seqdesc_per_bioseq.cpp File Reference

#include <ncbi_pch.hpp>
#include "discrepancy_core.hpp"
#include "utils.hpp"
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/valid/Comment_rule.hpp>
#include <objects/valid/Comment_set.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/validator/utilities.hpp>

Include dependency graph for seqdesc_per_bioseq.cpp:

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Enumerations
enum	EPrefixOrSuffixType { eType_none , eType_prefix , eType_suffix }

Functions
	USING_SCOPE (objects)
static EPrefixOrSuffixType	GetPrefixOrSuffixType (const CUser_field &field)
static bool	IsAppropriateRule (const CComment_rule &rule, const CUser_object &user)
const CComment_rule *	FindAppropriateRule (const CComment_set &rules, const CUser_object &user)

Variables
static constexpr CDiscrepancyCaseProps	s_testcase_props_RETROVIRIDAE_DNA = { CDiscrepancyVisitorImpl<eTestNames:: RETROVIRIDAE_DNA >::Create, eTestTypes:: SEQUENCE , eTestNames:: RETROVIRIDAE_DNA , "RETROVIRIDAE_DNA" , "Retroviridae DNA" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_NON_RETROVIRIDAE_PROVIRAL = { CDiscrepancyVisitorImpl<eTestNames:: NON_RETROVIRIDAE_PROVIRAL >::Create, eTestTypes:: SEQUENCE , eTestNames:: NON_RETROVIRIDAE_PROVIRAL , "NON_RETROVIRIDAE_PROVIRAL" , "Non-Retroviridae biosources that are proviral" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_BAD_MRNA_QUAL = { CDiscrepancyVisitorImpl<eTestNames:: BAD_MRNA_QUAL >::Create, eTestTypes:: SEQUENCE , eTestNames:: BAD_MRNA_QUAL , "BAD_MRNA_QUAL" , "mRNA sequence contains rearranged or germline" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_ORGANELLE_NOT_GENOMIC = { CDiscrepancyVisitorImpl<eTestNames:: ORGANELLE_NOT_GENOMIC >::Create, eTestTypes:: SEQUENCE , eTestNames:: ORGANELLE_NOT_GENOMIC , "ORGANELLE_NOT_GENOMIC" , "Organelle location should have genomic moltype" , eDisc | eOncaller , nullptr }
static const char *	kStructuredCommentPrefix = "StructuredCommentPrefix"
static const char *	kStructuredCommentSuffix = "StructuredCommentSuffix"
static constexpr CDiscrepancyCaseProps	s_testcase_props_SWITCH_STRUCTURED_COMMENT_PREFIX = { CDiscrepancyVisitorImpl<eTestNames:: SWITCH_STRUCTURED_COMMENT_PREFIX >::Create, eTestTypes:: DESC , eTestNames:: SWITCH_STRUCTURED_COMMENT_PREFIX , "SWITCH_STRUCTURED_COMMENT_PREFIX" , "Suspicious structured comment prefix" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_MISMATCHED_COMMENTS = { CDiscrepancyVisitorImpl<eTestNames:: MISMATCHED_COMMENTS >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISMATCHED_COMMENTS , "MISMATCHED_COMMENTS" , "Mismatched Comments" , eDisc , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_GENOMIC_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: GENOMIC_MRNA >::Create, eTestTypes:: DESC , eTestNames:: GENOMIC_MRNA , "GENOMIC_MRNA" , "Genomic mRNA is legal, but not expected" , eOncaller | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_AUTODEF_USER_OBJECT = { CDiscrepancyVisitorImpl<eTestNames:: AUTODEF_USER_OBJECT >::Create, eTestTypes:: SEQUENCE , eTestNames:: AUTODEF_USER_OBJECT , "AUTODEF_USER_OBJECT" , "Nucleotide sequence must have an autodef user object" , eOncaller , nullptr }

Enumeration Type Documentation

EPrefixOrSuffixType

enum EPrefixOrSuffixType

Enumerator
eType_none
eType_prefix
eType_suffix

Definition at line 132 of file seqdesc_per_bioseq.cpp.

Function Documentation

FindAppropriateRule()

const CComment_rule* FindAppropriateRule	(	const CComment_set &	rules,
		const CUser_object &	user
	)

Definition at line 177 of file seqdesc_per_bioseq.cpp.

References CComment_set_Base::Get(), IsAppropriateRule(), CComment_set_Base::IsSet(), and CComment_rule::IsValid().

GetPrefixOrSuffixType()

static EPrefixOrSuffixType GetPrefixOrSuffixType ( const CUser_field &  field )

static

Definition at line 140 of file seqdesc_per_bioseq.cpp.

References NStr::Equal(), eType_none, eType_prefix, eType_suffix, CUser_field_Base::GetData(), CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CUser_field_Base::IsSetData(), CUser_field_Base::IsSetLabel(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), kStructuredCommentPrefix, kStructuredCommentSuffix, and type.

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), and IsAppropriateRule().

IsAppropriateRule()

static bool IsAppropriateRule ( const CComment_rule &  rule, const CUser_object &  user  )

static

Definition at line 157 of file seqdesc_per_bioseq.cpp.

