util_cmds.cpp File Reference

#include <ncbi_pch.hpp>
#include <objects/taxon3/taxon3.hpp>
#include <misc/discrepancy/discrepancy.hpp>
#include <objmgr/seq_feat_handle.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <objtools/cleanup/cleanup.hpp>
#include <objtools/validator/validatorp.hpp>
#include <objtools/validator/go_term_validation_and_cleanup.hpp>
#include <gui/objutils/registry.hpp>
#include <gui/objutils/cmd_factory.hpp>
#include <gui/objutils/cmd_del_bioseq.hpp>
#include <gui/objutils/cmd_del_bioseq_set.hpp>
#include <gui/objutils/cmd_del_seq_feat.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/objutils/cmd_add_seqentry.hpp>
#include <gui/objutils/cmd_change_seq_entry.hpp>
#include <gui/objutils/descriptor_change.hpp>
#include <gui/objutils/cmd_create_feat.hpp>
#include <gui/objutils/cmd_create_desc.hpp>
#include <gui/objutils/cmd_change_bioseq_inst.hpp>
#include <gui/objutils/util_cmds.hpp>

Include dependency graph for util_cmds.cpp:

Go to the source code of this file.

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Functions
	USING_SCOPE (objects)
static bool	s_AreThereOtherCDSForThisProduct (const CSeq_feat_Handle &fh)
static bool	s_IsFarLocation (CSeq_feat_Handle fh)
CRef< CCmdComposite >	GetDeleteFeatureCommand (const CSeq_feat_Handle &fh, bool remove_proteins)
void	GetProductToCDSMap (CScope &scope, map< CBioseq_Handle, set< CSeq_feat_Handle > > &product_to_cds)
CRef< CCmdComposite >	GetDeleteFeatureCommand (const CSeq_feat_Handle &fh, bool remove_proteins, map< CBioseq_Handle, set< CSeq_feat_Handle > > &product_to_cds)
CRef< CCmdComposite >	GetDeleteSequenceCommand (CBioseq_Handle bsh)
static bool	s_IsNucLocation (CSeq_feat_Handle fh)
CRef< CCmdComposite >	GetDeleteAllFeaturesCommand (CSeq_entry_Handle seh, size_t &count, bool remove_proteins)
static void	s_GetSourceDescriptors (const CSeq_entry &se, vector< pair< const CSeqdesc *, const CSeq_entry * >> &src_descs)
CRef< CCmdComposite >	CleanupCommand (CSeq_entry_Handle orig_seh, bool extended, bool do_tax)
CRef< CCmdComposite >	CleanupHugeFileCommand (CSeq_entry_Handle orig_seh, bool extended, bool do_tax, objects::taxupdate_func_t &updater, bool rmv_user_object)
CRef< CCmdComposite >	TaxonomyLookupCommand (CSeq_entry_Handle seh)
CRef< CCmdComposite >	CachedTaxonomyLookupCommand (CSeq_entry_Handle seh, objects::taxupdate_func_t &updater)
CRef< CCmdComposite >	SpecificHostCleanupCommand (CSeq_entry_Handle seh)
CRef< CCmdComposite >	GetChangeStrainForwardingCommand (CSeq_entry_Handle seh, bool disable)
CRef< CCmdComposite >	GetDisableStrainForwardingCommand (CSeq_entry_Handle seh)
CRef< CCmdComposite >	GetEnableStrainForwardingCommand (CSeq_entry_Handle seh)
bool	s_IsSpeciesLevel (const COrg_ref &org)
CRef< CCmdComposite >	GetRmCultureNotesCommand (CSeq_entry_Handle seh)
CRef< CCmdComposite >	GetSynchronizeProductMolInfoCommand (CScope &scope, const CSeq_feat &cds)
CRef< CCmdComposite >	GetSynchronizeProteinPartialsCommand (CScope &scope, const CSeq_feat &cds)
