NCBI C++ ToolKit
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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_HandleCAnnot_CI::TSeqAnnotSet
 
typedef TSeqAnnotSet::const_iterator CAnnot_CI::TIterator
 
typedef vector< SAnnotTypeSelectorSAnnotSelector::TAdaptiveTriggers
 
typedef Uint1 SAnnotSelector::TAdaptiveDepthFlags
 
typedef size_t SAnnotSelector::TMaxSize
 
typedef unsigned SAnnotSelector::TMaxSearchSegments
 
typedef float SAnnotSelector::TMaxSearchTime
 
typedef vector< CAnnotNameSAnnotSelector::TAnnotsNames
 Object manager recognizes several fields of Seq-annot as annot name. More...
 
typedef map< string, intSAnnotSelector::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_HandleSAnnotSelector::TTSE_Limits
 
typedef vector< CSeq_entry_CICBioseq_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_HandleCFeat_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_CICSeq_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< TSeqPosSSeqMapSelector::TRange
 
typedef SSeqMapSelector::TFlags CSeqMap_CI::TFlags
 
typedef CSeqMap_CI_SegmentInfo CSeqMap_CI::TSegmentInfo
 
typedef vector< TSegmentInfoCSeqMap_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 TResidueCSeqVectorTypes::pointer
 
typedef const TResidueCSeqVectorTypes::reference
 
typedef AutoArray< char > CSeqVector_CI::TCacheData
 
typedef char * CSeqVector_CI::TCache_I
 
typedef vector< CSeqdesc::E_ChoiceCSeqdesc_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_CICAlign_CI::operator= (const CAlign_CI &iter)
 
virtual CAlign_CI::~CAlign_CI (void)
 
CAlign_CICAlign_CI::operator++ (void)
 Move to the next object in iterated sequence. More...
 
CAlign_CICAlign_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_CICAlign_CI::begin () const
 
CAlign_CI CAlign_CI::end () const
 
bool CAlign_CI::operator!= (const CAlign_CI &it) const
 
const CSeq_alignCAlign_CI::operator* (void) const
 Mapped alignment, not the original one. More...
 
const CSeq_alignCAlign_CI::operator-> (void) const
 Mapped alignment, not the original one. More...
 
const CSeq_alignCAlign_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_CICAnnot_CI::operator= (const CAnnot_CI &iter)
 
CAnnot_CICAnnot_CI::operator++ (void)
 Move to the next object in iterated sequence. More...
 
CAnnot_CICAnnot_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_HandleCAnnot_CI::operator* (void) const
 
const CSeq_annot_HandleCAnnot_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)
 
SAnnotSelectorSAnnotSelector::operator= (const SAnnotSelector &sel)
 
 SAnnotSelector::~SAnnotSelector (void)
 
SAnnotSelectorSAnnotSelector::SetAnnotType (TAnnotType type)
 Set annotation type (feat, align, graph) More...
 
SAnnotSelectorSAnnotSelector::SetFeatType (TFeatType type)
 Set feature type (also set annotation type to feat) More...
 
SAnnotSelectorSAnnotSelector::SetFeatSubtype (TFeatSubtype subtype)
 Set feature subtype (also set annotation and feat type) More...
 
SAnnotSelectorSAnnotSelector::IncludeAnnotType (TAnnotType type)
 Include annotation type in the search. More...
 
SAnnotSelectorSAnnotSelector::ExcludeAnnotType (TAnnotType type)
 Exclude annotation type from the search. More...
 
SAnnotSelectorSAnnotSelector::IncludeFeatType (TFeatType type)
 Include feature type in the search. More...
 
SAnnotSelectorSAnnotSelector::ExcludeFeatType (TFeatType type)
 Exclude feature type from the search. More...
 
SAnnotSelectorSAnnotSelector::IncludeFeatSubtype (TFeatSubtype subtype)
 Include feature subtype in the search. More...
 
