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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/deprecated__quals_8cpp_source.html below:

NCBI C++ ToolKit: src/misc/discrepancy/deprecated_quals.cpp Source File

49 class

xDeprecatedQualsMoreData:

public CObject 60

more_obj.

Reset

(

new

xDeprecatedQualsMoreData);

61

more_obj->m_qual = qual;

63 auto

disc_obj =

context

.BiosourceObjRef(*biosrc,

true

, more_obj);

64 auto key

"[n] bioseq[s] [has] '"

+ qual +

"' qualifier"

;

65 auto

& rec = report_node[

"Deprecated Qualifiers"

][

key

];

69 template

typename

_Container>

72 for

(

auto

& it : vec) {

74 if

(rec.IsDeprecated()) {

75 auto

qual = rec.GetSubtypeName(rec.GetSubtype(),

std::remove_cvref_t

<decltype(rec)>::eVocabulary_raw);

76

xRegisterBioSrc(

context

, biosrc, report_node, qual);

82 template

typename

_Container,

typename

_Removed>

83 unsigned

xRemoveDeprecated(_Removed& removed_quals, _Container& vec,

const

xDeprecatedQualsMoreData* qual_to_remove)

86 for

(

auto

it = vec.begin(); it != vec.end(); ) {

88 if

(rec.IsDeprecated()) {

89 auto

qual = rec.GetSubtypeName(rec.GetSubtype(),

std::remove_cvref_t

<decltype(rec)>::eVocabulary_raw);

90 if

(qual_to_remove ==

nullptr

|| (qual == qual_to_remove->m_qual)) {

91

removed_quals.insert(qual);

107 if

(biosrc->CanGetSubtype()) {

108 auto

& subtype = biosrc->GetSubtype();

109

xRegisterBioSrc(subtype,

context

, biosrc, m_Objs);

111 if

(biosrc->IsSetOrgMod()) {

112 auto

& mods = biosrc->GetOrg().GetOrgname().GetMod();

113

xRegisterBioSrc(mods,

context

, biosrc, m_Objs);

120 unsigned

removed = 0;

122

std::set<string> removed_quals;

126 auto

more_data =

static_cast<const

xDeprecatedQualsMoreData*

>

(obj->GetMoreInfo().GetPointerOrNull());

132

removed += xRemoveDeprecated(removed_quals, subtype, more_data);

135 auto

& mods = biosrc->

SetOrg

().SetOrgname().SetMod();

136

removed += xRemoveDeprecated(removed_quals, mods, more_data);

140 if

(removed && !removed_quals.empty() ) {

143 return Ref

(

new CAutofixReport

(

"DEPRECATED: [n] removed qualifier[s] ("

+ s +

")"

, removed));

153 for

(

auto

& rec: m_ReportItems) {

bool IsSetOrgMod(void) const

static void Add(TReportObjectList &list, TReportObjectSet &hash, CReportObj &obj, bool unique=true)

#define DISCREPANCY_AUTOFIX(name)

#define DISCREPANCY_CASE(name, type, group, descr)

#define DISCREPANCY_SUMMARIZE(name)

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

bool CanGetSubtype(void) const

Check if it is safe to call GetSubtype method.

void SetOrg(TOrg &value)

Assign a value to Org data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

CBioSource * GetBioSourceFromContext(CDiscrepancyObject *obj, CDiscrepancyContext &context)

const struct ncbi::grid::netcache::search::fields::KEY key

typename remove_cvref< T >::type remove_cvref_t

static CS_CONTEXT * context

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