go_term_validation_and_cleanup.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistr.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Object_id.hpp>
#include <objtools/validator/go_term_validation_and_cleanup.hpp>

Include dependency graph for go_term_validation_and_cleanup.cpp:

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Classes
class	CGoTermSortStruct

Functions
bool	operator< (const CGoTermSortStruct &l, const CGoTermSortStruct &r)
bool	IsGeneOntology (const CUser_object &user_object)
void	GetGoTermErrors (CUser_object::TData field_list, map< string, string > &id_terms, vector< TGoTermError > &errors)
vector< TGoTermError >	GetGoTermErrors (const CSeq_feat &feat)
bool	RemoveDuplicateGoTerms (CUser_object::TData &field_list)
bool	RemoveDuplicateGoTerms (CSeq_feat &feat)
void	SetGoTermValue (CUser_field &field, const string &val, const string &val_name)
void	SetGoTermValue (CUser_field &field, int val, const string &val_name)
void	ClearGoTermValue (CUser_field &field, const string &val_name)
void	SetGoTermId (CUser_field &field, const string &val)
void	SetGoTermText (CUser_field &field, const string &val)
void	SetGoTermPMID (CUser_field &field, int pmid)
void	AddGoTermEvidence (CUser_field &field, const string &val)
void	ClearGoTermEvidence (CUser_field &field)
void	ClearGoTermPMID (CUser_field &field)
void	AddGoTermToList (CSeq_feat &feat, CRef< CUser_field > field, const string &val_name)
void	AddProcessGoTerm (CSeq_feat &feat, CRef< CUser_field > field)
void	AddComponentGoTerm (CSeq_feat &feat, CRef< CUser_field > field)
void	AddFunctionGoTerm (CSeq_feat &feat, CRef< CUser_field > field)
size_t	CountGoTerms (const CSeq_feat &feat, const string &list_name)
size_t	CountProcessGoTerms (const CSeq_feat &feat)
size_t	CountComponentGoTerms (const CSeq_feat &feat)
size_t	CountFunctionGoTerms (const CSeq_feat &feat)

Variables
static const string	kGoTermText = "text string"
static const string	kGoTermID = "go id"
static const string	kGoTermPubMedID = "pubmed id"
static const string	kGoTermRef = "go ref"
static const string	kGoTermEvidence = "evidence"
static const string	kGoTermProcess = "Process"
static const string	kGoTermComponent = "Component"
static const string	kGoTermFunction = "Function"
static const string	kGeneOntology = "GeneOntology"

Function Documentation

AddComponentGoTerm()

void AddComponentGoTerm	(	CSeq_feat &	feat,
		CRef< CUser_field >	field
	)

Definition at line 491 of file go_term_validation_and_cleanup.cpp.

References AddGoTermToList(), and kGoTermComponent.

AddFunctionGoTerm()

void AddFunctionGoTerm	(	CSeq_feat &	feat,
		CRef< CUser_field >	field
	)

Definition at line 497 of file go_term_validation_and_cleanup.cpp.

References AddGoTermToList(), and kGoTermFunction.

AddGoTermEvidence()

void AddGoTermEvidence	(	CUser_field &	field,
		const string &	val
	)

Definition at line 435 of file go_term_validation_and_cleanup.cpp.

References kGoTermEvidence, CUser_field_Base::SetData(), CUser_field_Base::SetLabel(), and val.

Referenced by BOOST_AUTO_TEST_CASE(), and MakeGoTerm().

AddGoTermToList()

void AddGoTermToList	(	CSeq_feat &	feat,
		CRef< CUser_field >	field,
		const string &	val_name
	)

Definition at line 456 of file go_term_validation_and_cleanup.cpp.

References NStr::Equal(), CSeq_feat_Base::GetExt(), IsGeneOntology(), CUser_object_Base::IsSetData(), CSeq_feat_Base::IsSetExt(), kGeneOntology, CUser_field_Base::SetData(), CSeq_feat_Base::SetExt(), and CUser_field_Base::SetLabel().

Referenced by AddComponentGoTerm(), AddFunctionGoTerm(), and AddProcessGoTerm().

AddProcessGoTerm()

void AddProcessGoTerm	(	CSeq_feat &	feat,
		CRef< CUser_field >	field
	)

Definition at line 485 of file go_term_validation_and_cleanup.cpp.

References AddGoTermToList(), and kGoTermProcess.

Referenced by BOOST_AUTO_TEST_CASE(), and MakeGeneOntologyFeat().

ClearGoTermEvidence()

void ClearGoTermEvidence

(

CUser_field &

field

)

Definition at line 444 of file go_term_validation_and_cleanup.cpp.

References ClearGoTermValue(), and kGoTermEvidence.

