSeqMap_I	(	const CBioseq_EditHandle &	bioseq,
		const SSeqMapSelector &	selector,
		TSeqPos	pos = 0
	)

Definition at line 754 of file seq_map_ci.cpp.

CSeqMap_I() [3/5]

CSeqMap_I::CSeqMap_I	(	CRef< CSeqMap > &	seqmap,
		CScope *	scope,
		const SSeqMapSelector &	selector,
		const CRange< TSeqPos > &	range
	)

Definition at line 791 of file seq_map_ci.cpp.

CSeqMap_I() [4/5]

CSeqMap_I::CSeqMap_I	(	CRef< CSeqMap > &	seqmap,
		CScope *	scope,
		const SSeqMapSelector &	selector,
		TSeqPos	pos = 0
	)

Definition at line 778 of file seq_map_ci.cpp.

CSeqMap_I() [5/5]

CSeqMap_I::CSeqMap_I

(

void

)

Definition at line 749 of file seq_map_ci.cpp.

CSeqVector_CI() [1/5]

CSeqVector_CI::CSeqVector_CI	(	const CSeqVector &	seq_vector,
		ENa_strand	strand,
		TSeqPos	pos = 0,
		ECaseConversion	case_cvt = eCaseConversion_none
	)

Definition at line 153 of file seq_vector_ci.cpp.

References CSeqVector_CI::x_SetPos().

CSeqVector_CI() [2/5]

CSeqVector_CI::CSeqVector_CI	(	const CSeqVector &	seq_vector,
		TSeqPos	pos,
		ECaseConversion	case_cvt
	)

Definition at line 130 of file seq_vector_ci.cpp.

References CSeqVector_CI::x_SetPos().

CSeqVector_CI() [3/5]

CSeqVector_CI::CSeqVector_CI ( const CSeqVector &  seq_vector, TSeqPos  pos = 0  )

explicit

Definition at line 108 of file seq_vector_ci.cpp.

References CSeqVector_CI::x_SetPos().

CSeqVector_CI() [4/5]

CSeqVector_CI::CSeqVector_CI

(

const CSeqVector_CI &

sv_it

)

Definition at line 89 of file seq_vector_ci.cpp.

CSeqVector_CI() [5/5]

CSeqVector_CI::CSeqVector_CI

(

void

)

Definition at line 67 of file seq_vector_ci.cpp.

CTempValue()

CSeqVector_CI::CTempValue::CTempValue ( value_type  value )

inline

Definition at line 150 of file seq_vector_ci.hpp.

DECLARE_OPERATOR_BOOL() [1/11]

CAlign_CI::DECLARE_OPERATOR_BOOL

(

IsValid()

)

Check if iterator points to an object.

DECLARE_OPERATOR_BOOL() [2/11]

CFeat_CI::DECLARE_OPERATOR_BOOL

(

IsValid()

)

Check if iterator points to an object.

DECLARE_OPERATOR_BOOL() [3/11]

CGraph_CI::DECLARE_OPERATOR_BOOL

(

IsValid()

)

DECLARE_OPERATOR_BOOL() [4/11]

CSeq_entry_CI::DECLARE_OPERATOR_BOOL

(

IsValid()

)

Check if iterator points to an object.

DECLARE_OPERATOR_BOOL() [5/11]

CSeqMap_CI::DECLARE_OPERATOR_BOOL

(

IsValid()

)

DECLARE_OPERATOR_BOOL() [6/11]

CSeq_table_CI::DECLARE_OPERATOR_BOOL

(

IsValid()

)

DECLARE_OPERATOR_BOOL() [7/11]

CSeqVector_CI::DECLARE_OPERATOR_BOOL

(

IsValid()

)

DECLARE_OPERATOR_BOOL() [8/11]

CSeq_annot_CI::DECLARE_OPERATOR_BOOL

(

m_CurrentAnnot

)

Check if iterator points to an object.

DECLARE_OPERATOR_BOOL() [9/11]

CBioseq_CI::DECLARE_OPERATOR_BOOL

(

m_CurrentBioseq

)

Check if iterator points to an object.

DECLARE_OPERATOR_BOOL() [10/11]

CSeqdesc_CI::DECLARE_OPERATOR_BOOL

(

m_Entry

)

Check if iterator points to an object.

DECLARE_OPERATOR_BOOL() [11/11]

CAnnot_CI::DECLARE_OPERATOR_BOOL

(

x_IsValid()

)

Check if iterator points to an object.

DECLARE_OPERATOR_BOOL_REF()

CSeq_descr_CI::DECLARE_OPERATOR_BOOL_REF

(

m_CurrentBase

)

Check if iterator points to an object.

empty()

bool CAnnot_CI::empty ( void  ) const

inline

Check if iterator is empty.

Definition at line 187 of file annot_ci.hpp.

References set< Key, Compare >::empty(), and CAnnot_CI::m_SeqAnnotSet.

end() [1/4]

CAlign_CI CAlign_CI::end ( void  ) const

inline

Definition at line 183 of file align_ci.hpp.

end() [2/4]

CFeat_CI CFeat_CI::end ( void  ) const

inline

Definition at line 175 of file feat_ci.hpp.

References CAnnotTypes_CI::at_end, and CFeat_CI::CFeat_CI().

end() [3/4]

CGraph_CI CGraph_CI::end ( void  ) const

inline

Definition at line 341 of file graph_ci.hpp.

References CAnnotTypes_CI::at_end, and CGraph_CI::CGraph_CI().

end() [4/4]

CSeq_table_CI CSeq_table_CI::end ( void  ) const

inline

Definition at line 155 of file seq_table_ci.hpp.

ExcludeAnnotType()

SAnnotSelector & SAnnotSelector::ExcludeAnnotType

(

TAnnotType

type

)

Exclude annotation type from the search.

Definition at line 765 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_not_set, SAnnotTypeSelector::GetAnnotType(), CAnnotType_Index::GetAnnotTypeRange(), i, SAnnotSelector::IncludedAnnotType(), SAnnotSelector::m_AnnotTypesBitset, compile_time_bits::range(), and SAnnotSelector::x_InitializeAnnotTypesSet().

Referenced by NSearchFeatPanel::GatherFeatures().

ExcludedAnnotName()

bool SAnnotSelector::ExcludedAnnotName

(

const CAnnotName &

name

)

const

Definition at line 414 of file annot_selector.cpp.

References SAnnotSelector::IncludedAnnotName().

Referenced by CAnnot_Collector::x_SearchAll(), and CAnnot_Collector::x_SearchTSE2().

ExcludedTSE() [1/2]

bool SAnnotSelector::ExcludedTSE

(

const CSeq_entry_Handle &

tse

)

const

Definition at line 713 of file annot_selector.cpp.

