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NCBI C++ ToolKit: src/objmgr/annot_selector.cpp Source File

m_FeatProduct(feat_product),

m_OverlapType(eOverlap_Intervals),

m_ResolveMethod(eResolve_TSE),

m_SortOrder(eSortOrder_Normal),

m_LimitObjectType(eLimit_None),

m_UnresolvedFlag(eIgnoreUnresolved),

m_MaxSearchTime(FLT_MAX),

m_MaxSearchSegmentsAction(eMaxSearchSegmentsThrow),

m_AdaptiveDepthFlags(kAdaptive_None),

m_ExactDepth(

),

m_ExcludeExternal(

),

m_CollectSeq_annots(

),

m_CollectTypes(

),

m_CollectNames(

),

m_CollectCostOfLoading(

),

m_IgnoreStrand(

),

m_HasWildcardInAnnotsNames(

),

m_ExcludeIfGeneIsSuppressed(

),

m_SNPScaleLimit(

::eSNPScaleLimit_Default)

m_FeatProduct(feat_product),

m_OverlapType(eOverlap_Intervals),

m_ResolveMethod(eResolve_TSE),

m_SortOrder(eSortOrder_Normal),

m_LimitObjectType(eLimit_None),

m_UnresolvedFlag(eIgnoreUnresolved),

m_MaxSearchTime(FLT_MAX),

m_MaxSearchSegmentsAction(eMaxSearchSegmentsThrow),

m_NoMapping(

),

m_AdaptiveDepthFlags(kAdaptive_None),

m_ExactDepth(

),

m_ExcludeExternal(

),

m_CollectSeq_annots(

),

m_CollectTypes(

),

m_CollectNames(

),

m_CollectCostOfLoading(

),

m_IgnoreStrand(

),

m_HasWildcardInAnnotsNames(

),

m_ExcludeIfGeneIsSuppressed(

),

m_SNPScaleLimit(

::eSNPScaleLimit_Default)

m_FeatProduct(

),

m_OverlapType(eOverlap_Intervals),

m_ResolveMethod(eResolve_TSE),

m_SortOrder(eSortOrder_Normal),

m_LimitObjectType(eLimit_None),

m_UnresolvedFlag(eIgnoreUnresolved),

m_MaxSearchTime(FLT_MAX),

m_MaxSearchSegmentsAction(eMaxSearchSegmentsThrow),

m_NoMapping(

),

m_AdaptiveDepthFlags(kAdaptive_None),

m_ExactDepth(

),

m_ExcludeExternal(

),

m_CollectSeq_annots(

),

m_CollectTypes(

),

m_CollectNames(

),

m_CollectCostOfLoading(

),

m_IgnoreStrand(

),

m_HasWildcardInAnnotsNames(

),

m_ExcludeIfGeneIsSuppressed(

),

m_SNPScaleLimit(

::eSNPScaleLimit_Default)

(

!= &sel ) {

sx_HasWildcard(

& name,

* acc_ptr = 0)

& s = name.

();

( s.empty() || s.back() !=

) {

<

TNames,

TName>

sx_Has(

TNames&

,

TName& name)

<

TNames,

TName>

sx_Add(TNames&

,

TName& name)

( !sx_Has(

, name) ) {

.push_back(name);

<

TNames,

TName>

sx_Del(TNames&

,

TName& name)

has_match =

;

( arg_acc.empty() ) {

( incl_acc == arg_acc ) {

( arg_acc.empty() ) {

incl_level = it->second;

( incl_level != -1 && arg_level != incl_level ) {

( arg_acc.empty() ) {

( incl_acc == arg_acc ) {

( !

.IsNamed() ) {

vector_erase(vector<CAnnotName>& v,

& name)

v.erase(

(v.begin(), v.end(), name), v.end());

( zoom_level != 0 && zoom_part != zoom_level ) {

<<acc<<

<<zoom_level);

zoom_level = zoom_part;

(*m_NamedAnnotAccessions)[acc_part] = zoom_level;

( acc_size ==

) {

& tacc = it->first;

( tacc.size() == acc_size ) {

( tacc.size() == acc_size+2 &&

tacc[acc_size] ==

&&

tacc[acc_size+1] ==

) {

( !

