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CAutoDef Class Reference

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#include <objmgr/util/autodef.hpp>

+ Inheritance diagram for CAutoDef:
+ Collaboration diagram for CAutoDef:

Public Types

typedef set< CAutoDefAvailableModifierTAvailableModifierSet
 
using TSources = vector< CConstRef< objects::CBioSource > >
 
typedef vector< CRef< CAutoDefModifierCombo > > TModifierComboVector
 

Public Member Functions

 CAutoDef ()
 
 ~CAutoDef ()
 
void AddSources (CSeq_entry_Handle se)
 
void AddSources (CBioseq_Handle bh)
 
void AddDescriptors (const TSources &sources)
 
CRef< CAutoDefModifierComboFindBestModifierCombo ()
 
CAutoDefModifierComboGetAllModifierCombo ()
 
CAutoDefModifierComboGetEmptyCombo ()
 
unsigned int GetNumAvailableModifiers ()
 
string GetOneSourceDescription (const CBioseq_Handle &bh)
 
string GetOneFeatureClauseList (CBioseq_Handle bh, unsigned int genome_val)
 
string GetOneDefLine (CAutoDefModifierCombo *mod_combo, const CBioseq_Handle &bh, CRef< feature::CFeatTree > featTree=null)
 
string GetOneDefLine (const CBioseq_Handle &bh)
 
void SetOptionsObject (const CUser_object &user)
 
CRef< CUser_objectGetOptionsObject () const
 
void SetOptions (const CAutoDefModifierCombo &mod_combo)
 
void SetFeatureListType (CAutoDefOptions::EFeatureListType feature_list_type)
 
void SetMiscFeatRule (CAutoDefOptions::EMiscFeatRule misc_feat_rule)
 
void SetProductFlag (CBioSource::EGenome product_flag)
 
void SetNuclearCopyFlag (CBioSource::EGenome product_flag)
 
void SetSpecifyNuclearProduct (bool specify_nuclear_product)
 
void SetAltSpliceFlag (bool alt_splice_flag)
 
void SetSuppressLocusTags (bool suppress_locus_tags)
 
void SetSuppressAllele (bool suppress_allele)
 
void SetGeneClusterOppStrand (bool gene_opp_strand)
 
void SetSuppressFeatureAltSplice (bool suppress_alt_splice)
 
void SuppressMobileElementAndInsertionSequenceSubfeatures (bool suppress)
 
void SuppressMiscFeatSubfeatures (bool suppress)
 
void SetKeepExons (bool keep)
 
void SetKeepIntrons (bool keep)
 
void SetKeepRegulatoryFeatures (bool keep)
 
void SetKeepLTRs (bool keep)
 
void SetKeep3UTRs (bool keep)
 
void SetKeep5UTRs (bool keep)
 
void SetKeepuORFs (bool keep)
 
void SetKeepOptionalMobileElements (bool keep)
 
void SetKeepPrecursorRNA (bool keep)
 
void SetKeepRepeatRegion (bool keep)
 
void SetKeepMiscRecomb (bool keep)
 
void SetUseNcRNAComment (bool use_comment)
 
void SetUseFakePromoters (bool use_fake)
 
void SetCustomFeatureClause (const string &custom_feature_clause)
 
void SuppressFeature (const objects::CFeatListItem &feat)
 
void SuppressFeature (objects::CSeqFeatData::ESubtype subtype)
 
void GetAvailableModifiers (TAvailableModifierSet &mod_set)
 
void Cancel ()
 
bool Cancelled ()
 

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_objectCreateIDOptions (CSeq_entry_Handle seh)
 

Private Types

typedef vector< unsigned intTModifierIndexVector
 
typedef vector< CSeq_entry_HandleTSeqEntryHandleVector
 

Private Member Functions

void x_SortModifierListByRank (TModifierIndexVector &index_list, CAutoDefSourceDescription::TAvailableModifierVector &modifier_list)
 
void x_GetModifierIndexList (TModifierIndexVector &index_list, CAutoDefSourceDescription::TAvailableModifierVector &modifier_list)
 
string x_GetNonFeatureListEnding ()
 
string x_GetFeatureClauses (const CBioseq_Handle &bh)
 
string x_GetFeatureClauseProductEnding (const string &feature_clauses, CBioseq_Handle bh)
 
void x_RemoveOptionalFeatures (CAutoDefFeatureClause_Base *main_clause, const CBioseq_Handle &bh)
 
bool x_IsOrgModRequired (unsigned int mod_type)
 
bool x_IsSubSrcRequired (unsigned int mod_type)
 