References SAnnotSelector::ExcludedTSE(), and CSeq_entry_Handle::GetTSE_Handle().

ExcludedTSE() [2/2]

bool SAnnotSelector::ExcludedTSE

(

const CTSE_Handle &

tse

)

const

Definition at line 706 of file annot_selector.cpp.

References SAnnotSelector::m_ExcludedTSE.

Referenced by SAnnotSelector::ExcludedTSE(), and SAnnotSelector::ExcludeTSE().

ExcludeFeatSubtype()

SAnnotSelector & SAnnotSelector::ExcludeFeatSubtype

(

TFeatSubtype

subtype

)

Exclude feature subtype from the search.

Definition at line 828 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::ForceAnnotType(), SAnnotTypeSelector::GetAnnotType(), CAnnotType_Index::GetSubtypeIndex(), SAnnotSelector::IncludedFeatSubtype(), SAnnotSelector::m_AnnotTypesBitset, and SAnnotSelector::x_InitializeAnnotTypesSet().

Referenced by CFeatTableEdit::GenerateLocusIds(), CFeatTableEdit::GenerateLocusTags(), CDemoApp::Run(), s_SetSelection(), CFeatureGenerator::SImplementation::x_CopyAdditionalFeatures(), CBioseqIndex::x_DefaultSelector(), CFeatTableEdit::xGenerateLocusIdsRegenerate(), and CFeatTableEdit::xGenerateLocusIdsUseExisting().

ExcludeFeatType()

SAnnotSelector & SAnnotSelector::ExcludeFeatType

(

TFeatType

type

)

Exclude feature type from the search.

Definition at line 798 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::ForceAnnotType(), SAnnotTypeSelector::GetAnnotType(), CAnnotType_Index::GetFeatTypeRange(), i, SAnnotSelector::IncludedFeatType(), SAnnotSelector::m_AnnotTypesBitset, compile_time_bits::range(), and SAnnotSelector::x_InitializeAnnotTypesSet().

Referenced by CDemoApp::Run(), s_SetSelection(), and CBioseqIndex::x_DefaultSelector().

ExcludeNamedAnnotAccession()

SAnnotSelector & SAnnotSelector::ExcludeNamedAnnotAccession

(

const string &

acc

)

Definition at line 571 of file annot_selector.cpp.

References SAnnotSelector::m_NamedAnnotAccessions.

Referenced by CBioseqIndex::x_DefaultSelector(), CAnnot_Collector::x_FoundAllNamedAnnotAccessions(), and CScope_Impl::x_UpdateProcessedNAs().

ExcludeNamedAnnots() [1/2]

SAnnotSelector & SAnnotSelector::ExcludeNamedAnnots

(

const CAnnotName &

name

)

Add named annot to set of annots names to exclude.

Definition at line 499 of file annot_selector.cpp.

References SAnnotSelector::HasWildcardInAnnotsNames(), SAnnotSelector::m_ExcludeAnnotsNames, SAnnotSelector::m_HasWildcardInAnnotsNames, and SAnnotSelector::m_IncludeAnnotsNames.

Referenced by CGraphTrackFactory::CreateTracks(), CSeqTableGraphTrackFactory::CreateTracks(), SAnnotSelector::ExcludeNamedAnnots(), SAnnotSelector::ExcludeUnnamedAnnots(), ExtractExtraIds(), CSeqUtils::GetAnnotSelector(), GetBestCdsForMrna(), GetBestMrnaForCds(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeqUtils::GetMrnaForCds(), CAsn2FastaApp::HandleSeqEntry(), CId1FetchApp::LookUpGI(), CFeatCompareJob_Align::Run(), CDemoApp::Run(), CFeatTreeSampleApp::Run(), s_GetRnaMappingLocs(), s_SetSelection(), CBioseqIndex::x_DefaultSelector(), x_GetAnnotSelector(), and CFeatureGraph::x_StartJob().

ExcludeNamedAnnots() [2/2]

SAnnotSelector & SAnnotSelector::ExcludeNamedAnnots

(

const char *

name

)

Definition at line 510 of file annot_selector.cpp.

References SAnnotSelector::ExcludeNamedAnnots().

ExcludeTSE() [1/2]

SAnnotSelector & SAnnotSelector::ExcludeTSE

(

const CSeq_entry_Handle &

tse

)

Definition at line 692 of file annot_selector.cpp.

References SAnnotSelector::ExcludeTSE(), and CSeq_entry_Handle::GetTSE_Handle().

ExcludeTSE() [2/2]

SAnnotSelector & SAnnotSelector::ExcludeTSE

(

const CTSE_Handle &

tse

)

Definition at line 682 of file annot_selector.cpp.

References SAnnotSelector::ExcludedTSE(), and SAnnotSelector::m_ExcludedTSE.

Referenced by SAnnotSelector::ExcludeTSE(), CFlatGatherer::x_GatherFeatures(), and CFlatGatherer::x_GatherFeaturesIdx().

ExcludeUnnamedAnnots()

SAnnotSelector & SAnnotSelector::ExcludeUnnamedAnnots

(

void

)

Add unnamed annots to set of annots names to exclude.

Definition at line 516 of file annot_selector.cpp.

References SAnnotSelector::ExcludeNamedAnnots().

Referenced by CGraphUtils::CalcGraphLevels(), CSeqUtils::GetAnnotSelector(), CSeqUtils::GetMrnaForCds(), NSnp::IsSnpKnown(), SAnnotSelector::SetAllNamedAnnots(), and CFeatureGenerator::x_SetAnnotName().

ExtractZoomLevel()

bool ExtractZoomLevel	(	const string &	full_name,
		string *	acc_ptr,
		int *	zoom_level_ptr
	)

Extract optional zoom level suffix from named annotation string.

returns true if zoom level explicitly defined in the full_name argument. The accession string without zoom level will be written by acc_ptr pointer if it's not null. Zoom level will be written by zoom_level_ptr pointer if it's not null. Absent zoom level will be represented by value 0. Wildcard zoom level will be represented by value -1.

Definition at line 965 of file annot_selector.cpp.

References CSeq_annot::ExtractZoomLevel().

Referenced by CGraphUtils::CalcGraphLevels(), NSnpAnnot::GetGraph_CI(), CGBDataLoader_Native::GetNamedAnnotAccessions(), SAnnotSelector::HasIncludedOnlyNamedAnnotAccessions(), SAnnotSelector::IncludedAnnotName(), SAnnotSelector::IncludeNamedAnnotAccession(), CProcessor_AnnotInfo::LoadBlob(), s_CreateNAChunk(), CHistogramGlyph::SetAnnotName(), CSnpJob::x_FetchGraphs(), CAnnot_Collector::x_FoundAllNamedAnnotAccessions(), and CId2ReaderBase::x_UpdateLoadedSet().

