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#ifndef DYNAMITEpairbaseHEADERFILE
#define DYNAMITEpairbaseHEADERFILE
#ifdef _cplusplus
extern "C" {
#endif
#include "codon.h"
#include "probability.h"
#include "codonmatrix.h"
#include <stdio.h>
typedef char pairbase_type;
typedef int pairbase_codon_type;
#define BASE_GAP 5
#define BASE_OPEN 6
#define IS_NOT_BASE(a) (a == BASE_GAP ? 1 : a == BASE_OPEN ? 1 : 0)
#define MAKE_PAIRBASE(anchor,informant) (anchor*7+informant)
#define PAIRBASE_LENGTH (7*7)
#define PAIRBASE_CODON_LENGTH (PAIRBASE_LENGTH*PAIRBASE_LENGTH*PAIRBASE_LENGTH)
struct Wise2_PairBaseModel {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
Probability base[PAIRBASE_LENGTH];
} ;
/* PairBaseModel defined */
#ifndef DYNAMITE_DEFINED_PairBaseModel
typedef struct Wise2_PairBaseModel Wise2_PairBaseModel;
#define PairBaseModel Wise2_PairBaseModel
#define DYNAMITE_DEFINED_PairBaseModel
#endif
struct Wise2_PairBaseCodonModel {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
Probability codon[PAIRBASE_CODON_LENGTH];
} ;
/* PairBaseCodonModel defined */
#ifndef DYNAMITE_DEFINED_PairBaseCodonModel
typedef struct Wise2_PairBaseCodonModel Wise2_PairBaseCodonModel;
#define PairBaseCodonModel Wise2_PairBaseCodonModel
#define DYNAMITE_DEFINED_PairBaseCodonModel
#endif
struct Wise2_PairBaseModelScore {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
Score base[PAIRBASE_LENGTH];
} ;
/* PairBaseModelScore defined */
#ifndef DYNAMITE_DEFINED_PairBaseModelScore
typedef struct Wise2_PairBaseModelScore Wise2_PairBaseModelScore;
#define PairBaseModelScore Wise2_PairBaseModelScore
#define DYNAMITE_DEFINED_PairBaseModelScore
#endif
struct Wise2_PairBaseCodonModelScore {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
Score codon[PAIRBASE_CODON_LENGTH];
} ;
/* PairBaseCodonModelScore defined */
#ifndef DYNAMITE_DEFINED_PairBaseCodonModelScore
typedef struct Wise2_PairBaseCodonModelScore Wise2_PairBaseCodonModelScore;
#define PairBaseCodonModelScore Wise2_PairBaseCodonModelScore
#define DYNAMITE_DEFINED_PairBaseCodonModelScore
#endif
/***************************************************/
/* Callable functions */
/* These are the functions you are expected to use */
/***************************************************/
/* Function: diagonal_tweak_PairBaseCodonModel(m,ratio_on,ratio_off_positive,ratio_off_negative)
*
* Descrip: Tweaks a PairBaseCodonModel with on and off diagonal ratios
*
*
* Arg: m [UNKN ] Undocumented argument [PairBaseCodonModel *]
* Arg: ratio_on [UNKN ] Undocumented argument [double]
* Arg: ratio_off_positive [UNKN ] Undocumented argument [double]
* Arg: ratio_off_negative [UNKN ] Undocumented argument [double]
*
*/
void Wise2_diagonal_tweak_PairBaseCodonModel(PairBaseCodonModel * m,double ratio_on,double ratio_off_positive,double ratio_off_negative);
#define diagonal_tweak_PairBaseCodonModel Wise2_diagonal_tweak_PairBaseCodonModel
/* Function: flatten_diagonal_PairBaseCodonModel(m,ct)
*
* Descrip: flattens out the diagonal signal
*
*
* Arg: m [UNKN ] Undocumented argument [PairBaseCodonModel *]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
*/
void Wise2_flatten_diagonal_PairBaseCodonModel(PairBaseCodonModel * m,CodonTable * ct);
#define flatten_diagonal_PairBaseCodonModel Wise2_flatten_diagonal_PairBaseCodonModel
/* Function: flatten_diagonal_PairBaseCodonModelScore(m,ct)
*
* Descrip: flattens out the diagonal signal - for scores!