SAnnotSelectorSAnnotSelector::ExcludeFeatSubtype (TFeatSubtype subtype)
 Exclude feature subtype from the search. More...
 
bool SAnnotSelector::CheckAnnotType (TAnnotType type) const
 Check annot type (ignore subtypes). More...
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::SetOverlapType (EOverlapType overlap_type)
 Set overlap type. More...
 
SAnnotSelectorSAnnotSelector::SetOverlapIntervals (void)
 Check overlapping of individual intervals. More...
 
SAnnotSelectorSAnnotSelector::SetOverlapTotalRange (void)
 Check overlapping only of total ranges. More...
 
ESortOrder SAnnotSelector::GetSortOrder (void) const
 Get the selected sort order. More...
 
SAnnotSelectorSAnnotSelector::SetSortOrder (ESortOrder sort_order)
 Set sort order of annotations. More...
 
SAnnotSelectorSAnnotSelector::SetFeatComparator (IFeatComparator *comparator)
 
SAnnotSelectorSAnnotSelector::ResetFeatComparator (void)
 
bool SAnnotSelector::IsSetFeatComparator (void) const
 
IFeatComparatorSAnnotSelector::GetFeatComparator (void) const
 
EResolveMethod SAnnotSelector::GetResolveMethod (void) const
 GetResolveMethod() returns current value of resolve_method. More...
 
SAnnotSelectorSAnnotSelector::SetResolveMethod (EResolveMethod resolve_method)
 SetResolveMethod() controls visibility of subsegments depending on whether it's packaged together with master sequence. More...
 
SAnnotSelectorSAnnotSelector::SetResolveNone (void)
 SetResolveNone() is equivalent to SetResolveMethod(eResolve_None). More...
 
SAnnotSelectorSAnnotSelector::SetResolveTSE (void)
 SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE). More...
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::SetAdaptiveDepth (bool value=true)
 SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower level of segments. More...
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::SetAdaptiveTrigger (const SAnnotTypeSelector &sel)
 SetAdaptiveTrigger() allows to change default set of adaptive trigger annotations. More...
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::SetMaxSearchSegments (TMaxSearchSegments max_segments)
 Set maximum number of empty segments to search before giving up. More...
 
EMaxSearchSegmentsAction SAnnotSelector::GetMaxSearchSegmentsAction (void) const
 
SAnnotSelectorSAnnotSelector::SetMaxSearchSegmentsAction (EMaxSearchSegmentsAction action)
 
TMaxSearchTime SAnnotSelector::GetMaxSearchTime (void) const
 Get maximum time (in seconds) to search before giving up. More...
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::SetLimitNone (void)
 Remove restrictions on the parent object of annotations. More...
 
SAnnotSelectorSAnnotSelector::SetLimitTSE (const CTSE_Handle &limit)
 Limit annotations to those from the TSE only. More...
 
SAnnotSelectorSAnnotSelector::SetLimitTSE (const CSeq_entry_Handle &limit)
 
SAnnotSelectorSAnnotSelector::SetLimitSeqEntry (const CSeq_entry_Handle &limit)
 Limit annotations to those from the seq-entry only. More...
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::SetUnresolvedFlag (EUnresolvedFlag flag)
 Set method of handling unresolved seq-ids. More...
 
SAnnotSelectorSAnnotSelector::SetIgnoreUnresolved (void)
 
SAnnotSelectorSAnnotSelector::SetSearchUnresolved (void)
 
SAnnotSelectorSAnnotSelector::SetFailUnresolved (void)
 
SAnnotSelectorSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::SetSearchExternal (const CTSE_Handle &tse)
 Set all flags for searching standard GenBank external annotations. More...
 
SAnnotSelectorSAnnotSelector::SetSearchExternal (const CSeq_entry_Handle &tse)
 
SAnnotSelectorSAnnotSelector::SetSearchExternal (const CBioseq_Handle &seq)
 
SAnnotSelectorSAnnotSelector::ResetAnnotsNames (void)
 Select annotations from all Seq-annots. More...
 
