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#ifndef DYNAMITEgenewisemodelHEADERFILE
#define DYNAMITEgenewisemodelHEADERFILE
#ifdef _cplusplus
extern "C" {
#endif
#include "geneparser21.h"
#include "geneparameter.h"
#include "threestatemodel.h"
#include "codonmapper.h"
#include "cdparser.h"
#include "genefrequency.h"
#include "geneutil.h"
#define GeneWiseScoreLISTLENGTH 128
#define GeneWiseLISTLENGTH 128
#define MAX_PROTEIN_GENEWISE 4096
enum GeneWiseTransition {
GW_MATCH2MATCH,
GW_MATCH2INSERT,
GW_MATCH2DELETE,
GW_MATCH2END,
GW_INSERT2MATCH,
GW_INSERT2INSERT,
GW_INSERT2DELETE,
GW_INSERT2END,
GW_DELETE2MATCH,
GW_DELETE2INSERT,
GW_DELETE2DELETE,
GW_DELETE2END,
GW_START2MATCH,
GW_START2INSERT,
GW_START2DELETE,
GW_MATCH_BALANCE_5SS,
GW_INSERT_BALANCE_5SS,
GW_MATCH_BALANCE_3SS,
GW_INSERT_BALANCE_3SS,
GW_TRANSITION_LEN
};
#define GW_EMISSION_LEN 126
/* Object GeneWiseSegment
*
* Descrip: This is a particular HMM node, with
* match and insert emissions in the codon space
* and the transitions
*
* intron/frameshifting transitions are stored
* in a different datastructure, as they are
* not position dependent
*
*
*/
struct Wise2_GeneWiseSegment {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
Probability match[GW_EMISSION_LEN];
Probability insert[GW_EMISSION_LEN];
Probability transition[GW_TRANSITION_LEN];
} ;
/* GeneWiseSegment defined */
#ifndef DYNAMITE_DEFINED_GeneWiseSegment
typedef struct Wise2_GeneWiseSegment Wise2_GeneWiseSegment;
#define GeneWiseSegment Wise2_GeneWiseSegment
#define DYNAMITE_DEFINED_GeneWiseSegment
#endif
/* Object GeneWise
*
* Descrip: This is an expand HMM for codon
* matching, suitable for genewise and
* estwise type algorithms. It is simple
* a list of nodes
*
*
*/
struct Wise2_GeneWise {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
GeneWiseSegment ** seg;
int len;/* len for above seg */
int maxlen; /* maxlen for above seg */
char * name;
} ;
/* GeneWise defined */
#ifndef DYNAMITE_DEFINED_GeneWise
typedef struct Wise2_GeneWise Wise2_GeneWise;
#define GeneWise Wise2_GeneWise
#define DYNAMITE_DEFINED_GeneWise
#endif
/* Object GeneWiseScoreSegment
*
* Descrip: This is the log space equivalent
* of GeneWiseSegment
*
*
*/
struct Wise2_GeneWiseScoreSegment {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
Score match[GW_EMISSION_LEN];
Score insert[GW_EMISSION_LEN];
Score transition[GW_TRANSITION_LEN];
} ;
/* GeneWiseScoreSegment defined */
#ifndef DYNAMITE_DEFINED_GeneWiseScoreSegment
typedef struct Wise2_GeneWiseScoreSegment Wise2_GeneWiseScoreSegment;
#define GeneWiseScoreSegment Wise2_GeneWiseScoreSegment
#define DYNAMITE_DEFINED_GeneWiseScoreSegment
#endif
/* Object GeneWiseScore
*
* Descrip: This is the log space equivalent
* of the GeneWise
*
*
*/
struct Wise2_GeneWiseScore {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
GeneWiseScoreSegment ** seg;
int len;/* len for above seg */
int maxlen; /* maxlen for above seg */
char * name;
} ;
/* GeneWiseScore defined */
#ifndef DYNAMITE_DEFINED_GeneWiseScore
typedef struct Wise2_GeneWiseScore Wise2_GeneWiseScore;
#define GeneWiseScore Wise2_GeneWiseScore
#define DYNAMITE_DEFINED_GeneWiseScore
#endif
/* Object GeneWiseScoreFlat
*
* Descrip: This is a specialised datastructure
* which is equivalent to the GeneWiseScore
* object, but layed out more efficiently
* for memory lookup. The actual code is
* usually 10% faster. If you have a really
* large model however it might barf!