(OBJMGR, ADAPTIVE_DEPTH_BY_NAMED_ACC)::GetDefault() ) {

( default_value ) {

(

= range.first;

< range.second; ++

) {

(

= range.first;

< range.second; ++

) {

(

= range.first;

< range.second; ++

) {

(

= range.first;

< range.second; ++

) {

(

= range.first;

< range.second; ++

) {

(

= 0;

< range.first; ++

) {

(

= range.first;

< range.second; ++

) {

(

= range.first;

< range.second; ++

) {

* acc_ptr,

* zoom_level_ptr)

NCBI_PARAM_DEF(bool, OBJMGR, ADAPTIVE_DEPTH_BY_NAMED_ACC, true)

NCBI_PARAM_DECL(bool, OBJMGR, ADAPTIVE_DEPTH_BY_NAMED_ACC)

static SAnnotSelector::TAdaptiveDepthFlags s_DefaultAdaptiveDepthFlags

Annotation iterators exceptions.

const string & GetName(void) const

TFeatSubtype GetFeatSubtype(void) const

TFeatType GetFeatType(void) const

TAnnotType GetAnnotType(void) const

pair< size_t, size_t > TIndexRange

static TIndexRange GetFeatTypeRange(CSeqFeatData::E_Choice type)

static size_t GetSubtypeIndex(CSeqFeatData::ESubtype subtype)

static TIndexRange GetIndexRange(const SAnnotTypeSelector &sel)

static TIndexRange GetAnnotTypeRange(CSeq_annot::C_Data::E_Choice type)

void AddLocation(const CSeq_loc &loc, ETransSplicing trans_splcing=eNoTransSplicing)

static E_Choice GetTypeFromSubtype(ESubtype subtype)

static string CombineWithZoomLevel(const string &acc, int zoom_level)

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

static void AddZoomLevel(string &acc, int zoom_level)

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

Extract optional zoom level suffix from named annotation string.

void Reset(void)

Reset to null state.

const CTSE_Info & x_GetTSE_Info(void) const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

container_type::const_iterator const_iterator

static const struct name_t names[]

static void DLIST_NAME() remove(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const string & GetMsg(void) const

Get message string.

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

const CTSE_Handle & GetTSE_Handle(void) const

const CTSE_Handle & GetTSE_Handle(void) const

const CSeq_entry_Info & x_GetInfo(void) const

const CSeq_annot_Info & x_GetInfo(void) const

vector< SAnnotTypeSelector > TAdaptiveTriggers

AutoPtr< CHandleRangeMap > m_SourceLoc

bool m_CollectCostOfLoading

EResolveMethod m_ResolveMethod

SAnnotSelector(TAnnotType annot=CSeq_annot::C_Data::e_not_set, TFeatType feat=CSeqFeatData::e_not_set, bool feat_product=false)

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetAdaptiveTrigger(const SAnnotTypeSelector &sel)

SetAdaptiveTrigger() allows to change default set of adaptive trigger annotations.

SAnnotSelector & SetResolveTSE(void)

SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE).

SAnnotSelector & ExcludeFeatSubtype(TFeatSubtype subtype)

Exclude feature subtype from the search.

SAnnotSelector & operator=(const SAnnotSelector &sel)

CBioseq_Handle m_IgnoreFarLocationsForSorting

SAnnotSelector & ForceAnnotType(TAnnotType type)

Set annot type, include all subtypes.

SAnnotSelector & ResetUnnamedAnnots(void)

Reset special processing of unnamed annots (added or excluded)

SAnnotSelector & SetAllNamedAnnots(void)

Look for all named Seq-annots Resets the filter, and then excludes unnamed annots.

TTSE_Limits m_ExcludedTSE

TAdaptiveDepthFlags m_AdaptiveDepthFlags

SAnnotSelector & ExcludeFeatType(TFeatType type)

Exclude feature type from the search.

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

SAnnotSelector & ExcludeAnnotType(TAnnotType type)

Exclude annotation type from the search.

SAnnotSelector & SetSearchExternal(const CTSE_Handle &tse)

Set all flags for searching standard GenBank external annotations.

EUnresolvedFlag m_UnresolvedFlag

virtual ~IFeatComparator()

CConstRef< CObject > m_LimitObject

bool HasWildcardInAnnotsNames() const

void CheckLimitObjectType(void) const

SAnnotSelector & SetSourceLoc(const CSeq_loc &loc)

Set filter for source location of annotations.

bool IsIncludedNamedAnnotAccession(const string &acc) const

check if named annot accession is included in the search

SAnnotSelector & ResetAnnotsNames(void)

Select annotations from all Seq-annots.

