NCBI C++ ToolKit
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CAutoDefWithTaxonomy Class Reference

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#include <objtools/edit/autodef_with_tax.hpp>

+ Inheritance diagram for CAutoDefWithTaxonomy:
+ Collaboration diagram for CAutoDefWithTaxonomy:

Public Member Functions

 CAutoDefWithTaxonomy ()
 
 ~CAutoDefWithTaxonomy ()
 
string GetDocsumDefLine (CSeq_entry_Handle se)
 
- Public Member Functions inherited from CAutoDef
 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 GetDocsumOrgDescription (CSeq_entry_Handle se)
 
static bool RegeneratePopsetTitles (CSeq_entry_Handle se)
 
static bool RegenerateDefLines (CSeq_entry_Handle se)
 
- Static Public Member Functions inherited from CAutoDef
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)
 

Additional Inherited Members

- Public Types inherited from CAutoDef
typedef set< CAutoDefAvailableModifierTAvailableModifierSet
 
using TSources = vector< CConstRef< objects::CBioSource > >
 
typedef vector< CRef< CAutoDefModifierCombo > > TModifierComboVector
 

Detailed Description

Definition at line 42 of file autodef_with_tax.hpp.

Constructor & Destructor Documentation

◆ CAutoDefWithTaxonomy()

CAutoDefWithTaxonomy::CAutoDefWithTaxonomy ( )
inline

Definition at line 45 of file autodef_with_tax.hpp.

◆ ~CAutoDefWithTaxonomy()

CAutoDefWithTaxonomy::~CAutoDefWithTaxonomy ( )
inline

Definition at line 46 of file autodef_with_tax.hpp.

Member Function Documentation

◆ GetDocsumDefLine()

string CAutoDefWithTaxonomy::GetDocsumDefLine ( CSeq_entry_Handle  se)

◆ GetDocsumOrgDescription()

string CAutoDefWithTaxonomy::GetDocsumOrgDescription ( CSeq_entry_Handle  se)
static

◆ RegenerateDefLines()

bool CAutoDefWithTaxonomy::RegenerateDefLines ( CSeq_entry_Handle  se)
static

◆ RegeneratePopsetTitles()

bool CAutoDefWithTaxonomy::RegeneratePopsetTitles ( CSeq_entry_Handle  se)
static

The documentation for this class was generated from the following files:
Modified on Sat Feb 24 07:49:13 2024 by modify_doxy.py rev. 669887