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NCBI C++ ToolKit: include/objmgr/annot_selector.hpp Source File

feat_product =

);

feat_product =

);

( GetAnnotType() !=

) {

x_ClearAnnotTypesSet();

x_ClearAnnotTypesSet();

x_ClearAnnotTypesSet();

GetAnnotType() ==

;

IncludedAnnotType(TAnnotType

)

;

IncludedFeatType(TFeatType

)

;

IncludedFeatSubtype(TFeatSubtype subtype)

;

m_FeatProduct;

m_FeatProduct = byProduct;

m_OverlapType;

m_OverlapType = overlap_type;

SetOverlapType(eOverlap_Intervals);

SetOverlapType(eOverlap_TotalRange);

m_FeatComparator = comparator;

m_FeatComparator.Reset();

(0 != m_FeatComparator);

m_FeatComparator.GetNCPointerOrNull();

m_ResolveMethod;

m_ResolveMethod = resolve_method;

SetResolveMethod(eResolve_None);

SetResolveMethod(eResolve_TSE);

SetResolveMethod(eResolve_All);

m_ResolveDepth;

m_ResolveDepth =

;

fAdaptive_Default = 1,

kAdaptive_Default = fAdaptive_Default,

fAdaptive_ByTriggers = 1<<1,

fAdaptive_BySubtypes = 1<<2,

fAdaptive_ByPolicy = 1<<3,

fAdaptive_BySeqClass = 1<<4,

fAdaptive_ByNamedAcc = 1<<5,

kAdaptive_All = (fAdaptive_ByTriggers | fAdaptive_BySubtypes |

fAdaptive_ByPolicy | fAdaptive_BySeqClass |

fAdaptive_ByNamedAcc),

kAdaptive_DefaultBits= (fAdaptive_ByTriggers | fAdaptive_ByPolicy |

fAdaptive_BySeqClass | fAdaptive_ByNamedAcc)

m_AdaptiveDepthFlags != 0;

m_AdaptiveDepthFlags;

TAdaptiveDepthFlags GetDefaultAdaptiveDepthFlags();

SetDefaultAdaptiveDepthFlags(TAdaptiveDepthFlags

);

m_ExactDepth =

;

m_MaxSearchSegments;

eMaxSearchSegmentsSilent

m_MaxSearchSegmentsAction;

m_MaxSearchSegmentsAction = action;

m_MaxSearchTime;

m_LimitObject.NotEmpty();

m_UnresolvedFlag;

m_UnresolvedFlag = flag;

m_UnresolvedFlag = eIgnoreUnresolved;

m_UnresolvedFlag = eSearchUnresolved;

m_UnresolvedFlag = eFailUnresolved;

m_ExcludeExternal = exclude;

m_IncludeAnnotsNames;

m_ExcludeAnnotsNames;

!m_IncludeAnnotsNames.empty() ||

!m_ExcludeAnnotsNames.empty();

!m_IncludeAnnotsNames.empty();

m_HasWildcardInAnnotsNames;

!HasWildcardInAnnotsNames() && IsSetIncludedAnnotsNames();

IncludedAnnotName(

& name)

;

ExcludedAnnotName(

& name)

;

HasIncludedOnlyNamedAnnotAccessions()

;

*m_NamedAnnotAccessions;

m_NamedAnnotAccessions;

IsIncludedNamedAnnotAccession(

& acc)

;

m_NoMapping =

;

m_CollectSeq_annots =

;

m_CollectTypes =

;

m_CollectNames =

;

m_CollectCostOfLoading =

;

m_IgnoreStrand =

;

m_IgnoreFarLocationsForSorting = handle;

m_IgnoreFarLocationsForSorting;

m_FilterMask = filter_mask;

m_FilterBits = filter_bits & filter_mask;

m_FilterMask = m_FilterBits = 0;

m_FilterMask != 0;

m_ExcludeIfGeneIsSuppressed = exclude;

m_ExcludeIfGeneIsSuppressed;

CheckLimitObjectType(

)

;

x_InitializeAnnotTypesSet(

default_value);

x_ClearAnnotTypesSet(

);

eLimit_Seq_annot_Info

* acc_ptr,

* zoom_level_ptr);

namespace ncbi::objects::

static unsigned char depth[2 *(256+1+29)+1]

ESNPScaleLimit

SNP annotation scale limits.

