feature_item.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <serial/iterator.hpp>
#include <serial/enumvalues.hpp>
#include <algorithm>
#include <sstream>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Heterogen.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/OrgMod.hpp>
#include <objects/seqfeat/PCRPrimerSet.hpp>
#include <objects/seqfeat/PCRPrimer.hpp>
#include <objects/seqfeat/PCRReaction.hpp>
#include <objects/seqfeat/PCRReactionSet.hpp>
#include <objects/seqfeat/Code_break.hpp>
#include <objects/seqfeat/Delta_item.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/Gene_nomenclature.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objects/seqfeat/Genetic_code_table.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/RNA_gen.hpp>
#include <objects/seqfeat/RNA_qual_set.hpp>
#include <objects/seqfeat/RNA_qual.hpp>
#include <objects/seqfeat/Trna_ext.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seqfeat/Variation_ref.hpp>
#include <objects/seqfeat/Variation_inst.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Packed_seqpnt.hpp>
#include <objects/seqloc/Textseq_id.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/util/weight.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <util/static_set.hpp>
#include <util/static_map.hpp>
#include <util/sequtil/sequtil.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objtools/format/formatter.hpp>
#include <objtools/format/items/feature_item.hpp>
#include <objtools/format/items/gene_finder.hpp>
#include <objtools/format/context.hpp>
#include <objtools/format/items/qualifiers.hpp>
#include <objmgr/util/objutil.hpp>
#include "inst_info_map.hpp"

Include dependency graph for feature_item.cpp:

Go to the source code of this file.

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Classes
class	CGoQualLessThan
class	BadECNumberChar
struct	SLegalImport
class	CInStringPred

Macros
#define	DO_IMPORT(x)   { #x, eFQ_##x }
#define	DO_QUAL(x)   x_FormatQual(eFQ_##x, #x, qvec)
#define	DO_NOTE(x)   x_FormatNoteQual(eFQ_##x, GetStringOfFeatQual(eFQ_##x), qvec)
#define	DO_NOTE_PREPEND_NEWLINE(x)   x_FormatNoteQual(eFQ_##x, GetStringOfFeatQual(eFQ_##x), qvec, IFlatQVal::fPrependNewline )
#define	DO_QUAL(x)   x_FormatQual(eSQ_##x, GetStringOfSourceQual(eSQ_##x), qvec)
#define	DO_QUAL(x)   x_FormatQual(eSQ_##x, GetStringOfSourceQual(eSQ_##x), qvec)
#define	DO_NOTE(x)   x_FormatNoteQual(eSQ_##x, #x, qvec)

Typedefs
typedef CStaticArraySet< const char *, PNocase >	TLegalPseudoGeneText
typedef CStaticArraySet< const char *, PNocase_CStr >	TLegalExceptText
typedef CStaticArraySet< const char *, PNocase >	TLegalRefSeqExceptText
typedef SStaticPair< const char *, bool >	TMobileElemTypeKey
typedef CStaticPairArrayMap< const char *, bool, PCase_CStr >	TMobileElemTypeMap
typedef SStaticPair< EFeatureQualifier, CSeqFeatData::EQualifier >	TQualPair
typedef CStaticPairArrayMap< EFeatureQualifier, CSeqFeatData::EQualifier >	TQualMap

