NSearchFeatPanel Namespace Reference

Classes
class	CTrackFeatSubtype

Functions
void	GatherFeatures (const string &text, bool match_case, objects::CBioseq_Handle bsh, objects::CScope &scope, CFeaturePanel *panel, vector< CMappedFeatOrObject > &search_results)
TSeqRange	SplitPosOrRange (const string &text)
void	GetSubtypesForType (set< objects::CSeqFeatData::ESubtype > &subtypes, objects::CSeqFeatData::E_Choice feat)
void	s_GetFeatureLabel (const CSeq_feat &feat, vector< string > &feat_labels, CScope *scope)
void	GatherFeatures (const string &text, bool match_case, CBioseq_Handle bsh, CScope &scope, CFeaturePanel *panel, vector< CMappedFeatOrObject > &search_results)
void	GetSubtypesForType (set< CSeqFeatData::ESubtype > &subtypes, CSeqFeatData::E_Choice feat)
bool	s_UseCustomLabel (const CSeq_feat &feat)
void	s_GetCustomLabel (const CSeq_feat &feat, string &label)
void	s_GetSeqLabel (const CSeq_id &id, string *label, CScope *scope)
void	s_GetSeq_TotalRangeLabel (const CSeq_loc &loc, string *label, CScope *scope)
void	s_LabelFromQualifiers (const CSeq_feat &feat, string &label)
bool	s_IncludeFeatureTypeInLabel (const objects::CSeq_feat &feat)

Function Documentation

GatherFeatures() [1/2]

void NSearchFeatPanel::GatherFeatures	(	const string &	text,
		bool	match_case,
		CBioseq_Handle	bsh,
		CScope &	scope,
		CFeaturePanel *	panel,
		vector< CMappedFeatOrObject > &	search_results
	)

Definition at line 116 of file search_utils.cpp.

References SAnnotSelector::AddNamedAnnots(), SAnnotSelector::AddUnnamedAnnots(), CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CSeq_annot_Base::C_Data::e_Ids, CSeq_annot_Base::C_Data::e_Locs, CSeq_annot_Base::C_Data::e_not_set, CSeq_annot_Base::C_Data::e_Seq_table, CSeqUtils::eAnnot_Unnamed, NStr::eCase, set< Key, Compare >::empty(), NStr::eNocase, CSeqFeatData::eSubtype_variation, CSeqFeatData::eSubtype_variation_ref, SAnnotSelector::ExcludeAnnotType(), f(), NSearchFeatPanel::CTrackFeatSubtype::GetAnnots(), CSeqUtils::GetAnnotSelector(), NSearchFeatPanel::CTrackFeatSubtype::GetAnnotsSnp(), NSearchFeatPanel::CTrackFeatSubtype::GetAnnotsVar(), CSeq_loc::GetId(), CVariantPlacement_Base::GetLoc(), CVcfVariant::GetLocation(), NSearchFeatPanel::CTrackFeatSubtype::GetNamedAnnotSubtypes(), NSearchFeatPanel::CTrackFeatSubtype::GetNonAsnBlobs(), CMappedFeat::GetSeq_feat_Handle(), CBioseq_Handle::GetSeqId(), NSearchFeatPanel::CTrackFeatSubtype::GetSubtypes(), CSeq_loc::GetTotalRange(), CMappedFeat::GetTotalRange(), SAnnotSelector::IncludeFeatSubtype(), SAnnotSelector::IncludeNamedAnnotAccession(), CRegexp::IsMatch(), IsSameBioseq(), CVariantPlacement_Base::IsSetLoc(), kEmptyStr, CSeqUtils::NameTypeStrToValue(), NCBI_ASSERT, NON_CONST_ITERATE, NSearchFeatPanel::CTrackFeatSubtype::NonAsnDataExists(), SAnnotSelector::ResetAnnotsNames(), result, results, s_GetFeatureLabel(), NSNPWebServices::Search(), SAnnotSelector::SetFeatSubtype(), CMappedFeatOrObject::SetMappedFeat(), CMappedFeatOrObject::SetObject(), CMappedFeatOrObject::SetRange(), NSearchFeatPanel::CTrackFeatSubtype::SnpTrackExists(), NStr::StartsWith(), text(), CTrackContainer::Traverse(), and NSearchFeatPanel::CTrackFeatSubtype::VarTrackExists().

GatherFeatures() [2/2]

void NSearchFeatPanel::GatherFeatures	(	const string &	text,
		bool	match_case,
		objects::CBioseq_Handle	bsh,
		objects::CScope &	scope,
		CFeaturePanel *	panel,
		vector< CMappedFeatOrObject > &	search_results
	)

Referenced by CFeaturePanel::FindText().

GetSubtypesForType() [1/2]

void NSearchFeatPanel::GetSubtypesForType	(	set< CSeqFeatData::ESubtype > &	subtypes,
		CSeqFeatData::E_Choice	feat
	)

Definition at line 334 of file search_utils.cpp.

References CSeqFeatData::eSubtype_max, CSeqFeatData::GetTypeFromSubtype(), i, and set< Key, Compare >::insert().

GetSubtypesForType() [2/2]

void NSearchFeatPanel::GetSubtypesForType	(	set< objects::CSeqFeatData::ESubtype > &	subtypes,
		objects::CSeqFeatData::E_Choice	feat
	)

Referenced by CAggregateFeatureTrack::SetFeatTypes(), and CGeneModelTrack::x_AdjustSelector().

s_GetCustomLabel()

void NSearchFeatPanel::s_GetCustomLabel	(	const CSeq_feat &	feat,
		string &	label
	)

Definition at line 552 of file search_utils.cpp.

References CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_region, CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetRegion(), CSeqFeatData::GetSubtype(), CSeqFeatData_Base::IsRegion(), CSeq_feat_Base::IsSetComment(), label, s_IncludeFeatureTypeInLabel(), s_LabelFromQualifiers(), and CSeqFeatData::SubtypeValueToName().

Referenced by s_GetFeatureLabel().

s_GetFeatureLabel()

void NSearchFeatPanel::s_GetFeatureLabel	(	const CSeq_feat &	feat,
		vector< string > &	feat_labels,
		CScope *	scope
	)

Definition at line 349 of file search_utils.cpp.

References CVariation_ref_Base::CanGetId(), NStr::EqualCase(), NStr::EqualNocase(), CSeqFeatData_Base::eSite_other, CSeqFeatData::eSubtype_clone, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_imp, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_seq, CSeqFeatData::eSubtype_site, CSeqFeatData::eSubtype_variation, CSeqFeatData::eSubtype_variation_ref, fFGL_Content, fFGL_NoComments, fFGL_NoQualifiers, CSeqFeatData_Base::GetClone(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CDbtag_Base::GetDb(), CImp_feat_Base::GetDescr(), CSeqFeatData_Base::GetGene(), GetId(), CObject_id_Base::GetId(), CVariation_ref_Base::GetId(), CSeqFeatData_Base::GetImp(), GetLabel(), CSeq_feat_Base::GetLocation(), CGene_ref_Base::GetLocus_tag(), CClone_ref_Base::GetName(), CSeq_feat::GetNamedQual(), CSeq_feat_Base::GetProduct(), CSeq_feat_Base::GetQual(), NSnp::GetRsid(), CSeqFeatData_Base::GetSeq(), CSeqFeatData_Base::GetSite(), CObject_id_Base::GetStr(), CSeqFeatData::GetSubtype(), CDbtag_Base::GetTag(), CSeq_feat_Base::GetTitle(), CSeqFeatData_Base::GetVariation(), NStr::IntToString(), CObject_id_Base::IsId(), CSeq_feat_Base::IsSetComment(), CImp_feat_Base::IsSetDescr(), CSeq_feat_Base::IsSetLocation(), CGene_ref_Base::IsSetLocus_tag(), CClone_ref_Base::IsSetName(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Base::IsSetQual(), CSeq_feat_Base::IsSetTitle(), ITERATE, label, NStr::NumericToString(), s_GetCustomLabel(), s_GetSeq_TotalRangeLabel(), s_GetSeqLabel(), and s_UseCustomLabel().

Referenced by GatherFeatures().

s_GetSeq_TotalRangeLabel()

void NSearchFeatPanel::s_GetSeq_TotalRangeLabel	(	const CSeq_loc &	loc,
		string *	label,
		CScope *	scope
	)

Definition at line 594 of file search_utils.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, NStr::fWithCommas, CPacked_seqint_Base::Get(), CSeq_loc_mix_Base::Get(), GetId(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CPacked_seqpnt_Base::GetPoints(), GetStrand(), CSeq_loc::GetTotalRange(), NStr::IntToString(), kEmptyStr, label, compile_time_bits::range(), s_GetSeqLabel(), NStr::SizetToString(), and CSeq_loc_Base::Which().

Referenced by s_GetFeatureLabel().

s_GetSeqLabel()

void NSearchFeatPanel::s_GetSeqLabel	(	const CSeq_id &	id,
		string *	label,
		CScope *	scope
	)

Definition at line 579 of file search_utils.cpp.

References CSeq_id::eContent, CSeq_id::fLabel_Default, CSeq_id::GetLabel(), and label.

Referenced by s_GetFeatureLabel(), and s_GetSeq_TotalRangeLabel().

s_IncludeFeatureTypeInLabel()

bool NSearchFeatPanel::s_IncludeFeatureTypeInLabel

(

const objects::CSeq_feat &

feat

)

Definition at line 541 of file search_utils.cpp.

References rapidjson::value.

Referenced by s_GetCustomLabel().

s_LabelFromQualifiers()

void NSearchFeatPanel::s_LabelFromQualifiers	(	const CSeq_feat &	feat,
		string &	label
	)

Definition at line 526 of file search_utils.cpp.

References CSeq_feat::GetNamedQual(), label, and rapidjson::value.

Referenced by s_GetCustomLabel().

s_UseCustomLabel()

bool NSearchFeatPanel::s_UseCustomLabel

(

const CSeq_feat &

feat

)

Definition at line 517 of file search_utils.cpp.

References CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_misc_recomb, CSeqFeatData::eSubtype_misc_structure, CSeqFeatData::eSubtype_mobile_element, CSeqFeatData::eSubtype_oriT, CSeqFeatData::eSubtype_protein_bind, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_regulatory, CSeqFeatData::eSubtype_rep_origin, CSeqFeatData::eSubtype_repeat_region, CSeqFeatData::eSubtype_stem_loop, CSeq_feat_Base::GetData(), and CSeqFeatData::GetSubtype().

Referenced by s_GetFeatureLabel().

SplitPosOrRange()

TSeqRange NSearchFeatPanel::SplitPosOrRange

(

const string &

text

)

Definition at line 279 of file search_utils.cpp.

References ctll::empty(), NStr::EndsWith(), NStr::eNocase, CRegexp::fCompile_ignore_case, CRegexp::fMatch_default, CRegexp::GetMatch(), CRegexp::GetSub(), CRegexp::IsMatch(), CRegexp::NumFound(), text(), and NStr::TrimSuffixInPlace().

Referenced by CSeqGraphicPane::FindText().