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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/OrgMod_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seqfeat/OrgMod.cpp Source File

replace(name.begin(), name.end(),

,

);

replace(name.begin(), name.end(),

,

);

(name ==

|| name ==

) {

}

(name ==

) {

replace(name.begin(), name.end(),

,

);

replace(name.begin(), name.end(),

,

);

name ==

||

name ==

) {

(name ==

|| name ==

) {

:

;

(pos == string::npos) {

inst =

.substr(0, pos);

=

.substr(pos + 1);

(pos != string::npos) {

coll =

.substr(0, pos);

=

.substr(pos + 1);

vector<string> tokens;

(tokens.size() < 3) {

& vouch_types = tokens[1];

(

= 0;

< vouch_types.size();

++) {

(vouch_types[

]) {

vector<string> synonyms;

builtin_timestamp

(

time_t

(kInstitutionCollectionCodeList_Timestamp));

}

(

)

(getenv(

)) {

(

);

num_codes =

(kInstitutionCollectionCodeList) /

(

*);

(

= 0;

< num_codes;

++) {

*p = kInstitutionCollectionCodeList[

];

(getenv(

)) {

(

+

+

);

}

( !

->AtEOF() );

& is_miscapitalized,

& correct_cap,

& needs_country,

& erroneous_country)

(it != code_map.

()) {

is_miscapitalized =

;

correct_cap = it->first;

(pos == string::npos) {

= inst_coll +

;

it = code_map.

();

(it != code_map.

()) {

needs_country =

;

is_miscapitalized =

;

correct_cap = it->first.substr(0, inst_coll.length());

inst_sub = inst_coll.substr(0, pos);

it = code_map.

(inst_sub);

(it != code_map.

()) {

erroneous_country =

;

code_map.

();

(

& inst_coll,

&voucher_type,

& is_miscapitalized,

& correct_cap,

& needs_country,

& erroneous_country)

is_miscapitalized =

;

needs_country =

;

erroneous_country =

;

syn_is_miscapitalized =

;

syn_correct_cap =

;

syn_needs_country =

;

syn_erroneous_country =

;

syn_needs_country, syn_erroneous_country);

is_miscapitalized = syn_is_miscapitalized;

correct_cap = syn_correct_cap;

needs_country = syn_needs_country;

erroneous_country = syn_erroneous_country;

voucher_type = is->second;

}

(erroneous_country) {

syn_is_miscapitalized =

;

syn_correct_cap =

;

syn_needs_country =

;

syn_erroneous_country =

;

syn_needs_country, syn_erroneous_country);

is_miscapitalized = syn_is_miscapitalized;

correct_cap = syn_correct_cap;

needs_country = syn_needs_country;

erroneous_country = syn_erroneous_country;

voucher_type = is->second;

voucher_type = ic->second;

voucher_type = it->second;

(

(culture_collection,

) == string::npos) {

;

(

(specimen_voucher,

) == string::npos) {

(

(biomaterial,

) == string::npos) {

=

;

inst_coll = inst_code;

inst_coll = inst_code +

+ coll_code;

is_miscapitalized;

erroneous_country;

+ inst_coll +

;

}

(erroneous_country) {

+ inst_coll +

;

}

(is_miscapitalized) {

+ inst_coll +

+ correct_cap;

+ inst_coll +

;

+ inst_coll +

;

+ inst_coll +

;

;

+ inst_coll +

;

}

(

(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country)) {

+ inst_coll +

;

}

(erroneous_country) {

+ inst_code +

;

}

(is_miscapitalized) {

+ inst_code +

+ correct_cap;

;

+ inst_code +

+ inst_coll +

;

+ inst_coll +

;

rval = inst +

+ id;

rval = inst +

+ coll +

+ id;

string::iterator sit =

.begin();

inst_code =

.substr(0,

);

remainder =

.substr(

);

sit = remainder.begin();

(sit != remainder.end()) {

(it != code_map.