Referenced by BOOST_AUTO_TEST_CASE().

ClearGoTermPMID()

void ClearGoTermPMID

(

CUser_field &

field

)

Definition at line 450 of file go_term_validation_and_cleanup.cpp.

References ClearGoTermValue(), and kGoTermPubMedID.

Referenced by BOOST_AUTO_TEST_CASE().

ClearGoTermValue()

void ClearGoTermValue	(	CUser_field &	field,
		const string &	val_name
	)

Definition at line 401 of file go_term_validation_and_cleanup.cpp.

References NStr::Equal(), CUser_field_Base::GetData(), CUser_field_Base::C_Data::IsFields(), CUser_field_Base::IsSetData(), and CUser_field_Base::SetData().

Referenced by ClearGoTermEvidence(), and ClearGoTermPMID().

CountComponentGoTerms()

size_t CountComponentGoTerms

(

const CSeq_feat &

feat

)

Definition at line 527 of file go_term_validation_and_cleanup.cpp.

References CountGoTerms(), and kGoTermComponent.

CountFunctionGoTerms()

size_t CountFunctionGoTerms

(

const CSeq_feat &

feat

)

Definition at line 533 of file go_term_validation_and_cleanup.cpp.

References CountGoTerms(), and kGoTermFunction.

CountGoTerms()

size_t CountGoTerms	(	const CSeq_feat &	feat,
		const string &	list_name
	)

Definition at line 503 of file go_term_validation_and_cleanup.cpp.

References NStr::Equal(), CUser_object_Base::GetData(), CSeq_feat_Base::GetExt(), IsGeneOntology(), CUser_object_Base::IsSetData(), and CSeq_feat_Base::IsSetExt().

Referenced by CountComponentGoTerms(), CountFunctionGoTerms(), and CountProcessGoTerms().

CountProcessGoTerms()

size_t CountProcessGoTerms

(

const CSeq_feat &

feat

)

Definition at line 521 of file go_term_validation_and_cleanup.cpp.

References CountGoTerms(), and kGoTermProcess.

Referenced by CheckGeneOntologyTermDuplicate(), and CheckGeneOntologyTermNotDuplicate().

GetGoTermErrors() [1/2]

vector<TGoTermError> GetGoTermErrors

(

const CSeq_feat &

feat

)

Definition at line 237 of file go_term_validation_and_cleanup.cpp.

References eErr_SEQ_FEAT_BadGeneOntologyFormat, CUser_object_Base::GetData(), CSeq_feat_Base::GetExt(), GetGoTermErrors(), IsGeneOntology(), CGoTermSortStruct::IsLegalGoTermType(), CUser_object_Base::IsSetData(), and CSeq_feat_Base::IsSetExt().

Referenced by CSingleFeatValidator::x_ValidateExtUserObject().

GetGoTermErrors() [2/2]

void GetGoTermErrors	(	CUser_object::TData	field_list,
		map< string, string > &	id_terms,
		vector< TGoTermError > &	errors
	)

Definition at line 196 of file go_term_validation_and_cleanup.cpp.

References a, eErr_SEQ_FEAT_BadGeneOntologyFormat, eErr_SEQ_FEAT_DuplicateGeneOntologyTerm, eErr_SEQ_FEAT_GeneOntologyTermMissingGOID, eErr_SEQ_FEAT_InconsistentGeneOntologyTermAndId, map_checker< Container >::end(), NStr::Equal(), map_checker< Container >::find(), set< Key, Compare >::insert(), NStr::IsBlank(), msg(), and set< Key, Compare >::size().

Referenced by GetGoTermErrors().

IsGeneOntology()

bool IsGeneOntology

(

const CUser_object &

user_object

)

Definition at line 185 of file go_term_validation_and_cleanup.cpp.

References NStr::EqualCase(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), and kGeneOntology.

Referenced by AddGoTermToList(), CountGoTerms(), GetGoTermErrors(), and RemoveDuplicateGoTerms().

operator<()

bool operator<	(	const CGoTermSortStruct &	l,
		const CGoTermSortStruct &	r
	)

Definition at line 138 of file go_term_validation_and_cleanup.cpp.

References NStr::Compare(), l(), and r().

RemoveDuplicateGoTerms() [1/2]

bool RemoveDuplicateGoTerms

(

CSeq_feat &

feat

)

Definition at line 304 of file go_term_validation_and_cleanup.cpp.

References IsGeneOntology(), CGoTermSortStruct::IsLegalGoTermType(), CUser_object_Base::IsSetData(), CSeq_feat_Base::IsSetExt(), RemoveDuplicateGoTerms(), CUser_object_Base::SetData(), and CSeq_feat_Base::SetExt().

