suspect_product_names.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbi_autoinit.hpp>
#include <objects/macro/Suspect_rule_set.hpp>
#include <objects/macro/Suspect_rule.hpp>
#include <objects/seqfeat/RNA_gen.hpp>
#include <objects/macro/Search_func.hpp>
#include <objects/macro/Replace_func.hpp>
#include <objects/macro/Simple_replace.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/misc/sequence_util_macros.hpp>
#include <serial/objistrasn.hpp>
#include "discrepancy_core.hpp"
#include "utils.hpp"

Include dependency graph for suspect_product_names.cpp:

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Typedefs
typedef std::function< CRef< CSeq_feat >) >	GetFeatureFunc

Functions
	USING_SCOPE (objects)
string	GetTwoFieldSubfield (const string &str, unsigned subfield)
static string	GetFirstGBQualMatch (const vector< CRef< CGb_qual > > &quals, const string &qual_name, unsigned subfield=0, const CString_constraint *str_cons=nullptr)
static string	GetRNAProductString (const CSeq_feat &seq_feat)
static string	GetRuleText (const CSuspect_rule &rule)
static string	GetRuleMatch (const CSuspect_rule &rule)
static bool	ContainsLetters (const string &prod_name)
static string	ReplaceNoCase (const string &input, const string &search, const string &replace)
static void	GetProtAndRnaForCDS (const CSeq_feat &cds, CScope &scope, CSeq_feat *&prot, CSeq_feat *&mrna)
string	FixProductName (const CSuspect_rule *rule, CScope &, string &prot_name, GetFeatureFunc get_mrna, GetFeatureFunc get_cds)
static CConstRef< CSuspect_rule_set >	s_GetrRNAProductsSuspectRuleSet ()
static void	s_SummarizeStringConstraint (ostream &out_strm, const CString_constraint &string_constraint)
static void	s_SummarizeSearchFunc (ostream &out_strm, const CSearch_func &search_func)
static void	s_SummarizeSuspectRule (ostream &out_strm, const CSuspect_rule &rule)

Variables
static const string	kSuspectProductNames = "[n] product_name[s] contain[S] suspect phrase[s] or character[s]"
static constexpr CDiscrepancyCaseProps	s_testcase_props_SUSPECT_PRODUCT_NAMES = { CDiscrepancyVisitorImpl<eTestNames:: SUSPECT_PRODUCT_NAMES >::Create, eTestTypes:: FEAT , eTestNames:: SUSPECT_PRODUCT_NAMES , "SUSPECT_PRODUCT_NAMES" , "Suspect Product Name" , eDisc | eOncaller | eSubmitter | eSmart | eTSA | eFatal , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_ORGANELLE_PRODUCTS = { CDiscrepancyVisitorImpl<eTestNames:: ORGANELLE_PRODUCTS >::Create, eTestTypes:: FEAT , eTestNames:: ORGANELLE_PRODUCTS , "ORGANELLE_PRODUCTS" , "Organelle products on non-organelle sequence: on when neither bacteria nor virus" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_SUSPECT_RRNA_PRODUCTS = { CDiscrepancyVisitorImpl<eTestNames:: SUSPECT_RRNA_PRODUCTS >::Create, eTestTypes:: FEAT , eTestNames:: SUSPECT_RRNA_PRODUCTS , "SUSPECT_RRNA_PRODUCTS" , "rRNA product names should not contain 'partial' or 'domain'" , eDisc | eSubmitter | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props__SUSPECT_PRODUCT_NAMES = { CDiscrepancyVisitorImpl<eTestNames:: _SUSPECT_PRODUCT_NAMES >::Create, eTestTypes:: STRING , eTestNames:: _SUSPECT_PRODUCT_NAMES , "_SUSPECT_PRODUCT_NAMES" , "Suspect Product Names for asndisc -N option" , 0 , nullptr }

Typedef Documentation

GetFeatureFunc

typedef std::function< CRef<CSeq_feat>) > GetFeatureFunc

Definition at line 300 of file suspect_product_names.cpp.

Function Documentation

ContainsLetters()

static bool ContainsLetters ( const string &  prod_name )

static

Definition at line 210 of file suspect_product_names.cpp.

References isalpha().

FixProductName()

string FixProductName	(	const CSuspect_rule *	rule,
		CScope &	,
		string &	prot_name,
		GetFeatureFunc	get_mrna,
		GetFeatureFunc	get_cds
	)

Definition at line 301 of file suspect_product_names.cpp.

References AddComment(), CSuspect_rule_Base::GetFind(), CString_constraint_Base::GetMatch_text(), CReplace_rule_Base::GetMove_to_note(), CSimple_replace_Base::GetReplace(), CSuspect_rule_Base::GetReplace(), CReplace_rule_Base::GetReplace_func(), CReplace_func_Base::GetSimple_replace(), CSearch_func_Base::GetString_constraint(), CSimple_replace_Base::GetWhole_string(), CReplace_func_Base::IsHaem_replace(), CReplace_func_Base::IsSimple_replace(), and ReplaceNoCase().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix().