TBitFilter GetFilterMask(void) const

vector< SAnnotTypeSelector > TAdaptiveTriggers

bool HasLimit(void)

Check if the parent object of annotations is set.

AutoPtr< CHandleRangeMap > m_SourceLoc

SAnnotSelector & SetCollectSeq_annots(bool value=true)

Try to avoid collecting multiple objects from the same seq-annot.

TBitFilter GetFilterBits(void) const

bool m_CollectCostOfLoading

EResolveMethod m_ResolveMethod

bool GetExactDepth(void) const

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

SAnnotSelector & SetResolveTSE(void)

SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE).

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

SAnnotSelector & SetExactDepth(bool value=true)

SetExactDepth() specifies that annotations will be searched on the segment level specified by SetReso...

vector< CAnnotName > TAnnotsNames

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

CBioseq_Handle m_IgnoreFarLocationsForSorting

TMaxSearchTime GetMaxSearchTime(void) const

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

bitset< CSeqFeatData::eSubtype_max+3 > TAnnotTypesBitset

ESortOrder

Flag to indicate sorting method.

SAnnotSelector & SetIgnoreUnresolved(void)

TTSE_Limits m_ExcludedTSE

SAnnotSelector & SetCollectTypes(bool value=true)

Collect available annot types rather than annots.

TAdaptiveDepthFlags m_AdaptiveDepthFlags

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetOverlapTotalRange(void)

Check overlapping only of total ranges.

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

bool GetAdaptiveDepth(void) const

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

EUnresolvedFlag m_UnresolvedFlag

const TAnnotsNames & GetExcludedAnnotsNames(void) const

bool IsSetFeatComparator(void) const

CConstRef< CObject > m_LimitObject

bool HasWildcardInAnnotsNames() const

vector< CTSE_Handle > TTSE_Limits

TMaxSearchSegments GetMaxSearchSegments(void) const

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

SAnnotSelector & SetMaxSearchSegmentsAction(EMaxSearchSegmentsAction action)

EMaxSearchSegmentsAction GetMaxSearchSegmentsAction(void) const

SAnnotSelector & SetResolveMethod(EResolveMethod resolve_method)

SetResolveMethod() controls visibility of subsegments depending on whether it's packaged together wit...

IFeatComparator * GetFeatComparator(void) const

SAnnotSelector & SetByProduct(bool byProduct=true)

Set flag indicating if the features should be searched by their product rather than location.

int GetResolveDepth(void) const

GetResolveDepth() returns current limit of subsegment resolution in searching annotations.

ELimitObject m_LimitObjectType

EResolveMethod GetResolveMethod(void) const

GetResolveMethod() returns current value of resolve_method.

SAnnotSelector & SetOverlapType(EOverlapType overlap_type)

Set overlap type.

bool HasBitFilter(void) const

TAnnotTypesBitset m_AnnotTypesBitset

SAnnotSelector & SetNoMapping(bool value=true)

SAnnotSelector & SetExcludeIfGeneIsSuppressed(bool exclude=true)

Exclude features with empty gene xref: xref { { data gene { } } }.

string CombineWithZoomLevel(const string &acc, int zoom_level)

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

EUnresolvedFlag GetUnresolvedFlag(void) const

Get current method of handling unresolved seq-ids.

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

TMaxSearchTime m_MaxSearchTime

TAdaptiveTriggers m_AdaptiveTriggers

TMaxSize GetMaxSize(void) const

Get maximum allowed number of annotations to find.

SAnnotSelector & SetIgnoreFarLocationsForSorting(const CBioseq_Handle &handle)

Set handle used for determining what locations are "near".

AutoPtr< TNamedAnnotAccessions > m_NamedAnnotAccessions

EOverlapType GetOverlapType(void) const

Get the selected overlap type.

SAnnotSelector & SetFeatComparator(IFeatComparator *comparator)

SAnnotSelector & SetSearchUnresolved(void)

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

EOverlapType

Flag to indicate location overlapping method.

virtual bool Less(const CSeq_feat &f1, const CSeq_feat &f2, CScope *scope)=0

SAnnotSelector & ResetFeatComparator(void)

void AddZoomLevel(string &acc, int zoom_level)

EUnresolvedFlag

Flag to indicate handling of unresolved seq-ids.

