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NCBI C++ ToolKit: src/objtools/cleanup/cleanup_user_object.cpp Source File

any_change =

;

( user_object.IsSetType() && user_object.GetType().IsStr() ) {

(user_object.IsSetData()) {

(

field : user_object.SetData()) {

any_change |= x_CleanupUserField(*field);

any_change |= s_CleanupGeneOntology(user_object);

any_change |= s_CleanupStructuredComment(user_object);

any_change |= s_CleanupDBLink(user_object);

any_change =

;

(

sub_obj : field.

().SetObjects()) {

(

sub_field : field.

().SetFields()) {

{

,

}

any_change =

;

*

sc_bsecGoQualType[] = {

,

,

,

(

outer_field : obj.

()) {

(outer_field->IsSetLabel() && outer_field->GetLabel().IsStr() &&

outer_field->IsSetData() && outer_field->GetData().IsFields()

&& sc_GoQualArray.find(outer_field->GetLabel().GetStr().c_str()) != sc_GoQualArray.end()) {

(

term : outer_field->SetData().SetFields()) {

(

inner_term_iter : field.

().SetFields()) {

find_term = sc_OntologyTermCleanupMap.find(inner_label.c_str());

(find_term != sc_OntologyTermCleanupMap.end() &&

inner_field.

().SetStr().erase(0, strlen(find_term->second));

any_change =

;

genome_assembly_data =

;

ibol_data =

;

prefix_present =

;

suffix_present =

;

kBarcode =

;

(

field_i : obj.

()) {

prefix_present =

;

suffix_present =

;

(is_prefix || is_suffix) {

field.

().SetStr(new_val);

genome_assembly_data =

;

}

( core == kBarcode ) {

(prefix_present && !suffix_present) {

suffix->

().SetStr(

);

.push_back(suffix);

(!prefix_present && suffix_present) {

prefix->

().SetStr(

);

.emplace(

.begin(), prefix);

( genome_assembly_data ) {

{

,

},

{

,

},

{

,

},

{

,

}

any_change =

;

(

field_i : obj.

()) {

replace = sc_FinishingCleanupMap.find(field.

().

().c_str());

(replace != sc_FinishingCleanupMap.end()) {

field.

().SetStr(replace->second);

&field_str = field.

().SetStr();

ambiguous =

;

coll_date->

(&day,

);

coll_date->

(&month,

);

month = month.substr(0, 3);

coll_date->

(&year,

);

new_date += day +

;

new_date += month +

;

field_str = new_date;

any_change =

;

CUser_object::TData::iterator it = obj.

().begin();

(it != obj.

().end()) {

is_blank =

;

((*it)->IsSetData()) {

((*it)->GetData().IsStr()) {

&

= (*it)->GetData().GetStr();

it = obj.

().erase(it);

changed =

;

(

& it : obj.

()) {

(it->IsSetData() && it->GetData().IsStr()) {

= it->GetData().GetStr();

it->SetData().SetStrs().push_back(

);

any_change =

;

static bool s_CleanupDBLink(CUser_object &obj)

static bool s_CleanupGeneOntology(CUser_object &obj)

static bool s_CleanupStructuredComment(CUser_object &obj)

static bool s_CleanupGenomeAssembly(CUser_object &obj)

static bool CleanupUserObject(CUser_object &object)

static bool x_CleanupUserField(CUser_field &field)

static bool s_AddNumToUserField(CUser_field &field)

static bool s_RemoveEmptyFields(CUser_object &obj)

void GetDate(string *label, bool year_only=false) const

Append a standardized string representation of the date to the label.

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

static string FixDateFormat(const string &orig_date)

Attempt to fix the format of the date Returns a blank if the format of the date cannot be determined.

static CRef< CDate > DateFromCollectionDate(const string &str) THROWS((CException))

CUser_field & SetString(const char *value)

@ eObjectType_StructuredComment

EObjectType GetObjectType() const

SStaticPair< const char *, const char * > TFinishingCleanupElem

DEFINE_STATIC_ARRAY_MAP(TOntologyCleanupMap, sc_OntologyTermCleanupMap, k_ontology_term_cleanup_map)

SStaticPair< const char *, const char * > TOntologyCleanupElem

CStaticArrayMap< const char *, const char *, PNocase_CStr > TFinishingCleanupMap

static const TOntologyCleanupElem k_ontology_term_cleanup_map[]

CStaticArrayMap< const char *, const char *, PNocase_CStr > TOntologyCleanupMap

static const TFinishingCleanupElem k_finishing_cleanup_map[]

bool CleanVisString(string &str)

bool Asn2gnbkCompressSpaces(string &val)

weird space compression from C Toolkit

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const char * str(char *buf, int n)

#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 bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static CStringUTF8 AsUTF8(const CTempString &src, EEncoding encoding, EValidate validate=eNoValidate)

Convert into UTF8 from a C/C++ string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ eNocase

Case insensitive compare.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetData(void) const

the object itself Check if a value has been assigned to Data data member.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

bool IsSetYear(void) const

full year (including 1900) Check if a value has been assigned to Year data member.

bool IsStd(void) const

Check if variant Std is selected.

const TStrs & GetStrs(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TOss & GetOss(void) const

Get the variant data.

bool IsFields(void) const

Check if variant Fields is selected.

bool IsSetDay(void) const

day of month (1-31) Check if a value has been assigned to Day data member.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetLabel(void) const

field label Check if a value has been assigned to Label data member.

TData & SetData(void)

Assign a value to Data data member.

void SetNum(TNum value)

Assign a value to Num data member.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetNum(void) const

required for strs, ints, reals, oss Check if a value has been assigned to Num data member.

void SetLabel(TLabel &value)

Assign a value to Label data member.

const TReals & GetReals(void) const

Get the variant data.

bool IsSetMonth(void) const

month (1-12) Check if a value has been assigned to Month data member.

void SetData(TData &value)

Assign a value to Data data member.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

bool IsSetData(void) const

Check if a value has been assigned to Data data member.

const TStd & GetStd(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TInts & GetInts(void) const

Get the variant data.

TNum GetNum(void) const

Get the Num member data.

@ e_Object

for using other definitions

@ e_not_set

No variant selected.

const string kGenomeAssemblyData

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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