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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/BioSource_8cpp_source.html below:

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

108  if

(pgcode > 0)

return

pgcode;

174  if

(g_iter == sm_GenomeKeys.end()) {

179

gtype = g_iter->second;

189  match

= g_iter->first;

191  if

(organelle.length() ==

match

.length()

192

|| (

match

.length() < organelle.length() &&

isspace

(organelle[

match

.length()]))) {

193

gtype = g_iter->second;

200  if

(

NStr::Equal

(organelle,

"mitochondrial"

, use_case)) {

204  if

(

NStr::Equal

(organelle, g_iter->first, use_case)) {

205

gtype = g_iter->second;

220  while

(g_iter != sm_GenomeKeys.end() &&

221  unsigned

(g_iter->second) != genome) {

224  if

(g_iter != sm_GenomeKeys.end()) {

225

organelle = g_iter->first;

260  if

(g_iter == sm_OriginKeys.end ()) {

261

g_iter = sm_OriginSynonyms.find (

origin

.c_str());

262  if

(g_iter != sm_OriginSynonyms.end ()) {

263

gtype = g_iter->second;

266

gtype = g_iter->second;

273  while

(g_iter != sm_OriginKeys.end() && !found) {

274  match

= g_iter->first;

278

gtype = g_iter->second;

285

g_iter = sm_OriginSynonyms.begin();

286  while

(g_iter != sm_OriginSynonyms.end() && !found) {

287  match

= g_iter->first;

291

gtype = g_iter->second;

299  while

(g_iter != sm_OriginKeys.end() && !found) {

301

gtype = g_iter->second;

306

g_iter = sm_OriginSynonyms.begin();

307  while

(g_iter != sm_OriginSynonyms.end() && !found) {

309

gtype = g_iter->second;

322  string

origin_str =

""

;

324  while

(g_iter != sm_OriginKeys.end() &&

325  unsigned

(g_iter->second) !=

origin

) {

328  if

(g_iter != sm_OriginKeys.end()) {

329

origin_str = g_iter->first;

425  if

((*sit)->IsSetSubtype() && (*sit)->IsSetName()){

427  string

name =(*sit)->GetName();

442  if

(bioprojtype ==

"eSegment"

)

461  return "kinetoplast"

;

492  return "eExtrachrom"

;

506  return "eLinkageGroup"

;

518  return "eChromosome"

;

525  return "eNuclearProkaryote"

;

533  return "eVirionPhage"

;

542  return "eNuclearProkaryote"

;

550  return "eNuclearProkaryote"

;

553  return "eMitochondrion"

;

556  return "eKinetoplast"

;

559  return "eChloroplast"

;

562  return "eChromoplast"

;

568  return "eMacronuclear"

;

575  return "eProviralProphage"

;

581  return "eVirionPhage"

;

589  return "eNucleomorph"

;

592  return "eApicoplast"

;

595  return "eLeucoplast"

;

598  return "eProplastid"

;

601  return "eHydrogenosome"

;

604  return "eChromatophore"

;

613  return "eNuclearProkaryote"

;

678

COrgName::TMod::iterator it = org_ref.

SetOrgname

().SetMod().begin();

679  while

(it != org_ref.

SetOrgname

().SetMod().end()) {

681

it = org_ref.

SetOrgname

().SetMod().erase(it);

716  string label

= (*it)->GetFieldName();

717  bool

skipStopWord =

true

;

721

skipStopWord =

false

;

736  string

sample_val = (*it)->GetSampleVal();

737  if

(skipStopWord &&

IsStopWord

(sample_val)) {

747  mod

->SetSubtype(subtype);

748  mod

->SetSubname(sample_val);

749

mods.push_back(

mod

);

763

subtypes.push_back(sub);

775

subtypes.push_back(sub);

789  if

(!subtypes.empty()) {

802

CBioSource::TSubtype::iterator it =

SetSubtype

().begin();

855  if

(stop1 && stop2) {

891  if

((*it)->IsSetSubname() && (*it)->IsSetSubtype()) {

912  if

((*it)->IsSetName() && (*it)->IsSetSubtype()) {

920  string val

= (*it)->GetName();

942  "metagenome-source"

