NCBI C++ ToolKit
|
Search Toolkit Book for CAutoDef
#include <objmgr/util/autodef.hpp>
Public Types | |
typedef set< CAutoDefAvailableModifier > | TAvailableModifierSet |
using | TSources = vector< CConstRef< objects::CBioSource > > |
typedef vector< CRef< CAutoDefModifierCombo > > | TModifierComboVector |
Static Public Member Functions | |
static string | GetKeywordPrefix (CBioseq_Handle bh) |
static bool | RegenerateSequenceDefLines (CSeq_entry_Handle se) |
static string | RegenerateDefLine (CBioseq_Handle bh) |
static CRef< CUser_object > | CreateIDOptions (CSeq_entry_Handle seh) |
Private Types | |
typedef vector< unsigned int > | TModifierIndexVector |
typedef vector< CSeq_entry_Handle > | TSeqEntryHandleVector |
Private Attributes | |
CAutoDefModifierCombo | m_OrigModCombo |
CAutoDefOptions | m_Options |
bool | m_Cancelled |
CRef< feature::CFeatTree > | m_Feat_Tree |
Definition at line 61 of file autodef.hpp.
Definition at line 64 of file autodef.hpp.
typedef vector<CRef<CAutoDefModifierCombo> > CAutoDef::TModifierComboVector |
Definition at line 117 of file autodef.hpp.
|
private |
Definition at line 132 of file autodef.hpp.
|
private |
Definition at line 133 of file autodef.hpp.
using CAutoDef::TSources = vector<CConstRef<objects::CBioSource> > |
Definition at line 71 of file autodef.hpp.
CAutoDef::CAutoDef | ( | ) |
Definition at line 60 of file autodef.cpp.
CAutoDef::~CAutoDef | ( | ) |
Definition at line 66 of file autodef.cpp.
Definition at line 110 of file autodef.cpp.
References CAutoDefModifierCombo::AddSource(), CAutoDefModifierCombo::GetDefaultExcludeSp(), m_OrigModCombo, and CAutoDefModifierCombo::SetExcludeSpOrgs().
Referenced by BOOST_AUTO_TEST_CASE(), CheckDeflineMatches(), CheckRegulatoryFeatures(), MakeRegulatoryFeatureTest(), TestForRecomb(), and TestRepeatRegion().
void CAutoDef::AddSources | ( | CBioseq_Handle | bh | ) |
void CAutoDef::AddSources | ( | CSeq_entry_Handle | se | ) |
Definition at line 93 of file autodef.cpp.
References CAutoDefModifierCombo::AddSource(), CSeqdesc_Base::e_Source, CSeq_inst_Base::eMol_na, CBioseq_Handle::GetCompleteBioseq(), CAutoDefModifierCombo::GetDefaultExcludeSp(), CSeqdesc_Base::GetSource(), kEmptyStr, m_OrigModCombo, s_NeedFeatureClause(), CAutoDefModifierCombo::SetExcludeSpOrgs(), and x_GetFeatureClauses().
Referenced by BOOST_AUTO_TEST_CASE(), CheckDeflineMatches(), CheckRegulatoryFeatures(), ConfigureAutodefForSeqEntry(), ConfigureAutodefParamsForBestCombo(), ConfigureParamsForPrefixCombo(), CreateIDOptions(), MakeRegulatoryFeatureTest(), CAutoDefWithTaxonomy::RegeneratePopsetTitles(), CMacroFunction_Autodef::s_AutodefSeqEntryNoTitle(), CMacroFunction_Autodef::s_AutodefSequenceNoTitle(), CMacroFunction_AutodefId::s_ConfigureAutodefOptionsForID(), CMacroFunction_RefreshDefline::s_RefreshDeflineCommand(), TestForRecomb(), TestRepeatRegion(), CMacroFunction_AutodefComplete::TheFunction(), CMacroFunction_Autodef::x_AddModifiersToOptions(), CMacroFunction_AutodefComplete::x_AddModifiersToOptions(), CAutodefJob::x_MakeChanges(), and CAutodefToolManager::x_SelectCompatibleInputObjects().
|
inline |
Definition at line 121 of file autodef.hpp.
|
inline |
Definition at line 122 of file autodef.hpp.
|
static |
Definition at line 1442 of file autodef.cpp.