FeaturePolicyWasApplied()

bool CSeqMap_CI::FeaturePolicyWasApplied ( void  ) const

inline

Definition at line 799 of file seq_map_ci.hpp.

References CSeqMap_CI::m_FeaturePolicyWasApplied.

Referenced by CAnnot_Collector::x_SearchMapped().

ForceAnnotType()

SAnnotSelector & SAnnotSelector::ForceAnnotType

(

TAnnotType

type

)

Set annot type, include all subtypes.

Definition at line 840 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, CAnnotType_Index::GetAnnotTypeRange(), i, SAnnotSelector::m_AnnotTypesBitset, compile_time_bits::range(), and SAnnotSelector::SetAnnotType().

Referenced by CAnnotTypes_CI::CAnnotTypes_CI(), SAnnotSelector::ExcludeFeatSubtype(), SAnnotSelector::ExcludeFeatType(), SAnnotSelector::IncludeFeatSubtype(), and SAnnotSelector::IncludeFeatType().

GetA()

double CMappedGraph::GetA ( void  ) const

inline

Definition at line 165 of file graph_ci.hpp.

References CSeq_graph_Base::GetA(), and CMappedGraph::GetOriginalGraph().

Referenced by NSnpAnnot::EstimateSNPCount(), CSGAnnotJob::x_AddGraphToMap(), and CSnpJob::x_FetchGraphs().

GetAdaptiveDepth()

bool SAnnotSelector::GetAdaptiveDepth ( void  ) const

inline

GetAdaptiveDepth() returns current value of 'adaptive depth' flag.

See also

SetAdaptiveDepth()

Definition at line 354 of file annot_selector.hpp.

References SAnnotSelector::m_AdaptiveDepthFlags.

GetAdaptiveDepthFlags()

TAdaptiveDepthFlags SAnnotSelector::GetAdaptiveDepthFlags ( void  ) const

inline

GetAdaptiveDepthFlags() returns current set of adaptive depth heuristics flags.

See also

SetAdaptiveDepthFlags()

Definition at line 402 of file annot_selector.hpp.

References SAnnotSelector::m_AdaptiveDepthFlags.

Referenced by CDemoApp::Run(), CAnnot_Collector::x_CheckAdaptive(), CAnnot_Collector::x_CollectSegments(), CAnnot_Collector::x_Initialize(), CAnnot_Collector::x_Initialize0(), CAnnot_Collector::x_SearchSegments(), and CAnnot_Collector::x_SearchTSE2().

GetAnnot()

CSeq_annot_Handle CMappedGraph::GetAnnot

(

void

)

const

Get containing annot handle.

Definition at line 99 of file graph_ci.cpp.

References CAnnotObject_Ref::GetSeq_annot_Handle(), and CMappedGraph::m_GraphRef.

Referenced by CGraphGlyph::CGraphGlyph(), CMappedGraph::GetSeq_graph_Handle(), CMappedGraph::operator<(), CMappedGraph::operator==(), CSGAnnotJob::x_AddGraphObject(), CSGAnnotJob::x_GetGraphName(), and CSGAnnotJob::x_PercentileButNotMax().

GetB()

double CMappedGraph::GetB ( void  ) const

inline

Definition at line 174 of file graph_ci.hpp.

References CSeq_graph_Base::GetB(), and CMappedGraph::GetOriginalGraph().

Referenced by NSnpAnnot::EstimateSNPCount(), CSGAnnotJob::x_AddGraphToMap(), and CSnpJob::x_FetchGraphs().

GetBufferEnd()

const char * CSeqVector_CI::GetBufferEnd ( size_t  size ) const

inline

Get pointer to current position+size.

Throw exception if current pos + size is not in the buffer.

Definition at line 543 of file seq_vector_ci.hpp.

References CSeqVector_CI::m_Cache, CSeqVector_CI::m_CacheEnd, ncbi::grid::netcache::search::fields::size, and CSeqVector_CI::x_ThrowOutOfRange().

GetBufferPtr()

const char * CSeqVector_CI::GetBufferPtr ( void  ) const

inline

Get pointer to current char in the buffer.

Definition at line 536 of file seq_vector_ci.hpp.

References CSeqVector_CI::m_Cache.

Referenced by CFastaOstream::x_WriteSequence().

GetBufferSize()

TSeqPos CSeqVector_CI::GetBufferSize ( void  ) const

inline

Get number of chars from current position to the current buffer end.

Definition at line 529 of file seq_vector_ci.hpp.

References CSeqVector_CI::m_Cache, and CSeqVector_CI::m_CacheEnd.

Referenced by GetProteinWeight(), s_CalcDistanceUntilNextSignificantGapOrEnd(), and CFastaOstream::x_WriteSequence().

GetCoding()

CSeqVector_CI::TCoding CSeqVector_CI::GetCoding ( void  ) const

inline

Definition at line 310 of file seq_vector_ci.hpp.

References CSeqVector_CI::m_Coding.

Referenced by CSeqVector_CI::operator=().

GetComment()

const string& CMappedGraph::GetComment ( void  ) const

inline

Definition at line 121 of file graph_ci.hpp.

References CSeq_graph_Base::GetComment(), and CMappedGraph::GetOriginalGraph().

Referenced by CSGAnnotJob::x_PercentileButNotMax().

GetComp()

TSeqPos CMappedGraph::GetComp ( void  ) const

inline

Definition at line 156 of file graph_ci.hpp.

References CSeq_graph_Base::GetComp(), and CMappedGraph::GetOriginalGraph().

Referenced by NSnpAnnot::EstimateSNPCount(), CSGAnnotJob::x_AddGraphToMap(), and CSnpJob::x_FetchGraphs().

GetCurrentSeqMap_CI()

const CSeqMap_CI & CSeqVector_CI::GetCurrentSeqMap_CI ( void  ) const

inline

Definition at line 479 of file seq_vector_ci.hpp.

References CSeqVector_CI::m_Seg.

Referenced by CSGSegmentSmearJob::x_LoadGaps(), CSequenceTrack::x_RenderGaps(), and CFastaOstream::x_WriteSequence().

GetData()

const CSeq_data & CSeqMap_CI::GetData

(

void

)

const

will allow only regular data segments (whole, plus strand)

Definition at line 267 of file seq_map_ci.cpp.

References CSeqMap_CI::GetRefData(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), and NCBI_THROW.

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), GetGapType(), GetLinkage(), CSeqMap_I::GetSequence(), s_NewGapItem(), and WriteLinkageEvidence().

GetDefaultAdaptiveDepthFlags()

SAnnotSelector::TAdaptiveDepthFlags SAnnotSelector::GetDefaultAdaptiveDepthFlags ( )

static

Get default set of adaptive depth flags.

