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NCBI C++ ToolKit: src/objects/general/User_object.cpp Source File

+

);

list<string>::iterator iter = toks.begin();

(++iter; iter != toks.end(); ++iter) {

( !sub.empty() ) {

( !sub.empty() ) {

(*field_iter)->

(sub, delim, use_case);

& delim,

& delim,

& obj_subtype,

& delim,

field_ref = *field_iter;

field_ref->

().SetStr(toks.front());

().push_back(field_ref);

&

,

vector<string>&

)

vector<int>&

)

vector<double>&

)

*

=

;

*

=

;

().front()->GetData().GetObject();

;

obj.

().front()->GetData().GetObject();

(

&&

->GetData().IsStr()) {

( !

.empty() ) {

( !

.empty() ) {

;

it = sc_ObjectTypeMap.find(

.c_str());

(it == sc_ObjectTypeMap.end()) {

(

it = sc_ObjectTypeMap.begin(); it != sc_ObjectTypeMap.end(); it++) {

(it->second == obj_type) {

CUser_object::TData::iterator it =

().begin();

(it !=

().end()) {

CUser_object::TData::iterator it =

().begin();

(it !=

().end()) {

method->

(

);

(it !=

().end()) {

do_remove =

;

((*it)->IsSetLabel()) {

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

(

((*it)->GetLabel().GetStr(), field_name, ecase)) {

}

((*it)->GetLabel().IsId()) {

(

((*it)->GetLabel().GetStr(), field_name, ecase)) {

fturl->

().SetStr(url);

url =

+ upload_id;

(

.empty()) {

(

it = sc_RefGeneTrackingStatusMap.begin(); it != sc_RefGeneTrackingStatusMap.end(); it++) {

(it->second == status) {

it = sc_RefGeneTrackingStatusMap.find(field->

().

().c_str());

(it != sc_RefGeneTrackingStatusMap.end()) {

top->

().SetFields().push_back(uf);

top->

().SetFields().push_back(uf);

top->

().SetFields().push_back(uf);

top->

().SetFields().push_back(uf);

top->

().SetFields().push_back(uf);

top->

().SetFields().push_back(uf);

accession, acc_name, comment;

(it->IsSetLabel() && it->GetLabel().IsStr() && it->IsSetData()) {

&

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

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

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

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

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

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

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

(it->GetData().IsInt()) {

from = it->GetData().GetInt();

(it->GetData().IsInt()) {

to = it->GetData().GetInt();

(rval->IsEmpty()) {

field.

().SetFields().push_back(ident);

(

it : acc_list) {

field.

().SetFields().push_back(acc);

rval.push_back(acc);

static const TObjectTypePair k_object_type_map[]

CStaticArrayMap< const char *, CUser_object::ERefGeneTrackingStatus, PNocase_CStr > TRefGeneTrackingStatusMap

static const char * kFileTrack

const string kRGTAComment

const string kRefGeneTrackingGenerated

static const char * kAutoDefOptions

static const char * kRefGeneTracking

static const char * s_expres

static const char * kUnreviewed

static const char * kStructuredComment

static const char * s_count

static const char * kOrigIdAltSpell

SStaticPair< const char *, CUser_object::ERefGeneTrackingStatus > TRefGeneTrackingStatusPair

static const char * s_ncbi

static const char * kUnverified

const string kRGTAAccession

static const char * kValidationSuppression

const string kRefGeneTrackingCollaborator

const string kRefGeneTrackingCollaboratorURL

SStaticPair< const char *, CUser_object::EObjectType > TObjectTypePair

static const char * s_exp

static const char * kOriginalId

DEFINE_STATIC_ARRAY_MAP(TObjectTypeMap, sc_ObjectTypeMap, k_object_type_map)

const string kRefGeneTrackingStatus

static const char * kDBLink

const string kRefGeneTrackingIdenticalTo

static string s_GetUserObjectContent(const CUser_object &obj)

static const char * kNcbiCleanup

CStaticArrayMap< const char *, CUser_object::EObjectType, PNocase_CStr > TObjectTypeMap

const string kRefGeneTrackingAssembly

SAFE_CONST_STATIC_STRING(kUnverifiedOrganism, "Organism")

const string kRefGeneTrackingGenomicSource

static string s_GetUserObjectType(const CUser_object &obj)

static const TRefGeneTrackingStatusPair k_refgene_tracking_status_map[]

static const char * s_sage

static const char * s_tag

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

CRef< CUser_field > SetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase)

Return a field reference representing the tokenized key, or a NULL reference if the key cannot be cre...

CUser_field & SetString(const char *value)

CUser_field & SetGi(TGi gi)

CUser_field & SetValue(int value)

set a data field to a given value Int8 and TGi values can be stored into 'str' field if the value doe...

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Return a field reference representing the tokenized key, or a NULL reference if the key doesn't exist...