References CAutoDefOptions::AddOrgMod(), AddSources(), CAutoDefOptions::AddSubSource(), COrgMod_Base::eSubtype_bio_material, COrgMod_Base::eSubtype_breed, CSubSource_Base::eSubtype_clone, COrgMod_Base::eSubtype_cultivar, COrgMod_Base::eSubtype_culture_collection, COrgMod_Base::eSubtype_ecotype, CSubSource_Base::eSubtype_haplotype, COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_specimen_voucher, COrgMod_Base::eSubtype_strain, FindBestModifierCombo(), GetOptionsObject(), i, CAutoDefOptions::InitFromUserObject(), CAutoDefOptions::MakeUserObject(), and s_ChooseModInModList().
Referenced by CCleanup::AutodefId().
CRef< CAutoDefModifierCombo > CAutoDef::FindBestModifierCombo | ( | ) |
Definition at line 210 of file autodef.cpp.
References ITERATE, m_OrigModCombo, ct::sort(), and tmp.
Referenced by BOOST_AUTO_TEST_CASE(), CheckDeflineMatches(), CheckRegulatoryFeatures(), ConfigureAutodefParamsForBestCombo(), ConfigureParamsForPrefixCombo(), CreateIDOptions(), GetOneSourceDescription(), CMacroFunction_AutodefId::s_SelectModifiersforAutodefID(), TestRepeatRegion(), CMacroFunction_Autodef::x_AddModifiersToOptions(), CMacroFunction_AutodefComplete::x_AddModifiersToOptions(), and CAutodefToolManager::x_SelectCompatibleInputObjects().
CAutoDefModifierCombo * CAutoDef::GetAllModifierCombo | ( | ) |
Definition at line 265 of file autodef.cpp.
References CAutoDefModifierCombo::AddOrgMod(), CAutoDefModifierCombo::AddSubsource(), CAutoDefModifierCombo::GetAvailableModifiers(), CAutoDefModifierCombo::HasOrgMod(), CAutoDefModifierCombo::HasSubSource(), and m_OrigModCombo.
void CAutoDef::GetAvailableModifiers | ( | CAutoDef::TAvailableModifierSet & | mod_set | ) |
Definition at line 1184 of file autodef.cpp.
References set< Key, Compare >::clear(), CAutoDefModifierCombo::GetAvailableModifiers(), set< Key, Compare >::insert(), and m_OrigModCombo.
CAutoDefModifierCombo * CAutoDef::GetEmptyCombo | ( | ) |
Definition at line 296 of file autodef.cpp.
References m_OrigModCombo.
Referenced by ConfigureAutodefForSeqEntry(), GetOneDefLine(), CMacroFunction_Autodef::s_AutodefSeqEntryNoTitle(), CMacroFunction_Autodef::s_AutodefSequenceNoTitle(), CMacroFunction_AutodefComplete::TheFunction(), and CAutodefJob::x_MakeChanges().
|
static |
Definition at line 1033 of file autodef.cpp.
References CSeqdesc_Base::e_Genbank, CSeqdesc_Base::e_Molinfo, NStr::EqualNocase(), CMolInfo_Base::eTech_tsa, CSeqdesc_Base::GetGenbank(), CGB_block_Base::GetKeywords(), CSeqdesc_Base::GetMolinfo(), CMolInfo_Base::GetTech(), CGB_block_Base::IsSetKeywords(), CMolInfo_Base::IsSetTech(), and ITERATE.
Referenced by GetOneDefLine().
|
private |
Definition at line 440 of file autodef.cpp.
References CBioseq_set_Handle::CanGetClass(), CBioseq_Handle::CanGetInst_Repr(), CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::eRepr_seg, CBioseq_Handle::GetBioseqLength(), CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetInst_Repr(), CBioseq_Handle::GetParentEntry(), CSeq_entry_Handle::GetParentEntry(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSet(), offset, and compile_time_bits::range().
Referenced by x_GetFeatureClauses().
unsigned int CAutoDef::GetNumAvailableModifiers | ( | ) |
Definition at line 184 of file autodef.cpp.