Definition at line 639 of file annot_selector.cpp.

References SAnnotSelector::fAdaptive_ByNamedAcc, SAnnotSelector::fAdaptive_Default, flags, SAnnotSelector::kAdaptive_DefaultBits, NCBI_PARAM_TYPE, and s_DefaultAdaptiveDepthFlags.

Referenced by SAnnotSelector::SetAdaptiveDepth(), and SAnnotSelector::SetAdaptiveDepthFlags().

GetDepth() [1/2]

int CSeq_entry_CI::GetDepth

(

void

)

const

Returns the current depth, which may vary depending on flags.

If fIncludeGivenEntry is set, it returns the current depth relative to the initially given seq-entry (or initially given bioseq-set), where the given has depth "0", its direct children have depth "1", and so on. If fIncludeGivenEntry is NOT set, then the returned values are 1 less. That is, "0" for direct descendents of the given, "1" for the direct descendents of those, etc.

See also

fIncludeGivenEntry

Definition at line 205 of file seq_entry_ci.cpp.

References _ASSERT, CSeq_entry_CI::fIncludeGivenEntry, CSeq_entry_CI::m_Flags, CSeq_entry_CI::m_Parent, and CSeq_entry_CI::m_SubIt.

GetDepth() [2/2]

size_t CSeqMap_CI::GetDepth ( void  ) const

inline

return the depth of current segment

Definition at line 602 of file seq_map_ci.hpp.

References CSeqMap_CI::m_Stack.

Referenced by CSeq_loc_Mapper::x_InitializeSeqMapDown(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), and CSeq_loc_Mapper::x_InitializeSeqMapUp().

GetEndPosition()

TSeqPos CSeqMap_CI::GetEndPosition ( void  ) const

inline

return end position of current segment in sequence (exclusive)

Definition at line 679 of file seq_map_ci.hpp.

References SSeqMapSelector::m_Length, SSeqMapSelector::m_Position, and CSeqMap_CI::m_Selector.

Referenced by CGapAnalysis::AddBioseqGaps(), CValidError_bioseq::GapByGapInst(), CSeqVector_CI::GetGapSizeForward(), CAdvancedAlignCleanup::GetProsplignCompartments(), CResolveRequest::Process(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), s_NewGapItem(), UpdateSeqLength(), CAnnot_Collector::x_CollectMapped(), CFlatGatherer::x_CollectSourceDescriptors(), CComponentSearchJob::x_DoSearch(), CSeqVector_CI::x_FillCache(), CBioseqGaps_CI::x_FindNextGapOnBioseq(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), CSeqVector_CI::x_IncSeg(), CSeqVector_CI::x_InitSeg(), CSeqMap_CI::x_Prev(), CSequenceTrack::x_RenderGaps(), CSplign::x_RunOnCompartment(), CAnnot_Collector::x_SearchMapped(), CSequenceAmbigTrimmer::x_SegmentGetEndInclusive(), CSeqVector_CI::x_SetPos(), CVectorTrimPanel::x_SetSeqData(), CSequenceAmbigTrimmer::x_SliceBioseq(), CSeqVector_CI::x_UpdateCacheDown(), CSeqVector_CI::x_UpdateCacheUp(), and CSeqVector_CI::x_UpdateSeg().

GetExactDepth()

bool SAnnotSelector::GetExactDepth ( void  ) const

inline

GetExactDepth() returns current value of 'exact depth' flag.

See also

SetExactDepth()

Definition at line 443 of file annot_selector.hpp.

References SAnnotSelector::m_ExactDepth.

Referenced by CAnnot_Collector::x_CollectSegments(), CAnnot_Collector::x_Initialize(), CAnnot_Collector::x_Initialize0(), CAnnot_Collector::x_SearchSegments(), and CAnnot_Collector::x_SearchTSE2().

GetExcludedAnnotsNames()

const TAnnotsNames& SAnnotSelector::GetExcludedAnnotsNames ( void  ) const

inline

Definition at line 648 of file annot_selector.hpp.

References SAnnotSelector::m_ExcludeAnnotsNames.

GetExcludeIfGeneIsSuppressed()

bool SAnnotSelector::GetExcludeIfGeneIsSuppressed ( void  ) const

inline

Definition at line 823 of file annot_selector.hpp.

References SAnnotSelector::m_ExcludeIfGeneIsSuppressed.

Referenced by CAnnot_Collector::x_SearchRange().

GetFeatComparator()

IFeatComparator* SAnnotSelector::GetFeatComparator ( void  ) const

inline

Definition at line 254 of file annot_selector.hpp.

References CRef< C, Locker >::GetNCPointerOrNull(), and SAnnotSelector::m_FeatComparator.

GetFeatProduct()

bool SAnnotSelector::GetFeatProduct ( void  ) const

inline

Return true if the features should be searched using their product rather than location.

Definition at line 185 of file annot_selector.hpp.

References SAnnotSelector::m_FeatProduct.

Referenced by CIdRangeMap::CIdRangeMap(), and CFeat_CI::x_AddFeaturesWithId().

GetFilterBits()

TBitFilter SAnnotSelector::GetFilterBits ( void  ) const

inline

Definition at line 811 of file annot_selector.hpp.

References SAnnotSelector::m_FilterBits.

Referenced by CSeqTableInfo::MatchBitFilter().

GetFilterMask()

TBitFilter SAnnotSelector::GetFilterMask ( void  ) const

inline

Definition at line 807 of file annot_selector.hpp.

References SAnnotSelector::m_FilterMask.

Referenced by CSeqTableInfo::MatchBitFilter().

GetFlags()

CSeqMap_CI::TFlags CSeqMap_CI::GetFlags ( void  ) const

inline

Definition at line 785 of file seq_map_ci.hpp.

References SSeqMapSelector::m_Flags, and CSeqMap_CI::m_Selector.

Referenced by CSeqMap_CI::x_Found(), CSeqMap_CI::x_GetBioseq(), and CSeqMap_CI::x_Push().

GetGapChar()

CSeqVector_CI::TResidue CSeqVector_CI::GetGapChar ( void  ) const

inline

returns character representation of gap in sequence

Definition at line 622 of file seq_vector_ci.hpp.

References CSeqVector_CI::m_CaseConversion, CSeqVector_CI::m_Coding, and CSeqVectorTypes::sx_GetGapChar().

Referenced by CSeqVector_CI::x_FillCache().

GetGapSeq_literal()

CConstRef< CSeq_literal > CSeqVector_CI::GetGapSeq_literal

(

void

)

const

returns gap Seq-data object ref returns null if it's not a gap or an unspecified gap

Definition at line 340 of file seq_vector_ci.cpp.

