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NCBI C++ ToolKit: include/objects/seqfeat/Genetic_code_table.hpp Source File

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37 #ifndef OBJECTS_SEQFEAT_GENETIC_CODE_TABLE_HPP 38 #define OBJECTS_SEQFEAT_GENETIC_CODE_TABLE_HPP 102  static int

SetCodonState (

unsigned char ch1

,

105  static int

NextCodonState (

int state

,

107  static int

RevCompState (

int state

);

110  char

GetCodonResidue (

int state

)

const

;

111  char

GetStartResidue (

int state

)

const

;

112  char

GetStopResidue (

int state

)

const

;

114  bool

IsOrfStart (

int state

)

const

;

115  bool

IsAmbigStart (

int state

)

const

;

116  bool

IsAnyStart (

int state

)

const

;

117  bool

IsOrfStop (

int state

)

const

;

118  bool

IsATGStart (

int state

)

const

;

119  bool

IsAltStart (

int state

)

const

;

123  static int

sm_NextState [4097];

124  static int

sm_RvCmpState [4097];

125  static int

sm_BaseToIdx [256];

128  static void

x_InitFsaTable (

void

);

131  mutable char

m_AminoAcid [4097];

132  mutable char

m_OrfStart [4097];

133  mutable char

m_OrfStop [4097];

136  void

x_InitFsaTransl (

const string

*ncbieaa,

137  const string

*sncbieaa)

const

;

157  static const string

& GetNcbieaa(

int id

);

161  static const string

& GetSncbieaa(

int id

);

162  static const string

& GetSncbieaa(

const CGenetic_code

& gc);

165  static string

IndexToCodon(

int

index);

168  static int

CodonToIndex(

char

base1,

char

base2,

char

base3);

169  static int

CodonToIndex(

const string

& codon);

182  static void

x_InitImplementation(

void

);

273  static const int

k_ATG_state = 389;

280  static const int

k_ATG_state = 389;

static AutoPtr< CGen_code_table_imp > sm_Implementation

static CGen_code_table_imp & x_GetImplementation(void)

static void x_InitImplementation(void)

CGenetic_code_table_Base Tparent

CGenetic_code_table(const CGenetic_code_table &value)

CGenetic_code_table(void)

CGenetic_code_table & operator=(const CGenetic_code_table &value)

bool IsAmbigStart(int state) const

static int RevCompState(int state)

char GetStartResidue(int state) const

bool IsATGStart(int state) const

char GetCodonResidue(int state) const

bool IsAltStart(int state) const

static int sm_NextState[4097]

bool IsOrfStart(int state) const

static int SetCodonState(unsigned char ch1, unsigned char ch2, unsigned char ch3)

bool IsAnyStart(int state) const

static int NextCodonState(int state, unsigned char ch)

static int sm_RvCmpState[4097]

static int sm_BaseToIdx[256]

bool IsOrfStop(int state) const

char GetStopResidue(int state) const

element_type * get(void) const

Get pointer.

ESerialDataFormat

Data file format.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_SEQFEAT_EXPORT

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

const GenericPointer< typename T::ValueType > T2 value

static const BitmapCharRec ch3

static const BitmapCharRec ch1

static const BitmapCharRec ch2

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