void	SetProteinFeature (CSeq_feat &prot, CBioseq_Handle product, const CSeq_feat &cds)
void	AdjustProteinFeature (CSeq_feat &prot, CBioseq_Handle product, CSeq_feat &cds, bool &cds_change)
CRef< CCmdComposite >	CreateOrAdjustProteinFeature (CBioseq_Handle product, CSeq_feat &cds, bool &cds_change)
CRef< CCmdComposite >	TranslateCDSCommand (CScope &scope, CSeq_feat &cds, bool &cds_change, int &offset, bool create_general_only)
CRef< CCmdComposite >	GetRetranslateCDSCommand (CScope &scope, CSeq_feat &cds, bool &cds_change, bool create_general_only)
CRef< CCmdComposite >	GetRetranslateCDSCommand (CScope &scope, CSeq_feat &cds, bool &cds_change, int &offset, bool create_general_only)
CRef< CCmdComposite >	GetRetranslateCDSCommand (CScope &scope, const CSeq_feat &cds, bool create_general_only)
CRef< CCmdComposite >	GetRetranslateCDSCommand (CScope &scope, const CSeq_feat &cds, int &offset, bool create_general_only)
CRef< CCmdComposite >	SetTranslExcept (CSeq_entry_Handle seh, const string &comment, bool strict, bool extend, bool adjust_gene)
	SetTranslExcept A function to set a code break at the 3' end of coding regions in a Seq-entry to indicate that the stop codon is formed by the addition of a poly-A tail. More...
CRef< CCmdComposite >	GetReverseComplimentSequenceCommand (CBioseq_Handle bsh)
CRef< CCmdComposite >	TrimStopsFromCompleteCDS (const CSeq_feat &cds, CScope &scope)
	TrimStopsFromCompleteCDS If the CDS is 3' complete and the protein sequence ends with a stop codon, the function removes the stop codon, shortens the protein length and adjusts the features on the protein sequence so that they do not extend past the "new" end of the sequence. More...
static string	s_GetProductRules ()
CRef< CCmdComposite >	AutofixCommand (CSeq_entry_Handle orig_seh, const string &test_name, string *output, const string &suspect_rules)
CRef< CCmdComposite >	AutofixCommandHugeMode (CSeq_entry_Handle orig_seh, const string &str_test_name, map< string, size_t > &report, const string &suspect_rules)
CRef< CCmdComposite >	GetEditLocationCommand (const edit::CLocationEditPolicy &policy, bool retranslate, bool adjust_gene, const CSeq_feat &orig_feat, CScope &scope, int &offset, bool create_general_only)
	GetEditLocationCommand Changes the location properties of a feature according to a location policy. More...
CRef< CCmdChangeSeq_feat >	AdjustGene (const CSeq_feat &orig_feat, const CSeq_feat &new_feat, CScope &scope)
bool	GetNormalizeGeneQualsCommand (CBioseq_Handle bsh, CRef< CCmdComposite > cmd)
CRef< CCmdComposite >	GetNormalizeGeneQualsCommand (CSeq_entry_Handle seh)
bool	GetRemoveDuplicateGOTermsCommand (CBioseq_Handle bsh, CRef< CCmdComposite > cmd)
CRef< CCmdComposite >	GetRemoveDuplicateGOTermsCommand (CSeq_entry_Handle seh)
CRef< CCmdComposite >	UpdatemRNAProduct (const CSeq_feat &protein, CScope &scope, string &message)
CRef< CCmdComposite >	UpdatemRNAProduct (const string &prot_product, CConstRef< CObject > object, CScope &scope)