References CSeqMap_CI::GetRefGapLiteral(), CSeqVector_CI::IsInGap(), and CSeqVector_CI::m_Seg.

Referenced by CSeqVector::GetGapSeq_literal(), and CSequenceTrack::GetTooltip().

GetGapSizeBackward()

TSeqPos CSeqVector_CI::GetGapSizeBackward

(

void

)

const

returns number of gap symbols before current symbol returns 0 if current position is not in gap

Definition at line 362 of file seq_vector_ci.cpp.

References CSeqVector_CI::GetPos(), CSeqMap_CI::GetPosition(), CSeqVector_CI::IsInGap(), and CSeqVector_CI::m_Seg.

Referenced by CGenbankFormatter::FormatSequence(), s_CalcDistanceUntilNextSignificantGapOrEnd(), and CSeqVector_CI::SkipGapBackward().

GetGapSizeForward()

TSeqPos CSeqVector_CI::GetGapSizeForward

(

void

)

const

returns number of gap symbols ahead including current symbol returns 0 if current position is not in gap

Definition at line 351 of file seq_vector_ci.cpp.

References CSeqMap_CI::GetEndPosition(), CSeqVector_CI::GetPos(), CSeqVector_CI::IsInGap(), and CSeqVector_CI::m_Seg.

Referenced by CSeqVector::GetGapSizeForward(), CBlastBioseqMaker::HasSequence(), CSeqVector_CI::SkipGap(), and CFastaOstream::x_WriteSequence().

GetGraph()

const CSeq_graph::C_Graph & CMappedGraph::GetGraph

(

void

)

const

Definition at line 192 of file graph_ci.cpp.

References CSeq_graph_Base::GetGraph(), CAnnotObject_Ref::GetMappingInfo(), CMappedGraph::GetOriginalGraph(), CAnnotMapping_Info::IsPartial(), CMappedGraph::m_GraphRef, CMappedGraph::m_MappedGraph, and CMappedGraph::MakeMappedGraph().

Referenced by NSnpAnnot::EstimateSNPCount(), CSGAnnotJob::x_AddGraphObject(), CSnpJob::x_FetchGraphs(), CVectorTrimPanel::x_TrimSeqGraphData(), and CReportTrim::x_TrimSeqGraphData().

GetIgnoreFarLocationsForSorting()

const CBioseq_Handle& SAnnotSelector::GetIgnoreFarLocationsForSorting ( void  ) const

inline

Definition at line 782 of file annot_selector.hpp.

References SAnnotSelector::m_IgnoreFarLocationsForSorting.

GetIncludedAnnotsNames()

const TAnnotsNames& SAnnotSelector::GetIncludedAnnotsNames ( void  ) const

inline

Definition at line 644 of file annot_selector.hpp.

References SAnnotSelector::m_IncludeAnnotsNames.

Referenced by CAnnot_Collector::x_SearchTSE2().

GetLength()

TSeqPos CSeqMap_CI::GetLength ( void  ) const

inline

return length of current segment

Definition at line 672 of file seq_map_ci.hpp.

References SSeqMapSelector::m_Length, and CSeqMap_CI::m_Selector.

Referenced by CGapAnalysis::AddBioseqGaps(), CAlignmentAssistant::AdjustBioseq(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CSeqMap::CanResolveRange(), CGapCache::CGapCache(), CSeqMapSwitchPoint::ChangeSwitchPoint(), CFeatGapInfo::CollectGaps(), CEditSequence::CreateControls(), CSeqMap_CI::GetRefEndPosition(), CDemoApp::Run(), s_NewGapItem(), CSeq_loc_Conversion::SetConversion(), CEditSeqEndsWithAlign::TrimBeforeAfter(), UpdateSeqLength(), CGapAnalysis::x_AddGapsFromBases(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CSeq_loc_Mapper::x_InitializeSeqMapUp(), CSeqMap_CI::x_Push(), CVectorTrimPanel::x_SetSeqData(), CSequenceAmbigTrimmer::x_SliceBioseq(), and CSeqVector_CI::x_UpdateSeg().

GetLoc()

const CSeq_loc& CMappedGraph::GetLoc ( void  ) const

inline

Definition at line 126 of file graph_ci.hpp.

References CMappedGraph::m_MappedLoc, and CMappedGraph::MakeMappedLoc().

Referenced by NSnpAnnot::EstimateSNPCount(), CMappedGraph::MakeMappedGraph(), CMappedGraph::MakeMappedLoc(), CDemoApp::Run(), CReportTrim::TrimSeqGraphs(), CSGAnnotJob::x_AddGraphToMap(), CSnpJob::x_FetchGraphs(), and CVectorTrimPanel::x_TrimSeqGraphs().

GetLocation()

const CSeq_loc & CMappedFeat::GetLocation ( void  ) const

virtual

Reimplemented from CSeq_feat_Handle.

Definition at line 183 of file mapped_feat.cpp.

References CSeq_feat_Base::GetLocation(), CMappedFeat::GetMappedLocation(), CSeq_feat_Handle::GetOriginalSeq_feat(), CAnnotMapping_Info::IsMappedLocation(), and CMappedFeat::m_MappingInfoPtr.