References CAutoDefModifierCombo::GetAvailableModifiers(), and m_OrigModCombo.
string CAutoDef::GetOneDefLine | ( | CAutoDefModifierCombo * | mod_combo, |
const CBioseq_Handle & | bh, | ||
CRef< feature::CFeatTree > | featTree = null |
||
) |
Definition at line 1095 of file autodef.cpp.
References CBioSource_Base::CanGetGenome(), CBioseq_Handle::CanGetInst(), CSeq_inst_Base::CanGetMol(), CSeqdesc_Base::e_Source, CBioSource_Base::eGenome_chromosome, CBioSource_Base::eGenome_unknown, CSeq_inst_Base::eMol_aa, CAutoDefOptions::GetCustomFeatureClause(), CBioSource_Base::GetGenome(), CBioseq_Handle::GetInst(), GetKeywordPrefix(), CSeq_inst_Base::GetMol(), GetOneFeatureClauseList(), CAutoDefModifierCombo::GetSourceDescriptionString(), CAutoDefModifierCombo::InitOptions(), isalpha(), NStr::IsBlank(), m_Feat_Tree, m_Options, s_IsBioseqGenomic(), s_IsRefSeq(), NStr::StartsWith(), NStr::ToUpper(), and x_trim().
Referenced by CheckDeflineMatches(), CDeflineGenerator::GenerateDefline(), RegenerateDefLine(), CMacroFunction_RefreshDefline::s_RefreshDeflineCommand(), and CAutodefJob::x_MakeChanges().
string CAutoDef::GetOneDefLine | ( | const CBioseq_Handle & | bh | ) |
Definition at line 1147 of file autodef.cpp.
References CBioSource_Base::CanGetGenome(), CBioseq_Handle::CanGetInst(), CSeq_inst_Base::CanGetMol(), CSeqdesc_Base::e_Source, CBioSource_Base::eGenome_unknown, CSeq_inst_Base::eMol_aa, GetEmptyCombo(), CBioSource_Base::GetGenome(), CBioseq_Handle::GetInst(), GetKeywordPrefix(), CSeq_inst_Base::GetMol(), GetOneFeatureClauseList(), isalpha(), m_Options, and NStr::ToUpper().
string CAutoDef::GetOneFeatureClauseList | ( | CBioseq_Handle | bh, |
unsigned int | genome_val | ||
) |
Definition at line 971 of file autodef.cpp.
References data, CAutoDefOptions::eListAllFeatures, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, FOR_EACH_SEQFEAT_ON_SEQANNOT, CAutoDefOptions::GetAltSpliceFlag(), CSeq_annot_Handle::GetCompleteSeq_annot(), CAutoDefOptions::GetCustomFeatureClause(), CSeq_feat_Base::GetData(), CAutoDefOptions::GetFeatureListType(), IsBioseqmRNA(), NStr::IsBlank(), IsInGenProdSet(), m_Options, x_GetFeatureClauseProductEnding(), x_GetFeatureClauses(), and x_GetOneNonFeatureClause().
Referenced by CAutoDefWithTaxonomy::GetDocsumDefLine(), GetOneDefLine(), and s_AreFeatureClausesUnique().
string CAutoDef::GetOneSourceDescription | ( | const CBioseq_Handle & | bh | ) |
Definition at line 304 of file autodef.cpp.
References CSeqdesc_Base::e_Source, FindBestModifierCombo(), and NULL.
|
inline |
Definition at line 84 of file autodef.hpp.
Referenced by CheckDeflineMatches(), CreateIDOptions(), CMacroFunction_Autodef::s_AddAutodefOptions(), and CAutodefJob::x_MakeChanges().
|
private |
Definition at line 424 of file autodef.cpp.
References CBioseq_set_Handle::CanGetClass(), CBioseq_set_Base::eClass_parts, CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetParentEntry(), CSeq_entry_Handle::GetParentEntry(), CSeq_entry_Handle::GetSet(), and CSeq_entry_Handle::IsSet().
Referenced by x_RemoveOptionalFeatures().
|
static |
Definition at line 1225 of file autodef.cpp.