SAnnotSelectorSAnnotSelector::ResetUnnamedAnnots (void)
 Reset special processing of unnamed annots (added or excluded) More...
 
SAnnotSelectorSAnnotSelector::ResetNamedAnnots (const CAnnotName &name)
 Reset special processing of named annots (added or excluded) More...
 
SAnnotSelectorSAnnotSelector::ResetNamedAnnots (const char *name)
 
SAnnotSelectorSAnnotSelector::AddUnnamedAnnots (void)
 Add unnamed annots to set of annots names to look for. More...
 
SAnnotSelectorSAnnotSelector::AddNamedAnnots (const CAnnotName &name)
 Add named annot to set of annots names to look for. More...
 
SAnnotSelectorSAnnotSelector::AddNamedAnnots (const char *name)
 
SAnnotSelectorSAnnotSelector::ExcludeUnnamedAnnots (void)
 Add unnamed annots to set of annots names to exclude. More...
 
SAnnotSelectorSAnnotSelector::ExcludeNamedAnnots (const CAnnotName &name)
 Add named annot to set of annots names to exclude. More...
 
SAnnotSelectorSAnnotSelector::ExcludeNamedAnnots (const char *name)
 
SAnnotSelectorSAnnotSelector::SetAllNamedAnnots (void)
 Look for all named Seq-annots Resets the filter, and then excludes unnamed annots. More...
 
SAnnotSelectorSAnnotSelector::SetDataSource (const string &name)
 Look for named annot. More...
 
const TAnnotsNamesSAnnotSelector::GetIncludedAnnotsNames (void) const
 
const TAnnotsNamesSAnnotSelector::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
 
SAnnotSelectorSAnnotSelector::ResetNamedAnnotAccessions (void)
 Add named annot accession (NA*) in the search. More...
 
SAnnotSelectorSAnnotSelector::IncludeNamedAnnotAccession (const string &acc, int zoom_level=0)
 
SAnnotSelectorSAnnotSelector::ExcludeNamedAnnotAccession (const string &acc)
 
const TNamedAnnotAccessionsSAnnotSelector::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...
 
SAnnotSelectorSAnnotSelector::ExcludeTSE (const CTSE_Handle &tse)
 
SAnnotSelectorSAnnotSelector::ExcludeTSE (const CSeq_entry_Handle &tse)
 
SAnnotSelectorSAnnotSelector::ResetExcludedTSE (void)
 
bool SAnnotSelector::ExcludedTSE (const CTSE_Handle &tse) const
 
bool SAnnotSelector::ExcludedTSE (const CSeq_entry_Handle &tse) const
 
bool SAnnotSelector::GetNoMapping (void) const
 
SAnnotSelectorSAnnotSelector::SetNoMapping (bool value=true)
 
SAnnotSelectorSAnnotSelector::SetCollectSeq_annots (bool value=true)
 Try to avoid collecting multiple objects from the same seq-annot. More...
 
SAnnotSelectorSAnnotSelector::SetCollectTypes (bool value=true)
 Collect available annot types rather than annots. More...
 
SAnnotSelectorSAnnotSelector::SetCollectNames (bool value=true)
 Collect available annot names rather than annots. More...
 
SAnnotSelectorSAnnotSelector::SetCollectCostOfLoading (bool value=true)
 Collect cost of loading requested data. More...
 
SAnnotSelectorSAnnotSelector::SetIgnoreStrand (bool value=true)
 Ignore strand when testing for range overlap. More...
 
SAnnotSelectorSAnnotSelector::SetSourceLoc (const CSeq_loc &loc)
 Set filter for source location of annotations. More...
 
SAnnotSelectorSAnnotSelector::ResetSourceLoc (void)
 Reset filter for source location of annotations. More...
 