Functions
	USING_SCOPE (sequence)
static bool	s_ValidId (const CSeq_id &id)
static bool	s_StrEqualDisregardFinalPeriod (const string &s1, const string &s2, NStr::ECase use_case)
static bool	s_CheckQuals_cdregion (const CMappedFeat &feat, const CSeq_loc &loc, CBioseqContext &ctx)
static bool	s_HasPub (const CMappedFeat &feat, CBioseqContext &ctx)
static bool	s_HasCompareOrCitation (const CMappedFeat &feat, CBioseqContext &ctx)
static bool	s_CheckQuals_conflict (const CMappedFeat &feat, CBioseqContext &ctx)
static bool	s_CheckQuals_old_seq (const CMappedFeat &feat, CBioseqContext &ctx)
static bool	s_CheckQuals_gene (const CMappedFeat &feat)
static bool	s_CheckQuals_bind (const CMappedFeat &feat)
static bool	s_CheckQuals_mod_base (const CMappedFeat &feat)
static bool	s_CheckQuals_gap (const CMappedFeat &feat)
static bool	s_CheckQuals_assembly_gap (const CMappedFeat &feat)
static bool	s_CheckQuals_ncRNA (const CMappedFeat &feat)
static bool	s_CheckQuals_regulatory (const CMappedFeat &feat)
static bool	s_CheckMandatoryQuals (const CMappedFeat &feat, const CSeq_loc &loc, CBioseqContext &ctx)
static bool	s_SkipFeature (const CMappedFeat &feat, const CSeq_loc &loc, CBioseqContext &ctx)
static bool	s_IsLegalECNumber (const string &ec_number)
static const string &	s_GetBondName (CSeqFeatData::TBond bond)
static void	s_QualVectorToNote (const CFlatFeature::TQuals &qualVector, bool noRedundancy, string &note, string &punctuation, bool &addPeriod)
static void	s_NoteFinalize (bool addPeriod, string &noteStr, CFlatFeature &flatFeature, ETildeStyle style=eTilde_newline)
static int	s_GetOverlap (const CMappedFeat &feat)
static CMappedFeat	s_GetBestProtFeature (const CBioseq_Handle &seq)
	The best protein feature is defined as the one that has the most overlap with the given DNA. More...
static bool	s_CheckFuzz (const CInt_fuzz &fuzz)
static bool	s_LocIsFuzz (const CMappedFeat &feat, const CSeq_loc &loc)
static void	s_AddPcrPrimersQualsAppend (string &output, const string &name, const string &str)
static void	s_SplitCommaSeparatedStringInParens (vector< string > &output_vec, const string &string_to_split)
	DEFINE_STATIC_ARRAY_MAP (TLegalPseudoGeneText, sc_ValidPseudoGeneText, sc_ValidPseudoGene)
static bool	s_IsValidPseudoGene (objects::CFlatFileConfig::TMode mode, const string &text)
	DEFINE_STATIC_ARRAY_MAP (TLegalExceptText, sc_LegalExceptText, sc_ValidExceptionText)
static bool	s_IsValidExceptionText (const string &text)
	DEFINE_STATIC_ARRAY_MAP (TLegalRefSeqExceptText, sc_LegalRefSeqExceptText, sc_ValidRefSeqExceptionText)
static bool	s_IsValidRefSeqExceptionText (const string &text)
static bool	s_TransSplicingFeatureAllowed (const CSeqFeatData &data)
static const string &	s_AaName (int aa)
static int	s_ToIupacaa (int aa)
static int	s_ScoreSeqIdHandle (const CSeq_id_Handle &idh)
CSeq_id_Handle	s_FindBestIdChoice (const CBioseq_Handle::TId &ids)
static const string &	s_GetSiteName (CSeqFeatData::TSite site)
static void	s_ParseParentQual (const CGb_qual &gbqual, list< string > &vals)
static bool	s_IsValidDirection (const string &direction)
static bool	s_IsValidnConsSplice (const string &cons_splice)
static void	s_HTMLizeExperimentQual (string &out_new_val, const string &val)
static bool	s_IsValidRegulatoryClass (const string &type)
static bool	s_IsValidRecombinationClass (const string &type)
	DEFINE_STATIC_ARRAY_MAP (TMobileElemTypeMap, sm_MobileElemTypeKeys, mobile_element_key_to_suffix_required)
bool	s_ValidateMobileElementType (const string &mobile_element_type_value)
	DEFINE_STATIC_ARRAY_MAP (TQualMap, sc_QualMap, sc_GbToFeatQualMap)
static CSeqFeatData::EQualifier	s_GbToSeqFeatQual (EFeatureQualifier qual)
static const string	s_GetSubtypeString (const COrgMod::TSubtype &subtype)
static const string	s_GetSubsourceString (const CSubSource::TSubtype &subtype)
static ESourceQualifier	s_OrgModToSlot (const COrgMod &om)
static string	s_GetSpecimenVoucherText (CBioseqContext &ctx, const string &strRawName)
static ESourceQualifier	s_SubSourceToSlot (const CSubSource &ss)

Variables
static const char *const	sc_ValidPseudoGene []
static const char *const	sc_ValidExceptionText []
static const char *const	sc_ValidRefSeqExceptionText []
static const string	s_TrnaList []
static const TMobileElemTypeKey	mobile_element_key_to_suffix_required []
static const TQualPair	sc_GbToFeatQualMap []

Macro Definition Documentation

DO_IMPORT

#define DO_IMPORT

(

x

)

{ #x, eFQ_##x }

DO_NOTE [1/2]

#define DO_NOTE

(

x

)

x_FormatNoteQual(eFQ_##x, GetStringOfFeatQual(eFQ_##x), qvec)

DO_NOTE [2/2]

#define DO_NOTE

(

x

)

x_FormatNoteQual(eSQ_##x, #x, qvec)

DO_NOTE_PREPEND_NEWLINE

#define DO_NOTE_PREPEND_NEWLINE

(

x

)

x_FormatNoteQual(eFQ_##x, GetStringOfFeatQual(eFQ_##x), qvec, IFlatQVal::fPrependNewline )

DO_QUAL [1/3]

#define DO_QUAL

(

x

)

x_FormatQual(eFQ_##x, #x, qvec)

DO_QUAL [2/3]

#define DO_QUAL

(

x

)

x_FormatQual(eSQ_##x, GetStringOfSourceQual(eSQ_##x), qvec)

DO_QUAL [3/3]

#define DO_QUAL

(

x

)

x_FormatQual(eSQ_##x, GetStringOfSourceQual(eSQ_##x), qvec)

Typedef Documentation

TLegalExceptText

typedef CStaticArraySet<const char*, PNocase_CStr> TLegalExceptText

Definition at line 939 of file feature_item.cpp.