Referenced by CheckGeneOntologyTermDuplicate(), CheckGeneOntologyTermNotDuplicate(), and GetRemoveDuplicateGOTermsCommand().

RemoveDuplicateGoTerms() [2/2]

bool RemoveDuplicateGoTerms

(

CUser_object::TData &

field_list

)

Definition at line 276 of file go_term_validation_and_cleanup.cpp.

References a, set< Key, Compare >::begin(), set< Key, Compare >::end(), set< Key, Compare >::find(), and set< Key, Compare >::insert().

Referenced by RemoveDuplicateGoTerms().

SetGoTermId()

void SetGoTermId	(	CUser_field &	field,
		const string &	val
	)

Definition at line 417 of file go_term_validation_and_cleanup.cpp.

References kGoTermID, SetGoTermValue(), and val.

Referenced by BOOST_AUTO_TEST_CASE(), and MakeGoTerm().

SetGoTermPMID()

void SetGoTermPMID	(	CUser_field &	field,
		int	pmid
	)

Definition at line 429 of file go_term_validation_and_cleanup.cpp.

References kGoTermPubMedID, and SetGoTermValue().

Referenced by MakeGoTerm().

SetGoTermText()

void SetGoTermText	(	CUser_field &	field,
		const string &	val
	)

Definition at line 423 of file go_term_validation_and_cleanup.cpp.

References kGoTermText, SetGoTermValue(), and val.

Referenced by MakeGoTerm().

SetGoTermValue() [1/2]

void SetGoTermValue	(	CUser_field &	field,
		const string &	val,
		const string &	val_name
	)

Definition at line 337 of file go_term_validation_and_cleanup.cpp.

References NStr::Equal(), CUser_field_Base::GetData(), CUser_field_Base::C_Data::IsFields(), CUser_field_Base::IsSetData(), CUser_field_Base::SetData(), CUser_field_Base::SetLabel(), and val.

Referenced by SetGoTermId(), SetGoTermPMID(), and SetGoTermText().

SetGoTermValue() [2/2]

void SetGoTermValue	(	CUser_field &	field,
		int	val,
		const string &	val_name
	)

Definition at line 369 of file go_term_validation_and_cleanup.cpp.

References NStr::Equal(), CUser_field_Base::GetData(), CUser_field_Base::C_Data::IsFields(), CUser_field_Base::IsSetData(), CUser_field_Base::SetData(), CUser_field_Base::SetLabel(), and val.

Variable Documentation

kGeneOntology

const string kGeneOntology = "GeneOntology"

static

Definition at line 58 of file go_term_validation_and_cleanup.cpp.

Referenced by AddGoTermToList(), and IsGeneOntology().

kGoTermComponent

const string kGoTermComponent = "Component"

static

Definition at line 55 of file go_term_validation_and_cleanup.cpp.

Referenced by AddComponentGoTerm(), CountComponentGoTerms(), and CGoTermSortStruct::IsLegalGoTermType().

kGoTermEvidence

const string kGoTermEvidence = "evidence"

static

Definition at line 52 of file go_term_validation_and_cleanup.cpp.

Referenced by AddGoTermEvidence(), CGoTermSortStruct::CGoTermSortStruct(), and ClearGoTermEvidence().

kGoTermFunction

const string kGoTermFunction = "Function"

static

Definition at line 56 of file go_term_validation_and_cleanup.cpp.

Referenced by AddFunctionGoTerm(), CountFunctionGoTerms(), and CGoTermSortStruct::IsLegalGoTermType().

kGoTermID

const string kGoTermID = "go id"

static

Definition at line 49 of file go_term_validation_and_cleanup.cpp.

Referenced by CGoTermSortStruct::CGoTermSortStruct(), and SetGoTermId().

kGoTermProcess

const string kGoTermProcess = "Process"

static

Definition at line 54 of file go_term_validation_and_cleanup.cpp.

Referenced by AddProcessGoTerm(), CountProcessGoTerms(), and CGoTermSortStruct::IsLegalGoTermType().

kGoTermPubMedID

const string kGoTermPubMedID = "pubmed id"

static

Definition at line 50 of file go_term_validation_and_cleanup.cpp.

Referenced by CGoTermSortStruct::CGoTermSortStruct(), ClearGoTermPMID(), and SetGoTermPMID().

kGoTermRef

const string kGoTermRef = "go ref"

static

Definition at line 51 of file go_term_validation_and_cleanup.cpp.

Referenced by CGoTermSortStruct::CGoTermSortStruct().

kGoTermText

const string kGoTermText = "text string"

static

Definition at line 48 of file go_term_validation_and_cleanup.cpp.

Referenced by CGoTermSortStruct::CGoTermSortStruct(), and SetGoTermText().