SAnnotSelectorSAnnotSelector::SetIgnoreFarLocationsForSorting (const CBioseq_Handle &handle)
 Set handle used for determining what locations are "near". More...
 
const CBioseq_HandleSAnnotSelector::GetIgnoreFarLocationsForSorting (void) const
 
SAnnotSelectorSAnnotSelector::SetBitFilter (TBitFilter filter_bits, TBitFilter filter_mask=TBitFilter(-1))
 
SAnnotSelectorSAnnotSelector::ResetBitFilter (void)
 
bool SAnnotSelector::HasBitFilter (void) const
 
TBitFilter SAnnotSelector::GetFilterMask (void) const
 
TBitFilter SAnnotSelector::GetFilterBits (void) const
 
SAnnotSelectorSAnnotSelector::SetExcludeIfGeneIsSuppressed (bool exclude=true)
 Exclude features with empty gene xref: xref { { data gene { } } }. More...
 
bool SAnnotSelector::GetExcludeIfGeneIsSuppressed (void) const
 
TSNPScaleLimit SAnnotSelector::GetSNPScaleLimit (void) const
 
SAnnotSelectorSAnnotSelector::SetSNPScaleLimit (TSNPScaleLimit value)
 
SAnnotSelectorSAnnotSelector::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)
 
CScopeCBioseq_CI::GetScope (void) const
 Get the current scope for the iterator. More...
 
CBioseq_CICBioseq_CI::operator= (const CBioseq_CI &bioseq_ci)
 
CBioseq_CICBioseq_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_HandleCBioseq_CI::operator* (void) const
 
const CBioseq_HandleCBioseq_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_CICFeat_CI::operator= (const CFeat_CI &iter)
 
CFeat_CICFeat_CI::operator++ (void)
 Move to the next object in iterated sequence. More...
 
CFeat_CICFeat_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_CICFeat_CI::begin () const
 
CFeat_CI CFeat_CI::end () const
 
bool CFeat_CI::operator!= (const CFeat_CI &it) const
 
const CMappedFeatCFeat_CI::operator* (void) const
 
const CMappedFeatCFeat_CI::operator-> (void) const
 
CFeat_CICFeat_CI::operator++ (int)
 
CFeat_CICFeat_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_graphCMappedGraph::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_graphCMappedGraph::GetMappedGraph (void) const
 Graph mapped to the master sequence. More...
 
bool CMappedGraph::IsSetTitle (void) const
 
const stringCMappedGraph::GetTitle (void) const
 
bool CMappedGraph::IsSetComment (void) const
 
const stringCMappedGraph::GetComment (void) const
 
const CSeq_locCMappedGraph::GetLoc (void) const
 
bool CMappedGraph::IsSetTitle_x (void) const
 
const stringCMappedGraph::GetTitle_x (void) const
 
bool CMappedGraph::IsSetTitle_y (void) const
 
const stringCMappedGraph::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_GraphCMappedGraph::GetGraph (void) const
 
const TRangeCMappedGraph::GetMappedGraphTotalRange (void) const
 Get the range of graph data used in the mapped graph. More...
 
const TGraphRangesCMappedGraph::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_CICGraph_CI::operator= (const CGraph_CI &iter)
 
virtual CGraph_CI::~CGraph_CI (void)
 
CGraph_CICGraph_CI::operator++ (void)
 
CGraph_CICGraph_CI::operator-- (void)
 
void CGraph_CI::Rewind (void)
 
 CGraph_CI::DECLARE_OPERATOR_BOOL (IsValid())
 
const CGraph_CICGraph_CI::begin () const
 
CGraph_CI CGraph_CI::end () const
 
bool CGraph_CI::operator!= (const CGraph_CI &it) const
 
const CMappedGraphCGraph_CI::operator* (void) const
 
const CMappedGraphCGraph_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)
 