TLegalPseudoGeneText

typedef CStaticArraySet<const char*, PNocase> TLegalPseudoGeneText

Definition at line 918 of file feature_item.cpp.

TLegalRefSeqExceptText

typedef CStaticArraySet<const char*, PNocase> TLegalRefSeqExceptText

Definition at line 965 of file feature_item.cpp.

TMobileElemTypeKey

typedef SStaticPair<const char *, bool> TMobileElemTypeKey

Definition at line 4968 of file feature_item.cpp.

TMobileElemTypeMap

typedef CStaticPairArrayMap<const char*, bool, PCase_CStr> TMobileElemTypeMap

Definition at line 4981 of file feature_item.cpp.

TQualMap

typedef CStaticPairArrayMap<EFeatureQualifier, CSeqFeatData::EQualifier> TQualMap

Definition at line 5370 of file feature_item.cpp.

TQualPair

typedef SStaticPair<EFeatureQualifier, CSeqFeatData::EQualifier> TQualPair

Definition at line 5253 of file feature_item.cpp.

Function Documentation

DEFINE_STATIC_ARRAY_MAP() [1/5]

DEFINE_STATIC_ARRAY_MAP	(	TLegalExceptText	,
		sc_LegalExceptText	,
		sc_ValidExceptionText
	)

DEFINE_STATIC_ARRAY_MAP() [2/5]

DEFINE_STATIC_ARRAY_MAP	(	TLegalPseudoGeneText	,
		sc_ValidPseudoGeneText	,
		sc_ValidPseudoGene
	)

Referenced by CFeatureItem::x_AddQualProteinId(), and CFeatureItem::x_ImportQuals().

DEFINE_STATIC_ARRAY_MAP() [3/5]

DEFINE_STATIC_ARRAY_MAP	(	TLegalRefSeqExceptText	,
		sc_LegalRefSeqExceptText	,
		sc_ValidRefSeqExceptionText
	)

DEFINE_STATIC_ARRAY_MAP() [4/5]

DEFINE_STATIC_ARRAY_MAP	(	TMobileElemTypeMap	,
		sm_MobileElemTypeKeys	,
		mobile_element_key_to_suffix_required
	)

DEFINE_STATIC_ARRAY_MAP() [5/5]

DEFINE_STATIC_ARRAY_MAP	(	TQualMap	,
		sc_QualMap	,
		sc_GbToFeatQualMap
	)

s_AaName()

static const string& s_AaName ( int  aa )

static

Definition at line 2126 of file feature_item.cpp.

References ArraySize(), kEmptyStr, and s_TrnaList.

Referenced by CFeatureItem::x_AddQualsRna().

s_AddPcrPrimersQualsAppend()

static void s_AddPcrPrimersQualsAppend ( string &  output, const string &  name, const string &  str  )

static

Definition at line 874 of file feature_item.cpp.

References output, and str().

Referenced by CSourceFeatureItem::x_AddPcrPrimersQuals().

s_CheckFuzz()

static bool s_CheckFuzz ( const CInt_fuzz &  fuzz )

static

Definition at line 801 of file feature_item.cpp.

References CInt_fuzz_Base::eLim_unk, CInt_fuzz_Base::GetLim(), and CInt_fuzz_Base::IsLim().

Referenced by s_LocIsFuzz().

s_CheckMandatoryQuals()

static bool s_CheckMandatoryQuals ( const CMappedFeat &  feat, const CSeq_loc &  loc, CBioseqContext &  ctx  )

static

Definition at line 431 of file feature_item.cpp.

References ctx, CSeqFeatData::eSubtype_assembly_gap, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_conflict, CSeqFeatData::eSubtype_gap, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_binding, CSeqFeatData::eSubtype_modified_base, CSeqFeatData::eSubtype_ncRNA, CSeqFeatData::eSubtype_old_sequence, CSeqFeatData::eSubtype_protein_bind, CSeqFeatData::eSubtype_regulatory, CSeq_feat_Handle::GetData(), CSeqFeatData::GetSubtype(), s_CheckQuals_assembly_gap(), s_CheckQuals_bind(), s_CheckQuals_cdregion(), s_CheckQuals_conflict(), s_CheckQuals_gap(), s_CheckQuals_gene(), s_CheckQuals_mod_base(), s_CheckQuals_ncRNA(), s_CheckQuals_old_seq(), and s_CheckQuals_regulatory().

Referenced by s_SkipFeature().

s_CheckQuals_assembly_gap()

static bool s_CheckQuals_assembly_gap ( const CMappedFeat &  feat )

static

Definition at line 396 of file feature_item.cpp.

References CSeq_feat_Handle::GetNamedQual().