Variables
static const char *	kDiscrepancyEdit = "Dialogs.Edit.Discrepancy"

Function Documentation

AdjustGene()

CRef<CCmdChangeSeq_feat> AdjustGene	(	const CSeq_feat &	orig_feat,
		const CSeq_feat &	new_feat,
		CScope &	scope
	)

Definition at line 1576 of file util_cmds.cpp.

References CSerialObject::Assign(), eExtreme_Biological, CSeq_feat_Base::GetLocation(), GetOverlappingGene(), CScope::GetSeq_featHandle(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), Ref(), SeqLocExtend(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetPartial().

Referenced by GetEditLocationCommand().

AdjustProteinFeature()

void AdjustProteinFeature	(	CSeq_feat &	prot,
		CBioseq_Handle	product,
		CSeq_feat &	cds,
		bool &	cds_change
	)

Definition at line 939 of file util_cmds.cpp.

References CSeq_feat_Base::GetXref(), CSeq_feat_Base::IsSetXref(), NON_CONST_ITERATE, prot, CSeq_feat_Base::ResetXref(), SetProteinFeature(), and CSeq_feat_Base::SetXref().

Referenced by CreateOrAdjustProteinFeature().

AutofixCommand()

CRef<CCmdComposite> AutofixCommand	(	CSeq_entry_Handle	orig_seh,
		const string &	test_name,
		string *	output,
		const string &	suspect_rules
	)

Definition at line 1430 of file util_cmds.cpp.

References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), cmd, copy(), CSeq_entry_Handle::GetCompleteSeq_entry(), CObjectManager::GetInstance(), J, output, result, s_GetProductRules(), test_name, and tests.

AutofixCommandHugeMode()

CRef<CCmdComposite> AutofixCommandHugeMode	(	CSeq_entry_Handle	orig_seh,
		const string &	str_test_name,
		map< string, size_t > &	report,
		const string &	suspect_rules
	)

Definition at line 1487 of file util_cmds.cpp.

References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), cmd, copy(), CSeq_entry_Handle::GetCompleteSeq_entry(), GetDiscrepancyCaseName(), CObjectManager::GetInstance(), s_GetProductRules(), and test_name.

CachedTaxonomyLookupCommand()

CRef<CCmdComposite> CachedTaxonomyLookupCommand	(	CSeq_entry_Handle	seh,
		objects::taxupdate_func_t &	updater
	)

Definition at line 481 of file util_cmds.cpp.

References CSerialObject::Assign(), chunk_size, cmd, variation::Equals(), Error(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetScope(), CScope::GetSeq_entryHandle(), CScope::GetSeq_featHandle(), i, NStr::IsBlank(), ITERATE, len, LOG_POST, min(), n, NULL, CSeq_feat_Base::SetData(), CBioSource_Base::SetOrg(), and CSeqdesc_Base::SetSource().

Referenced by CleanupHugeFileCommand().

CleanupCommand()

CRef<CCmdComposite> CleanupCommand	(	CSeq_entry_Handle	orig_seh,
		bool	extended,
		bool	do_tax
	)

Definition at line 280 of file util_cmds.cpp.

References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), cleanup(), cmd, copy(), CCleanup::eClean_KeepTopSet, CCleanup::eClean_SyncGenCodes, Error(), CCmdComposite::Execute(), CSeq_entry_Handle::GetCompleteSeq_entry(), CObjectManager::GetInstance(), CException::GetMsg(), LOG_POST, and TaxonomyLookupCommand().

CleanupHugeFileCommand()

CRef<CCmdComposite> CleanupHugeFileCommand	(	CSeq_entry_Handle	orig_seh,
		bool	extended,
		bool	do_tax,
		objects::taxupdate_func_t &	updater,
		bool	rmv_user_object
	)

Definition at line 321 of file util_cmds.cpp.

References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), CachedTaxonomyLookupCommand(), cleanup(), cmd, copy(), CCleanup::eClean_KeepTopSet, CCleanup::eClean_NoNcbiUserObjects, CCleanup::eClean_SyncGenCodes, Error(), CCmdComposite::Execute(), CSeq_entry_Handle::GetCompleteSeq_entry(), CObjectManager::GetInstance(), CException::GetMsg(), and LOG_POST.

CreateOrAdjustProteinFeature()

CRef<CCmdComposite> CreateOrAdjustProteinFeature	(	CBioseq_Handle	product,
		CSeq_feat &	cds,
		bool &	cds_change
	)

Definition at line 960 of file util_cmds.cpp.

References AdjustProteinFeature(), cleanup(), cmd, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetSeq_entry_Handle(), and prot.

GetChangeStrainForwardingCommand()

CRef<CCmdComposite> GetChangeStrainForwardingCommand	(	CSeq_entry_Handle	seh,
		bool	disable
	)

Definition at line 696 of file util_cmds.cpp.

References CSerialObject::Assign(), cmd, CSeqFeatData_Base::e_Biosrc, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetScope(), CScope::GetSeq_entryHandle(), CMappedFeat::GetSeq_feat(), CScope::GetSeq_featHandle(), s_GetSourceDescriptors(), CSeq_feat_Base::SetData(), CBioSource::SetDisableStrainForwarding(), and CSeqdesc_Base::SetSource().

Referenced by GetDisableStrainForwardingCommand(), and GetEnableStrainForwardingCommand().

GetDeleteAllFeaturesCommand()

CRef<CCmdComposite> GetDeleteAllFeaturesCommand	(	CSeq_entry_Handle	seh,
		size_t &	count,
		bool	remove_proteins
	)

Definition at line 240 of file util_cmds.cpp.