CMappedFeatCMappedFeat::operator= (const CMappedFeat &feat)
 
 CMappedFeat::~CMappedFeat (void)
 
const CSeq_featCMappedFeat::GetOriginalFeature (void) const
 Get original feature with unmapped location/product. More...
 
const CSeq_feat_HandleCMappedFeat::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_featCMappedFeat::GetMappedFeature (void) const
 Feature mapped to the master sequence. More...
 
bool CMappedFeat::IsSetPartial (void) const
 
bool CMappedFeat::GetPartial (void) const
 
const CSeq_locCMappedFeat::GetProduct (void) const
 
const CSeq_locCMappedFeat::GetLocation (void) const
 
CConstRef< CSeq_featCMappedFeat::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
 
CMappedFeatCMappedFeat::Set (CAnnot_Collector &collector, const CAnnotObject_Ref &feat_ref)
 
void CMappedFeat::Reset (void)
 
CConstRef< CSeq_locCMappedFeat::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_CICSeq_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_CICSeq_annot_CI::operator++ (void)
 Move to the next object in iterated sequence. More...
 
CScopeCSeq_annot_CI::GetScope (void) const
 Get the current scope of the iterator. More...
 
const CSeq_annot_HandleCSeq_annot_CI::operator* (void) const
 
const CSeq_annot_HandleCSeq_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 TAnnotsCSeq_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_CICSeq_descr_CI::operator= (const CSeq_descr_CI &iter)
 
CSeq_descr_CICSeq_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_descrCSeq_descr_CI::operator* (void) const
 
const CSeq_descrCSeq_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_InfoCSeq_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_CICSeq_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_CICSeq_entry_CI::operator++ (void)
 Move to the next object in iterated sequence. More...
 
const CSeq_entry_HandleCSeq_entry_CI::operator* (void) const
 
const CSeq_entry_HandleCSeq_entry_CI::operator-> (void) const
 
const CBioseq_set_HandleCSeq_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_CICSeq_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_ICSeq_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_ICSeq_entry_I::operator++ (void)
 
const CSeq_entry_EditHandle CSeq_entry_I::operator* (void) const
 
unique_ptr< const CSeq_entry_EditHandleCSeq_entry_I::operator-> (void) const
 
CBioseq_set_EditHandle CSeq_entry_I::GetParentBioseq_set (void) const
 
CSeq_entry_ICSeq_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 CSeqMapCSeqMap_CI_SegmentInfo::x_GetSeqMap (void) const
 
size_t CSeqMap_CI_SegmentInfo::x_GetIndex (void) const
 
const CSeqMap::CSegmentCSeqMap_CI_SegmentInfo::x_GetSegment (void) const
 
const CSeqMap::CSegmentCSeqMap_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)
 
SSeqMapSelectorSSeqMapSelector::SetPosition (TSeqPos pos)
 Find segment containing the position. More...
 
SSeqMapSelectorSSeqMapSelector::SetRange (TSeqPos start, TSeqPos length)
 Set range for iterator. More...
 
SSeqMapSelectorSSeqMapSelector::SetRange (const TRange &range)
 Set range for iterator - CRange<> version. More...
 
SSeqMapSelectorSSeqMapSelector::SetStrand (ENa_strand strand)
 Set strand to iterate over. More...
 
SSeqMapSelectorSSeqMapSelector::SetResolveCount (size_t res_cnt)
 Set max depth of resolving seq-map. More...
 
SSeqMapSelectorSSeqMapSelector::SetLinkUsedTSE (bool link=true)
 
SSeqMapSelectorSSeqMapSelector::SetLinkUsedTSE (const CTSE_Handle &top_tse)
 
SSeqMapSelectorSSeqMapSelector::SetLinkUsedTSE (vector< CTSE_Handle > &used_tses)
 
SSeqMapSelectorSSeqMapSelector::SetLimitTSE (const CSeq_entry_Handle &tse)
 Limit TSE to resolve references. More...
 