CUser_field & SetBool(bool value)

static CRef< CRefGeneTrackingAccession > MakeAccessionFromUserField(const CUser_field &field)

CRef< CUser_field > MakeAccessionField() const

const string & GetRefGeneTrackingCollaborator() const

void SetObjectType(EObjectType obj_type)

void ResetRefGeneTrackingAssembly()

void ResetRefGeneTrackingStatus()

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

void RemoveUnreviewedUnannotated()

void RemoveUnverifiedFeature()

void AddUnverifiedOrganism()

void SetRefGeneTrackingCollaboratorURL(const string &collaborator_url)

ECategory GetCategory(void) const

accessors: classify a given user object

void AddUnreviewedUnannotated()

bool x_IsUnverifiedType(const string &val) const

const string & GetRefGeneTrackingCollaboratorURL() const

void AddUnverifiedContaminant()

@ eRefGeneTrackingStatus_INFERRED

@ eRefGeneTrackingStatus_VALIDATED

@ eRefGeneTrackingStatus_WGS

@ eRefGeneTrackingStatus_PREDICTED

@ eRefGeneTrackingStatus_Error

@ eRefGeneTrackingStatus_NotSet

@ eRefGeneTrackingStatus_PROVISIONAL

@ eRefGeneTrackingStatus_PIPELINE

@ eRefGeneTrackingStatus_REVIEWED

void ResetRefGeneTrackingCollaboratorURL()

CUser_object & SetCategory(ECategory category)

format a user object as a given type.

void SetRefGeneTrackingAssembly(const TRefGeneTrackingAccessions &acc_list)

void ResetRefGeneTrackingGenerated()

void RemoveUnverifiedMisassembled()

ECategory

enums for implicit typing of user objects

void x_AddUnverifiedType(const string &val)

void ResetRefGeneTrackingGenomicSource()

void SetRefGeneTrackingStatus(ERefGeneTrackingStatus status)

void RemoveUnverifiedContaminant()

void SetRefGeneTrackingCollaborator(const string &collaborator)

void SetRefGeneTrackingIdenticalTo(const CRefGeneTrackingAccession &accession)

const string & x_GetRefGeneTrackingField(const string &field_name) const

bool RemoveNamedField(const string &field_name, NStr::ECase ecase=NStr::eCase)

void SetRefGeneTrackingGenomicSource(const string &genomic_source)

@ eObjectType_RefGeneTracking

@ eObjectType_StructuredComment

@ eObjectType_AutodefOptions

@ eObjectType_ValidationSuppression

bool IsUnverifiedMisassembled() const

void GetLabel(string *label, ELabelContent mode=eContent) const

Append a label to label.

void SetRefGeneTrackingGenerated(bool val=true)

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

void SetFileTrackUploadId(const string &upload_id)

vector< CConstRef< CRefGeneTrackingAccession > > TRefGeneTrackingAccessions

const string & GetRefGeneTrackingGenomicSource() const

void x_RemoveUnreviewedType(const string &val)

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

~CUser_object(void)

destructor

bool IsUnverifiedOrganism() const

bool GetRefGeneTrackingGenerated() const

void ResetRefGeneTrackingCollaborator()

ERefGeneTrackingStatus GetRefGeneTrackingStatus() const

bool x_IsUnreviewedType(const string &val) const

ELabelContent

enum controlling what to return for a label this mirrors a request inside of feature::GetLabel()

EExperiment

sub-category experiment

EExperiment GetExperimentType(void) const

sub-category accessors:

bool IsUnverifiedContaminant() const

TRefGeneTrackingAccessions GetRefGeneTrackingAssembly() const

void x_RemoveUnverifiedType(const string &val)

void SetFileTrackURL(const string &url)

void x_AddUnreviewedType(const string &val)

bool IsUnverifiedFeature() const

void UpdateNcbiCleanup(int version)

void RemoveUnverifiedOrganism()

CUser_object(void)

constructor

void AddUnverifiedMisassembled()

const CUser_object & GetExperiment(void) const

bool IsUnreviewedUnannotated() const

CConstRef< CRefGeneTrackingAccession > GetRefGeneTrackingIdenticalTo() const

CUser_field & SetField(const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

Access a named field in this user object.

CRef< CUser_field > SetFieldRef(const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

EParseField

how to interpret the value in the AddField() conversion functions below.

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

void ResetRefGeneTrackingIdenticalTo()

CUser_object & SetExperiment(EExperiment category)

format a user object as a given type.

void x_SetRefGeneTrackingField(const string &field_name, const string &value)

EObjectType GetObjectType() const

void AddUnverifiedFeature()

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

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

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

Join strings using the specified delimiter.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

ECase

Which type of string comparison.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

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.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

int Year(void) const

Get year.

int Day(void) const

Get day.

int Month(void) const

Get month.

@ eCurrent

Use current time. See also CCurrentTime.

static const char label[]

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.

const TData & GetData(void) const

Get the Data member data.

TClass & SetClass(void)

Assign a value to Class data member.

const TFields & GetFields(void) const

Get the variant data.

TBool GetBool(void) const

Get the variant data.

bool IsFields(void) const

Check if variant Fields is selected.

bool IsSetClass(void) const

endeavor which designed this object Check if a value has been assigned to Class data member.

const TClass & GetClass(void) const

Get the Class member data.

bool IsStr(void) const

Check if variant Str is selected.

TType & SetType(void)

Assign a value to Type data member.

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.

const TStr & GetStr(void) const

Get the variant data.

void SetLabel(TLabel &value)

Assign a value to Label data member.

TStr & SetStr(void)

Select the variant.

virtual void Reset(void)

Reset the whole object.

const TData & GetData(void) const

Get the Data member data.

const TObject & GetObject(void) const

Get the variant data.

void ResetType(void)

Reset Type data member.

void ResetData(void)

Reset Data 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.

bool IsBool(void) const

Check if variant Bool is selected.

void ResetData(void)

Reset Data data member.

vector< CRef< CUser_field > > TData

@ e_Object

for using other definitions

constexpr bool empty(list< Ts... >) noexcept

const string version

version string

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

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

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