Referenced by CFeatTree::AddFeaturesFor(), CReportTrim::AdjustAndTranslate(), CEditSequence::AdjustFeatureLocations(), AdjustSingleFeature(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), BOOST_AUTO_TEST_CASE(), BuildFeatureSeqTableFromSeqEntry(), CheckAdjustStart(), CheckAdjustStartAndStop(), CheckAdjustStop(), variation::CVariationUtil::CheckExonBoundary(), CLDBlockGlyph::CLDBlockGlyph(), CAnnotCompare::CompareFeats(), CWriteUtil::CompareFeatures(), CFeatureGenerator::CreateMicroIntrons(), CSourceFeatureItem::CSourceFeatureItem(), CAnnotationASN1::ExtractModels(), variation::CVariationUtil::FindLocationProperties(), CValidError_bioseq::GapByGapInst(), CScore_StartStopCodon::Get(), CScore_CdsScore::Get(), GetAlignmentForRna(), CGeneFinder::GetAssociatedGeneInfo(), CGenbankIdResolve::GetBestId(), GetBestOverlappingFeat(), CFeatureGenerator::SImplementation::GetCds(), CInternalStopFinder::GetCDSNucleotideSequence(), GetCdsOnMrna(), variation::CVariationUtil::GetEffectiveTranscriptLength(), CValidator::CCacheImpl::GetFeatStrKeyToFeats(), GetFeatureProtein(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CSeqUtils::GetMappingInfo(), GetMrnasForGene(), GetOverlappingFeatures(), GetParentFeature(), CSeqTextDataSourceInterval::GetSeqData(), CFlatFileGenerator::GetSeqFeatText(), CValidError_imp::GetTSACDSOnMinusStrandErrors(), CValidError_bioseqset::IsCDSProductInGPS(), NSnp::IsSnpKnown(), CSeqTextDataSourceInterval::LookForSpliceJunctions(), MakemRNAforCDS(), SFeatLengthPredicate::operator()(), SFeatSortPredicate::operator()(), SChildLess::operator()(), operator<<(), CGeneFinder::CGeneSearchPlugin::processMainLoop(), variation::CVariationUtil::RemapToAnnotatedTarget(), CNewCleanup_imp::ResynchPeptidePartials(), CFeatCompareJob_Align::Run(), CFeatCompareJob_Location::Run(), CFeatureRetrievalJob::Run(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), s_CdsCountAmbiguities(), s_CdsLength(), s_CdsStopCodon(), s_CheckQuals_cdregion(), s_CodingPropensity(), s_CoincidingGapFeatures(), s_CollectBestOverlaps(), s_GetCdregionPlusUpstream(), s_GetFeatureKey(), s_GetFeatureKeyLinkLocation(), s_GetLinkFeatureKey(), s_GetOverlap(), s_PrematureStopCodon(), s_TitleFromSegment(), s_Utrs(), CCleanup::SetGenePartialByLongestContainedFeature(), SetTranslExcept(), CValidError_bioseq::ValidateFeatPartialInContext(), CVcfWriter::WriteAnnot(), CGuiObjectInfoSeq_feat::x_AddExtraInfo(), CFeatureItem::x_AddQualCodedBy(), CFeatureItem::x_AddQualOperon(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualsRna(), CGvfWriteRecord::x_AssignAttributeEndRange(), CGvfWriteRecord::x_AssignAttributeStartRange(), CValidError_bioseq::x_CheckSingleStrandedRNAViruses(), CFlatGatherer::x_CollectSourceFeatures(), CFlatGatherer::x_CopyCDSFromCDNA(), CSGFeatureJob::x_CreateCloneFeature(), CSGAlignmentJob::x_CreateFeatGlyph(), CSGFeatureJob::x_CreateFeatHist(), CSGFeatureJob::x_CreateFeatSmear(), CSGFeatureJob::x_CreateFeature1(), CFeatureGenerator::SImplementation::x_CreateGeneFeature(), COrfSearchJob::x_DoSearch(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), variation_ref::CHgvsParser::x_general_pos(), variation::CHgvsParser::x_general_pos(), CCdregionValidator::x_HasGoodParent(), variation::CVariationUtil::CCdregionIndex::x_Index(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CBioseqIndex::x_InitFeats(), CValidError_bioseq::x_IsSameAsCDS(), CBatchFeatJob::x_LoadFeatProducts(), CMacroFunction_FeatStrandednessConstraint::x_Match(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CNewCleanup_imp::x_MoveCDSFromNucAnnotToSetAnnot(), CValidError_bioseq::x_PartialAdjacentToIntron(), variation::CHgvsParser::x_PlacementCoordsToStr(), CReportTrim::x_RetranslateCDS(), CFlatFeatureRetrieveJob::x_Run(), variation_ref::CHgvsParser::x_SeqLocToStr(), CBioseqContext::x_SetHasMultiIntervalGenes(), x_ToBlastVec(), CValidError_bioseq::x_ValidateAbuttingRNA(), CSingleFeatValidator::x_ValidateGeneXRef(), CVcfWriter::x_WriteFeature(), CGff3Writer::xAssignFeature(), CGff2Writer::xAssignFeatureAttributeIsOrdered(), CGff2Writer::xAssignFeatureAttributePartial(), CGff2Writer::xAssignFeatureEndpoints(), CGtfWriter::xAssignFeatureMethod(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGff2Writer::xAssignFeatureStrand(), CGff3Writer::xAssignFeatureStrand(), CGtfWriter::xAssignFeaturesTranscript(), CFeatTableEdit::xConvertToGeneralIds(), CGffIdGenerator::xExtractFeatureLocation(), CGff2Writer::xGenerateMissingTranscript(), CExonNumberAssigner::xInitialize(), CFeatTableEdit::xPutErrorMissingLocustag(), CFeatTableEdit::xPutErrorMissingProteinId(), CFeatTableEdit::xPutErrorMissingTranscriptId(), CGtfWriter::xWriteFeatureExons(), CGff3Writer::xWriteFeatureGeneric(), CGff3Writer::xWriteFeatureProtein(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteFeatureTrna(), CGff3Writer::xWriteNucleotideFeature(), CGff3Writer::xWriteNucleotideFeatureTransSpliced(), and CGff3Writer::xWriteProteinFeature().

GetLocationId()

CSeq_id_Handle CMappedFeat::GetLocationId ( void  ) const

virtual

Reimplemented from CSeq_feat_Handle.

Definition at line 190 of file mapped_feat.cpp.

References CSeq_id_Handle::GetHandle(), CAnnotMapping_Info::GetLocationId(), CSeq_feat_Handle::GetLocationId(), CAnnotMapping_Info::IsMappedLocation(), and CMappedFeat::m_MappingInfoPtr.

Referenced by CGenbankIdResolve::GetBestId(), CSeqMasterIndex::GetBioseqIndex(), CBioseqIndex::GetFeatureForProduct(), CDemoApp::Run(), CUpdateSeq_Input::x_ReadAccession(), CGff2Writer::x_WriteSeqEntryHandle(), CGff3Writer::xAssignFeatureMethod(), and CFeatTableEdit::xGenerateMissingGeneForFeats().

GetLocationTotalRange()

TRange CMappedFeat::GetLocationTotalRange ( void  ) const

inline

Definition at line 98 of file mapped_feat.hpp.

References CMappedFeat::GetRange().

Referenced by CGffIdGenerator::xExtractFeatureLocation().

GetMappedFeature()

const CSeq_feat & CMappedFeat::GetMappedFeature

(

void

)

const

Feature mapped to the master sequence.

WARNING! The function is rather slow and should be used with care.

Definition at line 152 of file mapped_feat.cpp.

References CMappedFeat::GetSeq_feat().