bool x_IsFeatureSuppressed (CSeqFeatData::ESubtype subtype)
 
void GetMasterLocation (CBioseq_Handle &bh, CRange< TSeqPos > &range)
 
bool IsSegment (const CBioseq_Handle &bh)
 
bool x_Is5SList (CFeat_CI feat_ci)
 
bool x_IsSingleMiscFeat (CFeat_CI feat_ci)
 
string x_GetHumanSTRFeatureClauses (CBioseq_Handle bh, const CUser_object &comment)
 
string x_GetHumanSTRv2FeatureClauses (CBioseq_Handle bh, const CUser_object &comment)
 
bool x_IsHumanSTR (const CUser_object &obj)
 
string x_GetOneNonFeatureClause (CBioseq_Handle bh, unsigned int genome_val)
 

Private Attributes

CAutoDefModifierCombo m_OrigModCombo
 
CAutoDefOptions m_Options
 
bool m_Cancelled
 
CRef< feature::CFeatTree > m_Feat_Tree
 

Detailed Description

Definition at line 61 of file autodef.hpp.

Member Typedef Documentation

◆ TAvailableModifierSet

Definition at line 64 of file autodef.hpp.

◆ TModifierComboVector

Definition at line 117 of file autodef.hpp.

◆ TModifierIndexVector

typedef vector<unsigned int> CAutoDef::TModifierIndexVector
private

Definition at line 132 of file autodef.hpp.

◆ TSeqEntryHandleVector

Definition at line 133 of file autodef.hpp.

◆ TSources

using CAutoDef::TSources = vector<CConstRef<objects::CBioSource> >

Definition at line 71 of file autodef.hpp.

Constructor & Destructor Documentation

◆ CAutoDef()

CAutoDef::CAutoDef ( )

Definition at line 60 of file autodef.cpp.

◆ ~CAutoDef()

CAutoDef::~CAutoDef ( )

Definition at line 66 of file autodef.cpp.

Member Function Documentation

◆ AddDescriptors()

void CAutoDef::AddDescriptors ( const TSources sources)

◆ AddSources() [1/2]

void CAutoDef::AddSources ( CBioseq_Handle  bh)

◆ AddSources() [2/2]

void CAutoDef::AddSources ( CSeq_entry_Handle  se)

◆ Cancel()

void CAutoDef::Cancel ( void  )
inline

Definition at line 121 of file autodef.hpp.

◆ Cancelled()

bool CAutoDef::Cancelled ( )
inline

Definition at line 122 of file autodef.hpp.

◆ CreateIDOptions()

CRef< CUser_object > CAutoDef::CreateIDOptions ( CSeq_entry_Handle  seh)
static

◆ FindBestModifierCombo()

CRef< CAutoDefModifierCombo > CAutoDef::FindBestModifierCombo ( )

◆ GetAllModifierCombo()

CAutoDefModifierCombo * CAutoDef::GetAllModifierCombo ( )

◆ GetAvailableModifiers()

void CAutoDef::GetAvailableModifiers ( CAutoDef::TAvailableModifierSet mod_set)

◆ GetEmptyCombo()

CAutoDefModifierCombo * CAutoDef::GetEmptyCombo ( )

◆ GetKeywordPrefix()

string CAutoDef::GetKeywordPrefix ( CBioseq_Handle  bh)
static

◆ GetMasterLocation()

void CAutoDef::GetMasterLocation ( CBioseq_Handle bh,
CRange< TSeqPos > &  range 
)
private

◆ GetNumAvailableModifiers()

unsigned int CAutoDef::GetNumAvailableModifiers ( )

Definition at line 184 of file autodef.cpp.

References CAutoDefModifierCombo::GetAvailableModifiers(), and m_OrigModCombo.

◆ GetOneDefLine() [1/2]

string CAutoDef::GetOneDefLine ( CAutoDefModifierCombo mod_combo,
const CBioseq_Handle bh,
CRef< feature::CFeatTree >  featTree = null 
)

◆ GetOneDefLine() [2/2]

string CAutoDef::GetOneDefLine ( const CBioseq_Handle bh)

◆ GetOneFeatureClauseList()

string CAutoDef::GetOneFeatureClauseList ( CBioseq_Handle  bh,
unsigned int  genome_val 
)

◆ GetOneSourceDescription()

string CAutoDef::GetOneSourceDescription ( const CBioseq_Handle bh)

Definition at line 304 of file autodef.cpp.

References CSeqdesc_Base::e_Source, FindBestModifierCombo(), and NULL.