,

1026  if

(val1 > 180.0 || val2 > 180.0) {

1031

sprintf(buf1,

"%0.2f"

, val1);

1032

sprintf(buf2,

"%0.2f"

, val2);

1033  if

(

strcmp

(buf1, buf2) == 0) {

1045  bool

skipStopWord =

true

;

1049

skipStopWord =

false

;

1096  switch

(ignore_type) {

1118  bool

src_format_correct, src_precision_correct,

1119

src_lat_in_range, src_lon_in_range;

1120  double

src_lat_value, src_lon_value;

1122

src_lat_in_range, src_lon_in_range,

1123

src_lat_value, src_lon_value);

1124  bool

smpl_format_correct, smpl_precision_correct,

1125

smpl_lat_in_range, smpl_lon_in_range;

1126  double

smpl_lat_value, smpl_lon_value;

1128

smpl_lat_in_range, smpl_lon_in_range,

1129

smpl_lat_value, smpl_lon_value);

1130  if

(src_format_correct && smpl_format_correct

1142  if

(src_date && smpl_date && src_date->

Equals

(*smpl_date)) {

1169

vector<bool> matched1;

1170  for

(

size_t i

= 0;

i

< list1.size();

i

++) {

1171

matched1.push_back(

false

);

1174

vector<bool> matched2;

1175  for

(

size_t i

= 0;

i

< list2.size();

i

++) {

1176

matched2.push_back(

false

);

1178  for

(

size_t i

= 0;

i

< list1.size();

i

++) {

1179  bool

found =

false

;

1180  for

(

size_t

j = 0; j < list2.size(); j++) {

1184

matched2[j] =

true

;

1190

matched1[

i

] =

true

;

1193  for

(

size_t i

= 0;

i

< list1.size();

i

++) {

1194  if

(!matched1[

i

]) {

1195  bool

reported =

false

;

1196  for

(

size_t

j = 0; j < list2.size(); j++) {

1199

list.push_back(diff);

1201

matched2[j] =

true

;

1207

list.push_back(diff);

1211  for

(

size_t

j = 0; j < list2.size(); j++) {

1214

list.push_back(diff);

1225

CBioSource::TNameValList::iterator it1 = list1.begin();

1226

CBioSource::TNameValList::iterator it2 = list2.begin();

1227

vector<bool> matched;

1229  while

(it1 != list1.end() && it2 != list2.end()) {

1234

list.push_back(diff);

1237

}

else if

(

cmp

> 0) {

1240

list.push_back(diff);

1245  const string

& val_name = it1->first;

1248

v1.push_back(it1->second);

1249  v2

.push_back(it2->second);

1252  while

(it1 != list1.end() &&

NStr::Equal

(it1->first, val_name)) {

1253

v1.push_back(it1->second);

1256  while

(it2 != list2.end() &&

NStr::Equal

(it2->first, val_name)) {

1257  v2

.push_back(it2->second);

1264  while

(it1 != list1.end()) {

1267

list.push_back(diff);

1271  while

(it2 != list2.end()) {

1274

list.push_back(diff);

1283  string

src_tax =

""

;

1287  string

sample_tax =

""

;

1291

TFieldDiffList::iterator it = diff_list.begin();

1292  while

(it != diff_list.end()) {

1296

&&

NStr::Find

(sample_tax, (*it)->GetSrcVal()) != string::npos) {

1301

&&

NStr::Find

(src_tax, (*it)->GetSampleVal()) != string::npos) {

1308

it = diff_list.erase(it);

1318

TFieldDiffList::iterator it = diff_list.begin();

1319  while

(it != diff_list.end()) {

1321

it = diff_list.erase(it);

1365  "missing: control sample"

,

1366  "missing: data agreement established pre-2023"

,

1367  "missing: endangered species"

,

1368  "missing: human-identifiable"

,

1369  "missing: lab stock"

,

1370  "missing: sample group"

,

1371  "missing: synthetic construct"

,

1372  "missing: third party data"

,

1384  "restricted access"

,

1400  "missing: control sample"

,

1401  "missing: data agreement established pre-2023"

,

1402  "missing: endangered species"

,

1403  "missing: human-identifiable"

,

1404  "missing: lab stock"