References CCmdComposite::AddCommand(), cmd, count, GetDeleteFeatureCommand(), GetProductToCDSMap(), CSeq_entry_Handle::GetScope(), and s_IsNucLocation().

GetDeleteFeatureCommand() [1/2]

CRef<CCmdComposite> GetDeleteFeatureCommand	(	const CSeq_feat_Handle &	fh,
		bool	remove_proteins
	)

Definition at line 107 of file util_cmds.cpp.

References cmd, data, CScope::GetBioseqHandle(), CSeq_feat_Handle::GetData(), CSeq_feat_Handle::GetLocationId(), CSeq_entry_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CSeq_feat_Handle::GetProductId(), CSeq_feat_Handle::GetScope(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_id_Handle::GetSeqId(), CBioseq_Handle::IsProtein(), CSeq_feat_Handle::IsSetProduct(), CCmdFactory::RemoveCitations(), s_AreThereOtherCDSForThisProduct(), and s_IsFarLocation().

Referenced by GetDeleteAllFeaturesCommand().

GetDeleteFeatureCommand() [2/2]

CRef<CCmdComposite> GetDeleteFeatureCommand	(	const CSeq_feat_Handle &	fh,
		bool	remove_proteins,
		map< CBioseq_Handle, set< CSeq_feat_Handle > > &	product_to_cds
	)

Definition at line 164 of file util_cmds.cpp.

References cmd, data, CScope::GetBioseqHandle(), CSeq_feat_Handle::GetData(), CSeq_feat_Handle::GetLocationId(), CSeq_entry_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CSeq_feat_Handle::GetProductId(), CSeq_feat_Handle::GetScope(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_id_Handle::GetSeqId(), CBioseq_Handle::IsProtein(), CSeq_feat_Handle::IsSetProduct(), CCmdFactory::RemoveCitations(), and s_IsFarLocation().

GetDeleteSequenceCommand()

CRef<CCmdComposite> GetDeleteSequenceCommand

(

CBioseq_Handle

bsh

)

Definition at line 204 of file util_cmds.cpp.

References cmd, CBioseq_set_Base::eClass_nuc_prot, eUnknown, CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CBioseq_Handle::GetSeq_entry_Handle(), CBioseq_Handle::GetTopLevelEntry(), CBioseq_set_Handle::GetTopLevelEntry(), CBioseq_Handle::IsNa(), CBioseq_set_Handle::IsSetClass(), and NCBI_THROW.

GetDisableStrainForwardingCommand()

CRef<CCmdComposite> GetDisableStrainForwardingCommand

(

CSeq_entry_Handle

seh

)

Definition at line 729 of file util_cmds.cpp.

References GetChangeStrainForwardingCommand().

GetEditLocationCommand()

CRef<CCmdComposite> GetEditLocationCommand	(	const edit::CLocationEditPolicy &	policy,
		bool	retranslate,
		bool	adjust_gene,
		const CSeq_feat &	orig_feat,
		CScope &	scope,
		int &	offset,
		bool	create_general_only
	)

GetEditLocationCommand Changes the location properties of a feature according to a location policy.

Definition at line 1528 of file util_cmds.cpp.

References AdjustGene(), CSerialObject::Assign(), cmd, eExtreme_Biological, CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), GetRetranslateCDSCommand(), CScope::GetSeq_featHandle(), GetSynchronizeProteinPartialsCommand(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::IsSetProduct(), NULL, offset, and CSeq_feat_Base::SetPartial().

GetEnableStrainForwardingCommand()

CRef<CCmdComposite> GetEnableStrainForwardingCommand

(

CSeq_entry_Handle

seh

)

Definition at line 734 of file util_cmds.cpp.

References GetChangeStrainForwardingCommand().

GetNormalizeGeneQualsCommand() [1/2]

bool GetNormalizeGeneQualsCommand	(	CBioseq_Handle	bsh,
		CRef< CCmdComposite >	cmd
	)

Definition at line 1617 of file util_cmds.cpp.

References CSerialObject::Assign(), cmd, CCleanup::GetNormalizableGeneQualPairs(), and CCleanup::NormalizeGeneQuals().

Referenced by GetNormalizeGeneQualsCommand().

GetNormalizeGeneQualsCommand() [2/2]

CRef<CCmdComposite> GetNormalizeGeneQualsCommand

(

CSeq_entry_Handle

seh

)

Definition at line 1639 of file util_cmds.cpp.