◆ GetOptionsObject()

CRef<CUser_object> CAutoDef::GetOptionsObject ( ) const
inline

◆ IsSegment()

bool CAutoDef::IsSegment ( const CBioseq_Handle bh)
private

◆ RegenerateDefLine()

string CAutoDef::RegenerateDefLine ( CBioseq_Handle  bh)
static

◆ RegenerateSequenceDefLines()

bool CAutoDef::RegenerateSequenceDefLines ( CSeq_entry_Handle  se)
static

◆ SetAltSpliceFlag()

void CAutoDef::SetAltSpliceFlag ( bool  alt_splice_flag)
inline

◆ SetCustomFeatureClause()

void CAutoDef::SetCustomFeatureClause ( const string custom_feature_clause)
inline

◆ SetFeatureListType()

void CAutoDef::SetFeatureListType ( CAutoDefOptions::EFeatureListType  feature_list_type)
inline

◆ SetGeneClusterOppStrand()

void CAutoDef::SetGeneClusterOppStrand ( bool  gene_opp_strand)
inline

◆ SetKeep3UTRs()

void CAutoDef::SetKeep3UTRs ( bool  keep)
inline

◆ SetKeep5UTRs()

void CAutoDef::SetKeep5UTRs ( bool  keep)
inline

◆ SetKeepExons()

void CAutoDef::SetKeepExons ( bool  keep)
inline

◆ SetKeepIntrons()

void CAutoDef::SetKeepIntrons ( bool  keep)
inline

◆ SetKeepLTRs()

void CAutoDef::SetKeepLTRs ( bool  keep)
inline

Definition at line 275 of file autodef.hpp.

References m_Options, and CAutoDefOptions::SetKeepLTRs().

Referenced by ConfigureAutodefForSeqEntry().

◆ SetKeepMiscRecomb()

void CAutoDef::SetKeepMiscRecomb ( bool  keep)
inline

Definition at line 321 of file autodef.hpp.

References m_Options, and CAutoDefOptions::SetKeepMiscRecomb().

Referenced by ConfigureAutodefForSeqEntry(), and TestForRecomb().

◆ SetKeepOptionalMobileElements()

void CAutoDef::SetKeepOptionalMobileElements ( bool  keep)
inline

Definition at line 303 of file autodef.hpp.

References m_Options, and CAutoDefOptions::SetKeepMobileElements().

Referenced by BOOST_AUTO_TEST_CASE().

◆ SetKeepPrecursorRNA()

void CAutoDef::SetKeepPrecursorRNA ( bool  keep)
inline

Definition at line 309 of file autodef.hpp.

References m_Options, and CAutoDefOptions::SetKeepPrecursorRNA().

◆ SetKeepRegulatoryFeatures()

void CAutoDef::SetKeepRegulatoryFeatures ( bool  keep)
inline

◆ SetKeepRepeatRegion()

void CAutoDef::SetKeepRepeatRegion ( bool  keep)
inline

Definition at line 315 of file autodef.hpp.

References m_Options, and CAutoDefOptions::SetKeepRepeatRegion().

Referenced by ConfigureAutodefForSeqEntry(), and TestRepeatRegion().

◆ SetKeepuORFs()

void CAutoDef::SetKeepuORFs ( bool  keep)
inline

Definition at line 296 of file autodef.hpp.

References m_Options, and CAutoDefOptions::SetKeepuORFs().

Referenced by BOOST_AUTO_TEST_CASE().

◆ SetMiscFeatRule()

void CAutoDef::SetMiscFeatRule ( CAutoDefOptions::EMiscFeatRule  misc_feat_rule)
inline

◆ SetNuclearCopyFlag()

void CAutoDef::SetNuclearCopyFlag ( CBioSource::EGenome  product_flag)
inline

◆ SetOptions()

void CAutoDef::SetOptions ( const CAutoDefModifierCombo mod_combo)

◆ SetOptionsObject()

void CAutoDef::SetOptionsObject ( const CUser_object user)

◆ SetProductFlag()

void CAutoDef::SetProductFlag ( CBioSource::EGenome  product_flag)
inline

◆ SetSpecifyNuclearProduct()

void CAutoDef::SetSpecifyNuclearProduct ( bool  specify_nuclear_product)
inline

◆ SetSuppressAllele()

void CAutoDef::SetSuppressAllele ( bool  suppress_allele)

◆ SetSuppressFeatureAltSplice()

void CAutoDef::SetSuppressFeatureAltSplice ( bool  suppress_alt_splice)
inline

◆ SetSuppressLocusTags()

void CAutoDef::SetSuppressLocusTags ( bool  suppress_locus_tags)
inline

◆ SetUseFakePromoters()

void CAutoDef::SetUseFakePromoters ( bool  use_fake)
inline

◆ SetUseNcRNAComment()

void CAutoDef::SetUseNcRNAComment ( bool  use_comment)
inline

◆ SuppressFeature() [1/2]

void CAutoDef::SuppressFeature ( const objects::CFeatListItem &  feat)

◆ SuppressFeature() [2/2]

void CAutoDef::SuppressFeature ( objects::CSeqFeatData::ESubtype  subtype)

Definition at line 418 of file autodef.cpp.