*
*
* Arg: m [UNKN ] Undocumented argument [PairBaseCodonModelScore *]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
*/
void Wise2_flatten_diagonal_PairBaseCodonModelScore(PairBaseCodonModelScore * m,CodonTable * ct);
#define flatten_diagonal_PairBaseCodonModelScore Wise2_flatten_diagonal_PairBaseCodonModelScore
/* Function: zero_PairBaseModelScore(void)
*
* Descrip: a 0 pairbasemodel score
*
*
*
* Return [UNKN ] Undocumented return value [PairBaseModelScore *]
*
*/
PairBaseModelScore * Wise2_zero_PairBaseModelScore(void);
#define zero_PairBaseModelScore Wise2_zero_PairBaseModelScore
/* Function: very_simple_PairBaseCodonModel(id,rnd,nonm,gap,ct)
*
* Descrip: Makes a PairBaseCodonModel from just a one parameter! Wow!
*
*
* Arg: id [UNKN ] Undocumented argument [Probability]
* Arg: rnd [UNKN ] Undocumented argument [Probability]
* Arg: nonm [UNKN ] Undocumented argument [Probability]
* Arg: gap [UNKN ] Undocumented argument [Probability]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModel *]
*
*/
PairBaseCodonModel * Wise2_very_simple_PairBaseCodonModel(Probability id,Probability rnd,Probability nonm,Probability gap,CodonTable * ct);
#define very_simple_PairBaseCodonModel Wise2_very_simple_PairBaseCodonModel
/* Function: make_flat_PairBaseCodonModel(cp,nonm,gap,ct)
*
* Descrip: Makes a PairBaseCodonModel from a protein matrix - assumming a flat
* mapping to CodonMatrix
*
*
* Arg: cp [UNKN ] Undocumented argument [CompProb *]
* Arg: nonm [UNKN ] Undocumented argument [Probability]
* Arg: gap [UNKN ] Undocumented argument [Probability]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModel *]
*
*/
PairBaseCodonModel * Wise2_make_flat_PairBaseCodonModel(CompProb * cp,Probability nonm,Probability gap,CodonTable * ct);
#define make_flat_PairBaseCodonModel Wise2_make_flat_PairBaseCodonModel
/* Function: make_start_PairBaseCodonModelScore(ct)
*
* Descrip: Makes a PairBaseCodonModel score for start codon
*
*
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModelScore *]
*
*/
PairBaseCodonModelScore * Wise2_make_start_PairBaseCodonModelScore(CodonTable * ct);
#define make_start_PairBaseCodonModelScore Wise2_make_start_PairBaseCodonModelScore
/* Function: make_stop_PairBaseCodonModelScore(ct)
*
* Descrip: Makes a PairBaseCodonModel score for start codon
*
*
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModelScore *]
*
*/
PairBaseCodonModelScore * Wise2_make_stop_PairBaseCodonModelScore(CodonTable * ct);
#define make_stop_PairBaseCodonModelScore Wise2_make_stop_PairBaseCodonModelScore
/* Function: make_conserved_PairBaseCodonModel(cons,non_cons,aa_var,ct)
*
* Descrip: Makes a PairBaseCodonModel for a particular character in the CodonTable
*
*
* Arg: cons [UNKN ] Undocumented argument [Probability]
* Arg: non_cons [UNKN ] Undocumented argument [Probability]
* Arg: aa_var [UNKN ] Undocumented argument [char]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModel *]
*
*/
PairBaseCodonModel * Wise2_make_conserved_PairBaseCodonModel(Probability cons,Probability non_cons,char aa_var,CodonTable * ct);
#define make_conserved_PairBaseCodonModel Wise2_make_conserved_PairBaseCodonModel
/* Function: make_PairBaseCodonModel(codon_matrix,nonm,gap,ct)
*
* Descrip: Makes a PairBaseCodonModel from a CodonMatrix and parameters
*
*
* Arg: codon_matrix [UNKN ] Undocumented argument [CodonMatrix *]
* Arg: nonm [UNKN ] Undocumented argument [Probability]
* Arg: gap [UNKN ] Undocumented argument [Probability]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModel *]
*
*/
PairBaseCodonModel * Wise2_make_PairBaseCodonModel(CodonMatrix * codon_matrix,Probability nonm,Probability gap,CodonTable * ct);
#define make_PairBaseCodonModel Wise2_make_PairBaseCodonModel
/* Function: simple_PairBaseModel(iden,other,gap)
*
* Descrip: Makes a pair base model from simple leading diagonal
*
*
* Arg: iden [UNKN ] Undocumented argument [Probability]
* Arg: other [UNKN ] Undocumented argument [Probability]
* Arg: gap [UNKN ] Undocumented argument [Probability]
*
* Return [UNKN ] Undocumented return value [PairBaseModel *]
*
*/
