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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Seq__feat_8cpp_source.html below:

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

116 if

( type1 != type2 ) {

120 int

diff = order1 - order2;

139 int

diff = subtype1 - subtype2;

173 if

(diff)

return

diff;

177 return

s1.str().compare(s2.str());

185 if

((*it)->IsSetData () && (*it)->GetData ().IsGene ()) {

186 return

&((*it)->GetData ().GetGene ());

204

xref.push_back(gref);

205

gref->SetData().SetGene(

value

);

214 return

ref.

SetData

().SetGene();

218

xref.push_back(gref);

219 return

gref->SetData().SetGene();

226 if

((*it)->IsSetData () && (*it)->GetData ().IsProt ()) {

227 return

&((*it)->GetData ().GetProt ());

245

xref.push_back(pref);

246

pref->SetData().SetProt(

value

);

256 return

ref.

SetData

().SetProt();

260

xref.push_back(pref);

261 return

pref->SetData().SetProt();

271 if

((*xit)->IsSetId() && (*xit)->GetId().Equals(

id

)) {

285

x1->SetId().Assign(

id

);

300 const string

& qual_name,

const string

& qual_val)

304 if

( (*iter)->GetQual() == qual_name ) {

305

(*iter)->SetVal(qual_val);

331 if

( (*iter)->GetQual() != qual_name ) {

332

new_qual_vec.push_back(*iter);

336 if

( new_qual_vec.size() !=

GetQual

().

size

() ) {

338 if

( new_qual_vec.empty() ) {

380 if

( ! sCurrentExceptTextContents.empty() ) {

381

sCurrentExceptTextContents +=

", "

;

392

list<CTempString> list_of_except_texts;

396 string

new_except_texts;

397 ITERATE

(list<CTempString>, text_it, list_of_except_texts) {

399 if

( ! new_except_texts.empty() ) {

400

new_except_texts +=

", "

;

407 if

( new_except_texts.empty() ) {

419 if

( (*iter)->GetDb() == db) {

433 if

( (*iter)->GetQual() == qual_name && (*iter)->IsSetVal()) {

434 return

(*iter)->GetVal();

454

vector<CTempStringEx> exception_parts;

457 ITERATE

( vector<CTempStringEx>, part_it, exception_parts ) {

469 if

( sCleanedInputText.

empty

() ) {

478 return

( p_exception_text_set->find(sCleanedInputText) !=

479

p_exception_text_set->end() );

487

{

"16S ribosomal RNA and 23S ribosomal RNA overlap"

true

488

{

"16S ribosomal RNA and 5S ribosomal RNA overlap"

true

489

{

"23S ribosomal RNA and 16S ribosomal RNA overlap"

true

490

{

"23S ribosomal RNA and 5S ribosomal RNA overlap"

true

491

{

"5S ribosomal RNA and 16S ribosomal RNA overlap"

true

492

{

"5S ribosomal RNA and 23S ribosomal RNA overlap"

true

493

{

"adjusted for low-quality genome"

true

494

{

"alternative processing"

false

495

{

"alternative start codon"

false

496

{

"annotated by transcript or proteomic data"

false

497

{

"artificial frameshift"

false

498

{

"artificial location"

false

499

{

"circular RNA"

false

500

{

"dicistronic gene"

false

501

{

"gene split at contig boundary"

false

502

{

"gene split at sequence boundary"

false

503

{

"genetic code exception"

false

504

{

"heterogeneous population sequenced"

false

505

{

"low-quality sequence region"

false

506

{

"mismatches in transcription"

true

507

{

"mismatches in translation"

true

508

{

"modified codon recognition"

false

509

{

"nonconsensus splice site"

false

510

{

"rearrangement required for product"

false

511

{

"reasons given in citation"

false

512

{

"ribosomal slippage"

false

513

{

"RNA editing"

false

514

{

"trans-splicing"

false

515

{

"transcribed product replaced"

false

516

{

"transcribed pseudogene"

false

517

{

"translated product replaced"

false

518

{

"translation initiation by tRNA-Leu at CUG codon"

true

519

{

"unclassified transcription discrepancy"

true

520

{

"unclassified translation discrepancy"

true

521

{

"unextendable partial coding region"

false

}

528

vector<string> exception_list;

531 while

(it != sc_ExceptionPairMap.end()) {

532 if

(include_refseq || !it->second) {

533

exception_list.push_back(it->first);

538 return

exception_list;

545 if

(it != sc_ExceptionPairMap.end() && (allow_refseq || !it->second)) {

556 if

(it == sc_ExceptionPairMap.end()) {

569 const CObject_id

& obj_type = (*it)->GetType();

570 if

( obj_type.