Referenced by CLinkUtils::AddDbxrefLinksForSNP(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CReportEntry::CReportEntry(), CExploreProcess::DoOneBioseq(), CSnpTrack::GenerateAsn1(), CFeatureTrack::GenerateAsn1(), CGeneModelTrack::GenerateAsn1(), CSeqUtils::GetCdsMappingInfoFromRna(), CGeneXrefsFromFeats::GetCommand(), CGuiObjectInfoVariation::GetLinks(), CSeqUtils::GetMappingInfo(), GetOverlappingFeatures(), GetProtAndRnaForCDS(), CLinkedFeatsGroup::GetTooltip(), CAsn2FastaApp::HandleSeqEntry(), CWriteUtil::IsTransspliced(), CSelectFeatureDlg::OnFeatureEdit(), SChildLess::operator()(), CFeatIdRemapper::RemapIds(), variation::CVariationUtil::RemapToAnnotatedTarget(), CFeatureLoadingJob::Run(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), s_AdjustToAnnotatedCDS(), s_GetFeatureKey(), s_GetRnaMappingLocs(), variation::CHgvsParser::CContext::SetId(), variation_ref::CHgvsParser::CContext::SetId(), ProjectCDS::transform_align(), CFeatureItem::x_AddQualsIdx(), CSGAlignmentJob::x_CreateFeatGlyph(), CSGAlignmentJob::x_CreateGeneModels(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CAnnotGetter::x_GetCompleteSeqAnnot(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CAutoDef::x_GetFeatureClauses(), CSelectFeatureDlg::x_LoadFeatures(), CFeatureSearchJob::x_SearchFeatures(), CReportEntry::x_SetFeature(), CAdjustForConsensusSpliceSite::x_UpdateExonFeatures(), CGtfWriter::xAssignFeaturesCds(), and CGff3Writer::xWriteFeatureCds().

GetMappedGraph()

const CSeq_graph& CMappedGraph::GetMappedGraph ( void  ) const

inline

Graph mapped to the master sequence.

WARNING! The function is rather slow and should be used with care.

Definition at line 100 of file graph_ci.hpp.

References CMappedGraph::m_MappedGraph, and CMappedGraph::MakeMappedGraph().

Referenced by CSnpTrack::GenerateAsn1(), CDemoApp::Run(), CSGAlignStatJob::x_CollectAlignStats(), CAnnot_Collector::x_GetMappedObject(), and CSGAlnQualityScore::x_RetrieveQualityMap().

GetMappedGraphRanges()

const CMappedGraph::TGraphRanges & CMappedGraph::GetMappedGraphRanges

(

void

)

const

Get all mapped graph ranges.

The ranges are provided in the sequence coordinates, to get array index divide each value by 'comp'.

Definition at line 212 of file graph_ci.cpp.

References _ASSERT, CAnnotMapping_Info::GetGraphRanges(), CAnnotObject_Ref::GetMappingInfo(), CGraphRanges::GetRanges(), and CMappedGraph::m_GraphRef.

Referenced by CMappedGraph::GetNumval(), and CMappedGraph::MakeMappedGraphData().

GetMappedGraphTotalRange()

const CMappedGraph::TRange & CMappedGraph::GetMappedGraphTotalRange

(

void

)

const

Get the range of graph data used in the mapped graph.

The range is provided in the sequence coordinates, to get array index divide each value by 'comp'.

Definition at line 203 of file graph_ci.cpp.

References _ASSERT, CAnnotMapping_Info::GetGraphRanges(), CAnnotObject_Ref::GetMappingInfo(), CGraphRanges::GetTotalRange(), and CMappedGraph::m_GraphRef.

GetMappedLocation() [1/2]

CConstRef< CSeq_loc > CMappedFeat::GetMappedLocation ( void  ) const

private

Definition at line 129 of file mapped_feat.cpp.

References CCreatedFeat_Ref::GetMappedLocation(), CMappedFeat::m_MappedFeat, and CMappedFeat::m_MappingInfoPtr.

Referenced by CMappedFeat::GetLocation(), and CMappedFeat::GetProduct().

GetMappedLocation() [2/2]

const CSeq_loc & CSeq_table_CI::GetMappedLocation

(

void

)

const

Definition at line 156 of file seq_table_ci.cpp.

References CAnnotTypes_CI::Get(), CAnnotObject_Ref::GetMappingInfo(), CSeq_table_CI::GetOriginalLocation(), info, and CSeq_table_CI::m_MappedLoc.

Referenced by CSGSeqGraphJob::x_LoadSeqTable().

GetMaxSearchSegments()

TMaxSearchSegments SAnnotSelector::GetMaxSearchSegments ( void  ) const

inline

Get maximum number of empty segments to search before giving up.

Definition at line 464 of file annot_selector.hpp.

References SAnnotSelector::m_MaxSearchSegments.

Referenced by CAnnot_Collector::x_Initialize0().

GetMaxSearchSegmentsAction()

EMaxSearchSegmentsAction SAnnotSelector::GetMaxSearchSegmentsAction ( void  ) const

inline

Definition at line 482 of file annot_selector.hpp.

References SAnnotSelector::m_MaxSearchSegmentsAction.

Referenced by CAnnot_Collector::x_Initialize0().

GetMaxSearchTime()

TMaxSearchTime SAnnotSelector::GetMaxSearchTime ( void  ) const

inline

Get maximum time (in seconds) to search before giving up.

Definition at line 494 of file annot_selector.hpp.

References SAnnotSelector::m_MaxSearchTime.

Referenced by CAnnot_Collector::x_Initialize0(), and CAnnot_Collector::x_SearchMapped().

GetMaxSize()

TMaxSize SAnnotSelector::GetMaxSize ( void  ) const

inline

Get maximum allowed number of annotations to find.

Definition at line 450 of file annot_selector.hpp.

References SAnnotSelector::m_MaxSize.

Referenced by CAnnot_Collector::x_NoMoreObjects(), and CAnnot_Collector::x_SearchRange().

GetNamedAnnotAccessions()

const TNamedAnnotAccessions& SAnnotSelector::GetNamedAnnotAccessions ( void  ) const

inline

Definition at line 684 of file annot_selector.hpp.

References SAnnotSelector::m_NamedAnnotAccessions.

Referenced by CPSGDataLoader_Impl::GetAnnotRecordsNAOnce(), SCacheInfo::GetBlob_idsSubkey(), CSNPDataLoader_Impl::GetOrphanAnnotRecordsOnce(), CVDBGraphDataLoader_Impl::GetOrphanAnnotRecordsOnce(), CId1Reader::LoadSeq_idBlob_ids(), CId2ReaderBase::LoadSeq_idBlob_ids(), s_FormatCall(), CReaderRequestResult::s_KeyBlobIds(), CAnnot_Collector::x_FoundAllNamedAnnotAccessions(), CScope_Impl::x_GetAnnotRef_Info(), and CSGAnnotJob::x_LoadCoverageGraph().

GetNoMapping()

bool SAnnotSelector::GetNoMapping ( void  ) const

inline

Definition at line 704 of file annot_selector.hpp.

References SAnnotSelector::m_NoMapping.

GetNumval()

TSeqPos CMappedGraph::GetNumval ( void  ) const

inline

Definition at line 179 of file graph_ci.hpp.