PairBaseModel * Wise2_simple_PairBaseModel(Probability iden,Probability other,Probability gap);
#define simple_PairBaseModel Wise2_simple_PairBaseModel
/* Function: new_PairBaseCodonModelScore(pbcm)
*
* Descrip: Makes a codon score from a codon model
*
*
* Arg: pbcm [UNKN ] Undocumented argument [PairBaseCodonModel *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModelScore *]
*
*/
PairBaseCodonModelScore * Wise2_new_PairBaseCodonModelScore(PairBaseCodonModel * pbcm);
#define new_PairBaseCodonModelScore Wise2_new_PairBaseCodonModelScore
/* Function: new_PairBaseModelScore(pbm)
*
* Descrip: Makes a base score from a base model
*
*
* Arg: pbm [UNKN ] Undocumented argument [PairBaseModel *]
*
* Return [UNKN ] Undocumented return value [PairBaseModelScore *]
*
*/
PairBaseModelScore * Wise2_new_PairBaseModelScore(PairBaseModel * pbm);
#define new_PairBaseModelScore Wise2_new_PairBaseModelScore
/* Function: show_PairBaseModelScore(sc,ofp)
*
* Descrip: Debugging
*
*
* Arg: sc [UNKN ] Undocumented argument [PairBaseModelScore *]
* Arg: ofp [UNKN ] Undocumented argument [FILE *]
*
*/
void Wise2_show_PairBaseModelScore(PairBaseModelScore * sc,FILE * ofp);
#define show_PairBaseModelScore Wise2_show_PairBaseModelScore
/* Function: show_PairBaseCodonModelScore(sc,ct,ofp)
*
* Descrip: Debugging
*
*
* Arg: sc [UNKN ] Undocumented argument [PairBaseCodonModelScore *]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
* Arg: ofp [UNKN ] Undocumented argument [FILE *]
*
*/
void Wise2_show_PairBaseCodonModelScore(PairBaseCodonModelScore * sc,CodonTable * ct,FILE * ofp);
#define show_PairBaseCodonModelScore Wise2_show_PairBaseCodonModelScore
/* Function: reverse_pairbase_codon(codon)
*
* Descrip: Inverts pairbase codon
*
*
* Arg: codon [UNKN ] Undocumented argument [pairbase_codon_type]
*
* Return [UNKN ] Undocumented return value [pairbase_codon_type]
*
*/
pairbase_codon_type Wise2_reverse_pairbase_codon(pairbase_codon_type codon);
#define reverse_pairbase_codon Wise2_reverse_pairbase_codon
/* Function: complement_pairbase(b)
*
* Descrip: complements a pairbase
*
*
* Arg: b [UNKN ] Undocumented argument [pairbase_type]
*
* Return [UNKN ] Undocumented return value [pairbase_type]
*
*/
pairbase_type Wise2_complement_pairbase(pairbase_type b);
#define complement_pairbase Wise2_complement_pairbase
/* Function: pairbase_codon_from_seq(seq)
*
* Descrip: Makes a pairbase_codon from a pairbase_sequence
*
*
* Arg: seq [UNKN ] Undocumented argument [pairbase_type *]
*
* Return [UNKN ] Undocumented return value [pairbase_codon_type]
*
*/
pairbase_codon_type Wise2_pairbase_codon_from_seq(pairbase_type * seq);
#define pairbase_codon_from_seq Wise2_pairbase_codon_from_seq
/* Function: decompose_pairbase_codon(t,a,b,c)
*
* Descrip: Decomposes a pairbase codon
*
*
* Arg: t [UNKN ] Undocumented argument [pairbase_codon_type]
* Arg: a [UNKN ] Undocumented argument [pairbase_type *]
* Arg: b [UNKN ] Undocumented argument [pairbase_type *]
* Arg: c [UNKN ] Undocumented argument [pairbase_type *]
*
*/
void Wise2_decompose_pairbase_codon(pairbase_codon_type t,pairbase_type * a,pairbase_type * b,pairbase_type * c);
#define decompose_pairbase_codon Wise2_decompose_pairbase_codon
/* Function: anchor_base_from_pairbase(pairbase)
*
* Descrip: Finds the anchor base from a pair base
*
*
* Arg: pairbase [UNKN ] Undocumented argument [pairbase_type]
*
* Return [UNKN ] Undocumented return value [base]
*
*/
base Wise2_anchor_base_from_pairbase(pairbase_type pairbase);
#define anchor_base_from_pairbase Wise2_anchor_base_from_pairbase
/* Function: informant_base_from_pairbase(pairbase)
*
* Descrip: Finds the informant base from a pair base
*
*
* Arg: pairbase [UNKN ] Undocumented argument [pairbase_type]
*
* Return [UNKN ] Undocumented return value [base]
*
*/
base Wise2_informant_base_from_pairbase(pairbase_type pairbase);
#define informant_base_from_pairbase Wise2_informant_base_from_pairbase
/* Function: char_for_base(base)
*
* Descrip: gives back the character for the base
*
*
* Arg: base [UNKN ] Undocumented argument [int]
*
* Return [UNKN ] Undocumented return value [char]
*
*/
char Wise2_char_for_base(int base);
