NCBI C++ ToolKit
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Search Toolkit Book for CGff2Record
#include <objtools/readers/gff2_data.hpp>
Public Types | |
typedef map< string, string > | TAttributes |
typedef TAttributes::iterator | TAttrIt |
typedef TAttributes::const_iterator | TAttrCit |
Public Types inherited from CGffBaseColumns | |
using | TFrame = CCdregion::EFrame |
using | TReaderFlags = long |
using | SeqIdResolver = CRef< CSeq_id >(*)(const string &, TReaderFlags, bool) |
Static Public Member Functions | |
static void | TokenizeGFF (vector< CTempStringEx > &columns, const CTempStringEx &line) |
Static Public Member Functions inherited from CGffBaseColumns | |
static unsigned int | NextId () |
static void | ResetId () |
Protected Member Functions | |
virtual bool | xAssignAttributesFromGff (const string &, const string &) |
bool | xSplitGffAttributes (const string &, vector< string > &) const |
virtual bool | xMigrateAttributes (TReaderFlags, CRef< CSeq_feat >) const |
virtual bool | xInitFeatureData (TReaderFlags, CRef< CSeq_feat >) const |
virtual bool | xUpdateFeatureData (TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const |
virtual bool | xMigrateAttributesSubSource (TReaderFlags, CRef< CSeq_feat >, TAttributes &) const |
virtual bool | xMigrateAttributesOrgName (TReaderFlags, CRef< CSeq_feat >, TAttributes &) const |
virtual bool | xMigrateAttributesGo (TReaderFlags, CRef< CSeq_feat >, TAttributes &) const |
Static Protected Member Functions | |
static string | xNormalizedAttributeKey (const CTempString &) |
static string | xNormalizedAttributeValue (const CTempString &) |
static bool | xMigrateAttributeDefault (TAttributes &, const string &, CRef< CSeq_feat >, const string &, TReaderFlags) |
static bool | xMigrateAttributeSingle (TAttributes &, const string &, CRef< CSeq_feat >, const string &, TReaderFlags) |
Protected Attributes | |
string | m_strAttributes |
TAttributes | m_Attributes |
Protected Attributes inherited from CGffBaseColumns | |
string | mSeqId |
TSeqPos | m_uSeqStart |
TSeqPos | m_uSeqStop |
string | m_strSource |
string | m_strType |
string | m_strNormalizedType |
double * | m_pdScore |
ENa_strand * | m_peStrand |
TFrame * | m_pePhase |
Additional Inherited Members | |
Static Protected Attributes inherited from CGffBaseColumns | |
static unsigned int | msNextId = 0 |
Definition at line 42 of file gff2_data.hpp.
Definition at line 49 of file gff2_data.hpp.
typedef map<string, string> CGff2Record::TAttributes |
Definition at line 47 of file gff2_data.hpp.
Definition at line 48 of file gff2_data.hpp.
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Definition at line 53 of file gff2_data.hpp.
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Definition at line 54 of file gff2_data.hpp.
References map_checker< Container >::begin(), map_checker< Container >::end(), map_checker< Container >::insert(), and m_Attributes.
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Definition at line 61 of file gff2_data.hpp.
Reimplemented in CGvfReadRecord, and CGff3ReadRecord.
Definition at line 214 of file gff2_data.cpp.
References columns, CObjReaderLineException::Create(), eDiag_Error, CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eNa_strand_both, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, ILineError::eProblem_FeatureBadStartAndOrStop, NStr::fAllowLeadingSpaces, CGffBaseColumns::m_pdScore, CGffBaseColumns::m_pePhase, CGffBaseColumns::m_peStrand, m_strAttributes, CGffBaseColumns::m_strNormalizedType, CGffBaseColumns::m_strSource, CGffBaseColumns::m_strType, CGffBaseColumns::m_uSeqStart, CGffBaseColumns::m_uSeqStop, CGffBaseColumns::mSeqId, CTempString::npos, string, NStr::StringToDouble(), NStr::StringToUInt(), TokenizeGFF(), NStr::ToLower(), and xAssignAttributesFromGff().