Referenced by s_CheckMandatoryQuals().

s_CheckQuals_bind()

static bool s_CheckQuals_bind ( const CMappedFeat &  feat )

static

Definition at line 376 of file feature_item.cpp.

References CSeq_feat_Handle::GetNamedQual(), and NStr::IsBlank().

Referenced by s_CheckMandatoryQuals().

s_CheckQuals_cdregion()

static bool s_CheckQuals_cdregion ( const CMappedFeat &  feat, const CSeq_loc &  loc, CBioseqContext &  ctx  )

static

Definition at line 219 of file feature_item.cpp.

References ctx, eExtreme_Biological, NStr::Find(), GetAccessionForGi(), CScope::GetBioseqHandleFromTSE(), CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetExcept(), CSeq_feat_Handle::GetExcept_text(), CSeqFeatData_Base::GetGene(), CSeq_feat_Handle::GetGeneXref(), CSeq_id_Base::GetGi(), GetId(), CBioseq_Handle::GetId(), GetLength(), CMappedFeat::GetLocation(), GetOverlappingGene(), CMappedFeat::GetProduct(), CGene_ref_Base::GetPseudo(), CSeq_feat_Base::GetPseudo(), CSeq_feat_Handle::GetPseudo(), CSeq_id::GetTextseq_Id(), CSeq_id_Base::IsGi(), CSeq_feat_Handle::IsSetExcept(), CSeq_feat_Handle::IsSetExcept_text(), CSeq_feat_Handle::IsSetProduct(), CSeq_feat_Base::IsSetPseudo(), CSeq_feat_Handle::IsSetPseudo(), IsValidAccession(), ITERATE, Loc, NPOS, CConstRef< C, Locker >::Reset(), s_ValidId(), and ZERO_GI.

Referenced by s_CheckMandatoryQuals().

s_CheckQuals_conflict()

static bool s_CheckQuals_conflict ( const CMappedFeat &  feat, CBioseqContext &  ctx  )

static

Definition at line 343 of file feature_item.cpp.

References ctx, CSeq_feat_Handle::GetComment(), NStr::IsBlank(), CSeq_feat_Handle::IsSetComment(), and s_HasCompareOrCitation().

Referenced by s_CheckMandatoryQuals().

s_CheckQuals_gap()

static bool s_CheckQuals_gap ( const CMappedFeat &  feat )

static

Definition at line 390 of file feature_item.cpp.

References CSeq_feat_Handle::GetNamedQual().

Referenced by s_CheckMandatoryQuals().

s_CheckQuals_gene()

static bool s_CheckQuals_gene ( const CMappedFeat &  feat )

static

Definition at line 361 of file feature_item.cpp.

References CSeq_feat_Handle::GetData(), CGene_ref_Base::GetDesc(), CSeqFeatData_Base::GetGene(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::GetSyn(), CGene_ref_Base::IsSetDesc(), CGene_ref_Base::IsSetLocus(), and CGene_ref_Base::IsSetLocus_tag().

Referenced by s_CheckMandatoryQuals().

s_CheckQuals_mod_base()

static bool s_CheckQuals_mod_base ( const CMappedFeat &  feat )

static

Definition at line 383 of file feature_item.cpp.

References CSeq_feat_Handle::GetNamedQual(), and NStr::IsBlank().

Referenced by s_CheckMandatoryQuals().

s_CheckQuals_ncRNA()

static bool s_CheckQuals_ncRNA ( const CMappedFeat &  feat )

static

Definition at line 405 of file feature_item.cpp.

References CRNA_gen_Base::GetClass(), CSeq_feat_Handle::GetData(), CRNA_ref_Base::GetExt(), CRNA_ref_Base::C_Ext::GetGen(), CSeq_feat_Handle::GetNamedQual(), CSeqFeatData_Base::GetRna(), NStr::IsBlank(), CRNA_ref_Base::C_Ext::IsGen(), CRNA_gen_Base::IsSetClass(), and CRNA_ref_Base::IsSetExt().

Referenced by s_CheckMandatoryQuals().

s_CheckQuals_old_seq()

static bool s_CheckQuals_old_seq ( const CMappedFeat &  feat, CBioseqContext &  ctx  )

static

Definition at line 355 of file feature_item.cpp.

References ctx, and s_HasCompareOrCitation().

Referenced by s_CheckMandatoryQuals().

s_CheckQuals_regulatory()

static bool s_CheckQuals_regulatory ( const CMappedFeat &  feat )

static

Definition at line 424 of file feature_item.cpp.

References CSeq_feat_Handle::GetNamedQual().

Referenced by s_CheckMandatoryQuals().

s_FindBestIdChoice()

CSeq_id_Handle s_FindBestIdChoice

(

const CBioseq_Handle::TId &

ids

)

Definition at line 3113 of file feature_item.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Other, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, int, ITERATE, and s_ScoreSeqIdHandle().