References cmd, CSeq_inst_Base::eMol_na, GetNormalizeGeneQualsCommand(), and NULL.

GetProductToCDSMap()

void GetProductToCDSMap	(	CScope &	scope,
		map< CBioseq_Handle, set< CSeq_feat_Handle > > &	product_to_cds
	)

Definition at line 145 of file util_cmds.cpp.

References CScope::eAllTSEs, CSeqFeatData::eSubtype_cdregion, CScope::GetAllTSEs(), CScope::GetBioseqHandle(), CSeq_feat_Handle::GetProductId(), and CSeq_id_Handle::GetSeqId().

Referenced by GetDeleteAllFeaturesCommand().

GetRemoveDuplicateGOTermsCommand() [1/2]

bool GetRemoveDuplicateGOTermsCommand	(	CBioseq_Handle	bsh,
		CRef< CCmdComposite >	cmd
	)

Definition at line 1656 of file util_cmds.cpp.

References CSerialObject::Assign(), cmd, f(), and RemoveDuplicateGoTerms().

Referenced by GetRemoveDuplicateGOTermsCommand().

GetRemoveDuplicateGOTermsCommand() [2/2]

CRef<CCmdComposite> GetRemoveDuplicateGOTermsCommand

(

CSeq_entry_Handle

seh

)

Definition at line 1676 of file util_cmds.cpp.

References cmd, CSeq_inst_Base::eMol_na, GetRemoveDuplicateGOTermsCommand(), and NULL.

GetRetranslateCDSCommand() [1/4]

CRef<CCmdComposite> GetRetranslateCDSCommand	(	CScope &	scope,
		const CSeq_feat &	cds,
		bool	create_general_only
	)

Definition at line 1165 of file util_cmds.cpp.

References GetRetranslateCDSCommand(), and offset.

GetRetranslateCDSCommand() [2/4]

CRef<CCmdComposite> GetRetranslateCDSCommand	(	CScope &	scope,
		const CSeq_feat &	cds,
		int &	offset,
		bool	create_general_only
	)

Definition at line 1172 of file util_cmds.cpp.

References CSerialObject::Assign(), cmd, ctll::empty(), CSeq_feat_Base::GetData(), GetRetranslateCDSCommand(), CScope::GetSeq_featHandle(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetData(), NULL, and offset.

GetRetranslateCDSCommand() [3/4]

CRef<CCmdComposite> GetRetranslateCDSCommand	(	CScope &	scope,
		CSeq_feat &	cds,
		bool &	cds_change,
		bool	create_general_only
	)

Definition at line 1036 of file util_cmds.cpp.

References offset.

Referenced by GetEditLocationCommand(), and GetRetranslateCDSCommand().

GetRetranslateCDSCommand() [4/4]

CRef<CCmdComposite> GetRetranslateCDSCommand	(	CScope &	scope,
		CSeq_feat &	cds,
		bool &	cds_change,
		int &	offset,
		bool	create_general_only
	)

Definition at line 1043 of file util_cmds.cpp.

References AdjustProteinFeaturePartialsToMatchCDS(), CSerialObject::Assign(), CSeq_feat_Base::CanGetLocation(), CSeq_interval_Base::CanGetTo(), cmd, CSeqFeatData_Base::e_Prot, eExtreme_Positional, CSeq_inst_Base::eMol_aa, ctll::empty(), NStr::EndsWith(), CSeq_inst_Base::eRepr_raw, CSeqFeatData::eSubtype_prot, CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeq_feat_Base::GetData(), CBioseq_Base::GetInst(), CBioseq_Handle::GetInst(), CSeq_loc_Base::GetInt(), CBioseq::GetLength(), CSeq_inst_Base::GetLength(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetSeqId(), CSeq_loc::GetStop(), GetSynchronizeProductMolInfoCommand(), CSeqFeatData_Base::IsCdregion(), CSeq_loc_Base::IsInt(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetData(), CBioseq_Base::IsSetInst(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetProduct(), CSeq_inst_Base::IsSetSeq_data(), NULL, offset, CRef< C, Locker >::Reset(), CBioseq_Base::ResetInst(), CSeq_loc::SetId(), CBioseq_Base::SetInst(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CSeqTranslator::Translate(), TranslateCDSCommand(), and CSeqTranslator::TranslateToProtein().

GetReverseComplimentSequenceCommand()

CRef<CCmdComposite> GetReverseComplimentSequenceCommand

(

CBioseq_Handle

bsh

)

Definition at line 1265 of file util_cmds.cpp.