References CSeqdesc_Base::e_User, CUser_object::eObjectType_AutodefOptions, CUser_object::GetObjectType(), GetOneDefLine(), CSeqdesc_Base::GetUser(), CAutoDefOptions::InitFromUserObject(), CBioseq_Handle::IsAa(), kEmptyStr, CAutoDefModifierCombo::SetOptions(), and SetOptionsObject().
Referenced by RegenerateSequenceDefLines().
|
static |
Definition at line 1248 of file autodef.cpp.
References CSeqdesc_Base::e_User, CUser_object::eObjectType_AutodefOptions, NStr::Equal(), CUser_object::GetObjectType(), CSeqdesc_Base::GetUser(), CBioseq_Handle::IsAa(), NON_CONST_ITERATE, RegenerateDefLine(), CBioseq_EditHandle::SetDescr(), and CSeqdesc_Base::SetTitle().
Referenced by CCleanup::AutodefId(), and CAutoDefWithTaxonomy::RegenerateDefLines().
|
inline |
Definition at line 213 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetAltSpliceFlag().
Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
Definition at line 341 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetCustomFeatureClause().
Referenced by BOOST_AUTO_TEST_CASE(), and ConfigureAutodefForSeqEntry().
|
inline |
Definition at line 178 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetFeatureListType().
Referenced by BOOST_AUTO_TEST_CASE(), CheckDeflineMatches(), CheckRegulatoryFeatures(), ConfigureAutodefForSeqEntry(), CMacroFunction_Autodef::s_AutodefSeqEntryNoTitle(), CMacroFunction_Autodef::s_AutodefSequenceNoTitle(), TestForRecomb(), TestRepeatRegion(), CMacroFunction_AutodefComplete::TheFunction(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 227 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetGeneClusterOppStrand().
Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 282 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeep3UTRs().
Referenced by BOOST_AUTO_TEST_CASE(), ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 289 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeep5UTRs().
Referenced by BOOST_AUTO_TEST_CASE(), ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 255 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeepExons().
Referenced by BOOST_AUTO_TEST_CASE(), ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 262 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeepIntrons().
Referenced by BOOST_AUTO_TEST_CASE(), ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 275 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeepLTRs().
Referenced by ConfigureAutodefForSeqEntry().
|
inline |
Definition at line 321 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeepMiscRecomb().
Referenced by ConfigureAutodefForSeqEntry(), and TestForRecomb().
|
inline |
Definition at line 303 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeepMobileElements().
Referenced by BOOST_AUTO_TEST_CASE().
|
inline |
Definition at line 309 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeepPrecursorRNA().
|
inline |
Definition at line 269 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeepRegulatoryFeatures().
Referenced by CheckRegulatoryFeatures(), ConfigureAutodefForSeqEntry(), MakeRegulatoryFeatureTest(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 315 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeepRepeatRegion().
Referenced by ConfigureAutodefForSeqEntry(), and TestRepeatRegion().
|
inline |
Definition at line 296 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetKeepuORFs().
Referenced by BOOST_AUTO_TEST_CASE().
|
inline |
Definition at line 185 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetMiscFeatRule().
Referenced by BOOST_AUTO_TEST_CASE(), CheckDeflineMatches(), ConfigureAutodefForSeqEntry(), CMacroFunction_Autodef::s_AutodefSeqEntryNoTitle(), CMacroFunction_Autodef::s_AutodefSequenceNoTitle(), CMacroFunction_AutodefComplete::TheFunction(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 199 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetNuclearCopyFlag().
Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
void CAutoDef::SetOptions | ( | const CAutoDefModifierCombo & | mod_combo | ) |
Definition at line 1201 of file autodef.cpp.
References CAutoDefModifierCombo::InitOptions(), and m_Options.
Referenced by AutodefSeqEntryNoTitle(), CheckDeflineMatches(), CMacroFunction_Autodef::s_AutodefBioseqsNoTitle(), CMacroFunction_Autodef::s_AutodefSequenceNoTitle(), and CMacroFunction_AutodefComplete::TheFunction().
void CAutoDef::SetOptionsObject | ( | const CUser_object & | user | ) |
Definition at line 1196 of file autodef.cpp.
References CAutoDefOptions::InitFromUserObject(), and m_Options.