,

1405  "missing: sample group"

,

1406  "missing: synthetic construct"

,

1407  "missing: third party data"

,

1418  "restricted access"

,

1441

CBioSource::TSubtype::iterator it =

SetSubtype

().begin();

1444  if

((*it)->IsSetSubtype()

1446

&& (!(*it)->IsSetName() ||

NStr::IsBlank

((*it)->GetName()))) {

1458  while

(it !=

SetOrg

().SetOrgname().SetMod().end()) {

1460  if

((*it)->IsSetSubtype()

1461

&& (!(*it)->IsSetSubname() ||

NStr::IsBlank

((*it)->GetSubname()))) {

1477

CBioSource::TSubtype::iterator it =

SetSubtype

().begin();

1510  "Tax class/lineage"

,

1511  "Taxonomic classification"

,

1512  "Taxonomic Classification is"

,

1523  if

(

str

.empty()) {

1533  if

(

text

.empty()) {

1536  bool match

=

true

, at_least_one =

false

;

1539  const char

* ch =

orig

;

1541  while

(

isspace

((

unsigned char

)(*ch)) ||

ispunct

((

unsigned char

)(*ch))) {

1544  while

(*ch != 0 &&

match

) {

1546  for

(TWordList::const_iterator word = word_list.begin(); word != word_list.end() && !

match

; ++word) {

1547  size_t

length = word->size();

1549  unsigned char next

= *(ch + length);

1553

at_least_one =

true

;

1557  while

(

isspace

((

unsigned char

)(*ch)) ||

ispunct

((

unsigned char

)(*ch))) {

1561  return

(

match

&& at_least_one);

1570  bool

any_removed =

false

;

1586

CBioSource::TSubtype::iterator it =

SetSubtype

().begin();

1589  bool

removed =

false

;

1596

any_removed =

true

;

1611  while

(iter !=

SetOrg

().SetOrgname().SetMod().end()) {

1613  bool

removed =

false

;

1620

any_removed =

true

;

1642

CBioSource::TSubtype::iterator it =

SetSubtype

().begin();

1644  if

((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {

1664

CBioSource::TSubtype::iterator it =

SetSubtype

().begin();

1666  if

((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype &&

1688  while

(it !=

SetOrg

().SetOrgname().SetMod().end()) {

1689  if

((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {

1710  while

(it !=

SetOrg

().SetOrgname().SetMod().end()) {

1711  if

((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype &&

1712

(*it)->IsSetSubname() &&

NStr::Equal

((*it)->GetSubname(),

val

)) {

1729  bool

has_env_sample =

false

;

1730  bool

has_metagenomic =

false

;

1731  bool

any_change =

false

;

1735  if

((*s)->IsSetSubtype()) {

1737

has_env_sample =

true

;

1739

has_metagenomic =

true

;

1741  if

(has_env_sample && has_metagenomic) {

1748  if

(!has_env_sample &&

1754

has_env_sample =

true

;

1758  if

(has_metagenomic && !has_env_sample) {

1761

has_env_sample =

true

;

1765  if

(!has_env_sample &&

1771

has_env_sample =

true

;

1779  if

(!has_env_sample) {

1781

has_env_sample =

true

;

1784  if

(!has_metagenomic) {

1786

has_metagenomic =

true

;

1794  bool

has_metagenome_source =

false

;

1797

has_metagenome_source =

true

;

1801  if

(has_metagenome_source) {

1802  if

(!has_env_sample) {

1804

has_env_sample =

true

;

1807  if

(!has_metagenomic) {

1809

has_metagenomic =

true

;

1820  bool

any_change =

false

;

1823

CBioSource::TSubtype::iterator s =

SetSubtype

().begin();

1826  if

(! (*s)->IsSetName()) {

1832  string

nm = (*s)->GetName();

1834  if

((*s)->IsSetSubtype()) {

1878  while

(m !=

SetOrg

().SetOrgname().SetMod().end()) {

1879  if

((*m)->IsSetSubname()) {

1880  string

nm = (*m)->GetSubname();

1923  bool

isViral =

IsViral

(lineage);

1924  bool

isBacteria =

false

;

1925  bool

isArchaea =

false

;

1926  bool

isFungal =

false

;