SSeqMapSelectorSSeqMapSelector::SetFlags (TFlags flags)
 Select segment type(s) More...
 
SSeqMapSelectorSSeqMapSelector::SetByFeaturePolicy (void)
 
SSeqMapSelectorSSeqMapSelector::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_HandleSSeqMapSelector::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_CICSeqMap_CI::operator++ (void)
 
CSeqMap_CICSeqMap_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_dataCSeqMap_CI::GetData (void) const
 will allow only regular data segments (whole, plus strand) More...
 
const CSeq_dataCSeqMap_CI::GetRefData (void) const
 will allow any data segments, user should check for position and strand More...
 
CConstRef< CSeq_literalCSeqMap_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
 
CScopeCSeqMap_CI::GetScope (void) const
 
const CTSE_HandleCSeqMap_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 TSegmentInfoCSeqMap_CI::x_GetSegmentInfo (void) const
 
TSegmentInfoCSeqMap_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 CSeqMapCSeqMap_CI::x_GetSeqMap (void) const
 
size_t CSeqMap_CI::x_GetIndex (void) const
 
const CSeqMap::CSegmentCSeqMap_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_ICSeqMap_I::InsertGap (TSeqPos length, CSeq_data *gap_data=0)
 Insert gap. On return the iterator points to the new segment. More...
 
CSeqMap_ICSeqMap_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_ICSeqMap_I::InsertData (TSeqPos length, CSeq_data &data)
 Insert data. On return the iterator points to the new segment. More...
 
CSeqMap_ICSeqMap_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_ICSeqMap_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_locCSeq_table_CI::GetMappedLocation (void) const
 
const CSeq_locCSeq_table_CI::GetOriginalLocation (void) const
 
 CSeq_table_CI::CSeq_table_CI (const CSeq_table_CI &iter)
 
CSeq_table_CICSeq_table_CI::operator= (const CSeq_table_CI &iter)
 
virtual CSeq_table_CI::~CSeq_table_CI (void)
 
CSeq_table_CICSeq_table_CI::operator++ (void)
 
CSeq_table_CICSeq_table_CI::operator-- (void)
 
 CSeq_table_CI::DECLARE_OPERATOR_BOOL (IsValid())
 
const CSeq_table_CICSeq_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_HandleCSeq_table_CI::operator* (void) const
 
const CSeq_annot_HandleCSeq_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_CICSeqVector_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_CICSeqVector_CI::operator++ (void)
 
CSeqVector_CICSeqVector_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_CICSeqVector_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_CICSeqVector_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_literalCSeqVector_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_CICSeqVector_CI::operator+= (TSeqPos value)
 
CSeqVector_CICSeqVector_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_CICSeqdesc_CI::operator= (const CSeqdesc_CI &iter)
 
CSeqdesc_CICSeqdesc_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 CSeqdescCSeqdesc_CI::operator* (void) const
 
const CSeqdescCSeqdesc_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_InfoCSeqdesc_CI::x_GetBaseInfo (void) const
 
void CSeqdesc_CI::x_CheckRef (const CBioseq_Handle &handle)
 

Variables

CConstRef< CSeq_alignCAlign_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< IFeatComparatorSAnnotSelector::m_FeatComparator
 
ELimitObject SAnnotSelector::m_LimitObjectType
 
EUnresolvedFlag SAnnotSelector::m_UnresolvedFlag
 
CConstRef< CObjectSAnnotSelector::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< TNamedAnnotAccessionsSAnnotSelector::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< CHandleRangeMapSAnnotSelector::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_CollectorCMappedGraph::m_Collector
 
const CAnnotObject_RefCMappedGraph::m_GraphRef
 
CConstRef< CSeq_graphCMappedGraph::m_MappedGraph
 
CConstRef< CSeq_locCMappedGraph::m_MappedLoc
 
CMappedGraph CGraph_CI::m_Graph
 
CAnnotMapping_InfoCMappedFeat::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_InfoCSeq_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_CICSeq_entry_CI::m_SubIt
 