Referenced by CheckDeflineMatches(), CDeflineGenerator::GenerateDefline(), RegenerateDefLine(), CAutoDefWithTaxonomy::RegeneratePopsetTitles(), and CMacroFunction_RefreshDefline::s_RefreshDeflineCommand().
|
inline |
Definition at line 192 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetProductFlag().
Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 206 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetSpecifyNuclearProduct().
Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
void CAutoDef::SetSuppressAllele | ( | bool | suppress_allele | ) |
|
inline |
Definition at line 234 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetSuppressFeatureAltSplice().
Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 220 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetSuppressLocusTags().
Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 334 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetUseFakePromoters().
Referenced by BOOST_AUTO_TEST_CASE(), CheckRegulatoryFeatures(), ConfigureAutodefForSeqEntry(), MakeRegulatoryFeatureTest(), and CAutodefJob::x_MakeChanges().
|
inline |
Definition at line 327 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetUseNcRNAComment().
Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
void CAutoDef::SuppressFeature | ( | const objects::CFeatListItem & | feat | ) |
Definition at line 408 of file autodef.cpp.
References CSeqFeatData_Base::e_not_set, m_Options, CAutoDefOptions::SuppressAllFeatures(), and CAutoDefOptions::SuppressFeature().
Referenced by BOOST_AUTO_TEST_CASE(), CheckDeflineMatches(), ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
void CAutoDef::SuppressFeature | ( | objects::CSeqFeatData::ESubtype | subtype | ) |
Definition at line 418 of file autodef.cpp.
References m_Options, and CAutoDefOptions::SuppressFeature().
|
inline |
Definition at line 248 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetSuppressMiscFeatureSubfeatures().
Referenced by ConfigureAutodefForSeqEntry().
|
inline |
Definition at line 241 of file autodef.hpp.
References m_Options, and CAutoDefOptions::SetSuppressMobileElementSubfeatures().
Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().
|
private |
Definition at line 797 of file autodef.cpp.
References CBioSource_Base::CanGetGenome(), CBioSource_Base::CanGetSubtype(), CSeqdesc_Base::e_Source, CBioSource_Base::eGenome_unknown, NStr::Equal(), CSubSource_Base::eSubtype_other, NStr::Find(), CBioSource_Base::GetGenome(), CAutoDefOptions::GetNuclearCopyFlag(), CAutoDefOptions::GetProductFlag(), CAutoDefOptions::GetSpecifyNuclearProduct(), CBioSource_Base::GetSubtype(), NStr::IsBlank(), ITERATE, m_Options, OrganelleByGenome(), and s_GetProductFlagFromCDSProductNames().
Referenced by GetOneFeatureClauseList().
|
private |
Definition at line 554 of file autodef.cpp.
References CAutoDefFeatureClause_Base::AddSubclause(), CSeq_id::Assign(), CAutoDefFeatureClause_Base::AssignGeneProductNames(), CSeq_id::BestRank(), CAutoDefFeatureClause_Base::ConsolidateRepeatedClauses(), CAutoDefFeatureClause_Base::CountUnknownGenes(), CSeqdesc_Base::e_Source, CSeqdesc_Base::e_User, NStr::EqualNocase(), CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_LTR, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_repeat_region, CAutoDefFeatureClause_Base::ExpandExonLists(), FeatureClauseFactory(), CAutoDefFeatureClause_Base::FindAltSplices(), FindBestChoice(), CBioseq_Handle::GetBioseqCore(), CAutoDefOptions::GetCustomFeatureClause(), COrg_ref::GetDivision(), CAutoDefOptions::GetGeneClusterOppStrand(), CBioseq_Base::GetId(), CBioseq_Handle::GetInst_Length(), CAutoDefOptions::GetKeepRepeatRegion(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetMappedFeature(), GetMasterLocation(), CBioSource_Base::GetOrg(), CMappedFeat::GetOriginalFeature(), CSeqdesc_Base::GetSource(), CAutoDefOptions::GetSuppressAlleles(), CAutoDefOptions::GetSuppressFeatureAltSplice(), CAutoDefOptions::GetSuppressMiscFeatureSubfeatures(), CAutoDefOptions::GetSuppressMobileElementSubfeatures(), CAutoDefOptions::GetUseFakePromoters(), CSeqdesc_Base::GetUser(), CAutoDefFeatureClause_Base::GroupAltSplicedExons(), CAutoDefFeatureClause_Base::GroupClauses(), CAutoDefFeatureClause_Base::GroupConsecutiveExons(), CAutoDefFeatureClause_Base::GroupGenes(), CAutoDefFeatureClause_Base::GroupmRNAs(), CAutoDefFeatureClause_Base::GroupSegmentedCDSs(), NStr::IsBlank(), COrg_ref::IsSetDivision(), CBioSource_Base::IsSetOrg(), CAutoDefFeatureClause_Base::Label(), CAutoDefFeatureClause_Base::ListClauses(), m_Options, compile_time_bits::range(), CAutoDefFeatureClause_Base::RemoveDeletedSubclauses(), CAutoDefFeatureClause_Base::RemoveFeaturesUnderType(), CAutoDefFeatureClause_Base::RemoveGenesMentionedElsewhere(), CAutoDefFeatureClause_Base::ReverseCDSClauseLists(), s_HasPromoter(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CAutoDefFeatureClause_Base::SuppressMobileElementAndInsertionSequenceSubfeatures(), x_GetHumanSTRFeatureClauses(), x_GetHumanSTRv2FeatureClauses(), x_Is5SList(), x_IsHumanSTR(), x_IsSingleMiscFeat(), and x_RemoveOptionalFeatures().
Referenced by AddSources(), and GetOneFeatureClauseList().
|
private |
Definition at line 1310 of file autodef.cpp.
References NStr::Equal(), NStr::EqualNocase(), CSeqFeatData::eSubtype_variation, f, CUser_object_Base::GetData(), CUser_object_Base::IsSetData(), ITERATE, label, and NStr::NumericToString().
Referenced by x_GetFeatureClauses().
|
private |
Definition at line 1366 of file autodef.cpp.
References NStr::EqualNocase(), CUser_object_Base::GetData(), CUser_object_Base::IsSetData(), ITERATE, and label.
Referenced by x_GetFeatureClauses().
|
private |
Definition at line 139 of file autodef.cpp.
References x_SortModifierListByRank().
|
private |
Definition at line 878 of file autodef.cpp.
References CAutoDefOptions::eCompleteGenome, CAutoDefOptions::eCompleteSequence, CAutoDefOptions::eListAllFeatures, CAutoDefOptions::ePartialGenome, CAutoDefOptions::ePartialSequence, CAutoDefOptions::eSequence, CAutoDefOptions::eWholeGenomeShotgunSequence, CAutoDefOptions::GetFeatureListType(), and m_Options.
Referenced by x_GetOneNonFeatureClause().
|
private |
Definition at line 935 of file autodef.cpp.
References CSeqdesc_Base::e_Molinfo, CMolInfo_Base::eBiomol_mRNA, CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_plastid, CAutoDefOptions::eSequence, CMolInfo_Base::GetBiomol(), CMolInfo::GetBiomolName(), CAutoDefOptions::GetFeatureListType(), CSeqdesc_Base::GetMolinfo(), NStr::IsBlank(), CMolInfo_Base::IsSetBiomol(), m_Options, OrganelleByGenome(), and x_GetNonFeatureListEnding().
Referenced by GetOneFeatureClauseList().
Definition at line 481 of file autodef.cpp.
References NStr::Equal(), CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_rRNA, CSeq_feat_Handle::GetComment(), CSeq_feat_Handle::GetData(), CRNA_ref_Base::GetExt(), CRNA_ref_Base::C_Ext::GetName(), CSeqFeatData_Base::GetRna(), CSeqFeatData::GetSubtype(), CRNA_ref_Base::C_Ext::IsName(), CSeq_feat_Handle::IsSetComment(), CRNA_ref_Base::IsSetExt(), and CFeat_CI::Rewind().
Referenced by x_GetFeatureClauses().
|
private |
Definition at line 402 of file autodef.cpp.
References CAutoDefOptions::IsFeatureSuppressed(), and m_Options.
|
private |
Definition at line 1287 of file autodef.cpp.
References CUser_object::eObjectType_StructuredComment, NStr::EqualNocase(), f, CUser_object_Base::GetData(), CUser_object::GetObjectType(), CUser_object_Base::IsSetData(), and ITERATE.