1936  if

(isViral || isBacteria || isArchaea || isFungal) {

1956  bool

isViral =

IsViral

(lineage);

1957  bool

isAnimal =

false

;

1958  bool

isPlant =

false

;

1968  if

(isViral || isAnimal || isPlant) {

1988  bool

any_change =

false

;

1992

TSubtype::iterator it =

SetSubtype

().begin();

1995  if

((*it)->IsSetSubtype()) {

2032  bool

any_change =

false

;

2034  while

(m !=

SetOrg

().SetOrgname().SetMod().end()){

2035  if

((*m)->IsUnexpectedViralOrgModQualifier()) {

2061 #define MAKE_COMMON_INT(o1,o2,o3,Field) \ 2062  if (o1.IsSet##Field() && o2.IsSet##Field() && o1.Get##Field() == o2.Get##Field()) o3.Set##Field(o1.Get##Field()); 2072  bool

found =

false

;

2074  if

((*it1)->Equals(**it2)) {

2110

common_src->

SetOrg

().Assign(*common_org);

2122  if

((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {

CStaticArraySet< const char *, PNocase_CStr > TCTaxNameElementQualsSet

static const char * s_SpecialLineageWords[]

static const char * kOrgModNote

bool s_CompareNameVals(const CBioSource::TNameVal &f1, const CBioSource::TNameVal &f2)

void GetFieldDiffsFromNameValLists(TFieldDiffList &list, CBioSource::TNameValList &list1, CBioSource::TNameValList &list2, bool is_local_copy)

CStaticArraySet< const char *, PNocase_CStr > TCStopWordStrSet

CStaticPairArrayMap< const char *, CBioSource::EGenome, PNocase_CStr > TGenomeMap

static const char *const s_TaxNameElementQuals[]

static const char * kOrganismName

SStaticPair< const char *, CBioSource::EGenome > TGenomeKey

CStaticArraySet< const char *, PNocase_CStr > TCIgnoreCaseQualsSet

static const TCIgnoreCaseQualsSet s_IgnoreCaseQualsSet(s_IgnoreCaseQuals, sizeof(s_IgnoreCaseQuals), __FILE__, __LINE__)

static const char * kTaxId

static IgnoreConflictData sIgnoreConflictList[]

bool s_IsTaxNameElement(const string &value)

struct ignoreconflict IgnoreConflictData

static const TCTaxNameElementQualsSet s_TaxNameElementQualsSet(s_TaxNameElementQuals, sizeof(s_TaxNameElementQuals), __FILE__, __LINE__)

static const char * kSubSrcNote

DEFINE_STATIC_ARRAY_MAP(TGenomeMap, sm_GenomeKeys, genome_key_to_subtype)

static bool s_IsPunct(char ch)

static const std::set< std::string > s_insdcNullTerms

bool s_SameExceptPrecision(double val1, double val2)

bool s_MayIgnoreCase(const string &value)

CStaticPairArrayMap< const char *, CBioSource::EOrigin, PNocase_CStr > TOriginMap

vector< CTempString > TWordList

static const TGenomeKey genome_key_to_subtype[]

static const char * kDisableStrainForwardAttrib

static const char *const s_StopWords[]

static const TOriginKey origin_key_to_subtype[]

void RemoveDiffByName(TFieldDiffList &diff_list, string pair_name)

SStaticPair< const char *, CBioSource::EOrigin > TOriginKey

int s_iCompareNameVals(const CBioSource::TNameVal &f1, const CBioSource::TNameVal &f2)

static const char *const s_IgnoreCaseQuals[]

static bool s_DoesTextContainOnlyTheseWords(const string &text, const TWordList &word_list)

bool s_MustCopy(int subtype)

static void s_GetWordListFromText(string &str, TWordList &word_list)

void CompareValLists(TFieldDiffList &list, const string &val_name, bool is_local_copy, const vector< string > &list1, const vector< string > &list2)

#define MAKE_COMMON_INT(o1, o2, o3, Field)

static const TCStopWordStrSet s_StopWordsSet(s_StopWords, sizeof(s_StopWords), __FILE__, __LINE__)

static const TOriginKey origin_synonyms[]

set< string > GetINSDCMissingValues()