GetFirstGBQualMatch()

static string GetFirstGBQualMatch ( const vector< CRef< CGb_qual > > &  quals, const string &  qual_name, unsigned  subfield = 0, const CString_constraint *  str_cons = nullptr  )

static

Definition at line 78 of file suspect_product_names.cpp.

References NStr::EqualNocase(), GetTwoFieldSubfield(), and str().

Referenced by GetRNAProductString().

GetProtAndRnaForCDS()

static void GetProtAndRnaForCDS ( const CSeq_feat &  cds, CScope &  scope, CSeq_feat *&  prot, CSeq_feat *&  mrna  )

static

Definition at line 280 of file suspect_product_names.cpp.

References CSeqFeatData::eSubtype_prot, GetBestMrnaForCds(), CScope::GetBioseqHandle(), CMappedFeat::GetMappedFeature(), CSeq_feat_Base::GetProduct(), prot, and rna.

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix().

GetRNAProductString()

static string GetRNAProductString ( const CSeq_feat &  seq_feat )

static

Definition at line 95 of file suspect_product_names.cpp.

References CRNA_gen_Base::CanGetProduct(), CSeq_feat_Base::CanGetQual(), CRNA_ref_Base::C_Ext::e_Gen, CRNA_ref_Base::C_Ext::e_Name, CRNA_ref_Base::C_Ext::e_TRNA, fFGL_Content, CSeq_feat_Base::GetData(), GetFirstGBQualMatch(), CRNA_ref_Base::C_Ext::GetGen(), GetLabel(), CRNA_ref_Base::C_Ext::GetName(), CSeq_feat::GetNamedQual(), CRNA_gen_Base::GetProduct(), CSeq_feat_Base::GetQual(), CSeqFeatData_Base::GetRna(), rna, and CRNA_ref_Base::C_Ext::Which().

GetRuleMatch()

static string GetRuleMatch ( const CSuspect_rule &  rule )

static

Definition at line 149 of file suspect_product_names.cpp.

References CSuspect_rule_Base::CanGetFind(), CSimple_replace_Base::CanGetReplace(), CSuspect_rule_Base::CanGetReplace(), CSuspect_rule_Base::CanGetRule_type(), CSearch_func_Base::e_All_caps, CSearch_func_Base::e_Contains_plural, CSearch_func_Base::e_Has_term, CSearch_func_Base::e_N_or_more_brackets_or_parentheses, CSearch_func_Base::e_Prefix_and_numbers, CSearch_func_Base::e_String_constraint, CSearch_func_Base::e_Three_numbers, CSearch_func_Base::e_Too_long, CSearch_func_Base::e_Unbalanced_paren, CSearch_func_Base::e_Underscore, eFix_type_quickfix, eFix_type_typo, eString_location_ends, eString_location_equals, eString_location_starts, CSuspect_rule_Base::GetDescription(), CSuspect_rule_Base::GetFind(), CString_constraint_Base::GetMatch_location(), CString_constraint_Base::GetMatch_text(), CSimple_replace_Base::GetReplace(), CSuspect_rule_Base::GetReplace(), CReplace_rule_Base::GetReplace_func(), CSuspect_rule_Base::GetRule_type(), CReplace_func_Base::GetSimple_replace(), CSearch_func_Base::GetString_constraint(), CSuspect_rule_Base::IsSetDescription(), CReplace_func_Base::IsSimple_replace(), NStr::ReplaceInPlace(), and CSearch_func_Base::Which().

GetRuleText()

static string GetRuleText ( const CSuspect_rule &  rule )

static

Definition at line 126 of file suspect_product_names.cpp.

References CSuspect_rule_Base::GetRule_type().

GetTwoFieldSubfield()

string GetTwoFieldSubfield	(	const string &	str,
		unsigned	subfield
	)

Definition at line 55 of file suspect_product_names.cpp.

References CTempString::empty(), kEmptyStr, str(), strtmp, and CTempString::substr().

Referenced by GetFirstGBQualMatch().

ReplaceNoCase()

static string ReplaceNoCase ( const string &  input, const string &  search, const string &  replace  )

static

Definition at line 264 of file suspect_product_names.cpp.

References NStr::FindNoCase(), input(), NPOS, and NStr::TruncateSpacesInPlace().

Referenced by FixProductName().

s_GetrRNAProductsSuspectRuleSet()

static CConstRef<CSuspect_rule_set> s_GetrRNAProductsSuspectRuleSet ( )

static

Definition at line 440 of file suspect_product_names.cpp.

References ConstRef(), CTempString::data(), DEFINE_STATIC_FAST_MUTEX, CAutoInitPtr_Base::IsInitialized(), CTempString::length(), and CObjectIStream::Read().

s_SummarizeSearchFunc()

static void s_SummarizeSearchFunc ( ostream &  out_strm, const CSearch_func &  search_func  )

static

Definition at line 504 of file suspect_product_names.cpp.

