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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gff2__data_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/gff2_data.cpp Source File

85  auto

& mix = pLoc->

SetMix

();

91  for

(

const auto

& token : tokens) {

92  auto

divPos = token.find(

".."

);

93  if

(divPos == string::npos) {

95

mix.AddInterval(

id

, point, point, strand);

99

mix.AddInterval(

id

, from, to, strand);

113  const string

cdstr_start =

"(pos:"

;

114  const string

cdstr_div =

",aa:"

;

115  const string

cdstr_end =

")"

;

121  size_t

pos_start = cdstr_start.length();

122  size_t

pos_stop =

str

.find(cdstr_div);

123  string

posstr =

str

.substr(pos_start, pos_stop-pos_start);

124  string

aaa =

str

.substr(pos_stop+cdstr_div.length());

125

aaa = aaa.substr(0, aaa.length()-cdstr_end.length());

127  const string

posstr_compl =

"complement("

;

130

posstr = posstr.substr(posstr_compl.length());

131

posstr = posstr.substr(0, posstr.length()-1);

137

posstr = posstr.substr(5);

138  _ASSERT

(posstr.back() ==

')'

);

139

posstr = posstr.substr(0, posstr.length() - 1);

142

pCodeBreak->

SetLoc

(*pLoc);

144  const string

posstr_div =

".."

;

145  size_t

pos_div = posstr.find(posstr_div);

146  if

(pos_div == string::npos) {

151  const auto

to =

NStr::StringToInt

(posstr.substr(pos_div + posstr_div.length())) - 1;

154

pCodeBreak->

SetLoc

().SetInt().SetId(

id

);

155

pCodeBreak->

SetLoc

().SetInt().SetFrom(from);

156

pCodeBreak->

SetLoc

().SetInt().SetTo(to);

157

pCodeBreak->

SetLoc

().SetInt().SetStrand(strand);

194  auto

it = AminoAcidMap.find(aaa);

195  char

aacode = (it != AminoAcidMap.end()) ? it->second :

'X'

;

197

pCodeBreak->

SetAa

().SetNcbieaa(aacode);

203  const string

& genome,

209

GENOME_MAP& sGenomeMap = *s_GenomeMap;

210  if

(sGenomeMap.empty()) {

234

GENOME_MAP::const_iterator cit = sGenomeMap.find(genome);

235  if

(cit != sGenomeMap.end()) {

243

vector<CTempStringEx>&

columns

,

273  if

(!isNumericCol3 && isNumericCol4 && isNumericNext) {

277  size_t

startof_col1 =

columns

[1].begin() - in_line.

begin

();

292  const string

& strRawInput )

295

vector< CTempStringEx >

columns

;

303  "Bad data line: not enough columns"

,

320  string

message =

"Bad data line: Both \"start\" and \"stop\" must be positive integers."

;

328  string

message =

"Bad data line: location start is greater than location stop (start=" 383  const string

& strKey,

384  string

& strValue )

const 387  TAttrCit

it = m_Attributes.find( strKey );

388  if

( it == m_Attributes.end() ) {

392

strValue = it->second;

398  const string

& strKey,

399

list<string>& values )

const 403  TAttrCit

it = m_Attributes.find(strKey);

404  if

(it == m_Attributes.end()) {

408  return

!values.empty();

426

strValue = strValue.

substr

( 1, string::npos );

429

strValue = strValue.

substr

( 0, strValue.

length

() - 1 );

439  bool

inQuotes =

false

;

441  for

(;

i

<

input

.length();

i

++)

444  if

(

input

[

i

] ==

'\"'

) {

449  if

(

input

[

i

] ==

';'

) {

458  if

(

input

[

i

] ==

'\"'

) {

478  bool

inQuotes =

false

;

480  while

(

input

[

i

] ==

';'

) {

484  for

(

i

=0;

i

<

input

.length();

i

++)

487  if

(

input

[

i

] ==

'\"'

) {

516

semicolon =

input

.length();