Referenced by CGff3ReadRecord::AssignFromGff().
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inline |
Definition at line 80 of file gff2_data.hpp.
References m_Attributes.
Referenced by CGvfReader::xFeatureSetExt(), and CGff3Reader::xInitializeFeature().
Definition at line 320 of file gff2_data.cpp.
References NStr::Split().
Definition at line 305 of file gff2_data.cpp.
Referenced by CGff3ReadRecord::AssignFromGff(), CGff3LocationRecord::CGff3LocationRecord(), CGffIdTracker::CheckAndIndexRecord(), IsMultiParent(), CGff2Reader::xAlignmentSetDenseg(), CGff2Reader::xAlignmentSetScore(), CGff2Reader::xAlignmentSetSpliced_seg(), CGvfReader::xFeatureSetExt(), CGvfReader::xFeatureSetLocationInterval(), CGvfReader::xFeatureSetLocationPoint(), CGff3Reader::xFindFeatureUnderConstruction(), CGff3LocationMerger::xGetLocationIds(), CGff3Reader::xMakeRecordId(), CGff3Reader::xUpdateAnnotCds(), CGff3Reader::xUpdateAnnotExon(), CGff3Reader::xUpdateAnnotGene(), CGff3Reader::xUpdateAnnotGeneric(), CGff3Reader::xUpdateAnnotRegion(), CGff3Reader::xUpdateAnnotRna(), CGvfReader::xVariationSetDeletions(), CGvfReader::xVariationSetId(), CGvfReader::xVariationSetInsertions(), CGvfReader::xVariationSetName(), CGvfReader::xVariationSetParent(), CGvfReader::xVariationSetProperties(), CGvfReader::xVariationSetSnvs(), and CGff3Reader::xVerifyCdsParents().
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Reimplemented from CGffBaseColumns.
Definition at line 508 of file gff2_data.cpp.
References flags, and CGffBaseColumns::InitializeFeature().
Referenced by CGff3Reader::xInitializeFeature(), CGff2Reader::xUpdateAnnotFeature(), and CGff3Reader::xUpdateAnnotRegion().
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Definition at line 72 of file gff2_data.hpp.
References NStr::EndsWith(), NStr::StartsWith(), and CGffBaseColumns::Type().
bool CGff2Record::IsMultiParent | ( | ) | const |
Definition at line 1171 of file gff2_data.cpp.
References GetAttribute().
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static |
Definition at line 165 of file gff2_data.cpp.
References CTempString::begin(), columns, CTempString::find_first_not_of(), CTempString::find_first_of(), NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, next(), CTempString::npos, NStr::Split(), and CTempStringEx::substr().
Referenced by AssignFromGff(), and CGff2Reader::IsAlignmentData().
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Definition at line 521 of file gff2_data.cpp.
References CSeqFeatData::eSubtype_cdregion, and flags.
Referenced by CGff3Reader::xUpdateAnnotExon(), CGff3Reader::xUpdateAnnotGene(), CGff3Reader::xUpdateAnnotGeneric(), and CGff3Reader::xUpdateAnnotRna().
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protectedvirtual |
Reimplemented in CGvfReadRecord, and CGtfReadRecord.
Definition at line 452 of file gff2_data.cpp.
References map_checker< Container >::clear(), input(), m_Attributes, next(), and x_GetNextAttribute().
Referenced by AssignFromGff().
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protectedvirtual |
Reimplemented from CGffBaseColumns.
Definition at line 1130 of file gff2_data.cpp.
References eDiag_Error, CGff2Reader::fGenbankMode, flags, CSoMap::SoTypeToFeature(), Type, and CGffBaseColumns::xInitFeatureData().
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Definition at line 936 of file gff2_data.cpp.
References CSeq_feat::AddQualifier(), attributes, NStr::Split(), rapidjson::value, and xNormalizedAttributeValue().
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Definition at line 589 of file gff2_data.cpp.