Referenced by CFeatureItem::x_AddProductIdQuals().

s_GbToSeqFeatQual()

static CSeqFeatData::EQualifier s_GbToSeqFeatQual ( EFeatureQualifier  qual )

static

Definition at line 5373 of file feature_item.cpp.

References CSeqFeatData::eQual_bad.

Referenced by CFeatureItem::x_DropIllegalQuals().

s_GetBestProtFeature()

static CMappedFeat s_GetBestProtFeature ( const CBioseq_Handle &  seq )

static

The best protein feature is defined as the one that has the most overlap with the given DNA.

If there is a tie between two protein features in overlap then the one with the lesser processing status is declared the winner.

Definition at line 744 of file feature_item.cpp.

References CSeqFeatData_Base::e_Prot, CProt_ref_Base::eProcessed_transit_peptide, CSeq_feat_Handle::GetData(), CProt_ref_Base::GetProcessed(), CSeqFeatData_Base::GetProt(), CBioseq_Handle::GetTSE_Handle(), s_GetOverlap(), and SAnnotSelector::SetLimitTSE().

Referenced by CFeatureItem::x_AddFTableCdregionQuals(), CFeatureItem::x_AddQualSeqfeatNote(), and CFeatureItem::x_GetAssociatedProtInfo().

s_GetBondName()

static const string& s_GetBondName ( CSeqFeatData::TBond  bond )

static

Definition at line 652 of file feature_item.cpp.

References CSeqFeatData_Base::eBond_other, and ENUM_METHOD_NAME.

Referenced by CFeatureItem::x_AddFTableBondQuals(), and CFeatureItem::x_AddQualsBond().

s_GetOverlap()

static int s_GetOverlap ( const CMappedFeat &  feat )

static

Definition at line 725 of file feature_item.cpp.

References CMappedFeat::GetLocation(), and ITERATE.

Referenced by s_GetBestProtFeature().

s_GetSiteName()

static const string& s_GetSiteName ( CSeqFeatData::TSite  site )

static

Definition at line 3389 of file feature_item.cpp.

References ENUM_METHOD_NAME, CSeqFeatData_Base::eSite_dna_binding, CSeqFeatData_Base::eSite_inhibit, CSeqFeatData_Base::eSite_other, and site.

Referenced by CFeatureItem::x_AddFTableSiteQuals(), and CFeatureItem::x_AddQualsSite().

s_GetSpecimenVoucherText()

static string s_GetSpecimenVoucherText ( CBioseqContext &  ctx, const string &  strRawName  )

static

Definition at line 6168 of file feature_item.cpp.

References ctx, COrgMod::GetInstitutionFullName(), CInstInfoMap::GetInstitutionVoucherInfo(), int, NStr::IsBlank(), COrgMod::ParseStructuredVoucher(), NStr::Replace(), NStr::StartsWith(), text(), NStr::TrimPrefixInPlace(), and NStr::TruncateSpacesInPlace().

Referenced by CSourceFeatureItem::x_AddQuals().

s_GetSubsourceString()

static const string s_GetSubsourceString ( const CSubSource::TSubtype &  subtype )

static

Definition at line 6008 of file feature_item.cpp.

References CSubSource_Base::eSubtype_cell_line, CSubSource_Base::eSubtype_cell_type, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_clone_lib, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_dev_stage, CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_frequency, CSubSource_Base::eSubtype_genotype, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_haplogroup, CSubSource_Base::eSubtype_haplotype, CSubSource_Base::eSubtype_insertion_seq_name, CSubSource_Base::eSubtype_isolation_source, CSubSource_Base::eSubtype_lab_host, CSubSource_Base::eSubtype_map, CSubSource_Base::eSubtype_other, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_plastid_name, CSubSource_Base::eSubtype_pop_variant, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_segment, CSubSource_Base::eSubtype_sex, CSubSource_Base::eSubtype_subclone, CSubSource_Base::eSubtype_tissue_lib, CSubSource_Base::eSubtype_tissue_type, CSubSource_Base::eSubtype_transgenic, CSubSource_Base::eSubtype_transposon_name, and kEmptyStr.

Referenced by CFeatureItem::x_AddFTableBiosrcQuals().

s_GetSubtypeString()

static const string s_GetSubtypeString ( const COrgMod::TSubtype &  subtype )

static

Definition at line 5959 of file feature_item.cpp.