()) {

= inst_code +

+ remainder;

(colon_pos != 0 && colon_pos != string::npos) {

(pos == string::npos) {

inst =

.substr(pos + 1,

.length() - pos - 2);

miscap =

, needs_country =

, wrong_country =

;

v_type = voucher_type;

(colon_pos == 0) {

= inst +

.substr(0, pos);

= inst +

+

.substr(0, pos);

new_inst_code = inst_code;

(

(it->second, v_type) != string::npos) {

new_inst_code = it->first;

&& inst_code.c_str()[it->first.length()] ==

) {

(vector<string>, it, vouchers) {

inst1, coll1, id1;

vector<string>::const_iterator it_next = it;

(++it_next; it_next != vouchers.end(); ++it_next) {

inst2, coll2, id2;

(coll1, coll2) && !

(coll1) ?

:

;

(

.find_first_not_of(

) ==

);

= strain.substr(prefix.length());

strain = prefix +

+

;

new_val = strain;

new_val = strain;

vector<string> words;

(

= 0;

<

;

++) {

(

= 0;

<

;

++) {

,

(

= 0;

<

;

++) {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

}

fix =

;

fix = possible_fix->second;

new_val =

;

deprecate_orgmods.test((

)subtype);

s1 = strain1;

s2 = strain2;

any_change =

;

,

,

,

,

,

fromEnv =

.Get(

);

(fromEnv ==

) {

}

(fromEnv ==

) {

fromConfig = reg.

(

,

,

);

(fromConfig ==

|| fromConfig ==

|| fromConfig ==

|| fromConfig ==

) {

static COrgMod::TInstitutionCodeMap s_CultureCollectionInstitutionCodeMap

bool FindInstCodeAndSpecID(COrgMod::TInstitutionCodeMap &code_map, string &val)

static const size_t sNumUnexpectedViralOrgModQualifiers

static COrgMod::TInstitutionCodeMap s_CompleteInstitutionFullNameMap

void s_HarmonizeString(string &s)

const char * sm_KnownHostWords[]

const char * sm_BadStrainValues[]

static const string sValidTypeMaterialPrefixes[]

static const int sNumValidTypeMaterialPrefixes

const string kMissingInst

static const COrgMod::TSubtype sUnexpectedViralOrgModQualifiers[]

const char * sm_BadIsolateValues[]

static const string sValidCultureTypeMaterialPrefixes[]

static constexpr auto s_hostFixupMap

static bool s_InstitutionCollectionCodeMapInitialized

static COrgMod::TInstitutionCodeMap s_BiomaterialInstitutionCodeMap

bool s_FixStrainForPrefix(const string &prefix, string &strain)

static COrgMod::TInstitutionCodeMap s_SpecimenVoucherInstitutionCodeMap

bool s_IsAllDigits(string str)

static COrgMod::TInstitutionCodeMap s_InstitutionCodeTypeMap

DEFINE_STATIC_FAST_MUTEX(s_InstitutionCollectionCodeMutex)

static COrgMod::TInstitutionCodeMap s_CompleteInstitutionCodeMap

string s_FixOneStrain(const string &strain)

static COrgMod::TInstitutionCodeMap s_InstitutionCodeSynonymsMap

static const int sNumValidCultureTypeMaterialPrefixes

static void s_InitializeInstitutionCollectionCodeMaps(void)

static bool s_init_LookForMultipleIsolates(void)

static void s_ProcessInstitutionCollectionCodeLine(const CTempString &line)

static CNcbiApplication * Instance(void)

Singleton method.