References CConstRef< C, Locker >::Empty(), eType_none, CComment_rule::FindFieldRuleRef(), CUser_object_Base::GetData(), GetPrefixOrSuffixType(), and CUser_object_Base::IsSetData().

Referenced by FindAppropriateRule().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

kStructuredCommentPrefix

const char* kStructuredCommentPrefix = "StructuredCommentPrefix"

static

Definition at line 129 of file seqdesc_per_bioseq.cpp.

Referenced by GetPrefixOrSuffixType().

kStructuredCommentSuffix

const char* kStructuredCommentSuffix = "StructuredCommentSuffix"

static

Definition at line 130 of file seqdesc_per_bioseq.cpp.

Referenced by GetPrefixOrSuffixType().

s_testcase_props_AUTODEF_USER_OBJECT

constexpr CDiscrepancyCaseProps s_testcase_props_AUTODEF_USER_OBJECT = { CDiscrepancyVisitorImpl<eTestNames:: AUTODEF_USER_OBJECT >::Create, eTestTypes:: SEQUENCE , eTestNames:: AUTODEF_USER_OBJECT , "AUTODEF_USER_OBJECT" , "Nucleotide sequence must have an autodef user object" , eOncaller , nullptr }

staticconstexpr

Definition at line 319 of file seqdesc_per_bioseq.cpp.

s_testcase_props_BAD_MRNA_QUAL

constexpr CDiscrepancyCaseProps s_testcase_props_BAD_MRNA_QUAL = { CDiscrepancyVisitorImpl<eTestNames:: BAD_MRNA_QUAL >::Create, eTestTypes:: SEQUENCE , eTestNames:: BAD_MRNA_QUAL , "BAD_MRNA_QUAL" , "mRNA sequence contains rearranged or germline" , eOncaller , nullptr }

staticconstexpr

Definition at line 94 of file seqdesc_per_bioseq.cpp.

s_testcase_props_GENOMIC_MRNA

constexpr CDiscrepancyCaseProps s_testcase_props_GENOMIC_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: GENOMIC_MRNA >::Create, eTestTypes:: DESC , eTestNames:: GENOMIC_MRNA , "GENOMIC_MRNA" , "Genomic mRNA is legal, but not expected" , eOncaller | eSmart , nullptr }

staticconstexpr

Definition at line 307 of file seqdesc_per_bioseq.cpp.

s_testcase_props_MISMATCHED_COMMENTS

constexpr CDiscrepancyCaseProps s_testcase_props_MISMATCHED_COMMENTS = { CDiscrepancyVisitorImpl<eTestNames:: MISMATCHED_COMMENTS >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISMATCHED_COMMENTS , "MISMATCHED_COMMENTS" , "Mismatched Comments" , eDisc , nullptr }

staticconstexpr

Definition at line 252 of file seqdesc_per_bioseq.cpp.

s_testcase_props_NON_RETROVIRIDAE_PROVIRAL

constexpr CDiscrepancyCaseProps s_testcase_props_NON_RETROVIRIDAE_PROVIRAL = { CDiscrepancyVisitorImpl<eTestNames:: NON_RETROVIRIDAE_PROVIRAL >::Create, eTestTypes:: SEQUENCE , eTestNames:: NON_RETROVIRIDAE_PROVIRAL , "NON_RETROVIRIDAE_PROVIRAL" , "Non-Retroviridae biosources that are proviral" , eOncaller , nullptr }

staticconstexpr

Definition at line 77 of file seqdesc_per_bioseq.cpp.

s_testcase_props_ORGANELLE_NOT_GENOMIC

constexpr CDiscrepancyCaseProps s_testcase_props_ORGANELLE_NOT_GENOMIC = { CDiscrepancyVisitorImpl<eTestNames:: ORGANELLE_NOT_GENOMIC >::Create, eTestTypes:: SEQUENCE , eTestNames:: ORGANELLE_NOT_GENOMIC , "ORGANELLE_NOT_GENOMIC" , "Organelle location should have genomic moltype" , eDisc | eOncaller , nullptr }

staticconstexpr

Definition at line 111 of file seqdesc_per_bioseq.cpp.

s_testcase_props_RETROVIRIDAE_DNA

constexpr CDiscrepancyCaseProps s_testcase_props_RETROVIRIDAE_DNA = { CDiscrepancyVisitorImpl<eTestNames:: RETROVIRIDAE_DNA >::Create, eTestTypes:: SEQUENCE , eTestNames:: RETROVIRIDAE_DNA , "RETROVIRIDAE_DNA" , "Retroviridae DNA" , eOncaller , nullptr }

staticconstexpr

Definition at line 50 of file seqdesc_per_bioseq.cpp.

s_testcase_props_SWITCH_STRUCTURED_COMMENT_PREFIX

constexpr CDiscrepancyCaseProps s_testcase_props_SWITCH_STRUCTURED_COMMENT_PREFIX = { CDiscrepancyVisitorImpl<eTestNames:: SWITCH_STRUCTURED_COMMENT_PREFIX >::Create, eTestTypes:: DESC , eTestNames:: SWITCH_STRUCTURED_COMMENT_PREFIX , "SWITCH_STRUCTURED_COMMENT_PREFIX" , "Suspicious structured comment prefix" , eOncaller , nullptr }

staticconstexpr

Definition at line 199 of file seqdesc_per_bioseq.cpp.