519

equal =

min

(space, semicolon);

526  return

!

key

.empty();

530  const string

& strType,

531  const string

& strRawAttributes )

549  const string

& strRawAttributes,

553  string

strCurrAttrib;

554  bool

inQuotes =

false

;

556  ITERATE

(

string

, iterChar, strRawAttributes) {

558  if

(*iterChar ==

'\"'

) {

561

strCurrAttrib += *iterChar;

563  if

(*iterChar ==

';'

) {

565  if

(!strCurrAttrib.empty())

567

strCurrAttrib.clear();

569  if

(*iterChar ==

'\"'

) {

572

strCurrAttrib += *iterChar;

578  if

(!strCurrAttrib.empty())

594  return

xMigrateAttributes(

flags

, pFeature);

604  auto

subtype = pFeature->GetData().GetSubtype();

605  auto

recType = NormalizedType();

608

pFeature->SetLocation().SetMix().AddSeqLoc(*pAddLoc);

609  if

(!xUpdateFeatureData(

flags

, pFeature)) {

614

GetAttribute(

"ID"

, cdsId);

615  if

(!cdsId.empty()) {

616

pFeature->AddOrReplaceQualifier(

"ID"

, cdsId);

629  const CSeq_loc

& target = pFeature->GetLocation();

647  if

(curStart == newStart) {

648

pFeature->SetData().SetCdregion().SetFrame(Phase());

655  if

(curStop == newStop) {

656

pFeature->SetData().SetCdregion().SetFrame(Phase());

671  TAttributes

attrs_left(m_Attributes.begin(), m_Attributes.end());

674

it = attrs_left.

find

(

"Note"

);

675  if

(it != attrs_left.

end

()) {

676

pFeature->SetComment(xNormalizedAttributeValue(it->second));

677

attrs_left.

erase

(it);

680

it = attrs_left.

find

(

"Dbxref"

);

681  if

(it != attrs_left.

end

()) {

682

vector<string> dbxrefs;

684  for

(vector<string>::iterator it1 = dbxrefs.begin(); it1 != dbxrefs.end();

686  string

dbtag = xNormalizedAttributeValue(*it1);

689

attrs_left.

erase

(it);

692

it = attrs_left.

find

(

"Is_circular"

);

693  if

(it != attrs_left.

end

()) {

694  if

(pFeature->GetData().IsBiosrc()) {

697

pSubSource->

SetName

(

"is_circular"

);

698

pFeature->SetData().SetBiosrc().SetSubtype().push_back(pSubSource);

702

it = attrs_left.

find

(

"Parent"

);

703  if

(it != attrs_left.

end

()) {

704  if

(

Type

() !=

"CDS"

) {

705

xMigrateAttributeSingle(

706

attrs_left,

"Parent"

, pFeature,

"Parent"

,

flags

);

708  else

attrs_left.

erase

(it);

711

it = attrs_left.

find

(

"Name"

);

712  if

(it != attrs_left.

end

()) {

713  auto

soType = NormalizedType();

715

GetAttribute(

"gbkey"

, gbKey);

716  if

(soType ==

"cds"

|| soType ==

"mrna"

|| soType ==

"biological_region"

||

717

(soType ==

"region"

&& gbKey !=

"Src"

)) {

718

attrs_left.

erase

(it);

722

it = attrs_left.

find

(

"codon_start"

);

723  if

(it != attrs_left.

end

()) {

726  switch

(codon_start) {

739

attrs_left.

erase

(it);

743

it = attrs_left.

find

(

"description"

);

744  if

(it != attrs_left.

end

()) {

745  if

(pFeature->GetData().IsGene()) {

746  string

description = xNormalizedAttributeValue(it->second);

747

pFeature->SetData().SetGene().SetDesc(description);

748

attrs_left.

erase

(it);

752

it = attrs_left.

find

(

"exception"

);

753  if

(it != attrs_left.

end

()) {

754

pFeature->SetExcept(

true

);