References m_Options, and CAutoDefOptions::SuppressFeature().

◆ SuppressMiscFeatSubfeatures()

void CAutoDef::SuppressMiscFeatSubfeatures ( bool  suppress)
inline

◆ SuppressMobileElementAndInsertionSequenceSubfeatures()

void CAutoDef::SuppressMobileElementAndInsertionSequenceSubfeatures ( bool  suppress)
inline

◆ x_GetFeatureClauseProductEnding()

string CAutoDef::x_GetFeatureClauseProductEnding ( const string feature_clauses,
CBioseq_Handle  bh 
)
private

◆ x_GetFeatureClauses()

string CAutoDef::x_GetFeatureClauses ( const CBioseq_Handle bh)
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().

◆ x_GetHumanSTRFeatureClauses()

string CAutoDef::x_GetHumanSTRFeatureClauses ( CBioseq_Handle  bh,
const CUser_object comment 
)
private

◆ x_GetHumanSTRv2FeatureClauses()

string CAutoDef::x_GetHumanSTRv2FeatureClauses ( CBioseq_Handle  bh,
const CUser_object comment 
)
private

◆ x_GetModifierIndexList()

void CAutoDef::x_GetModifierIndexList ( TModifierIndexVector index_list,
CAutoDefSourceDescription::TAvailableModifierVector modifier_list 
)
private

Definition at line 139 of file autodef.cpp.

References x_SortModifierListByRank().

◆ x_GetNonFeatureListEnding()

string CAutoDef::x_GetNonFeatureListEnding ( )
private

◆ x_GetOneNonFeatureClause()

string CAutoDef::x_GetOneNonFeatureClause ( CBioseq_Handle  bh,
unsigned int  genome_val 
)
private

◆ x_Is5SList()

bool CAutoDef::x_Is5SList ( CFeat_CI  feat_ci)
private

◆ x_IsFeatureSuppressed()

bool CAutoDef::x_IsFeatureSuppressed ( CSeqFeatData::ESubtype  subtype)
private

Definition at line 402 of file autodef.cpp.

References CAutoDefOptions::IsFeatureSuppressed(), and m_Options.

◆ x_IsHumanSTR()

bool CAutoDef::x_IsHumanSTR ( const CUser_object obj)
private

◆ x_IsOrgModRequired()

bool CAutoDef::x_IsOrgModRequired ( unsigned int  mod_type)
private

Definition at line 166 of file autodef.cpp.

◆ x_IsSingleMiscFeat()

bool CAutoDef::x_IsSingleMiscFeat ( CFeat_CI  feat_ci)
private

◆ x_IsSubSrcRequired()

bool CAutoDef::x_IsSubSrcRequired ( unsigned int  mod_type)
private

◆ x_RemoveOptionalFeatures()

void CAutoDef::x_RemoveOptionalFeatures ( CAutoDefFeatureClause_Base main_clause,
const CBioseq_Handle bh 
)
private

◆ x_SortModifierListByRank()

void CAutoDef::x_SortModifierListByRank ( TModifierIndexVector index_list,
CAutoDefSourceDescription::TAvailableModifierVector modifier_list 
)
private

Definition at line 121 of file autodef.cpp.

References tmp.

Referenced by x_GetModifierIndexList().

Member Data Documentation

◆ m_Cancelled

bool CAutoDef::m_Cancelled
private

Definition at line 140 of file autodef.hpp.

◆ m_Feat_Tree

CRef<feature::CFeatTree> CAutoDef::m_Feat_Tree
private

Definition at line 173 of file autodef.hpp.

Referenced by GetOneDefLine().

◆ m_Options

CAutoDefOptions CAutoDef::m_Options
private

◆ m_OrigModCombo

CAutoDefModifierCombo CAutoDef::m_OrigModCombo
private

The documentation for this class was generated from the following files:
Modified on Sat Jul 20 11:13:17 2024 by modify_doxy.py rev. 669887