References COrgMod_Base::eSubtype_acronym, COrgMod_Base::eSubtype_anamorph, COrgMod_Base::eSubtype_authority, COrgMod_Base::eSubtype_bio_material, COrgMod_Base::eSubtype_biotype, COrgMod_Base::eSubtype_biovar, COrgMod_Base::eSubtype_breed, COrgMod_Base::eSubtype_chemovar, COrgMod_Base::eSubtype_common, COrgMod_Base::eSubtype_cultivar, COrgMod_Base::eSubtype_culture_collection, COrgMod_Base::eSubtype_dosage, COrgMod_Base::eSubtype_ecotype, COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_forma_specialis, COrgMod_Base::eSubtype_gb_acronym, COrgMod_Base::eSubtype_gb_anamorph, COrgMod_Base::eSubtype_gb_synonym, COrgMod_Base::eSubtype_group, COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_metagenome_source, COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_old_lineage, COrgMod_Base::eSubtype_old_name, COrgMod_Base::eSubtype_other, COrgMod_Base::eSubtype_pathovar, COrgMod_Base::eSubtype_serogroup, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_serovar, COrgMod_Base::eSubtype_specimen_voucher, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_sub_species, COrgMod_Base::eSubtype_subgroup, COrgMod_Base::eSubtype_substrain, COrgMod_Base::eSubtype_subtype, COrgMod_Base::eSubtype_synonym, COrgMod_Base::eSubtype_teleomorph, COrgMod_Base::eSubtype_type, COrgMod_Base::eSubtype_type_material, COrgMod_Base::eSubtype_variety, and kEmptyStr.

Referenced by CFeatureItem::x_AddFTableBiosrcQuals().

s_HasCompareOrCitation()

static bool s_HasCompareOrCitation ( const CMappedFeat &  feat, CBioseqContext &  ctx  )

static

Definition at line 326 of file feature_item.cpp.

References ctx, CSeq_feat_Handle::GetNamedQual(), NStr::IsBlank(), CSeq_feat_Handle::IsSetCit(), and s_HasPub().

Referenced by s_CheckQuals_conflict(), and s_CheckQuals_old_seq().

s_HasPub()

static bool s_HasPub ( const CMappedFeat &  feat, CBioseqContext &  ctx  )

static

Definition at line 314 of file feature_item.cpp.

References ctx, CSeq_feat_Handle::GetCit(), and ITERATE.

Referenced by s_HasCompareOrCitation().

s_HTMLizeExperimentQual()

static void s_HTMLizeExperimentQual ( string &  out_new_val, const string &  val  )

static

Definition at line 4072 of file feature_item.cpp.

References copy(), isdigit(), NPOS, strLinkBasePubmed, and val.

Referenced by CFeatureItem::x_ImportQuals().

s_IsLegalECNumber()

static bool s_IsLegalECNumber ( const string &  ec_number )

static

Definition at line 608 of file feature_item.cpp.

References isdigit(), and ITERATE.

Referenced by CFeatureItem::x_AddQualProtEcNumber(), CFeatureItem::x_AddQualsProt(), and CFeatureItem::x_ImportQuals().

s_IsValidDirection()

static bool s_IsValidDirection ( const string &  direction )

static

Definition at line 4051 of file feature_item.cpp.

References NStr::EqualNocase().

Referenced by CSequenceAmbigTrimmer::x_FindWhereToTrim(), CFeatureItem::x_ImportQuals(), CSequenceAmbigTrimmer::x_SegmentGetEndInclusive(), and CSequenceAmbigTrimmer::x_SeqMapIterDoNext().

s_IsValidExceptionText()

static bool s_IsValidExceptionText ( const string &  text )

static

Definition at line 942 of file feature_item.cpp.

References text().

Referenced by CFeatureItem::x_AddQualExceptions().

s_IsValidnConsSplice()

static bool s_IsValidnConsSplice ( const string &  cons_splice )

static

Definition at line 4058 of file feature_item.cpp.

References NStr::EqualNocase().

Referenced by CFeatureItem::x_ImportQuals().

s_IsValidPseudoGene()

static bool s_IsValidPseudoGene ( objects::CFlatFileConfig::TMode  mode, const string &  text  )

static

Definition at line 921 of file feature_item.cpp.

References text().

Referenced by CFeatureItem::x_CleanQuals().

s_IsValidRecombinationClass()

static bool s_IsValidRecombinationClass ( const string &  type )

static

Definition at line 4514 of file feature_item.cpp.

References NStr::Equal(), FOR_EACH_STRING_IN_VECTOR, CSeqFeatData::GetRecombinationClassList(), and str().

Referenced by CFeatureItem::x_AddRecombinationClassQual().

s_IsValidRefSeqExceptionText()

static bool s_IsValidRefSeqExceptionText ( const string &  text )

static

Definition at line 968 of file feature_item.cpp.

References text().

Referenced by CFeatureItem::x_AddQualExceptions().

s_IsValidRegulatoryClass()

static bool s_IsValidRegulatoryClass ( const string &  type )

static

Definition at line 4502 of file feature_item.cpp.

References NStr::Equal(), FOR_EACH_STRING_IN_VECTOR, CSeqFeatData::GetRegulatoryClassList(), and str().