References map_checker< Container >::begin(), CSeq_feat_Base::eExp_ev_experimental, CSeq_feat_Base::eExp_ev_not_experimental, CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, map_checker< Container >::empty(), map_checker< Container >::end(), map_checker< Container >::erase(), CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_ncRNA, CSubSource_Base::eSubtype_other, CGff2Reader::fGenbankMode, map_checker< Container >::find(), flags, NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, GetSeqId(), ncbi::grid::netcache::search::fields::key, s_StringToCodeBreak(), s_StringToGenome(), CSubSource_Base::SetName(), CGb_qual_Base::SetQual(), CSubSource_Base::SetSubtype(), CGb_qual_Base::SetVal(), NStr::Split(), NStr::StringToInt(), tag, Type, val, rapidjson::value, and CGff2Reader::x_ParseDbtag().
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Definition at line 1033 of file gff2_data.cpp.
References CReadUtil::AddGeneOntologyTerm(), and NStr::StartsWith().
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Definition at line 914 of file gff2_data.cpp.
References CSeq_feat::AddQualifier(), attributes, rapidjson::value, and xNormalizedAttributeValue().
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Definition at line 966 of file gff2_data.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_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_variety, COrgMod_Base::SetSubname(), and COrgMod_Base::SetSubtype().
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Definition at line 1056 of file gff2_data.cpp.
References CSubSource_Base::eSubtype_altitude, 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_collected_by, CSubSource_Base::eSubtype_collection_date, 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_fwd_primer_name, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_genotype, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_haplogroup, CSubSource_Base::eSubtype_haplotype, CSubSource_Base::eSubtype_identified_by, CSubSource_Base::eSubtype_insertion_seq_name, CSubSource_Base::eSubtype_isolation_source, CSubSource_Base::eSubtype_lab_host, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_linkage_group, CSubSource_Base::eSubtype_map, CSubSource_Base::eSubtype_mating_type, CSubSource_Base::eSubtype_metagenomic, CSubSource_Base::eSubtype_other, CSubSource_Base::eSubtype_phenotype, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_plastid_name, CSubSource_Base::eSubtype_pop_variant, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_rev_primer_name, CSubSource_Base::eSubtype_rev_primer_seq, 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, CSubSource_Base::eSubtype_whole_replicon, CSubSource_Base::SetName(), and CSubSource_Base::SetSubtype().
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Definition at line 335 of file gff2_data.cpp.
References NStr::TruncateSpaces_Unsafe().
Referenced by CGff3ReadRecord::x_NormalizedAttributeKey(), and CGtfReadRecord::xAssignAttributesFromGff().
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Definition at line 343 of file gff2_data.cpp.
References NStr::EndsWith(), NStr::eUrlDec_Percent, CTempString::length(), NStr::StartsWith(), CTempString::substr(), NStr::TruncateSpaces_Unsafe(), and NStr::URLDecode().
Referenced by CGtfReadRecord::xAssignAttributesFromGff(), CGvfReadRecord::xAssignAttributesFromGff(), xMigrateAttributeDefault(), and xMigrateAttributeSingle().
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Definition at line 471 of file gff2_data.cpp.
References attributes, ITERATE, and NStr::TruncateSpacesInPlace().
Referenced by CGtfReadRecord::xAssignAttributesFromGff(), and CGvfReadRecord::xAssignAttributesFromGff().
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Definition at line 546 of file gff2_data.cpp.
References CSeq_interval_Base::CanGetStrand(), eExtreme_Positional, eNa_strand_minus, eNa_strand_plus, CSeqFeatData::eSubtype_cdregion, flags, CSeq_loc_Base::GetInt(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), and CSeq_interval_Base::GetStrand().
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Definition at line 171 of file gff2_data.hpp.
Referenced by CGff3ReadRecord::AssignFromGff(), CGvfReadRecord::AssignFromGff(), Attributes(), CGff2Record(), xAssignAttributesFromGff(), and CGvfReadRecord::xAssignAttributesFromGff().
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Definition at line 170 of file gff2_data.hpp.
Referenced by AssignFromGff().