755

pFeature->SetExcept_text(xNormalizedAttributeValue(it->second));

756

attrs_left.

erase

(it);

759

it = attrs_left.

find

(

"exon_number"

);

760  if

(it != attrs_left.

end

()) {

763

pQual->

SetVal

(it->second);

764

pFeature->SetQual().push_back(pQual);

765

attrs_left.

erase

(it);

768

it = attrs_left.

find

(

"experiment"

);

769  if

(it != attrs_left.

end

()) {

770  const string

strExperimentDefault(

771  "experimental evidence, no additional details recorded"

);

772  string value

= xNormalizedAttributeValue(it->second);

773  if

(

value

== strExperimentDefault) {

778

pQual->

SetQual

(

"experiment"

);

780

pFeature->SetQual().push_back(pQual);

782

attrs_left.

erase

(it);

785

it = attrs_left.

find

(

"gbkey"

);

786  if

(it != attrs_left.

end

()) {

787

attrs_left.

erase

(it);

790

it = attrs_left.

find

(

"gene"

);

791  if

(it != attrs_left.

end

()) {

792  if

(pFeature->GetData().IsGene()) {

793

list<string> geneValues;

796

list<string>::const_iterator cit = geneValues.begin();

797  if

(cit != geneValues.end()) {

798  value

= xNormalizedAttributeValue(*cit);

799

pFeature->SetData().SetGene().SetLocus(

value

);

801  while

(cit != geneValues.end()) {

802  value

= xNormalizedAttributeValue(*cit);

803

pFeature->SetData().SetGene().SetSyn().push_back(

value

);

807

attrs_left.

erase

(it);

811

it = attrs_left.

find

(

"genome"

);

812  if

(it != attrs_left.

end

()) {

813  if

(pFeature->GetData().IsBiosrc()) {

814

pFeature->SetData().SetBiosrc().SetGenome(

816

attrs_left.

erase

(it);

820

it = attrs_left.

find

(

"gene_synonym"

);

821  if

(it != attrs_left.

end

()) {

822  if

(pFeature->GetData().IsGene()) {

823

vector<string> synonyms;

825  for

(vector<string>::iterator it1 = synonyms.begin(); it1 != synonyms.end();

827  string

synonym = xNormalizedAttributeValue(*it1);

828

pFeature->SetData().SetGene().SetSyn().push_back(synonym);

831

attrs_left.

erase

(it);

834

it = attrs_left.

find

(

"inference"

);

835  if

(it != attrs_left.

end

()) {

836  auto

inferenceVal = it->second;

837  const string

strInferenceDefault(

838  "non-experimental evidence, no additional details recorded"

);

839  auto value

= xNormalizedAttributeValue(inferenceVal);

840  if

(

value

== strInferenceDefault) {

844

vector<string> inferenceVals;

846  for

(

auto val

: inferenceVals) {

848

pQual->

SetQual

(

"inference"

);

849

pQual->

SetVal

(xNormalizedAttributeValue(

val

));

850

pFeature->SetQual().push_back(pQual);

853

attrs_left.

erase

(it);

856

it = attrs_left.

find

(

"locus_tag"

);

857  if

(it != attrs_left.

end

()) {

858  if

(pFeature->GetData().IsGene()) {

859  string tag

= xNormalizedAttributeValue(it->second);

860

pFeature->SetData().SetGene().SetLocus_tag(

tag

);

862

attrs_left.

erase

(it);

865

it = attrs_left.

find

(

"map"

);

866  if

(it != attrs_left.

end

()) {

867  if

(pFeature->GetData().IsGene()) {

868

pFeature->SetData().SetGene().SetMaploc(

869

xNormalizedAttributeValue(it->second));

873

it = attrs_left.

find

(

"ncrna_class"

);

874  if

(it != attrs_left.

end

()) {

876

pFeature->SetData().SetRna().SetExt().SetGen().SetClass(

877

xNormalizedAttributeValue(it->second));