SAnnotSelector & ExcludeTSE(const CTSE_Handle &tse)

SAnnotSelector & ResetNamedAnnots(const CAnnotName &name)

Reset special processing of named annots (added or excluded)

void x_InitializeAnnotTypesSet(bool default_value)

ELimitObject m_LimitObjectType

SAnnotSelector & SetLimitNone(void)

Remove restrictions on the parent object of annotations.

SAnnotSelector & SetDataSource(const string &name)

Look for named annot.

bool IncludedFeatSubtype(TFeatSubtype subtype) const

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

TAnnotTypesBitset m_AnnotTypesBitset

bool ExcludedAnnotName(const CAnnotName &name) const

SAnnotSelector & SetAdaptiveDepthFlags(TAdaptiveDepthFlags flags)

SetAdaptiveDepthFlags() sets flags for adaptive depth heuristics.

string CombineWithZoomLevel(const string &acc, int zoom_level)

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

SAnnotSelector & SetLimitSeqAnnot(const CSeq_annot_Handle &limit)

Limit annotations to those from the seq-annot only.

TMaxSearchTime m_MaxSearchTime

TAdaptiveTriggers m_AdaptiveTriggers

bool IncludedAnnotType(TAnnotType type) const

Return true if at least one subtype of the type is included or selected type is not set (any).

AutoPtr< TNamedAnnotAccessions > m_NamedAnnotAccessions

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

SAnnotSelector & SetSearchUnresolved(void)

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

void AddZoomLevel(string &acc, int zoom_level)

TMaxSearchSegments m_MaxSearchSegments

EMaxSearchSegmentsAction m_MaxSearchSegmentsAction

SAnnotSelector & IncludeAnnotType(TAnnotType type)

Include annotation type in the search.

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

static TAdaptiveDepthFlags GetDefaultAdaptiveDepthFlags()

Get default set of adaptive depth flags.

SAnnotSelector & ResetExcludedTSE(void)

map< string, int > TNamedAnnotAccessions

TSNPScaleLimit m_SNPScaleLimit

bool IncludedAnnotName(const CAnnotName &name) const

bool HasIncludedOnlyNamedAnnotAccessions() const

bool m_ExcludeIfGeneIsSuppressed

static void SetDefaultAdaptiveDepthFlags(TAdaptiveDepthFlags flags)

Set default set of adaptive depth flags.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

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

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

bool ExcludedTSE(const CTSE_Handle &tse) const

Uint1 TAdaptiveDepthFlags

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

SAnnotSelector & SetLimitTSE(const CTSE_Handle &limit)

Limit annotations to those from the TSE only.

SAnnotSelector & ExcludeUnnamedAnnots(void)

Add unnamed annots to set of annots names to exclude.

bool m_HasWildcardInAnnotsNames

CIRef< IFeatComparator > m_FeatComparator

bool IsSetIncludedAnnotsNames(void) const

SAnnotSelector & ResetSourceLoc(void)

Reset filter for source location of annotations.

TAnnotsNames m_IncludeAnnotsNames

SAnnotSelector & AddUnnamedAnnots(void)

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

SAnnotSelector & ExcludeNamedAnnotAccession(const string &acc)

bool MatchType(const CAnnotObject_Info &annot_info) const

Check if type of the annotation matches the selector.

SAnnotSelector & ResetNamedAnnotAccessions(void)

Add named annot accession (NA*) in the search.

TAnnotsNames m_ExcludeAnnotsNames

bool IncludedFeatType(TFeatType type) const

SAnnotSelector & SetLimitSeqEntry(const CSeq_entry_Handle &limit)

Limit annotations to those from the seq-entry only.

void x_ClearAnnotTypesSet(void)

void Reset(void)

Reset reference object.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

#define numeric_limits

Pre-declaration of the "numeric_limits<>" template Forcibly overrides (using preprocessor) the origin...

#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.

NCBI_NS_STD::string::size_type SIZE_TYPE

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

E_Choice

Choice variants.

@ e_not_set

No variant selected.

@ e_not_set

No variant selected.

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

TFeatSubtype GetFeatSubtype(void) const

CSeq_annot::C_Data::E_Choice TAnnotType

TAnnotType GetAnnotType(void) const

TFeatType GetFeatType(void) const

void SetAnnotType(TAnnotType type)

void SetFeatType(TFeatType type)

void SetFeatSubtype(TFeatSubtype subtype)

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