Referenced by x_GetFeatureClauses().
Definition at line 166 of file autodef.cpp.
Definition at line 524 of file autodef.cpp.
References CSeqFeatData::eSubtype_misc_feature, CSeq_feat_Handle::GetData(), CSeqFeatData::GetSubtype(), CSeq_feat_Handle::IsSetComment(), and CFeat_CI::Rewind().
Referenced by x_GetFeatureClauses().
Definition at line 172 of file autodef.cpp.
References CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_plasmid_name, and CSubSource_Base::eSubtype_transgenic.
|
private |
Definition at line 319 of file autodef.cpp.
References CSeqFeatData::eSubtype_3UTR, CSeqFeatData::eSubtype_5UTR, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_LTR, CSeqFeatData::eSubtype_misc_recomb, CSeqFeatData::eSubtype_regulatory, CAutoDefOptions::GetKeep3UTRs(), CAutoDefOptions::GetKeep5UTRs(), CAutoDefOptions::GetKeepExons(), CAutoDefOptions::GetKeepIntrons(), CAutoDefOptions::GetKeepLTRs(), CAutoDefOptions::GetKeepMiscRecomb(), CAutoDefOptions::GetKeepMobileElements(), CAutoDefOptions::GetKeepPrecursorRNA(), CAutoDefOptions::GetKeepRegulatoryFeatures(), CAutoDefOptions::GetKeepRepeatRegion(), CAutoDefOptions::GetKeepuORFs(), CAutoDefFeatureClause_Base::GetMainFeatureSubtype(), CAutoDefFeatureClause_Base::GetNumSubclauses(), CAutoDefOptions::GetUseFakePromoters(), CAutoDefFeatureClause_Base::IsBioseqPrecursorRNA(), CAutoDefFeatureClause_Base::IsFeatureTypeLonely(), IsSegment(), m_Options, NULL, CAutoDefFeatureClause_Base::RemoveBioseqPrecursorRNAs(), CAutoDefFeatureClause_Base::RemoveDeletedSubclauses(), CAutoDefFeatureClause_Base::RemoveFeaturesByType(), CAutoDefFeatureClause_Base::RemoveFeaturesInmRNAsByType(), CAutoDefFeatureClause_Base::RemoveOptionalMobileElements(), CAutoDefFeatureClause_Base::RemoveUnwantedExons(), and CAutoDefFeatureClause_Base::RemoveuORFs().
Referenced by x_GetFeatureClauses().
|
private |
|
private |
Definition at line 140 of file autodef.hpp.
|
private |
Definition at line 173 of file autodef.hpp.
Referenced by GetOneDefLine().
|
private |
Definition at line 137 of file autodef.hpp.
Referenced by GetOneDefLine(), GetOneFeatureClauseList(), SetAltSpliceFlag(), SetCustomFeatureClause(), SetFeatureListType(), SetGeneClusterOppStrand(), SetKeep3UTRs(), SetKeep5UTRs(), SetKeepExons(), SetKeepIntrons(), SetKeepLTRs(), SetKeepMiscRecomb(), SetKeepOptionalMobileElements(), SetKeepPrecursorRNA(), SetKeepRegulatoryFeatures(), SetKeepRepeatRegion(), SetKeepuORFs(), SetMiscFeatRule(), SetNuclearCopyFlag(), SetOptions(), SetOptionsObject(), SetProductFlag(), SetSpecifyNuclearProduct(), SetSuppressFeatureAltSplice(), SetSuppressLocusTags(), SetUseFakePromoters(), SetUseNcRNAComment(), SuppressFeature(), SuppressMiscFeatSubfeatures(), SuppressMobileElementAndInsertionSequenceSubfeatures(), x_GetFeatureClauseProductEnding(), x_GetFeatureClauses(), x_GetNonFeatureListEnding(), x_GetOneNonFeatureClause(), x_IsFeatureSuppressed(), and x_RemoveOptionalFeatures().
|
private |
Definition at line 135 of file autodef.hpp.
Referenced by AddDescriptors(), AddSources(), FindBestModifierCombo(), GetAllModifierCombo(), GetAvailableModifiers(), GetEmptyCombo(), and GetNumAvailableModifiers().