References CSerialObject::Assign(), cmd, f(), CBioseq_Handle::GetInst(), CBioseq_Handle::GetScope(), CMappedFeat::GetSeq_feat(), CScope::GetSeq_featHandle(), NULL, ReverseComplement(), and ReverseComplementFeature().

GetRmCultureNotesCommand()

CRef<CCmdComposite> GetRmCultureNotesCommand

(

CSeq_entry_Handle

seh

)

Definition at line 769 of file util_cmds.cpp.

References CSerialObject::Assign(), cmd, CSeqFeatData_Base::e_Biosrc, CSeqFeatData_Base::GetBiosrc(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_feat_Handle::GetData(), CBioSource_Base::GetOrg(), CSeq_entry_Handle::GetScope(), CScope::GetSeq_entryHandle(), CMappedFeat::GetSeq_feat(), CScope::GetSeq_featHandle(), CSeqdesc_Base::GetSource(), CTaxon3::Init(), CBioSource::RemoveCultureNotes(), CFeat_CI::Rewind(), s_GetSourceDescriptors(), CTaxon3::SendRequest(), CSeq_feat_Base::SetData(), CTaxon3_request_Base::SetRequest(), and CSeqdesc_Base::SetSource().

GetSynchronizeProductMolInfoCommand()

CRef<CCmdComposite> GetSynchronizeProductMolInfoCommand	(	CScope &	scope,
		const CSeq_feat &	cds
	)

Definition at line 845 of file util_cmds.cpp.

References AdjustProteinMolInfoToMatchCDS(), CSerialObject::Assign(), cmd, CSeqdesc_Base::e_Molinfo, CMolInfo_Base::eBiomol_peptide, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeqdesc_Base::GetMolinfo(), CBioseq_Handle::GetParentEntry(), CSeq_feat_Base::GetProduct(), CSeqdesc_CI::GetSeq_entry_Handle(), CSeqFeatData_Base::IsCdregion(), CBioseq_Handle::IsNa(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetProduct(), NULL, CMolInfo_Base::SetBiomol(), and CSeqdesc_Base::SetMolinfo().

Referenced by GetRetranslateCDSCommand(), and GetSynchronizeProteinPartialsCommand().

GetSynchronizeProteinPartialsCommand()

CRef<CCmdComposite> GetSynchronizeProteinPartialsCommand	(	CScope &	scope,
		const CSeq_feat &	cds
	)

Definition at line 885 of file util_cmds.cpp.

References AdjustProteinFeaturePartialsToMatchCDS(), CSerialObject::Assign(), cmd, CSeqFeatData::eSubtype_prot, f(), CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetProduct(), GetSynchronizeProductMolInfoCommand(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetProduct(), and NULL.

Referenced by GetEditLocationCommand().

s_AreThereOtherCDSForThisProduct()

static bool s_AreThereOtherCDSForThisProduct ( const CSeq_feat_Handle &  fh )

static

Definition at line 65 of file util_cmds.cpp.

References CScope::eAllTSEs, CSeq_inst_Base::eMol_na, CSeqFeatData::eSubtype_cdregion, CScope::GetAllTSEs(), CSeq_feat_Handle::GetOriginalSeq_feat(), CConstRef< C, Locker >::GetPointer(), CSeq_feat_Handle::GetProduct(), CSeq_feat_Handle::GetScope(), and ITERATE.

Referenced by GetDeleteFeatureCommand().

s_GetProductRules()

static string s_GetProductRules ( )

static

Definition at line 1380 of file util_cmds.cpp.

References file, CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), kDiscrepancyEdit, and kEmptyStr.

Referenced by AutofixCommand(), and AutofixCommandHugeMode().

s_GetSourceDescriptors()

static void s_GetSourceDescriptors ( const CSeq_entry &  se, vector< pair< const CSeqdesc *, const CSeq_entry * >> &  src_descs  )

static

Definition at line 263 of file util_cmds.cpp.

References CSeq_descr_Base::Get(), CSeq_entry::GetDescr(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSet(), CSeq_entry::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), and ITERATE.

Referenced by GetChangeStrainForwardingCommand(), and GetRmCultureNotesCommand().

s_IsFarLocation()

static bool s_IsFarLocation ( CSeq_feat_Handle  fh )

static

Definition at line 86 of file util_cmds.cpp.