CTSE_Handle CSeqMap_CI_SegmentInfo::m_TSE
 
CConstRef< CSeqMapCSeqMap_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< CSeqMapCSeqMap_I::m_SeqMap
 
CConstRef< CSeq_locCSeq_table_CI::m_MappedLoc
 
static const char CSeqVectorTypes::sm_TrivialTable [256]
 
value_type CSeqVector_CI::CTempValue::m_Value
 
CHeapScope CSeqVector_CI::m_Scope
 
CConstRef< CSeqMapCSeqVector_CI::m_SeqMap
 
CTSE_Handle CSeqVector_CI::m_TSE
 
vector< CTSE_HandleCSeqVector_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< INcbi2naRandomizerCSeqVector_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

Definition at line 61 of file seq_vector_ci.hpp.

◆ 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

Definition at line 63 of file seq_vector_ci.hpp.

◆ reference

Definition at line 64 of file seq_vector_ci.hpp.

◆ size_type

Definition at line 60 of file seq_vector_ci.hpp.

◆ TAdaptiveDepthFlags

Definition at line 349 of file annot_selector.hpp.

◆ 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

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

Definition at line 841 of file annot_selector.hpp.

◆ 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

Definition at line 58 of file seq_vector_ci.hpp.

◆ 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

Search features with specified id.

Definition at line 142 of file feat_ci.hpp.

◆ TFeatureIdInt

Definition at line 143 of file feat_ci.hpp.

◆ TFeatureIdStr

Definition at line 144 of file feat_ci.hpp.

◆ TFlags [1/3]

bitwise OR of "EFlags"

Definition at line 82 of file seq_entry_ci.hpp.

◆ TFlags [2/3]

Definition at line 114 of file seq_map_ci.hpp.

◆ TFlags [3/3]

Definition at line 254 of file seq_map_ci.hpp.

◆ TGraphRanges

Definition at line 197 of file graph_ci.hpp.

◆ TIterator

Definition at line 138 of file annot_ci.hpp.

◆ TMaxSearchSegments

Definition at line 462 of file annot_selector.hpp.

◆ 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

Definition at line 610 of file annot_selector.hpp.

◆ TRange [1/2]

Definition at line 196 of file graph_ci.hpp.

◆ TRange [2/2]

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

Definition at line 337 of file seq_map_ci.hpp.

◆ TSeq_feat_Handles

Definition at line 199 of file feat_ci.hpp.

◆ TSeqAnnotSet

Definition at line 137 of file annot_ci.hpp.

◆ 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

Definition at line 59 of file seq_vector_ci.hpp.

Enumeration Type Documentation

◆ 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

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

Enumerator
eCaseConversion_none 
eCaseConversion_upper 
eCaseConversion_lower 

Definition at line 66 of file seq_vector_ci.hpp.

◆ EFlags [1/2]

Enumerator
eSearch_entry 
eSearch_recursive 

Definition at line 75 of file seq_annot_ci.hpp.

◆ EFlags [2/2]

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

Enumerator
eLimit_None 
eLimit_TSE_Info 
eLimit_Seq_entry_Info 
eLimit_Seq_annot_Info 

Definition at line 851 of file annot_selector.hpp.

◆ EMaxSearchSegmentsAction

Enumerator
eMaxSearchSegmentsThrow 
eMaxSearchSegmentsLog 
eMaxSearchSegmentsSilent 

Definition at line 477 of file annot_selector.hpp.