*
*
*/
struct Wise2_GeneWiseScoreFlat {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
GeneWiseScoreSegment * seg;
int len;
} ;
/* GeneWiseScoreFlat defined */
#ifndef DYNAMITE_DEFINED_GeneWiseScoreFlat
typedef struct Wise2_GeneWiseScoreFlat Wise2_GeneWiseScoreFlat;
#define GeneWiseScoreFlat Wise2_GeneWiseScoreFlat
#define DYNAMITE_DEFINED_GeneWiseScoreFlat
#endif
/***************************************************/
/* Callable functions */
/* These are the functions you are expected to use */
/***************************************************/
/* Function: pack_GeneWiseScore(gws)
*
* Descrip: Packing up the GeneWise model into a byte structure
*
*
* Arg: gws [UNKN ] Undocumented argument [GeneWiseScore *]
*
* Return [UNKN ] Undocumented return value [char *]
*
*/
char * Wise2_pack_GeneWiseScore(GeneWiseScore * gws);
#define pack_GeneWiseScore Wise2_pack_GeneWiseScore
/* Function: GeneWiseScoreFlat_from_GeneWiseScore(gws)
*
* Descrip: This produces a flattened GeneWiseSegment structure
* for use in quick implementations (memory lookup
* is much better due to everything being a single
* piece of memory).
*
*
* Arg: gws [UNKN ] Undocumented argument [GeneWiseScore *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScoreFlat *]
*
*/
GeneWiseScoreFlat * Wise2_GeneWiseScoreFlat_from_GeneWiseScore(GeneWiseScore * gws);
#define GeneWiseScoreFlat_from_GeneWiseScore Wise2_GeneWiseScoreFlat_from_GeneWiseScore
/* Function: free_GeneWiseScoreFlat(obj)
*
* Descrip: Frees the GeneWiseScoreFlat datastructure
*
* overrides the usual deconstructor
*
*
* Arg: obj [UNKN ] Undocumented argument [GeneWiseScoreFlat *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScoreFlat *]
*
*/
GeneWiseScoreFlat * Wise2_free_GeneWiseScoreFlat(GeneWiseScoreFlat * obj);
#define free_GeneWiseScoreFlat Wise2_free_GeneWiseScoreFlat
/* Function: map_phase0_codons_AlnBlock_GeneWise(alb,gws,cseq)
*
* Descrip: This function does something very
* sinister.
*
* It maps the phase 0 introns which
* have three base pairs added on the
* end.
*
* It actually changes the AlnBlock structure
*
*
* Arg: alb [UNKN ] Undocumented argument [AlnBlock *]
* Arg: gws [UNKN ] Undocumented argument [GeneWiseScore *]
* Arg: cseq [UNKN ] Undocumented argument [ComplexSequence *]
*
*/
void Wise2_map_phase0_codons_AlnBlock_GeneWise(AlnBlock * alb,GeneWiseScore * gws,ComplexSequence * cseq);
#define map_phase0_codons_AlnBlock_GeneWise Wise2_map_phase0_codons_AlnBlock_GeneWise
/* Function: flatten_balance_scores_GeneWise(gw)
*
* Descrip: This function is make all the balance scores 0 (hence prob-ratio to 1).
*
* Used when you are using naive models
*
*
* Arg: gw [UNKN ] genewise model to flatten [GeneWise *]
*
*/
void Wise2_flatten_balance_scores_GeneWise(GeneWise * gw);
#define flatten_balance_scores_GeneWise Wise2_flatten_balance_scores_GeneWise
/* Function: GeneWise_from_ThreeStateModel_cdna(tsm,cp,cm,allN)
*
* Descrip: This function makes a
* GeneWise model for the estwise
* type algorithms
*
*
* Arg: tsm [UNKN ] Undocumented argument [ThreeStateModel *]
* Arg: cp [UNKN ] Undocumented argument [cDNAParser *]
* Arg: cm [UNKN ] Undocumented argument [CodonMapper *]
* Arg: allN [UNKN ] Undocumented argument [Probability]
*
* Return [UNKN ] Undocumented return value [GeneWise *]
*
*/
GeneWise * Wise2_GeneWise_from_ThreeStateModel_cdna(ThreeStateModel * tsm,cDNAParser * cp,CodonMapper * cm,Probability allN);
#define GeneWise_from_ThreeStateModel_cdna Wise2_GeneWise_from_ThreeStateModel_cdna
/* Function: GeneWise_from_ThreeStateModel_setfactor(tsm,factor,cm,allN)
*
* Descrip: This function makes a
* GeneWise model for the estwise
* type algorithms
*
*
* Arg: tsm [UNKN ] Undocumented argument [ThreeStateModel *]
* Arg: factor [UNKN ] Undocumented argument [Probability]
* Arg: cm [UNKN ] Undocumented argument [CodonMapper *]
* Arg: allN [UNKN ] Undocumented argument [Probability]
*
* Return [UNKN ] Undocumented return value [GeneWise *]
*
*/
GeneWise * Wise2_GeneWise_from_ThreeStateModel_setfactor(ThreeStateModel * tsm,Probability factor,CodonMapper * cm,Probability allN);
#define GeneWise_from_ThreeStateModel_setfactor Wise2_GeneWise_from_ThreeStateModel_setfactor
/* Function: GeneWise_from_ThreeStateModel(tsm,gp,cm,allN,gwcm)
*
* Descrip: This makes a genewise model from a
* threestatemodel for the genewise type
* algorithms.