#define char_for_base Wise2_char_for_base
/* Function: hard_link_PairBaseModel(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj [UNKN ] Object to be hard linked [PairBaseModel *]
*
* Return [UNKN ] Undocumented return value [PairBaseModel *]
*
*/
PairBaseModel * Wise2_hard_link_PairBaseModel(PairBaseModel * obj);
#define hard_link_PairBaseModel Wise2_hard_link_PairBaseModel
/* Function: PairBaseModel_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [PairBaseModel *]
*
*/
PairBaseModel * Wise2_PairBaseModel_alloc(void);
#define PairBaseModel_alloc Wise2_PairBaseModel_alloc
/* Function: free_PairBaseModel(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [PairBaseModel *]
*
* Return [UNKN ] Undocumented return value [PairBaseModel *]
*
*/
PairBaseModel * Wise2_free_PairBaseModel(PairBaseModel * obj);
#define free_PairBaseModel Wise2_free_PairBaseModel
/* Function: hard_link_PairBaseCodonModel(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj [UNKN ] Object to be hard linked [PairBaseCodonModel *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModel *]
*
*/
PairBaseCodonModel * Wise2_hard_link_PairBaseCodonModel(PairBaseCodonModel * obj);
#define hard_link_PairBaseCodonModel Wise2_hard_link_PairBaseCodonModel
/* Function: PairBaseCodonModel_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModel *]
*
*/
PairBaseCodonModel * Wise2_PairBaseCodonModel_alloc(void);
#define PairBaseCodonModel_alloc Wise2_PairBaseCodonModel_alloc
/* Function: free_PairBaseCodonModel(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [PairBaseCodonModel *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModel *]
*
*/
PairBaseCodonModel * Wise2_free_PairBaseCodonModel(PairBaseCodonModel * obj);
#define free_PairBaseCodonModel Wise2_free_PairBaseCodonModel
/* Function: hard_link_PairBaseModelScore(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj [UNKN ] Object to be hard linked [PairBaseModelScore *]
*
* Return [UNKN ] Undocumented return value [PairBaseModelScore *]
*
*/
PairBaseModelScore * Wise2_hard_link_PairBaseModelScore(PairBaseModelScore * obj);
#define hard_link_PairBaseModelScore Wise2_hard_link_PairBaseModelScore
/* Function: PairBaseModelScore_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [PairBaseModelScore *]
*
*/
PairBaseModelScore * Wise2_PairBaseModelScore_alloc(void);
#define PairBaseModelScore_alloc Wise2_PairBaseModelScore_alloc
/* Function: free_PairBaseModelScore(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [PairBaseModelScore *]
*
* Return [UNKN ] Undocumented return value [PairBaseModelScore *]
*
*/
PairBaseModelScore * Wise2_free_PairBaseModelScore(PairBaseModelScore * obj);
#define free_PairBaseModelScore Wise2_free_PairBaseModelScore
/* Function: hard_link_PairBaseCodonModelScore(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj [UNKN ] Object to be hard linked [PairBaseCodonModelScore *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModelScore *]
*
*/
PairBaseCodonModelScore * Wise2_hard_link_PairBaseCodonModelScore(PairBaseCodonModelScore * obj);
#define hard_link_PairBaseCodonModelScore Wise2_hard_link_PairBaseCodonModelScore
/* Function: PairBaseCodonModelScore_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModelScore *]
*
*/
PairBaseCodonModelScore * Wise2_PairBaseCodonModelScore_alloc(void);
#define PairBaseCodonModelScore_alloc Wise2_PairBaseCodonModelScore_alloc
/* Function: free_PairBaseCodonModelScore(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [PairBaseCodonModelScore *]
*
* Return [UNKN ] Undocumented return value [PairBaseCodonModelScore *]
*
*/
PairBaseCodonModelScore * Wise2_free_PairBaseCodonModelScore(PairBaseCodonModelScore * obj);
#define free_PairBaseCodonModelScore Wise2_free_PairBaseCodonModelScore
/* Unplaced functions */
/* There has been no indication of the use of these functions */
/***************************************************/
/* Internal functions */
/* you are not expected to have to call these */
/***************************************************/
#ifdef _cplusplus
}
#endif
#endif
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