879

attrs_left.

erase

(it);

882

it = attrs_left.

find

(

"partial"

);

883  if

(it != attrs_left.

end

()) {

885

pFeature->AddQualifier(

"partial"

, it->second);

887

attrs_left.

erase

(it);

890

it = attrs_left.

find

(

"pseudo"

);

891  if

(it != attrs_left.

end

()) {

892

pFeature->SetPseudo(

true

);

893

attrs_left.

erase

(it);

896

it = attrs_left.

find

(

"regulatory_class"

);

897  if

(it != attrs_left.

end

()) {

898  if

(pFeature->GetData().IsImp() && (pFeature->GetData().GetImp().GetKey() ==

"regulatory"

)) {

900

pFeature->RemoveQualifier(

"regulatory_class"

);

901

pFeature->AddQualifier(

"regulatory_class"

, it->second);

902

attrs_left.

erase

(it);

907

it = attrs_left.

find

(

"rpt_type"

);

908  if

(it != attrs_left.

end

()) {

910

{

"microsatellite"

,

"microsatellite"

},

911

{

"minisatellite"

,

"minisatellite"

},

912

{

"satellite_DNA"

,

"satellite"

},

913

{

"satellite"

,

"satellite"

},

915

pFeature->RemoveQualifier(

"rpt_type"

);

916

pFeature->RemoveQualifier(

"satellite"

);

917  auto

rpt_type = it->second;

918  auto

satelliteIt = satellites.

find

(rpt_type);

919  if

(satelliteIt != satellites.

end

()) {

920

pFeature->AddQualifier(

"satellite"

, satelliteIt->second);

923

pFeature->AddQualifier(

"rpt_type"

, rpt_type);

925

attrs_left.

erase

(it);

928

it = attrs_left.

find

(

"satellite"

);

929  if

(it != attrs_left.

end

()) {

930  if

(pFeature->GetData().IsImp() && pFeature->GetData().GetImp().GetKey() ==

"repeat_region"

) {

931

attrs_left.

erase

(it);

935

it = attrs_left.

find

(

"transl_except"

);

936  if

(it != attrs_left.

end

()) {

937  if

(pFeature->GetData().IsCdregion()) {

938

vector<string> codebreaks;

940  for

(vector<string>::iterator it1 = codebreaks.begin();

941

it1 != codebreaks.end(); ++it1 ) {

942  string

breakData = xNormalizedAttributeValue(*it1);

948  string

message =

"Unable to parse code-break : \""

+ it->second +

"\""

;

953

pFeature->SetData().SetCdregion().SetCode_break().push_back(

957

attrs_left.

erase

(it);

961

it = attrs_left.

find

(

"transl_table"

);

962  if

(it != attrs_left.

end

()) {

963  if

(pFeature->GetData().IsCdregion()) {

966

pFeature->SetData().SetCdregion().SetCode().Set().push_back(pCe);

967

attrs_left.

erase

(it);

971  if

(!xMigrateAttributesGo(

flags

, pFeature, attrs_left)) {

975  if

(pFeature->GetData().IsBiosrc()) {

976  if

(!xMigrateAttributesSubSource(

flags

, pFeature, attrs_left)) {

979  if

(!xMigrateAttributesOrgName(

flags

, pFeature, attrs_left)) {

987  while

(!attrs_left.

empty

()) {

988  const string

&

key

= attrs_left.

begin

()->first;

989  if

(!xMigrateAttributeDefault(attrs_left,

key

, pFeature,

key

,

flags

)) {

999  const string

& attrKey,

1001  const string

& qualKey,

1021  const string

& attrKey,

1023  const string

& qualKey,

1034

list<CTempStringEx> values;

1036  for

(list<CTempStringEx>::const_iterator cit = values.begin(); cit != values.end();

1057

ORGMOD_MAP& sOrgModMap = *s_OrgModMap;