References CMappedGraph::GetMappedGraphRanges(), CAnnotObject_Ref::GetMappingInfo(), CSeq_graph_Base::GetNumval(), CMappedGraph::GetOriginalGraph(), CAnnotMapping_Info::IsMapped(), ITERATE, CMappedGraph::m_GraphRef, and CMappedGraph::m_MappedGraph.

GetOriginalFeature()

const CSeq_feat & CMappedFeat::GetOriginalFeature

(

void

)

const

Get original feature with unmapped location/product.

Definition at line 146 of file mapped_feat.cpp.

References CSeq_feat_Handle::GetOriginalSeq_feat().

Referenced by CReportTrim::AdjustAndTranslate(), CEditSequence::AdjustFeatureLocations(), AdjustSingleFeature(), CModifyStructuredComment::apply_to_seq_and_feat(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), BOOST_AUTO_TEST_CASE(), CFeatureItemBase::CFeatureItemBase(), CLDBlockGlyph::CLDBlockGlyph(), CAnnotCompare::CompareFeats(), CConvertCDSToProt::Convert(), Convert_Seq_loc_Seq_feat(), CCdsToMatPeptide::ConvertInner(), CSourceFeatureItem::CSourceFeatureItem(), CExploreProcess::DoOneBioseq(), CAnnotationASN1::ExtractModels(), CmRNAAndCDSIndex::FindMatchmRNA(), CFeatTableEdit::GenerateLocusTags(), NSnp::GetAlleles(), CPubField::GetApplyObjects(), CSrcTableColumnBase::GetApplyObjects(), GetBestMrnaForCds(), GetBioSourceForBioseq(), NSnp::GetBitfield(), CValidError_imp::GetCDSGivenProduct(), CmRNAFromGeneCdsExon::GetCommand(), CtRNAFromGene::GetCommand(), CTruncateCDS::GetCommand(), CBulkCDS::GetCommandFromValuesTable(), GetFeatureProtein(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CGeneModelFeatJob::GetFilters(), NSnp::GetLength(), CSeqUtils::GetMappingInfo(), GetmRNAForProduct(), CValidError_imp::GetmRNAGivenProduct(), GetMrnasForGene(), CCleanup::GetNormalizableGeneQualPairs(), CPubField::GetObjects(), CSrcTableColumnBase::GetObjects(), GetOverlappingFeatures(), GetProductName(), GetPROTForProduct(), NSnp::GetRsid(), NSnp::GetTag(), CBulkCDS::GetValuesTableFromSeqEntry(), CFeatTableEdit::InferPartials(), NSnp::IsSnp(), NSnp::IsSnpKnown(), SFeatSortPredicate::operator()(), operator<<(), CFeatTableEdit::ProcessCodonRecognized(), CCdsForMrnaPlugin::processMainLoop(), CGeneFinder::CGeneSearchPlugin::processMainLoop(), CGeneFinder::ResolveGeneObjectId(), RestoreModelFromPublicMrnaFeature(), RetranslateCdregion(), CExtendCDSToStop::RetranslateCDSCommand(), CRevCompSequencesDlg::RevCompBioSeq(), CGffExportJob::Run(), CGtfExportJob::Run(), CFeatCompareJob_Align::Run(), CFeatCompareJob_Location::Run(), CDemoApp::Run(), CTestBMApp::Run(), CSampleLds2Application::Run(), s_Code_break(), s_CompareProtProdToTrans(), s_GetCdsByProduct(), s_GetMappedFeat(), s_GetProductName(), s_IsSelenocysteine(), s_PassesFilter(), s_Render_SeqFeat(), s_SubsequentIntron(), CFixFeatureId::s_UpdateFeatureIds(), s_VerifyTree(), CGeneOverlapProcess::SeqEntryProcess(), CCleanup::SetGeneticCodes(), CCleanup::SetProteinName(), SetTranslExcept(), sGetCdsProductName(), CFeatTableEdit::SubmitFixProducts(), TrimSequenceAndAnnotation(), TrimStopsFromCompleteCDS(), CFeatureItem::x_AddFTableRnaQuals(), CFeatureItem::x_AddQualsCdregionIdx(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualTranslation(), CSGFeatureJob::x_CreateFeatHist(), CSGFeatureJob::x_CreateFeatSmear(), CGeneModelFeatJob::x_CreateFeaturesWithFilter(), CFeatureGenerator::SImplementation::x_CreateGeneFeature(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CSourceItem::x_GatherInfo(), CFlatGatherer::x_GatherReferences(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CAutoDef::x_GetFeatureClauses(), CDeflineGenerator::x_GetGeneRefViaCDS(), CLDBlockJob::x_LoadFtable(), CSnpJob::x_PreFetchFtable(), CVectorTrimPanel::x_RetranslateCDS(), CReportTrim::x_RetranslateCDS(), CFeatureSearchJob::x_SearchFeatures(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CDeflineGenerator::x_SetPrefix(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CVectorTrimPanel::x_TrimSelected(), CValidError_bioseq::x_ValidateAbuttingRNA(), CValidError_bioseq::x_ValidateCDSagainstVDJC(), CMRNAValidator::x_ValidateMrnaGene(), CFeatTableEdit::xAdjustExistingParentGene(), CGtfWriter::xAssignFeatureAttributeTranscriptBiotype(), CGff3Writer::xAssignFeatureType(), CFeatTableEdit::xCreateMissingParentGene(), CFeatTableEdit::xFeatureAddQualifier(), CFeatTableEdit::xFeatureRemoveQualifier(), CFeatTableEdit::xFeatureSetProduct(), CFeatTableEdit::xGenerateMissingMrnaForCds(), CFeatTableEdit::xGetLinkedFeature(), CGff3Writer::xWriteFeatureProtein(), CBedWriter::xWriteFeaturesThreeFeatData(), and CGff3Writer::xWriteProteinFeature().

GetOriginalGraph()

const CSeq_graph& CMappedGraph::GetOriginalGraph ( void  ) const

inline

Get original graph with unmapped location/product.

Definition at line 70 of file graph_ci.hpp.

References CAnnotObject_Ref::GetGraph(), and CMappedGraph::m_GraphRef.

Referenced by BOOST_AUTO_TEST_CASE(), Convert_Seq_loc_Seq_graph(), CMappedGraph::GetA(), CMappedGraph::GetB(), CMappedGraph::GetComment(), CMappedGraph::GetComp(), CMappedGraph::GetGraph(), CMappedGraph::GetNumval(), CMappedGraph::GetTitle(), CMappedGraph::GetTitle_x(), CMappedGraph::GetTitle_y(), CMappedGraph::IsSetA(), CMappedGraph::IsSetB(),