NCBI C++ ToolKit
go_term_validation_and_cleanup.hpp
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1 /* $Id: go_term_validation_and_cleanup.hpp 83485 2018-08-27 11:48:15Z bollin $
2  * ===========================================================================
3  *
4  * PUBLIC DOMAIN NOTICE
5  * National Center for Biotechnology Information
6  *
7  * This software/database is a "United States Government Work" under the
8  * terms of the United States Copyright Act. It was written as part of
9  * the author's official duties as a United States Government employee and
10  * thus cannot be copyrighted. This software/database is freely available
11  * to the public for use. The National Library of Medicine and the U.S.
12  * Government have not placed any restriction on its use or reproduction.
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14  * Although all reasonable efforts have been taken to ensure the accuracy
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24  * ===========================================================================
25  *`
26  * Author: Colleen Bollin, Jonathan Kans, Clifford Clausen, Aaron Ucko......
27  *
28  * File Description:
29  * For validating individual features
30  * .......
31  *
32  */
33 
34 #ifndef VALIDATOR___GO_TERM_VALIDATION_AND_CLEANUP__HPP
35 #define VALIDATOR___GO_TERM_VALIDATION_AND_CLEANUP__HPP
36 
37 #include <corelib/ncbistd.hpp>
39 
40 #include <objmgr/scope.hpp>
44 
47 
48 
49 
50 BEGIN_SCOPE(validator)
51 
52 bool IsGeneOntology(const CUser_object& user_object);
53 
54 typedef pair<EErrType, string> TGoTermError;
55 vector<TGoTermError> NCBI_VALIDATOR_EXPORT GetGoTermErrors(const CSeq_feat& feat);
57 
58 void NCBI_VALIDATOR_EXPORT SetGoTermId(CUser_field& field, const string& val);
59 void NCBI_VALIDATOR_EXPORT SetGoTermText(CUser_field& field, const string& val);
60 void NCBI_VALIDATOR_EXPORT SetGoTermPMID(CUser_field& field, int pmid);
61 void NCBI_VALIDATOR_EXPORT AddGoTermEvidence(CUser_field& field, const string& val);
64 
68 
72 
73 
74 END_SCOPE(validator)
77 
78 #endif /* VALIDATOR___GO_TERM_VALIDATION_AND_CLEANUP__HPP */
User-defined methods of the data storage class.
namespace ncbi::objects::
Definition: Seq_feat.hpp:58
Include a standard set of the NCBI C++ Toolkit most basic headers.
void SetGoTermPMID(CUser_field &field, int pmid)
size_t CountProcessGoTerms(const CSeq_feat &feat)
void AddFunctionGoTerm(CSeq_feat &feat, CRef< CUser_field > field)
size_t CountComponentGoTerms(const CSeq_feat &feat)
void ClearGoTermPMID(CUser_field &field)
void SetGoTermText(CUser_field &field, const string &val)
void AddProcessGoTerm(CSeq_feat &feat, CRef< CUser_field > field)
size_t CountFunctionGoTerms(const CSeq_feat &feat)
void ClearGoTermEvidence(CUser_field &field)
void SetGoTermId(CUser_field &field, const string &val)
void AddGoTermEvidence(CUser_field &field, const string &val)
void AddComponentGoTerm(CSeq_feat &feat, CRef< CUser_field > field)
bool RemoveDuplicateGoTerms(CSeq_feat &feat)
vector< TGoTermError > GetGoTermErrors(const CSeq_feat &feat)
bool IsGeneOntology(const CUser_object &user_object)
pair< EErrType, string > TGoTermError
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
#define NCBI_VALIDATOR_EXPORT
Definition: ncbi_export.h:913
Modified on Fri Apr 12 17:17:22 2024 by modify_doxy.py rev. 669887