@ eConflictIgnoreMissingInBioSample

@ eConflictIgnoreMissingInBioSource

vector< CRef< CFieldDiff > > TFieldDiffList

User-defined methods of the data storage class.

bool AllowMatingTypeQualifier() const

const string & GetLineage(void) const

bool BiosampleDiffsOkForUpdate(const TFieldDiffList &diffs) const

bool IsSetCommon(void) const

const string & GetTaxname(void) const

bool RemoveLineageSourceNotes()

bool FixEnvironmentalSample()

bool IsSetGcode(void) const

string GetRepliconName(void) const

CRef< CBioSource > MakeCommonExceptOrg(const CBioSource &other) const

static bool ShouldIgnoreConflict(const string &label, string src_val, string sample_val, bool is_local_copy=false)

TNameValList GetNameValPairs() const

bool IsSetOrgMod(void) const

static string GetOrganelleByGenome(unsigned int genome)

bool GetDisableStrainForwarding() const

pair< string, string > TNameVal

int GetPgcode(void) const

void RemoveCultureNotes(bool is_species_level=true)

int GetGenCode(int def=1) const

string GetBioprojectLocation(void) const

bool FixSexMatingTypeInconsistencies()

void x_ClearCoordinatedBioSampleSubSources()

void x_RemoveNameElementDiffs(const CBioSource &biosample, TFieldDiffList &diff_list) const

const string & GetCommon(void) const

const COrgName & GetOrgname(void) const

const string & GetDivision(void) const

CRef< CBioSource > MakeCommon(const CBioSource &other) const

bool FixGenomeForQualifiers()

static bool IsStopWord(const string &value)

static CBioSource::EOrigin GetOriginByString(const string &origin, NStr::ECase use_case=NStr::eCase, bool starts_with=false)

bool HasSubtype(CSubSource::TSubtype subtype) const

bool IsSetMgcode(void) const

bool IsSetOrgname(void) const

string GetBioprojectType(void) const

TNameValList x_GetSubtypeNameValPairs() const

bool RemoveOrgMod(int subtype)

vector< TNameVal > TNameValList

bool x_ShouldIgnoreNoteForBiosample() const

bool IsSetLineage(void) const

static void x_RemoveStopWords(COrg_ref &org_ref)

bool IsSetPgcode(void) const

bool IsSetDivision(void) const

void UpdateWithBioSample(const CBioSource &biosample, bool force, bool is_local_copy=false)

TNameValList x_GetOrgModNameValPairs() const

int GetMgcode(void) const

static CBioSource::EGenome GetGenomeByOrganelle(const string &organelle, NStr::ECase use_case=NStr::eCase, bool starts_with=false)

bool AllowSexQualifier() const

void SetDisableStrainForwarding(bool val)

static string GetStringFromOrigin(unsigned int origin)

bool IsSetTaxname(void) const

TFieldDiffList GetBiosampleDiffs(const CBioSource &biosample, bool is_local_copy=false) const

bool RemoveUnexpectedViralQualifiers()

bool RemoveSubSource(int subtype)

@OrgMod.hpp User-defined methods of the data storage class.

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

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

const string & GetLineage(void) const

const string & GetDivision(void) const

TTaxId SetTaxId(TTaxId tax_id)

CRef< COrg_ref > MakeCommon(const COrg_ref &other) const

int GetPgcode(void) const

bool IsSetDivision(void) const

bool IsSetPgcode(void) const

bool IsSetGcode(void) const

bool IsSetMgcode(void) const

int GetMgcode(void) const

bool IsSetOrgMod(void) const

bool IsSetLineage(void) const

const_iterator find(const key_type &key) const

Return a const_iterator pointing to the specified element, or to the end if the element is not found.

const_iterator end() const

Return the end of the controlled sequence.

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

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

static bool IsValidSexQualifierValue(const string &value)

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

static bool NeedsNoText(const TSubtype &subtype)

static void IsCorrectLatLonFormat(string lat_lon, bool &format_correct, bool &precision_correct, bool &lat_in_range, bool &lon_in_range, double &lat_value, double &lon_value)

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

static bool IsDiscouraged(const TSubtype subtype)

static void RemoveCultureNotes(string &value, bool is_species_level=true)

The NCBI C++ standard methods for dealing with std::string.