IsStr

() && obj_type.

GetStr

() == ext_type ) {

571

ret.

Reset

(it->GetPointer());

577 if

(

GetExt

().GetType().IsStr()) {

578 if

(

GetExt

().GetType().GetStr() == ext_type) {

581 else if

(

GetExt

().GetType().GetStr() ==

"CombinedFeatureUserObjects"

) {

584 if

(

.GetData().IsObject() &&

585 f

.GetData().GetObject().GetType().IsStr() &&

586 f

.GetData().GetObject().GetType().GetStr() == ext_type) {

587

ret.

Reset

.GetData().GetObject());

602 const CObject_id

& obj_type = (*it)->GetType();

603 if

( obj_type.

IsStr

() && obj_type.

GetStr

() == ext_type ) {

604

ret.

Reset

(it->GetPointer());

610 if

(

GetExt

().GetType().IsStr()) {

611 if

(

GetExt

().GetType().GetStr() == ext_type) {

614 else if

(

GetExt

().GetType().GetStr() ==

"CombinedFeatureUserObjects"

) {

617 if

(

.GetData().IsObject() &&

618 f

.GetData().GetObject().GetType().IsStr() &&

619 f

.GetData().GetObject().GetType().GetStr() == ext_type) {

620

ret.

Reset

.SetData().SetObject());

655 const CObject_id

& obj_type = (*it)->GetType();

656 if

( obj_type.

IsStr

() && obj_type.

GetStr

() == ext_type ) {

660 if

( exts.empty() ) {

665 if

(

GetExt

().GetType().IsStr()) {

666 if

(

GetExt

().GetType().GetStr() == ext_type) {

669 else if

(

GetExt

().GetType().GetStr() ==

"CombinedFeatureUserObjects"

) {

676 if

(

.GetData().IsObject() &&

677 f

.GetData().GetObject().GetType().IsStr() &&

678 f

.GetData().GetObject().GetType().GetStr() == ext_type) {

681

new_ext_data.push_back(*it);

684 if

( new_ext_data.empty() ) {

686

}

else if

( new_ext_data.size() != curr_ext_data.size() ) {

688

new_ext_data.swap(curr_ext_data);

bool IsReverse(ENa_strand s)

static int s_GetCdregionOrder(const CSeqFeatData &fd)

DEFINE_STATIC_ARRAY_MAP(TExceptionPairMap, sc_ExceptionPairMap, k_LegalExceptionMap)

static bool s_IsOperon(const CSeqFeatData &fd)

CStaticArrayMap< const char *, bool, PNocase_CStr > TExceptionPairMap

SStaticPair< const char *, bool > TExceptionPairElem

static const TExceptionPairElem k_LegalExceptionMap[]

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

ESubtype GetSubtype(void) const

namespace ncbi::objects::

const CProt_ref * GetProtXref(void) const

get protein (if present) from Seq-feat.xref list

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

int GetTypeSortingOrder(void) const

Return relative importance order of features by their type.

void RemoveExceptText(const string &exception_text)

Remove all instances of the given exception text in this feature, and reset the except flag if there ...

void AddExceptText(const string &exception_text)

Add the given exception_text and set the except flag to true.

bool HasSeqFeatXref(const CSeqFeatXref::TId &id) const

CProt_ref & SetProtXref(void)

int CompareNonLocation(const CSeq_feat &f2, const CSeq_loc &loc1, const CSeq_loc &loc2) const

Compare relative order of this feature and feature f2 similarily to the Compare() method,...

void RemoveExt(const string &ext_type)

Remove all Exts with the given type.

CConstRef< CDbtag > GetNamedDbxref(const CTempString &db) const

Return a specified DB xref.

int CompareStrict(const CSeq_feat &f2) const

Compare features more thoroughly than Compare() - return zero only if the features are identical,...

CConstRef< CUser_object > FindExt(const string &ext_type) const

Find extension by type in exts container.

