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NCBI C++ ToolKit: include/objtools/format/items/qualifiers.hpp Source File

fFlags_showEvenIfRedund = 1 << 0

TStyle style = eQuoted,

ETrim trim = eTrim_Normal );

TStyle style = eQuoted,

ETrim trim = eTrim_Normal );

&

(

)

{

m_Name; }

&

(

)

{

m_Value; }

&

(

)

{

m_Prefix; }

&

(

)

{

m_Suffix; }

fPrependNewline = 0x8

: m_Prefix(pfx), m_Suffix(sfx)

<

Key>

Find(

) != m_Quals.end();

m_Quals.find(

);

m_Quals.find(

);

(

!= end() ) {

m_Quals.erase(

);

m_Quals.find(

);

m_Quals.find(

);

m_Quals.size();

&

(

)

{

m_Value; }

TFlags

)

;

TFlags

)

;

TFlags

)

;

TFlags

)

;

: m_Value(

), m_Style(style) { }

list<string>::const_iterator& end,

: m_Value(begin, end), m_Style(style) { }

TFlags

)

;

m_Suffix = &kSemicolon;

TFlags

)

;

TFlags

)

;

TFlags

)

;

(

codon,

aa,

is_ascii =

);

& =

);

TFlags

)

;

TFlags

)

;

TFlags

)

;

TFlags

)

;

TFlags

)

;

TFlags

)

;

: m_Value(&

), m_GiPrefix(add_gi_prefix) { }

TFlags

)

;

TFlags

)

;

& fwd_name,

& fwd_seq,

& rev_name,

& rev_seq ) :

m_fwd_name( fwd_name ),

m_fwd_seq( fwd_seq ),

m_rev_name( rev_name ),

: m_Value(

), m_Quals(quals) { }

TFlags

)

;

x_XrefInGeneXref(

& dbtag)

;

TFlags

)

;

TFlags

)

;

& GetTextString(

)

;

GetPubmedId(

)

;

m_Anticodon(&ac), m_Aa(aa){ }

TFlags

)

;

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.

CConstRef< CSeq_loc > m_Anticodon

CFlatAnticodonQVal(const CSeq_loc &ac, const string &aa)

CFlatBondQVal(const string &value)

void Format(TFlatQuals &q, const CTempString &n, CBioseqContext &, TFlags) const

CFlatBoolQVal(bool value)

CCdregion::TCode_break m_Value

CFlatCodeBreakQVal(const CCdregion::TCode_break &value)

CFlatGeneQVal(const string &value)

CFlatGeneSynonymsQVal(const CGene_ref::TSyn &syns)

CFlatGoQVal(const CUser_field &value)

CConstRef< CUser_field > m_Value

CConstRef< CGb_qual > m_Value

CFlatIllegalQVal(const CGb_qual &value)

CFlatLabelQVal(const string &value)

CFlatModelEvQVal(const CUser_object &value)

CConstRef< CUser_object > m_Value

CFlatMolTypeQVal(TBiomol biomol, TMol mol)

CMolInfo::TBiomol TBiomol

CFlatNomenclatureQVal(const CGene_ref_Base::TFormal_name &value)

CConstRef< CGene_ref_Base::TFormal_name > m_Value

CFlatNumberQVal(const string &value)

CFlatOrgModQVal(const COrgMod &value)

CConstRef< COrgMod > m_Value

CFlatOrganelleQVal(CBioSource::TGenome value)

CBioSource::TGenome m_Value

CFlatProductNamesQVal(const CProt_ref::TName &value, const string &gene)

CProt_ref::TName & SetValue(void)

const CProt_ref::TName & GetValue(void) const

CFlatPubSetQVal(const CPub_set &value)

CConstRef< CPub_set > m_Value

CFlatSeqIdQVal(const CSeq_id &value, bool add_gi_prefix=false)

CConstRef< CSeq_id > m_Value

CConstRef< CSeq_loc > m_Value

void Format(TFlatQuals &q, const CTempString &n, CBioseqContext &ctx, TFlags) const

CFlatSeqLocQVal(const CSeq_loc &value)

CFlatSiteQVal(const string &value)

const TValue & GetValue(void) const

CFlatStringListQVal(const list< string >::const_iterator &begin, const list< string >::const_iterator &end, TStyle style=CFormatQual::eQuoted)

CFlatStringListQVal(const list< string > &value, TStyle style=CFormatQual::eQuoted)

IFlatQVal::TFlags m_AddPeriod

void SetAddPeriod(bool addPeriod=true)

const string & GetValue(void) const

CFlatSubSourcePrimer(const string &fwd_name, const string &fwd_seq, const string &rev_name, const string &rev_seq)

CConstRef< CSubSource > m_Value

CFlatSubSourceQVal(const CSubSource &value)

CFlatSubmitterSeqidQVal(TTech tech)

const string & m_Seqfeat_note

CFlatTrnaCodonsQVal(const CTrna_ext &trna, const string &comment)

CConstRef< CTrna_ext > m_Value

CFlatXrefQVal(const TXref &value, const TQuals *quals=0)

CQualContainer< EFeatureQualifier > TQuals

CConstRef< TQuals > m_Quals

void SetAddPeriod(bool add=true)

TFlags GetFlags(void) const

const string & GetSuffix(void) const

const string & GetName(void) const

TStyle GetStyle(void) const

const string & GetPrefix(void) const

ETrim GetTrim(void) const

const string & GetValue(void) const

bool GetAddPeriod(void) const

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

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

const_iterator begin(void) const

const_iterator Find(const Key &key) const

void RemoveQuals(const Key &key)

TQualMMap::iterator iterator

void AddQual(const Key &key, const IFlatQVal *value)

iterator Erase(iterator it)

iterator LowerBound(Key &key)

const_iterator end(void) const

const_iterator LowerBound(const Key &key) const

multimap< Key, CConstRef< IFlatQVal > > TQualMMap

iterator Find(const Key &key)

TQualMMap::size_type size_type

bool HasQual(const Key &key) const

TQualMMap::const_iterator const_iterator

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

static const string kSpace

static const string kSemicolonEOL

static const string kSemicolon

TFlatQual x_AddFQ(TFlatQuals &q, const CTempString &n, const CTempString &v, TStyle st=CFormatQual::eQuoted, CFormatQual::TFlags flags=0, ETrim trim=CFormatQual::eTrim_Normal) const

virtual void Format(TFlatQuals &quals, const CTempString &name, CBioseqContext &ctx, TFlags flags=0) const =0

CFormatQual::TStyle TStyle

IFlatQVal(const string *pfx=&kSpace, const string *sfx=&kEmptyStr)

static const string kComma

container_type::const_iterator const_iterator

container_type::size_type size_type

container_type::iterator iterator

container_type::value_type value_type

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)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string & ToLower(string &str)

Convert string to lower case – string& version.

#define NCBI_FORMAT_EXPORT

vector< CRef< CDbtag > > TDbxref

list< CRef< CCode_break > > TCode_break

EMol

molecule class in living organism

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

const GenericPointer< typename T::ValueType > T2 value

static bool Equals(const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)

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

vector< TFlatQual > TFlatQuals

CRef< CFormatQual > TFlatQual

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

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