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static void DLIST_NAME() remove(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

constexpr size_t ArraySize(const Element(&)[Size])

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define TAX_ID_FROM(T, value)

#define NCBI_THROW(exception_class, err_code, message)

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

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

#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 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 int strncasecmp(const char *s1, const char *s2, size_t n)

Case-insensitive comparison of two zero-terminated strings, narrowed to the specified number of chara...

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

Case-sensitive equality of a substring with another string.

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

Compare of a substring with another 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.

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.

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.

@ fSplit_Tokenize

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

@ eNocase

Case insensitive compare.

@ eCase

Case sensitive compare.

static const char label[]

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

const TPcr_primers & GetPcr_primers(void) const

Get the Pcr_primers member data.

TGenome GetGenome(void) const

Get the Genome member data.

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

bool IsSetOrg(void) const

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

bool CanGetOrg(void) const

Check if it is safe to call GetOrg method.

list< CRef< CSubSource > > TSubtype

bool IsSetSubtype(void) const

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

TGenome & SetGenome(void)

Assign a value to Genome data member.

bool IsSetPcr_primers(void) const

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

bool CanGetGenome(void) const

Check if it is safe to call GetGenome method.

const TOrg & GetOrg(void) const

Get the Org member data.

TOrg & SetOrg(void)

Assign a value to Org data member.

TSubtype GetSubtype(void) const

Get the Subtype member data.

bool IsSetGenome(void) const

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

bool IsSetSubtype(void) const

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

void SetPcr_primers(TPcr_primers &value)

Assign a value to Pcr_primers data member.

void SetOrg(TOrg &value)

Assign a value to Org data member.

void SetName(const TName &value)

Assign a value to Name data member.

const TName & GetName(void) const

Get the Name member data.

EGenome

biological context

bool IsSetName(void) const

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

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

void ResetSubtype(void)

Reset Subtype data member.

@ eSubtype_collection_date

DD-MMM-YYYY format.

@ eSubtype_environmental_sample

@ eSubtype_endogenous_virus_name

@ eOrigin_synthetic

purely synthetic

@ eOrigin_mut

artificially mutagenized

@ eOrigin_artificial

artificially engineered

@ eOrigin_natmut

naturally occurring mutant

@ eOrigin_natural

normal biological entity

@ eGenome_endogenous_virus

@ eGenome_plasmid_in_mitochondrion

@ eGenome_plasmid_in_plastid

const TMod & GetMod(void) const

Get the Mod member data.

TSubtype GetSubtype(void) const

Get the Subtype member data.

bool IsSetPgcode(void) const

plastid genetic code Check if a value has been assigned to Pgcode data member.

TMgcode GetMgcode(void) const

Get the Mgcode member data.

TGcode GetGcode(void) const

Get the Gcode 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 IsSetCommon(void) const

common name Check if a value has been assigned to Common data member.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

bool IsSetMgcode(void) const

mitochondrial genetic code Check if a value has been assigned to Mgcode data member.

void ResetTaxname(void)

Reset Taxname data member.

const TCommon & GetCommon(void) const

Get the Common member data.

void SetTaxname(const TTaxname &value)

Assign a value to Taxname data member.

list< CRef< COrgMod > > TMod

bool IsSetOrgname(void) const

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

bool IsSetSubname(void) const

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

bool IsSetTaxname(void) const

preferred formal name Check if a value has been assigned to Taxname data member.

bool IsSetGcode(void) const

genetic code (see CdRegion) Check if a value has been assigned to Gcode data member.

void SetOrgname(TOrgname &value)

Assign a value to Orgname data member.

TPgcode GetPgcode(void) const

Get the Pgcode member data.

const TAttrib & GetAttrib(void) const

Get the Attrib member data.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

@ eSubtype_other

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

@ eSubtype_metagenome_source

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

static void text(MDB_val *v)

constexpr auto sort(_Init &&init)

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

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

const GenericPointer< typename T::ValueType > T2 value

int strcmp(const char *str1, const char *str2)

Defines unified interface to application:

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

static const GLdouble origin[]

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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

EConflictIgnoreType ignore_type


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