Referenced by CFeatureItem::x_AddRegulatoryClassQual().

s_LocIsFuzz()

static bool s_LocIsFuzz ( const CMappedFeat &  feat, const CSeq_loc &  loc  )

static

Definition at line 806 of file feature_item.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_CI::eEmpty_Allow, eExtreme_Biological, CSeqFeatData::eSubtype_imp, CSeq_feat_Handle::GetData(), CSeqFeatData_Base::GetImp(), CImp_feat_Base::GetLoc(), CSeqFeatData::GetSubtype(), CSeqFeatData_Base::IsImp(), CImp_feat_Base::IsSetLoc(), l(), NPOS, and s_CheckFuzz().

Referenced by CFeatureItem::x_AddQualPartial().

s_NoteFinalize()

static void s_NoteFinalize ( bool  addPeriod, string &  noteStr, CFlatFeature &  flatFeature, ETildeStyle  style = eTilde_newline  )

static

Definition at line 705 of file feature_item.cpp.

References AddPeriod(), NStr::EndsWith(), ExpandTildes(), CFlatFeature::SetQuals(), and TrimSpacesAndJunkFromEnds().

Referenced by CFeatureItem::x_FormatNoteQuals(), and CSourceFeatureItem::x_FormatNoteQuals().

s_OrgModToSlot()

static ESourceQualifier s_OrgModToSlot ( const COrgMod &  om )

static

Definition at line 6163 of file feature_item.cpp.

References GetSourceQualOfOrgMod(), and om.

Referenced by CSourceFeatureItem::x_AddQuals().

s_ParseParentQual()

static void s_ParseParentQual ( const CGb_qual &  gbqual, list< string > &  vals  )

static

Definition at line 4013 of file feature_item.cpp.

References ConvertQuotes(), NStr::EndsWith(), eTilde_space, ExpandTildes(), NStr::fSplit_Tokenize, CGb_qual_Base::GetVal(), NStr::IsBlank(), CGb_qual_Base::IsSetVal(), NPOS, NStr::Split(), NStr::StartsWith(), and val.

Referenced by CFeatureItem::x_ImportQuals().

s_QualVectorToNote()

static void s_QualVectorToNote ( const CFlatFeature::TQuals &  qualVector, bool  noRedundancy, string &  note, string &  punctuation, bool &  addPeriod  )

static

Definition at line 659 of file feature_item.cpp.

References NStr::EndsWith(), CFormatQual::fFlags_showEvenIfRedund, ITERATE, and JoinString().

Referenced by CFeatureItem::x_FormatNoteQuals(), and CSourceFeatureItem::x_FormatNoteQuals().

s_ScoreSeqIdHandle()

static int s_ScoreSeqIdHandle ( const CSeq_id_Handle &  idh )

static

Definition at line 3104 of file feature_item.cpp.

References CSeq_id_Handle::GetSeqId(), and CSeq_id::Score().

Referenced by s_FindBestIdChoice().

s_SkipFeature()

static bool s_SkipFeature ( const CMappedFeat &  feat, const CSeq_loc &  loc, CBioseqContext &  ctx  )

static

Definition at line 484 of file feature_item.cpp.

References ctx, CSeqFeatData_Base::e_Bond, CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Comment, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Region, CSeqFeatData_Base::e_Rna, CSeqFeatData_Base::e_Site, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_transcribed_RNA, CSeqFeatData::eSubtype_allele, CSeqFeatData::eSubtype_bad, CSeqFeatData::eSubtype_biosrc, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_het, CSeqFeatData::eSubtype_imp, CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mutation, CSeqFeatData::eSubtype_preprotein, CSeqFeatData::eSubtype_pub, CSeqFeatData::eSubtype_rsite, CSeqFeatData::eSubtype_seq, CSeqFeatData::eSubtype_site_ref, CSeqFeatData::eSubtype_variation, CSeqFeatData::eSubtype_virion, CFlatFileConfig::GeneRNACDSFeatures(), CSeq_feat_Handle::GetData(), CDbtag_Base::GetDb(), CSeq_feat_Handle::GetDbxref(), CSeqFeatData::GetSubtype(), CFlatFileConfig::HideExonFeatures(), CFlatFileConfig::HideImpFeatures(), CFlatFileConfig::HideIntronFeatures(), CFlatFileConfig::HideMiscFeatures(), CFlatFileConfig::HideRemoteImpFeatures(), CFlatFileConfig::IsFormatDDBJ(), CFlatFileConfig::IsPolicyGenomes(), CDbtag_Base::IsSetDb(), ITERATE, CFlatFileConfig::NeedRequiredQuals(), s_CheckMandatoryQuals(), CFlatFileConfig::ValidateFeatures(), and CSeqFeatData_Base::Which().

Referenced by CFeatureItem::x_GatherInfoWithParent().

s_SplitCommaSeparatedStringInParens()

static void s_SplitCommaSeparatedStringInParens ( vector< string > &  output_vec, const string &  string_to_split  )

static

Definition at line 887 of file feature_item.cpp.

References NStr::Split().

Referenced by CFeatureItem::x_AddRptTypeQual().

s_StrEqualDisregardFinalPeriod()

static bool s_StrEqualDisregardFinalPeriod ( const string &  s1, const string &  s2, NStr::ECase  use_case  )

static

Definition at line 185 of file feature_item.cpp.