References CSeq_loc_CI::eEmpty_Skip, CScope::GetBioseqHandle(), CSeq_feat_Handle::GetLocation(), CSeq_feat_Handle::GetProduct(), CSeq_feat_Handle::GetScope(), CBioseq_Handle::GetSeq_entry_Handle(), and IsFarLocation().

Referenced by GetDeleteFeatureCommand().

s_IsNucLocation()

static bool s_IsNucLocation ( CSeq_feat_Handle  fh )

static

Definition at line 226 of file util_cmds.cpp.

References CSeq_loc_CI::eEmpty_Skip, CScope::GetBioseqHandle(), CSeq_feat_Handle::GetLocation(), CSeq_feat_Handle::GetScope(), and CBioseq_Handle::IsNa().

Referenced by GetDeleteAllFeaturesCommand().

s_IsSpeciesLevel()

bool s_IsSpeciesLevel

(

const COrg_ref &

org

)

Definition at line 740 of file util_cmds.cpp.

References CTaxon3::Init(), CTaxon3::SendRequest(), and CTaxon3_request_Base::SetRequest().

SetProteinFeature()

void SetProteinFeature	(	CSeq_feat &	prot,
		CBioseq_Handle	product,
		const CSeq_feat &	cds
	)

Definition at line 923 of file util_cmds.cpp.

References eExtreme_Biological, CBioseq_Handle::GetId(), CBioseq_Handle::GetInst_Length(), CSeq_feat_Base::GetLocation(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), and prot.

Referenced by AdjustProteinFeature().

SetTranslExcept()

CRef<CCmdComposite> SetTranslExcept	(	CSeq_entry_Handle	seh,
		const string &	comment,
		bool	strict,
		bool	extend,
		bool	adjust_gene
	)

SetTranslExcept A function to set a code break at the 3' end of coding regions in a Seq-entry to indicate that the stop codon is formed by the addition of a poly-A tail.

Parameters

seh	The Seq-entry to search for coding regions to adjust
comment	The string to place in the note on cds if a code break is added
strict	Only add code break if last partial codon consists of "TA" or just "T". If strict is false, add code break if first NT of last partial codon is T or N.
extend	If true, extend coding region to cover partial stop codon
adjust_gene	If true, adjust gene location to match coding region after adjustment

Definition at line 1211 of file util_cmds.cpp.

References CSerialObject::Assign(), cmd, CSeqFeatData_Base::e_Cdregion, eExtreme_Biological, eNa_strand_minus, ExtendStop(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetLocation(), CMappedFeat::GetOriginalFeature(), GetOverlappingGene(), CSeq_entry_Handle::GetScope(), CScope::GetSeq_featHandle(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), NULL, and CSeq_feat_Base::SetLocation().

SpecificHostCleanupCommand()

CRef<CCmdComposite> SpecificHostCleanupCommand

(

CSeq_entry_Handle

seh

)

Definition at line 593 of file util_cmds.cpp.

References CSerialObject::Assign(), chunk_size, cmd, variation::Equals(), Error(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetScope(), CScope::GetSeq_entryHandle(), CScope::GetSeq_featHandle(), i, CTaxon3::Init(), NStr::IsBlank(), ITERATE, len, LOG_POST, min(), n, NULL, CTaxon3::SendOrgRefList(), CSeq_feat_Base::SetData(), CBioSource_Base::SetOrg(), and CSeqdesc_Base::SetSource().

TaxonomyLookupCommand()

CRef<CCmdComposite> TaxonomyLookupCommand

(

CSeq_entry_Handle

seh

)

Definition at line 372 of file util_cmds.cpp.

References CSerialObject::Assign(), chunk_size, cmd, variation::Equals(), Error(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetScope(), CScope::GetSeq_entryHandle(), CScope::GetSeq_featHandle(), i, CTaxon3::Init(), NStr::IsBlank(), ITERATE, len, LOG_POST, min(), n, NULL, CTaxon3::SendOrgRefList(), CSeq_feat_Base::SetData(), CBioSource_Base::SetOrg(), and CSeqdesc_Base::SetSource().

Referenced by CleanupCommand().

TranslateCDSCommand()

CRef<CCmdComposite> TranslateCDSCommand	(	CScope &	scope,
		CSeq_feat &	cds,
		bool &	cds_change,
		int &	offset,
		bool	create_general_only
	)

Definition at line 981 of file util_cmds.cpp.