◆ 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

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

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

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)

◆ 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  )

◆ 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 
)

◆ 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 
)

◆ 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

◆ 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

◆ 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

◆ 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)

◆ CSeq_descr_CI() [4/5]

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

◆ 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

◆ 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 
)

◆ CSeqMap_CI() [2/6]

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

◆ 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

◆ CSeqMap_CI() [6/6]

CSeqMap_CI::CSeqMap_CI ( void  )

◆ 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)

◆ ExcludedAnnotName()

bool SAnnotSelector::ExcludedAnnotName ( const CAnnotName name) const

◆ ExcludedTSE() [1/2]

bool SAnnotSelector::ExcludedTSE ( const CSeq_entry_Handle tse) const

◆ ExcludedTSE() [2/2]

bool SAnnotSelector::ExcludedTSE ( const CTSE_Handle tse) const

◆ ExcludeFeatSubtype()

SAnnotSelector & SAnnotSelector::ExcludeFeatSubtype ( TFeatSubtype  subtype)

◆ ExcludeFeatType()

SAnnotSelector & SAnnotSelector::ExcludeFeatType ( TFeatType  type)

◆ ExcludeNamedAnnotAccession()

SAnnotSelector & SAnnotSelector::ExcludeNamedAnnotAccession ( const string acc)

◆ ExcludeNamedAnnots() [1/2]

SAnnotSelector & SAnnotSelector::ExcludeNamedAnnots ( const CAnnotName name)

◆ 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)

◆ ExcludeTSE() [2/2]

SAnnotSelector & SAnnotSelector::ExcludeTSE ( const CTSE_Handle tse)

◆ ExcludeUnnamedAnnots()

SAnnotSelector & SAnnotSelector::ExcludeUnnamedAnnots ( void  )

◆ 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)

◆ GetA()

double CMappedGraph::GetA ( void  ) const
inline

◆ 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

◆ GetAnnot()

CSeq_annot_Handle CMappedGraph::GetAnnot ( void  ) const

◆ GetB()

double CMappedGraph::GetB ( void  ) const
inline

◆ 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

◆ GetComp()

TSeqPos CMappedGraph::GetComp ( void  ) const
inline

◆ GetCurrentSeqMap_CI()

const CSeqMap_CI & CSeqVector_CI::GetCurrentSeqMap_CI ( void  ) const
inline

◆ GetData()

const CSeq_data & CSeqMap_CI::GetData ( void  ) const

◆ GetDefaultAdaptiveDepthFlags()

SAnnotSelector::TAdaptiveDepthFlags SAnnotSelector::GetDefaultAdaptiveDepthFlags ( )
static

◆ 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

◆ GetEndPosition()

TSeqPos CSeqMap_CI::GetEndPosition ( void  ) const
inline

◆ GetExactDepth()

bool SAnnotSelector::GetExactDepth ( void  ) const
inline

◆ 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

◆ GetFeatComparator()

IFeatComparator* SAnnotSelector::GetFeatComparator ( void  ) const
inline

◆ 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

◆ 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

◆ GetIgnoreFarLocationsForSorting()

const CBioseq_Handle& SAnnotSelector::GetIgnoreFarLocationsForSorting ( void  ) const
inline

◆ 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

◆ GetLoc()

const CSeq_loc& CMappedGraph::GetLoc ( void  ) const
inline

◆ 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(), 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_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(), 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

◆ 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

◆ GetMappedLocation() [2/2]

const CSeq_loc & CSeq_table_CI::GetMappedLocation ( void  ) const

◆ 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

◆ 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

◆ 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

◆ 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(), CmRNAFromGeneCdsExon::GetCommand(), CtRNAFromGene::GetCommand(), CTruncateCDS::GetCommand(), CBulkCDS::GetCommandFromValuesTable(), GetFeatureProtein(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CGeneModelFeatJob::GetFilters(), NSnp::GetLength(), CSeqUtils::GetMappingInfo(), GetMrnasForGene(), CCleanup::GetNormalizableGeneQualPairs(), CPubField::GetObjects(), CSrcTableColumnBase::GetObjects(), GetOverlappingFeatures(), GetProductName(), 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_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