NCBI C++ ToolKit
Functions
autodef_functions.cpp File Reference
#include <ncbi_pch.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/util/create_defline.hpp>
#include <gui/objutils/macro_fn_entry.hpp>
#include <gui/objutils/cmd_create_desc.hpp>
#include <gui/objutils/descriptor_change.hpp>
#include <gui/objutils/cmd_del_desc.hpp>
#include <gui/packages/pkg_sequence_edit/autodef_functions.hpp>
#include <objtools/edit/autodef_with_tax.hpp>
#include <objects/general/User_object.hpp>
#include <objmgr/seq_entry_ci.hpp>
+ Include dependency graph for autodef_functions.cpp:

Go to the source code of this file.

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Functions

 USING_SCOPE (objects)
 
void ConfigureAutodefParamsForBestCombo (SAutodefParams &params, CSeq_entry_Handle seh)
 
void ConfigureAutodefParamsForID (SAutodefParams &params, CSeq_entry_Handle seh)
 
unsigned int ConfigureParamsForPrefixCombo (SAutodefParams &params, CSeq_entry_Handle seh)
 
CAutoDefModifierComboConfigureAutodefForSeqEntry (CAutoDef &autodef, CSeq_entry_Handle entry, SAutodefParams *params)
 
CRef< CCmdCompositeAutodefSeqEntryNoTitle (CSeq_entry_Handle entry, SAutodefParams *params, bool docsum_only)
 
CRef< CCmdCompositeAutodefSeqEntryNoTitle (CSeq_entry_Handle entry, CBioseq_Handle target, SAutodefParams *params)
 
CRef< CCmdCompositeInstantiateProteinTitles (CSeq_entry_Handle entry)
 

Function Documentation

◆ AutodefSeqEntryNoTitle() [1/2]

CRef<CCmdComposite> AutodefSeqEntryNoTitle ( CSeq_entry_Handle  entry,
CBioseq_Handle  target,
SAutodefParams params 
)

◆ AutodefSeqEntryNoTitle() [2/2]

CRef<CCmdComposite> AutodefSeqEntryNoTitle ( CSeq_entry_Handle  entry,
SAutodefParams params,
bool  docsum_only 
)

Definition at line 165 of file autodef_functions.cpp.

References cmd, and ConfigureAutodefForSeqEntry().

◆ ConfigureAutodefForSeqEntry()

CAutoDefModifierCombo* ConfigureAutodefForSeqEntry ( CAutoDef autodef,
CSeq_entry_Handle  entry,
SAutodefParams params 
)

Definition at line 96 of file autodef_functions.cpp.

References CAutoDefModifierCombo::AddOrgMod(), CAutoDef::AddSources(), CAutoDefModifierCombo::AddSubsource(), CBioSource_Base::eGenome_unknown, CAutoDef::GetEmptyCombo(), ITERATE, SAutodefParams::m_AltSpliceFlag, SAutodefParams::m_CustomFeatureClause, SAutodefParams::m_DoNotApplyToAff, SAutodefParams::m_DoNotApplyToCf, SAutodefParams::m_DoNotApplyToNr, SAutodefParams::m_DoNotApplyToSp, SAutodefParams::m_FeatureListType, SAutodefParams::m_GeneClusterOppStrand, SAutodefParams::m_HIVRule, SAutodefParams::m_IncludeCountryText, SAutodefParams::m_Keep3UTRs, SAutodefParams::m_Keep5UTRs, SAutodefParams::m_KeepAfterSemicolon, SAutodefParams::m_KeepExons, SAutodefParams::m_KeepIntrons, SAutodefParams::m_KeepLTRs, SAutodefParams::m_KeepMiscRecomb, SAutodefParams::m_KeepRegulatoryFeatures, SAutodefParams::m_KeepRepeatRegion, SAutodefParams::m_LeaveParenthetical, SAutodefParams::m_MaxMods, SAutodefParams::m_MiscFeatRule, SAutodefParams::m_ModifierList, SAutodefParams::m_NeedHIVRule, SAutodefParams::m_NuclearCopyFlag, SAutodefParams::m_ProductFlag, SAutodefParams::m_SpecifyNuclearProduct, SAutodefParams::m_SuppressedFeatures, SAutodefParams::m_SuppressFeatureAltSplice, SAutodefParams::m_SuppressLocusTags, SAutodefParams::m_SuppressMiscFeatSubfeatures, SAutodefParams::m_SuppressMobileElementSubfeatures, SAutodefParams::m_UseFakePromoters, SAutodefParams::m_UseLabels, SAutodefParams::m_UseNcRNAComment, n, CAutoDef::SetAltSpliceFlag(), CAutoDef::SetCustomFeatureClause(), CAutoDefModifierCombo::SetExcludeAffOrgs(), CAutoDefModifierCombo::SetExcludeCfOrgs(), CAutoDefModifierCombo::SetExcludeNrOrgs(), CAutoDefModifierCombo::SetExcludeSpOrgs(), CAutoDef::SetFeatureListType(), CAutoDef::SetGeneClusterOppStrand(), CAutoDefModifierCombo::SetHIVCloneIsolateRule(), CAutoDef::SetKeep3UTRs(), CAutoDef::SetKeep5UTRs(), CAutoDefModifierCombo::SetKeepAfterSemicolon(), CAutoDefModifierCombo::SetKeepCountryText(), CAutoDef::SetKeepExons(), CAutoDef::SetKeepIntrons(), CAutoDef::SetKeepLTRs(), CAutoDef::SetKeepMiscRecomb(), CAutoDefModifierCombo::SetKeepParen(), CAutoDef::SetKeepRegulatoryFeatures(), CAutoDef::SetKeepRepeatRegion(), CAutoDefModifierCombo::SetMaxModifiers(), CAutoDef::SetMiscFeatRule(), CAutoDef::SetNuclearCopyFlag(), CAutoDef::SetProductFlag(), CAutoDef::SetSpecifyNuclearProduct(), CAutoDef::SetSuppressFeatureAltSplice(), CAutoDef::SetSuppressLocusTags(), CAutoDef::SetUseFakePromoters(), CAutoDefModifierCombo::SetUseModifierLabels(), CAutoDef::SetUseNcRNAComment(), CAutoDef::SuppressFeature(), CAutoDef::SuppressMiscFeatSubfeatures(), and CAutoDef::SuppressMobileElementAndInsertionSequenceSubfeatures().

Referenced by AutodefSeqEntryNoTitle().

◆ ConfigureAutodefParamsForBestCombo()

void ConfigureAutodefParamsForBestCombo ( SAutodefParams params,
CSeq_entry_Handle  seh 
)

◆ ConfigureAutodefParamsForID()

void ConfigureAutodefParamsForID ( SAutodefParams params,
CSeq_entry_Handle  seh 
)

◆ ConfigureParamsForPrefixCombo()

unsigned int ConfigureParamsForPrefixCombo ( SAutodefParams params,
CSeq_entry_Handle  seh 
)

◆ InstantiateProteinTitles()

CRef<CCmdComposite> InstantiateProteinTitles ( CSeq_entry_Handle  entry)

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Fri Mar 01 10:07:05 2024 by modify_doxy.py rev. 669887