NCBI C++ ToolKit
Classes | Functions | Variables
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:

Go to the source code of this file.

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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< TGoTermErrorGetGoTermErrors (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 
)

◆ AddGoTermToList()

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

◆ AddProcessGoTerm()

void AddProcessGoTerm ( CSeq_feat feat,
CRef< CUser_field field 
)

◆ 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 
)

◆ 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 
)

◆ CountProcessGoTerms()

size_t CountProcessGoTerms ( const CSeq_feat feat)

◆ GetGoTermErrors() [1/2]

vector<TGoTermError> GetGoTermErrors ( const CSeq_feat feat)

◆ GetGoTermErrors() [2/2]

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

◆ IsGeneOntology()

bool IsGeneOntology ( const CUser_object user_object)

◆ operator<()

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

◆ RemoveDuplicateGoTerms() [1/2]

bool RemoveDuplicateGoTerms ( CSeq_feat feat)

◆ RemoveDuplicateGoTerms() [2/2]

bool RemoveDuplicateGoTerms ( CUser_object::TData field_list)

◆ 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 
)

◆ SetGoTermValue() [2/2]

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

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

◆ kGoTermEvidence

const string kGoTermEvidence = "evidence"
static

◆ kGoTermFunction

const string kGoTermFunction = "Function"
static

◆ kGoTermID

const string kGoTermID = "go id"
static

◆ kGoTermProcess

const string kGoTermProcess = "Process"
static

◆ kGoTermPubMedID

const string kGoTermPubMedID = "pubmed id"
static

◆ kGoTermRef

const string kGoTermRef = "go ref"
static

◆ kGoTermText

const string kGoTermText = "text string"
static
Modified on Wed Feb 28 07:13:48 2024 by modify_doxy.py rev. 669887