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 char *	decode (char iupac, GB_alignment_type aliType, bool decode_amino_iupac_groups)

Variables
const Nuc_Group	nuc_group [26][2]
static const char *	aminoGroupMembers [AA_GROUP_COUNT]
static Amino_Group	amino_group [26]
static Setup	perform

Enumeration Type Documentation

enum iupac::Amino_Group

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

)

Definition at line 89 of file iupac.cxx.

References AA_GROUP_ILLEGAL, and amino_group.

Referenced by BaseFrequencies::build_consensus_string_to(), decode(), and getAAgroupDefinition().

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
	)

Definition at line 192 of file iupac.cxx.

References GB_AT_AA, GB_AT_RNA, ILL_CODE, and initialize_IUPAC_add().

Referenced by BaseFrequencies::build_consensus_string_to(), ClustalV_align(), combine(), and ED4_set_iupac().

const char * iupac::decode	(	char	iupac,
		GB_alignment_type	aliType,
		bool	decode_amino_iupac_groups
	)

Definition at line 239 of file iupac.cxx.

References AA_GROUP_COUNT, AA_GROUP_NONE, aminoGroupMembers, awt_assert, GB_AT_AA, GB_AT_RNA, get_amino_group_for(), group, IUPAC_EMPTY, iupac::Nuc_Group::members, and nuc_group.

Referenced by AWT_is_codon(), and BaseFrequencies::setup().

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 } }, 
        { _____________, _____________ }, 

        
    }

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().