NCBI C++ ToolKit
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macro_util.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbimisc.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/taxon3/taxon3.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objtools/edit/source_edit.hpp>
#include <objmgr/seq_entry_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <gui/objutils/macro_ex.hpp>
#include <gui/objutils/macro_fn_aecr.hpp>
#include <gui/objutils/macro_fn_pubfields.hpp>
#include <gui/objutils/macro_util.hpp>
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Namespaces

 NMacroUtil
 

Typedefs

using NMacroUtil::TFeatLabelMap = SStaticPair< const char *, CLabel::ELabelType >
 
using NMacroUtil::TLabelTypeToNameMap = CStaticPairArrayMap< string, CLabel::ELabelType >
 

Functions

 USING_SCOPE (objects)
 
objects::edit::EExistingText NMacroUtil::ActionTypeToExistingTextOption (const string &action_type, const string &delimiter)
 
objects::ECapChange NMacroUtil::ConvertStringtoCapitalOption (const string &cap_name)
 
CSeq_entry_Handle NMacroUtil::GetParentEntryForBioSource (const CBioSource &bsrc, const CSeq_entry_Handle &tse)
 
CConstRef< CBioseqNMacroUtil::GetBioseqForSeqdescObject (const CSerialObject *obj, const CSeq_entry_Handle &tse)
 
CObjectInfo NMacroUtil::GetPrimitiveObjInfo (const CObjectInfo &info)
 
void NMacroUtil::GetPrimitiveObjectInfos (CMQueryNodeValue::TObs &objs, const CMQueryNodeValue::SResolvedField &info)
 
void NMacroUtil::GetPrimitiveObjInfosWithContainers (CMQueryNodeValue::TObs &objs, const CMQueryNodeValue::SResolvedField &info)
 
CMQueryNodeValue::EType NMacroUtil::GetPrimitiveFromRef (CMQueryNodeValue &node)
 
void NMacroUtil::SwapGbQualWithValues (CMQueryNodeValue::TObs &objs)
 
void NMacroUtil::RemoveGeneXref (CSeq_feat &feat)
 
void NMacroUtil::RemoveEmptyDescriptors (CBioseq &bseq)
 
string NMacroUtil::GetStringValue (CRef< CMQueryNodeValue > &value)
 converts ints and doubles into string, by changing the type of the value More...
 
objects::CSeqFeatData::ESubtype NMacroUtil::GetFeatSubtype (const string &feat_type)
 
bool NMacroUtil::StringsAreEquivalent (const string &name1, const string &name2)
 
bool NMacroUtil::GetLocusTagFromGene (const CGene_ref &gene, string &locus_tag)
 
bool NMacroUtil::GetLocusTagFromProtRef (const CSeq_feat &prot_feat, CScope &scope, string &locus_tag)
 
CRef< objects::CSeqdesc > NMacroUtil::MakeNcbiAutofixUserObject ()
 
bool NMacroUtil::FindNcbiAutofixUserObject (const CSeq_entry_Handle &tse)
 
objects::CRNA_ref::EType NMacroUtil::GetRNAType (const string &rna_type)
 
bool NMacroUtil::IsBiosourceModifier (const string &field)
 
bool NMacroUtil::IsTaxname (CMQueryNodeValue::SResolvedField &res)
 
void NMacroUtil::CleanupForTaxnameChange (CObjectInfo oi)
 
void NMacroUtil::CleanupForTaxnameChange (CMQueryNodeValue::SResolvedField &res, CObjectInfo oi)
 
void NMacroUtil::s_SetInitials (CName_std &std_name, const string &middle_init)
 
bool NMacroUtil::ApplyFirstName (CName_std &std_name, const string &newValue, edit::EExistingText existing_text)
 
bool NMacroUtil::RemoveFirstName (CName_std &std_name)
 
bool NMacroUtil::ApplyMiddleInitial (CName_std &std_name, const string &newValue, edit::EExistingText existing_text)
 
bool NMacroUtil::RemoveMiddleInitial (CName_std &std_name)
 
unsigned NMacroUtil::ApplyAuthorNames (CAuth_list &auth_list, const string &newValue)
 
EStructVoucherPart NMacroUtil::GetSVPartFromString (const string voucher_part)
 
bool NMacroUtil::IsStructVoucherPart (const string &field)
 
void NMacroUtil::ConvertMultiSpaces (string &line, const string &delimiter)
 replace any instance of 2 or more spaces with a single instance of 'delimiter' More...
 
string NMacroUtil::TransformForCSV (const string &str)
 
 NMacroUtil::DEFINE_STATIC_ARRAY_MAP (TLabelTypeToNameMap, sm_CLabelMap, s_LabelTypeToName)
 
CLabel::ELabelType NMacroUtil::NameToLabelType (const string &name)
 
bool NMacroUtil::IsSatelliteSubfield (const string &field)
 
bool NMacroUtil::IsMobileElementTSubfield (const string &field)
 
EUnverifiedType NMacroUtil::GetUnverifiedType (const string &value)
 

Variables

static const TFeatLabelMap NMacroUtil::s_LabelTypeToName []
 
const char * kInst_suffix = "-inst"
 
const char * kColl_suffix = "-coll"
 
const char * kSpecid_suffix = "-specid"
 
const char * kSatelliteType = "satellite-type"
 
const char * kSatelliteName = "satellite-name"
 
const char * kMobileElementTQual = "mobile_element_type"
 
const char * kMobileElementTType = "mobile-element-type-type"
 
const char * kMobileElementTName = "mobile-element-type-name"
 
const char * kStrCommFieldValue = "fieldvalue"
 
const char * kStrCommDbname = "dbname"
 
const char * kStrCommFieldName = "fieldname"
 
Modified on Thu Feb 22 17:12:26 2024 by modify_doxy.py rev. 669887