1 #ifndef OBJTOOLS_FORMAT_ITEMS___QUALIFIERS__HPP
2 #define OBJTOOLS_FORMAT_ITEMS___QUALIFIERS__HPP
81 fFlags_showEvenIfRedund = 1 << 0
100 TStyle style = eQuoted,
102 ETrim trim = eTrim_Normal );
105 TStyle style = eQuoted,
107 ETrim trim = eTrim_Normal );
109 const string&
GetName (
void)
const {
return m_Name; }
110 const string&
GetValue (
void)
const {
return m_Value; }
112 const string&
GetPrefix(
void)
const {
return m_Prefix; }
113 const string&
GetSuffix(
void)
const {
return m_Suffix; }
142 fPrependNewline = 0x8
160 : m_Prefix(pfx), m_Suffix(sfx)
179 template<
typename Key>
203 return Find(
key) != m_Quals.end();
207 return m_Quals.find(
key);
211 return m_Quals.find(
key);
215 if (
next != end() ) {
225 return m_Quals.find(
key);
228 return m_Quals.find(
key);
231 return m_Quals.size();
281 const string&
GetValue(
void)
const {
return m_Value; }
344 : m_Value(
value), m_Style(style) { }
346 const list<string>::const_iterator& end,
348 : m_Value(begin, end), m_Style(style) { }
367 m_Suffix = &kSemicolon;
400 CFlatCodonQVal(
unsigned int codon,
unsigned char aa,
bool is_ascii =
true);
415 const string& =
"" );
528 : m_Value(&
value), m_GiPrefix(add_gi_prefix) { }
569 const string& fwd_name,
570 const string& fwd_seq,
571 const string& rev_name,
572 const string& rev_seq ) :
574 m_fwd_name( fwd_name ),
575 m_fwd_seq( fwd_seq ),
576 m_rev_name( rev_name ),
600 : m_Value(
value), m_Quals(quals) { }
605 bool x_XrefInGeneXref(
const CDbtag& dbtag)
const;
633 const string & GetTextString(
void)
const;
634 int GetPubmedId(
void)
const;
645 m_Anticodon(&ac), m_Aa(aa){ }
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
@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)