static bool FixStructuredVoucher(string &val, const string &voucher_type)

static bool NCBI_ValidateForMultipleIsolates(void)

static bool FuzzyStrainMatch(const string &strain1, const string &strain2)

static string IsCultureCollectionValid(const string &culture_collection)

static bool IsValidSubtypeName(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static const string & GetInstitutionShortName(const string &full_name)

static bool IsINSDCValidTypeMaterial(const string &type_material)

static bool IsInstitutionCodeValid(const string &inst_coll, string &voucher_type, bool &is_miscapitalized, string &correct_cap, bool &needs_country, bool &erroneous_country)

static bool AddStructureToVoucher(string &val, const string &voucher_type)

static bool IsStrainValid(const string &strain)

static bool IsMultipleValuesAllowed(TSubtype)

static bool IsDiscouraged(const TSubtype stype, bool indexer=false)

static const string & GetInstitutionFullName(const string &short_name)

static string IsStructuredVoucherValid(const string &val, const string &voucher_type)

static string FixHost(const string &value)

bool RemoveAbbreviation()

static bool IsValidTypeMaterial(const string &type_material)

static string IsBiomaterialValid(const string &biomaterial)

static string GetSubtypeName(TSubtype stype, EVocabulary vocabulary=eVocabulary_raw)

static string CheckMultipleVouchers(const vector< string > &)

static string FixHostCapitalization(const string &value)

static bool HoldsInstitutionCode(const TSubtype stype)

This indicates if the given Org-mod subtype is supposed to hold an institution code (Example: "ATCC:2...

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

bool IsUnexpectedViralOrgModQualifier() const

static bool IsIsolateValid(const string &isolate)

bool IsDeprecated() const

static bool RescueInstFromParentheses(string &val, const string &voucher_type)

static TInstitutionCodeMap::iterator FindInstitutionCode(const string &inst_coll, TInstitutionCodeMap &code_map, bool &is_miscapitalized, string &correct_cap, bool &needs_country, bool &erroneous_country)

static string MakeStructuredVoucher(const string &inst, const string &coll, const string &id)

static string IsSpecimenVoucherValid(const string &specimen_voucher)

static string FixStrain(const string &strain)

static bool ParseStructuredVoucher(const string &str, string &inst, string &coll, string &id)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

static constexpr auto construct(init_type const(&init)[N])

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

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

Utility macros and typedefs for exploring NCBI objects from general.asn.

const CNcbiEnvironment & GetEnvironment(void) const

Get the application's cached environment.

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

#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.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

#define ENUM_METHOD_NAME(EnumName)

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

virtual string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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

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

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

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

Join strings using the specified delimiter.

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

Case-sensitive equality of a substring with another string.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a 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 EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another 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.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ eReverseSearch

Search in a backward direction.

@ eNocase

Case insensitive compare.

@ eCase

Case sensitive compare.

TSubname & SetSubname(void)

Assign a value to Subname data member.

TSubtype GetSubtype(void) const

Get the Subtype member data.

bool IsSetSubtype(void) const

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

const TSubname & GetSubname(void) const

Get the Subname member data.

bool CanGetSubtype(void) const

Check if it is safe to call GetSubtype method.

bool IsSetSubname(void) const

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

@ eSubtype_gb_acronym

used by taxonomy database

@ eSubtype_gb_synonym

used by taxonomy database

@ eSubtype_other

ASN5: old-name (254) will be added to next spec.

@ eSubtype_dosage

chromosome dosage of hybrid

@ eSubtype_nat_host

natural host of this specimen

@ eSubtype_metagenome_source

@ eSubtype_specimen_voucher

@ eSubtype_nomenclature

code of nomenclature in subname (B,P,V,Z or combination)

@ eSubtype_gb_anamorph

used by taxonomy database

@ eSubtype_culture_collection

@ eSubtype_forma_specialis

Lightweight interface for getting lines of data with minimal memory copying.

const GenericPointer< typename T::ValueType > T2 value

#define FOR_EACH_STRING_IN_VECTOR(Itr, Var)

FOR_EACH_STRING_IN_VECTOR EDIT_EACH_STRING_IN_VECTOR.

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

string g_FindDataFile(const CTempString &name, CDirEntry::EType type=CDirEntry::eFile)

Look for an NCBI application data file or directory of the given name and type; in general,...

bool g_IsDataFileOld(const CTempString &path, const CTempString &id_line)

Check whether the given file (a full path, as returned by g_FindDataFile) is older than a built-in ve...

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