ARB
Classes | Enumerations | Functions | Variables
iupac Namespace Reference

Classes

struct  Nuc_Group
 
class  Setup
 

Enumerations

enum  Amino_Group {
  AA_GROUP_NONE = 0, AA_GROUP_ALPHA, AA_GROUP_BETA, AA_GROUP_GAMMA,
  AA_GROUP_DELTA, AA_GROUP_EPSILON, AA_GROUP_ZETA, AA_GROUP_ILLEGAL,
  AA_GROUP_COUNT = AA_GROUP_ILLEGAL
}
 

Functions

Amino_Group get_amino_group_for (char aa)
 
char get_amino_consensus_char (Amino_Group ag)
 
int to_index (char c)
 
char combine (char c1, char c2, GB_alignment_type ali)
 
char encode (const char bases[], GB_alignment_type aliType)
 
const chardecode (char iupac, GB_alignment_type aliType, bool decode_amino_iupac_groups)
 

Variables

const Nuc_Group nuc_group [26][2]
 
static const charaminoGroupMembers [AA_GROUP_COUNT]
 
static Amino_Group amino_group [26]
 
static Setup perform
 

Enumeration Type Documentation

Enumerator
AA_GROUP_NONE 
AA_GROUP_ALPHA 
AA_GROUP_BETA 
AA_GROUP_GAMMA 
AA_GROUP_DELTA 
AA_GROUP_EPSILON 
AA_GROUP_ZETA 
AA_GROUP_ILLEGAL 
AA_GROUP_COUNT 

Definition at line 26 of file iupac.h.

Function Documentation

Amino_Group iupac::get_amino_group_for ( char  aa)
char iupac::get_amino_consensus_char ( Amino_Group  ag)

Definition at line 95 of file iupac.cxx.

References AA_GROUP_ILLEGAL, AA_GROUP_NONE, and aminoGroupMembers.

Referenced by BaseFrequencies::build_consensus_string_to().

int iupac::to_index ( char  c)
inline

Definition at line 53 of file iupac.h.

References arb_assert.

Referenced by resolve_IUPAC_target_string().

char iupac::combine ( char  c1,
char  c2,
GB_alignment_type  ali 
)

Definition at line 231 of file iupac.cxx.

References buffer, and encode().

Referenced by buildMixedCodon().

char iupac::encode ( const char  bases[],
GB_alignment_type  aliType 
)
const char * iupac::decode ( char  iupac,
GB_alignment_type  aliType,
bool  decode_amino_iupac_groups 
)

Variable Documentation

const Nuc_Group iupac::nuc_group
Initial value:
= {
{ { "A", 1 }, { "A", 1 } },
{ { "CGT", 3 }, { "CGU", 3 } },
{ { "C", 1 }, { "C", 1 } },
{ { "AGT", 3 }, { "AGU", 3 } },
{ { "G", 1 }, { "G", 1 } },
{ { "ACT", 3 }, { "ACU", 3 } },
{ { "GT", 2 }, { "GU", 2 } },
{ { "AC", 2 }, { "AC", 2 } },
{ { "ACGT", 1 }, { "ACGU", 1 } },
{ { "AG", 2 }, { "AG", 2 } },
{ { "CG", 2 }, { "CG", 2 } },
{ { "T", 1 }, { "U", 1 } },
{ { "T", 1 }, { "U", 1 } },
{ { "ACG", 3 }, { "ACG", 3 } },
{ { "AT", 2 }, { "AU", 2 } },
{ { "CT", 2 }, { "CU", 2 } },
}
#define _____________
Definition: iupac.cxx:22

Definition at line 24 of file iupac.cxx.

Referenced by decode(), initialize_IUPAC_add(), and resolve_IUPAC_target_string().

const char* iupac::aminoGroupMembers[AA_GROUP_COUNT]
static
Initial value:
= {
"XOU",
"AGPST",
"DBENQZ",
"HKR",
"IJLMV",
"FWY",
"C",
}

Definition at line 57 of file iupac.cxx.

Referenced by decode(), and get_amino_consensus_char().

Amino_Group iupac::amino_group[26]
static

Definition at line 68 of file iupac.cxx.

Referenced by get_amino_group_for().

Setup iupac::perform
static

Definition at line 85 of file iupac.cxx.

Referenced by SimpleTester::perform_all().