TMaxSearchSegments m_MaxSearchSegments

SAnnotSelector & SetSNPScaleLimit(TSNPScaleLimit value)

TAdaptiveDepthFlags GetAdaptiveDepthFlags(void) const

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

TSNPScaleLimit GetSNPScaleLimit(void) const

bool HasExplicitAnnotsNames() const

bool IsSetAnnotsNames(void) const

EMaxSearchSegmentsAction m_MaxSearchSegmentsAction

SAnnotSelector & ResetBitFilter(void)

unsigned TMaxSearchSegments

bool CheckAnnotType(TAnnotType type) const

Check annot type (ignore subtypes).

EResolveMethod

Flag to indicate references resolution method.

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

const TAnnotsNames & GetIncludedAnnotsNames(void) const

SAnnotSelector & SetMaxSearchTime(TMaxSearchTime max_time)

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

bool GetFeatProduct(void) const

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

map< string, int > TNamedAnnotAccessions

Uint8 TBitFilter

Set bit filter for annotations that support it (SNP) If filter is set then collect only annotations t...

SAnnotSelector & ResetSNPScaleLimit(void)

TSNPScaleLimit m_SNPScaleLimit

SAnnotSelector & SetMaxSize(TMaxSize max_size)

Set maximum number of annotations to find.

SAnnotSelector & SetBitFilter(TBitFilter filter_bits, TBitFilter filter_mask=TBitFilter(-1))

SAnnotSelector & SetOverlapIntervals(void)

Check overlapping of individual intervals.

const CBioseq_Handle & GetIgnoreFarLocationsForSorting(void) const

bool m_ExcludeIfGeneIsSuppressed

bool GetNoMapping(void) const

SAnnotSelector & SetFailUnresolved(void)

SAnnotSelector & SetResolveNone(void)

SetResolveNone() is equivalent to SetResolveMethod(eResolve_None).

SAnnotSelector & SetUnresolvedFlag(EUnresolvedFlag flag)

Set method of handling unresolved seq-ids.

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

Extract optional zoom level suffix from named annotation string.

EOverlapType m_OverlapType

const TNamedAnnotAccessions & GetNamedAnnotAccessions(void) const

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

Uint1 TAdaptiveDepthFlags

SAnnotSelector & SetCollectCostOfLoading(bool value=true)

Collect cost of loading requested data.

SAnnotSelector & SetIgnoreStrand(bool value=true)

Ignore strand when testing for range overlap.

SAnnotSelector & SetSortOrder(ESortOrder sort_order)

Set sort order of annotations.

bool m_HasWildcardInAnnotsNames

CIRef< IFeatComparator > m_FeatComparator

bool IsSetIncludedAnnotsNames(void) const

TAnnotsNames m_IncludeAnnotsNames

SAnnotSelector & SetMaxSearchSegments(TMaxSearchSegments max_segments)

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

bool GetExcludeIfGeneIsSuppressed(void) const

TAnnotsNames m_ExcludeAnnotsNames

CSeq_id::ESNPScaleLimit TSNPScaleLimit

ESortOrder GetSortOrder(void) const

Get the selected sort order.

@ eSortOrder_Normal

default - increasing start, decreasing length

@ eSortOrder_None

do not sort annotations for faster retrieval

@ eOverlap_Intervals

default - overlapping of individual intervals

@ eIgnoreUnresolved

Ignore unresolved ids (default)

@ eSearchUnresolved

Search annotations for unresolvable IDs.

@ eResolve_TSE

default - search only on segments in the same TSE

@ eResolve_None

Do not search annotations on segments.

@ eMaxSearchSegmentsThrow

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOBJMGR_EXPORT

sort_order

Sort order declaration.

E_Choice

Choice variants.

@ e_not_set

No variant selected.

@ e_not_set

No variant selected.

const GenericPointer< typename T::ValueType > T2 value

CSeq_annot::C_Data::E_Choice TAnnotType

void SetAnnotType(TAnnotType type)

void SetFeatType(TFeatType type)

void SetFeatSubtype(TFeatSubtype subtype)

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