CGene_ref & SetGeneXref(void)

static vector< string > GetListOfLegalExceptions(bool include_refseq)

Produces the list of legal exceptions.

int TAddExt

binary OR of EAddExt

bool HasExceptionText(const string &exception_text) const

Returns whether or not the given exception_text is set for this feature.

int Compare(const CSeq_feat &f2) const

Compare relative order of this feature and feature f2, ordering first by features' coordinates,...

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

Add a qualifier to this feature, or replace the value for the first one if it already exists.

static bool IsExceptionTextInLegalList(const string &exception_text, bool allow_refseq)

Indicates whether this specific text occurs in the list of legal exceptions.

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

Add a qualifier to this feature.

void RemoveQualifier(const string &qual_name)

Remove all qualifiers with the given name; do nothing if no such qualifier exists.

@ fAddExt_ReplaceAll

Before adding, remove all previous.

AutoPtr< TExceptionTextSet > GetTempExceptionTextSet(void) const

Returns a case-insensitive set of exception texts.

const CGene_ref * GetGeneXref(void) const

See related function in util/feature.hpp.

void AddDbxref(const string &db_name, const string &db_key)

add a DB xref to this feature

void AddExt(CRef< CUser_object > ext, TAddExt add_flags=0)

Add an extension by type in exts container.

bool AddSeqFeatXref(const CSeqFeatXref::TId &id)

static bool IsExceptionTextRefSeqOnly(const string &exception_text)

Indicates whether this specific text is a RefSeq-only exception.

~CSeq_feat(void)

destructor

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

TBase::const_iterator const_iterator

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERASE_ITERATE(Type, Var, Cont)

Non-constant version with ability to erase current element, if container permits.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_USER_THROW(message)

Throw a quick-and-dirty runtime exception of type 'CException' with the given error message and error...

#define MSerial_AsnText

I/O stream manipulators â.

ENa_strand GetStrand(void) const

Get the location's strand.

int CompareSubLoc(const CSeq_loc &loc, ENa_strand strand, const ISubLocFilter *filter=NULL) const

Compare first-level sub-locations sequentially to order them by biological "complexity".

void Reset(void)

Reset reference object.

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 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.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

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

Truncate whitespace in a string.

@ fSplit_Tokenize

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

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.

void SetTag(TTag &value)

Assign a value to Tag data member.

TData & SetData(void)

Assign a value to Data data member.

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

void SetDb(const TDb &value)

Assign a value to Db data member.

vector< CRef< CUser_field > > TData

TXref & SetXref(void)

Assign a value to Xref data member.

void SetQual(const TQual &value)

Assign a value to Qual data member.

const TKey & GetKey(void) const

Get the Key member data.

vector< CRef< CDbtag > > TDbxref

TDbxref & SetDbxref(void)

Assign a value to Dbxref data member.

void SetData(TData &value)

Assign a value to Data data member.

const TData & GetData(void) const

Get the Data member data.

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

E_Choice Which(void) const

Which variant is currently selected.

const TExts & GetExts(void) const

Get the Exts member data.

bool IsProt(void) const

Check if variant Prot is selected.

bool IsSetExt(void) const

user defined structure extension Check if a value has been assigned to Ext data member.

TExcept & SetExcept(void)

Assign a value to Except data member.

list< CRef< CUser_object > > TExts

void ResetExcept(void)

Reset Except data member.

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

TExts & SetExts(void)

Assign a value to Exts data member.

E_Choice

Choice variants.

TData & SetData(void)

Assign a value to Data data member.

void ResetExts(void)

Reset Exts data member.

bool IsGene(void) const

Check if variant Gene is selected.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

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

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

const TCdregion & GetCdregion(void) const

Get the variant data.

void ResetExt(void)

Reset Ext data member.

void SetVal(const TVal &value)

Assign a value to Val data member.

bool IsSetExts(void) const

set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member.

TExt & SetExt(void)

Assign a value to Ext data member.

TExcept GetExcept(void) const

Get the Except member data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

vector< CRef< CGb_qual > > TQual

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

TQual & SetQual(void)

Assign a value to Qual data member.

const TExt & GetExt(void) const

Get the Ext member data.

TExcept_text & SetExcept_text(void)

Assign a value to Except_text data member.

void ResetQual(void)

Reset Qual data member.

const TImp & GetImp(void) const

Get the variant data.

@ eFrame_not_set

not set, code uses one

ENa_strand

strand of nucleic acid

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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