References ch1, ch2, NStr::eNocase, and toupper().

Referenced by CFeatureItem::x_AddQualsRegion(), and CFeatureItem::x_CleanQuals().

s_SubSourceToSlot()

static ESourceQualifier s_SubSourceToSlot ( const CSubSource &  ss )

static

Definition at line 6380 of file feature_item.cpp.

References GetSourceQualOfSubSource(), and CSubSource_Base::GetSubtype().

Referenced by CSourceFeatureItem::x_AddQuals().

s_ToIupacaa()

static int s_ToIupacaa ( int  aa )

static

Definition at line 2142 of file feature_item.cpp.

References CSeqConvert::Convert(), CSeqUtil::e_Iupacaa, CSeqUtil::e_Ncbieaa, i, and n.

Referenced by CFeatureItem::x_AddQualsRna().

s_TransSplicingFeatureAllowed()

static bool s_TransSplicingFeatureAllowed ( const CSeqFeatData &  data )

static

Definition at line 1373 of file feature_item.cpp.

References data, CSeqFeatData::eSubtype_3clip, CSeqFeatData::eSubtype_3UTR, CSeqFeatData::eSubtype_5clip, CSeqFeatData::eSubtype_5UTR, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_otherRNA, CSeqFeatData::eSubtype_preRNA, and CSeqFeatData::eSubtype_tRNA.

Referenced by CFeatureItem::x_AddQualExceptions().

s_ValidateMobileElementType()

bool s_ValidateMobileElementType

(

const string &

mobile_element_type_value

)

Definition at line 4985 of file feature_item.cpp.

Referenced by CFeatureItem::x_CleanQuals().

s_ValidId()

static bool s_ValidId ( const CSeq_id &  id )

static

Definition at line 176 of file feature_item.cpp.

Referenced by s_CheckQuals_cdregion().

USING_SCOPE()

USING_SCOPE

(

sequence

)

Variable Documentation

mobile_element_key_to_suffix_required

const TMobileElemTypeKey mobile_element_key_to_suffix_required[]

static

Initial value:

= {
    {  "LINE",                     false  },
    {  "MITE",                     false  },
    {  "SINE",                     false  },
    {  "insertion sequence",       false  },
    {  "integron",                 false  },
    {  "non-LTR retrotransposon",  false  },
    {  "other",                    true   },
    {  "retrotransposon",          false  },
    {  "transposon",               false  }
}

Definition at line 4969 of file feature_item.cpp.

s_TrnaList

const string s_TrnaList[]

static

Initial value:

= {
  "tRNA-Gap",
  "tRNA-Ala",
  "tRNA-Asx",
  "tRNA-Cys",
  "tRNA-Asp",
  "tRNA-Glu",
  "tRNA-Phe",
  "tRNA-Gly",
  "tRNA-His",
  "tRNA-Ile",
  "tRNA-Xle",
  "tRNA-Lys",
  "tRNA-Leu",
  "tRNA-Met",
  "tRNA-Asn",
  "tRNA-Pyl",
  "tRNA-Pro",
  "tRNA-Gln",
  "tRNA-Arg",
  "tRNA-Ser",
  "tRNA-Thr",
  "tRNA-Sec",
  "tRNA-Val",
  "tRNA-Trp",
  "tRNA-OTHER",
  "tRNA-Tyr",
  "tRNA-Glx",
  "tRNA-TERM"
}

Definition at line 2094 of file feature_item.cpp.

Referenced by s_AaName().

sc_GbToFeatQualMap

const TQualPair sc_GbToFeatQualMap[]

static

Definition at line 5254 of file feature_item.cpp.

sc_ValidExceptionText

const char* const sc_ValidExceptionText[]

static

Initial value:

= {
    "annotated by transcript or proteomic data",
    "rearrangement required for product",
    "reasons given in citation",
    "RNA editing"
}

Definition at line 933 of file feature_item.cpp.

sc_ValidPseudoGene

const char* const sc_ValidPseudoGene[]

static

Initial value:

= {
    "allelic",
    "processed",
    "unitary",
    "unknown",
    "unprocessed"
}

Definition at line 911 of file feature_item.cpp.

sc_ValidRefSeqExceptionText

const char* const sc_ValidRefSeqExceptionText[]

static

Initial value:

= {
    "adjusted for low-quality genome",
    "alternative processing",
    "alternative start codon",
    "artificial frameshift",
    "dicistronic gene",
    "mismatches in transcription",
    "mismatches in translation",
    "modified codon recognition",
    "nonconsensus splice site",
    "transcribed product replaced",
    "transcribed pseudogene",
    "translated product replaced",
    "unclassified transcription discrepancy",
    "unclassified translation discrepancy",
    "unextendable partial coding region"
}

Definition at line 948 of file feature_item.cpp.