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

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1 #ifndef OBJTOOLS_FORMAT_ITEMS___FLAT_SEQLOC__HPP 2 #define OBJTOOLS_FORMAT_ITEMS___FLAT_SEQLOC__HPP 85  TType type

= eType_location,

bool

show_all_accns =

false

,

86  bool

add_join =

false

,

bool

suppress_accession =

false

);

88  const string

&

GetString

(

void

)

const

{

return

m_String; }

107  bool

x_Add(

const CSeq_loc

& loc, ostream& oss,

109  bool

show_all_accns =

false

,

bool

join_whole_loc =

false

,

110  bool

suppress_accession =

false

);

113  bool

show_all_accns =

false

,

bool

suppress_accession =

false

);

114  bool

x_Add(

const CSeq_point

& pnt, ostream& oss,

116  bool

show_all_accns =

false

,

bool

suppress_accession =

false

);

118

EHTML html, EForce force = eForce_None, ESource

source

= eSource_Other,

119  bool

show_all_accns =

false

,

bool

suppress_accession =

false

);

120  void

x_AddID(

const CSeq_id

&

id

, ostream& oss,

122  bool

show_all_accns =

false

,

bool

suppress_accession =

false

);

void SetLength(const TLength &value)

CFlatGapLoc(TLength value)

TLength GetLength(void) const

const CInt_fuzz * GetFuzz() const

void SetFuzz(const CInt_fuzz *fuzz)

CFastMutex m_MutexForTheMap

std::map< CSeq_id_Handle, CSeq_id_Handle > TToAccessionMap

static CGuardedToAccessionMap m_ToAccessionMap

const string & GetString(void) const

static const char si[8][64]

unsigned int TSeqPos

Type for sequence locations and lengths.

void SetNull(void)

Override all setters to incorporate cache invalidation.

#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.

#define NCBI_FORMAT_EXPORT

const TYPE & Get(const CNamedParameterList *param)

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

Multi-threading – mutexes; rw-locks; semaphore.

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

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