1058  if

(sOrgModMap.empty()) {

1098

list<CRef<COrgMod> >& orgMod =

1099

pFeature->SetData().SetBiosrc().SetOrg().SetOrgname().SetMod();

1100  for

( ORGMOD_MAP::const_iterator sit = sOrgModMap.begin();

1101

sit != sOrgModMap.end(); ++sit) {

1103  if

(ait == attrs_left.end()) {

1109

orgMod.push_back(pOrgMod);

1110

attrs_left.erase(ait);

1122  for

(

auto

it = attrs.begin(); it != attrs.end();

) {

1129

it = attrs.erase(it);

1147

SUBSOURCE_MAP& sSubSourceMap = *s_SubSourceMap;

1148  if

(sSubSourceMap.empty()) {

1195

list<CRef<CSubSource> >& subType =

1196

pFeature->SetData().SetBiosrc().SetSubtype();

1197  for

( SUBSOURCE_MAP::const_iterator sit = sSubSourceMap.begin();

1198

sit != sSubSourceMap.end(); ++sit) {

1200  if

(ait == attrs_left.end()) {

1205

pSubSource->

SetName

(xNormalizedAttributeValue(ait->second));

1206

subType.push_back(pSubSource);

1207

attrs_left.erase(ait);

1218  auto

recognizedType = NormalizedType();

1220  if

(recognizedType ==

"region"

|| recognizedType ==

"biological_region"

) {

1222  if

(GetAttribute(

"gbkey"

, gbkey)) {

1223  if

(gbkey ==

"Src"

) {

1224

pFeature->SetData().SetBiosrc();

1230

GetAttribute(

"Name"

, name);

1231

pFeature->SetData().SetRegion(name);

1235  if

(recognizedType ==

"start_codon"

|| recognizedType ==

"stop_codon"

) {

1236

recognizedType =

"cds"

;

1241  Type

(), *pFeature, invalidFeaturesToRegion)) {

1242  string

message =

"Bad data line: Invalid feature type \""

+

Type

() +

"\""

;

1257

list<string> parentIds;

1261  return

(parentIds.size() > 1);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

static CRef< CDbtag > x_ParseDbtag(const CTempString &)

virtual bool xUpdateFeatureData(TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const

bool IsMultiParent() const

TAttributes::const_iterator TAttrCit

static string xNormalizedAttributeValue(const CTempString &)

virtual bool xMigrateAttributes(TReaderFlags, CRef< CSeq_feat >) const

TAttributes::iterator TAttrIt

bool GetAttribute(const string &, string &) const

virtual bool UpdateFeature(TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const

virtual bool AssignFromGff(const string &)

virtual bool InitializeFeature(TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const

static void TokenizeGFF(vector< CTempStringEx > &columns, const CTempStringEx &line)

virtual bool xInitFeatureData(TReaderFlags, CRef< CSeq_feat >) const

static bool xMigrateAttributeDefault(TAttributes &, const string &, CRef< CSeq_feat >, const string &, TReaderFlags)

static bool xMigrateAttributeSingle(TAttributes &, const string &, CRef< CSeq_feat >, const string &, TReaderFlags)

virtual bool xMigrateAttributesGo(TReaderFlags, CRef< CSeq_feat >, TAttributes &) const

virtual bool xMigrateAttributesOrgName(TReaderFlags, CRef< CSeq_feat >, TAttributes &) const

virtual bool xMigrateAttributesSubSource(TReaderFlags, CRef< CSeq_feat >, TAttributes &) const

bool xSplitGffAttributes(const string &, vector< string > &) const

static string xNormalizedAttributeKey(const CTempString &)

virtual bool xAssignAttributesFromGff(const string &, const string &)

virtual bool xInitFeatureData(TReaderFlags, CRef< CSeq_feat >) const

virtual bool InitializeFeature(TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const

string m_strNormalizedType

static CObjReaderLineException * Create(EDiagSev eSeverity, unsigned int uLine, const std::string &strMessage, EProblem eProblem=eProblem_GeneralParsingError, const std::string &strSeqId=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), CObjReaderLineException::EErrCode eErrCode=eFormat, const TVecOfLines &vecOfOtherLines=TVecOfLines())

Please use this instead of the constructor because the ctor is protected.