References AddEmptyProteinFeatureToProtein(), CSeq_id::Assign(), cmd, eExtreme_Biological, CScope::GetBioseqHandle(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), GetNewProtId(), CBioseq_Handle::GetParentEntry(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetTopLevelEntry(), CSeq_feat_Base::GetXref(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CBioseq_Base::IsSetId(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Base::IsSetXref(), NON_CONST_ITERATE, NULL, offset, prot, CRef< C, Locker >::Reset(), CSeq_feat_Base::ResetXref(), CBioseq_Base::SetId(), SetMolinfoForProtein(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), CSeq_feat_Base::SetXref(), and CSeqTranslator::TranslateToProtein().

Referenced by GetRetranslateCDSCommand().

TrimStopsFromCompleteCDS()

CRef<CCmdComposite> TrimStopsFromCompleteCDS	(	const CSeq_feat &	cds,
		CScope &	scope
	)

TrimStopsFromCompleteCDS If the CDS is 3' complete and the protein sequence ends with a stop codon, the function removes the stop codon, shortens the protein length and adjusts the features on the protein sequence so that they do not extend past the "new" end of the sequence.

The function does not modify either the CDS location or the nucleotide sequence.

Parameters

cds	Coding region feature which product will be examined
scope	The scope in which adjustments are to be made (if necessary)

Returns

True if stop codon was found, removed and features on the protein sequence were adjusted, false otherwise

Definition at line 1307 of file util_cmds.cpp.

References CSerialObject::Assign(), CSeq_feat_Base::CanGetLocation(), cmd, CSeq_data_Base::e_Ncbieaa, CSeqFeatData_Base::e_Prot, CBioseq_Handle::eCoding_Ncbi, eExtreme_Biological, ctll::empty(), NStr::EndsWith(), CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetInst(), CBioseq_Handle::GetInst_Seq_data(), CSeq_loc_Base::GetInt(), CSeq_inst_Base::GetLength(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetOriginalFeature(), CSeq_feat_Base::GetProduct(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_loc::GetStop(), CSeq_interval_Base::GetTo(), CSeqFeatData_Base::IsCdregion(), CSeq_loc_Base::IsInt(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsNcbieaa(), CSeq_loc::IsPartialStop(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetProduct(), CSeq_inst_Base::IsSetSeq_data(), NULL, CSeqVector::SetCoding(), CSeq_inst_Base::SetLength(), CSeq_feat_Base::SetLocation(), CSeq_inst_Base::SetSeq_data(), and CSeqVector::size().

UpdatemRNAProduct() [1/2]

CRef<CCmdComposite> UpdatemRNAProduct	(	const CSeq_feat &	protein,
		CScope &	scope,
		string &	message
	)

Definition at line 1693 of file util_cmds.cpp.

References CSerialObject::Assign(), cmd, NStr::Equal(), CSeqFeatData::eSubtype_prot, CRNA_ref_Base::eType_mRNA, CScope::GetBioseqHandle(), GetCDSForProduct(), CBioseq_Handle::GetCompleteBioseq(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), GetmRNAforCDS(), CProt_ref_Base::GetName(), CSeqFeatData_Base::GetProt(), CSeqFeatData_Base::GetRna(), CScope::GetSeq_featHandle(), CSeqFeatData::GetSubtype(), CRNA_ref_Base::GetType(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetData(), CProt_ref_Base::IsSetName(), kEmptyStr, rna, and CSeq_feat_Base::SetData().

UpdatemRNAProduct() [2/2]

CRef<CCmdComposite> UpdatemRNAProduct	(	const string &	prot_product,
		CConstRef< CObject >	object,
		CScope &	scope
	)

Definition at line 1736 of file util_cmds.cpp.

References CSerialObject::Assign(), cmd, ctll::empty(), CSeqFeatData::eSubtype_prot, CScope::GetBioseqHandle(), GetCDSForProduct(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), GetmRNAforCDS(), CScope::GetSeq_featHandle(), CSeqFeatData::GetSubtype(), CSeqFeatData_Base::IsRna(), NULL, CConstRef< C, Locker >::Reset(), and CSeq_feat_Base::SetData().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

kDiscrepancyEdit

const char* kDiscrepancyEdit = "Dialogs.Edit.Discrepancy"

static

Definition at line 1378 of file util_cmds.cpp.

Referenced by s_GetProductRules().