References CSearch_func_Base::GetString_constraint(), CSearch_func_Base::IsString_constraint(), NCBI_USER_THROW, and s_SummarizeStringConstraint().

Referenced by s_SummarizeSuspectRule().

s_SummarizeStringConstraint()

static void s_SummarizeStringConstraint ( ostream &  out_strm, const CString_constraint &  string_constraint  )

static

Definition at line 473 of file suspect_product_names.cpp.

References GET_FIELD_OR_DEFAULT, CString_constraint_Base::GetMatch_text(), CString_constraint_Base::IsSetCase_sensitive(), CString_constraint_Base::IsSetIgnore_punct(), CString_constraint_Base::IsSetIgnore_space(), CString_constraint_Base::IsSetIgnore_weasel(), CString_constraint_Base::IsSetIgnore_words(), CString_constraint_Base::IsSetIs_all_caps(), CString_constraint_Base::IsSetIs_all_lower(), CString_constraint_Base::IsSetIs_all_punct(), CString_constraint_Base::IsSetIs_first_cap(), CString_constraint_Base::IsSetIs_first_each_cap(), CString_constraint_Base::IsSetMatch_location(), CString_constraint_Base::IsSetNot_present(), and NCBI_USER_THROW.

Referenced by s_SummarizeSearchFunc().

s_SummarizeSuspectRule()

static void s_SummarizeSuspectRule ( ostream &  out_strm, const CSuspect_rule &  rule  )

static

Definition at line 528 of file suspect_product_names.cpp.

References _ASSERT, CSuspect_rule_Base::GetExcept(), CSuspect_rule_Base::GetFind(), CSuspect_rule_Base::IsSetDescription(), CSuspect_rule_Base::IsSetExcept(), CSuspect_rule_Base::IsSetFatal(), CSuspect_rule_Base::IsSetFeat_constraint(), CSuspect_rule_Base::IsSetFind(), CSuspect_rule_Base::IsSetReplace(), CSuspect_rule_Base::IsSetRule_type(), NCBI_USER_THROW, and s_SummarizeSearchFunc().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

kSuspectProductNames

const string kSuspectProductNames = "[n] product_name[s] contain[S] suspect phrase[s] or character[s]"

static

Definition at line 208 of file suspect_product_names.cpp.

s_testcase_props__SUSPECT_PRODUCT_NAMES

constexpr CDiscrepancyCaseProps s_testcase_props__SUSPECT_PRODUCT_NAMES = { CDiscrepancyVisitorImpl<eTestNames:: _SUSPECT_PRODUCT_NAMES >::Create, eTestTypes:: STRING , eTestNames:: _SUSPECT_PRODUCT_NAMES , "_SUSPECT_PRODUCT_NAMES" , "Suspect Product Names for asndisc -N option" , 0 , nullptr }

staticconstexpr

Definition at line 578 of file suspect_product_names.cpp.

s_testcase_props_ORGANELLE_PRODUCTS

constexpr CDiscrepancyCaseProps s_testcase_props_ORGANELLE_PRODUCTS = { CDiscrepancyVisitorImpl<eTestNames:: ORGANELLE_PRODUCTS >::Create, eTestTypes:: FEAT , eTestNames:: ORGANELLE_PRODUCTS , "ORGANELLE_PRODUCTS" , "Organelle products on non-organelle sequence: on when neither bacteria nor virus" , eOncaller , nullptr }

staticconstexpr

Definition at line 372 of file suspect_product_names.cpp.

s_testcase_props_SUSPECT_PRODUCT_NAMES

constexpr CDiscrepancyCaseProps s_testcase_props_SUSPECT_PRODUCT_NAMES = { CDiscrepancyVisitorImpl<eTestNames:: SUSPECT_PRODUCT_NAMES >::Create, eTestTypes:: FEAT , eTestNames:: SUSPECT_PRODUCT_NAMES , "SUSPECT_PRODUCT_NAMES" , "Suspect Product Name" , eDisc | eOncaller | eSubmitter | eSmart | eTSA | eFatal , nullptr }

staticconstexpr

Definition at line 221 of file suspect_product_names.cpp.

s_testcase_props_SUSPECT_RRNA_PRODUCTS

constexpr CDiscrepancyCaseProps s_testcase_props_SUSPECT_RRNA_PRODUCTS = { CDiscrepancyVisitorImpl<eTestNames:: SUSPECT_RRNA_PRODUCTS >::Create, eTestTypes:: FEAT , eTestNames:: SUSPECT_RRNA_PRODUCTS , "SUSPECT_RRNA_PRODUCTS" , "rRNA product names should not contain 'partial' or 'domain'" , eDisc | eSubmitter | eSmart , nullptr }

staticconstexpr

Definition at line 551 of file suspect_product_names.cpp.