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

static void AddGeneOntologyTerm(CSeq_feat &feature, const CTempString &qual, const CTempString &val)

void AddQualifier(const string &qual_name, const string &qual_val)

Add a qualifier to this feature.

static bool SoTypeToFeature(std::string_view, CSeq_feat &, bool=false)

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

@ eProblem_FeatureBadStartAndOrStop

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

#define MAKE_CONST_MAP(name, type1, type2,...)

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

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

static const struct attribute attributes[]

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

static const column_t columns[]

CBioSource::EGenome s_StringToGenome(const string &genome, CGff2Record::TReaderFlags flags)

CRef< CSeq_loc > s_GetCodeBreakSeqLocMix(const string &locString, const CSeq_id &id, ENa_strand strand)

CTempString x_GetNextAttribute(CTempString &input)

CRef< CCode_break > s_StringToCodeBreak(const string &str, CSeq_id &id, CGff2Record::TReaderFlags flags)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eDiag_Error

Error message.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

TSeqPos GetStop(ESeqLocExtremes ext) const

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 BEGIN_NCBI_SCOPE

Define ncbi namespace.

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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

Check if a string ends with a specified suffix value.

CTempStringEx substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

static string URLDecode(const CTempString str, EUrlDecode flag=eUrlDec_All)

URL-decode string.

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

Truncate whitespace in a string (in-place)

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

Check if a string starts with a specified prefix value.

size_type length(void) const

Return the length of the represented array.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

size_type find_first_not_of(const CTempString match, size_type pos=0) const

Find the first occurrence of any character not in the matching string within the current string,...

size_type find_first_of(const CTempString match, size_type pos=0) const

Find the first occurrence of any character in the matching string within the current string,...

static string & ToLower(string &str)

Convert string to lower case – string& version.

static const size_type npos

const_iterator begin() const

Return an iterator to the string's starting position.

@ fAllowLeadingSpaces

Ignore leading whitespace characters in converted string.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

@ eUrlDec_Percent

Decode only XX.

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

void SetName(const TName &value)

Assign a value to Name data member.

EGenome

biological context

@ eSubtype_collection_date

DD-MMM-YYYY format.

@ eSubtype_insertion_seq_name

@ eSubtype_transposon_name

@ eSubtype_fwd_primer_seq

sequence (possibly more than one; semicolon-separated)

@ eSubtype_lat_lon

+/- decimal degrees

@ eSubtype_rev_primer_name

@ eSubtype_collected_by

name of person who collected the sample

@ eSubtype_fwd_primer_name

@ eSubtype_rev_primer_seq

sequence (possibly more than one; semicolon-separated)

@ eSubtype_isolation_source

@ eSubtype_environmental_sample

@ eSubtype_endogenous_virus_name

@ eSubtype_identified_by

name of person who identified the sample

@ eSubtype_whole_replicon

@ eGenome_endogenous_virus

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

void SetSubname(const TSubname &value)

Assign a value 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_specimen_voucher

@ eSubtype_gb_anamorph

used by taxonomy database

@ eSubtype_culture_collection

@ eSubtype_forma_specialis

void SetAa(TAa &value)

Assign a value to Aa data member.

void SetQual(const TQual &value)

Assign a value to Qual data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

void SetVal(const TVal &value)

Assign a value to Val data member.

@ eExp_ev_experimental

any reasonable experimental check

@ eExp_ev_not_experimental

similarity, pattern, etc

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

ENa_strand

strand of nucleic acid

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

TStrand GetStrand(void) const

Get the Strand member data.

const TInt & GetInt(void) const

Get the variant data.

@ eNa_strand_both

in forward orientation

std::false_type tagStrNocase

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

const GenericPointer< typename T::ValueType > T2 value

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)


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