*
* Notice you have to provide the gene parameters
* being used
*
* Stop is now not used
*
*
* Arg: tsm [UNKN ] Undocumented argument [ThreeStateModel *]
* Arg: gp [UNKN ] Undocumented argument [GeneParser21 *]
* Arg: cm [UNKN ] Undocumented argument [CodonMapper *]
* Arg: allN [UNKN ] Undocumented argument [Probability]
* Arg: gwcm [UNKN ] Undocumented argument [GeneWiseCodonModel *]
*
* Return [UNKN ] Undocumented return value [GeneWise *]
*
*/
GeneWise * Wise2_GeneWise_from_ThreeStateModel(ThreeStateModel * tsm,GeneParser21 * gp,CodonMapper * cm,Probability allN,GeneWiseCodonModel * gwcm);
#define GeneWise_from_ThreeStateModel Wise2_GeneWise_from_ThreeStateModel
/* Function: GeneWise_fold_in_synchronised_RandomModel(gw,rm,cm,*ct,stop_codon_background)
*
* Descrip: This function places 'log-odd' scores of the
* genewise model assumming that the random model
* is a protein model with the codon mapper system
* added in, *and* that the path of the random model
* is synchronous with the query model.
*
* It fudges stop codons with the stop score given
* as a probability.
*
* In other words, this should give bits scores as
* if it was a protein, even though it is DNA
*
*
* Arg: gw [UNKN ] Undocumented argument [GeneWise *]
* Arg: rm [UNKN ] Undocumented argument [RandomModel *]
* Arg: cm [UNKN ] Undocumented argument [CodonMapper *]
* Arg: *ct [UNKN ] Undocumented argument [CodonTable]
* Arg: stop_codon_background [UNKN ] Undocumented argument [Probability]
*
*/
void Wise2_GeneWise_fold_in_synchronised_RandomModel(GeneWise * gw,RandomModel * rm,CodonMapper * cm,CodonTable *ct,Probability stop_codon_background);
#define GeneWise_fold_in_synchronised_RandomModel Wise2_GeneWise_fold_in_synchronised_RandomModel
/* Function: check_flat_insert(gw,should_force,should_warn,ct)
*
* Descrip: This function checks that the insert model is bang on
* zero, forcing it to zero
*
* Potentially it warns for non zeros as well
*
*
* Arg: gw [UNKN ] Undocumented argument [GeneWise *]
* Arg: should_force [UNKN ] Undocumented argument [boolean]
* Arg: should_warn [UNKN ] Undocumented argument [boolean]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_check_flat_insert(GeneWise * gw,boolean should_force,boolean should_warn,CodonTable * ct);
#define check_flat_insert Wise2_check_flat_insert
/* Function: GeneWise_fold_in_RandomModelDNA(gw,rmd)
*
* Descrip: This function folds in a simple random model
* (single base position) into a genewise model
*
*
* Arg: gw [UNKN ] Undocumented argument [GeneWise *]
* Arg: rmd [UNKN ] Undocumented argument [RandomModelDNA *]
*
*/
void Wise2_GeneWise_fold_in_RandomModelDNA(GeneWise * gw,RandomModelDNA * rmd);
#define GeneWise_fold_in_RandomModelDNA Wise2_GeneWise_fold_in_RandomModelDNA
/* Function: Protein_from_GeneWise_AlnColumn(dna,is_random_AlnColumn,col,position_in_aln,last_column,ct)
*
* Descrip: Produces a protein object from a genewise/estwise
* style label set, setting the last retrieved column
*
*
* Arg: dna [UNKN ] Undocumented argument [Sequence *]
* Arg: is_random_AlnColumn [UNKN ] Undocumented argument [NullString]
* Arg: col [UNKN ] Undocumented argument [AlnColumn *]
* Arg: position_in_aln [UNKN ] Undocumented argument [int]
* Arg: last_column [UNKN ] Undocumented argument [AlnColumn **]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
*
* Return [UNKN ] Undocumented return value [Protein *]
*
*/
Protein * Wise2_Protein_from_GeneWise_AlnColumn(Sequence * dna,AlnColumn * col,int position_in_aln,AlnColumn ** last_column,CodonTable * ct,boolean (*is_random_AlnColumn)(const AlnColumn *));
#define Protein_from_GeneWise_AlnColumn Wise2_Protein_from_GeneWise_AlnColumn
/* Function: GeneWiseScore_from_GeneWise(gw)
*
* Descrip: Makes a Score (log based) object from
* a probability based object
*
*
* Arg: gw [UNKN ] Undocumented argument [GeneWise *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScore *]
*
*/
GeneWiseScore * Wise2_GeneWiseScore_from_GeneWise(GeneWise * gw);
#define GeneWiseScore_from_GeneWise Wise2_GeneWiseScore_from_GeneWise
/* Function: hard_link_GeneWiseSegment(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 [GeneWiseSegment *]
*
* Return [UNKN ] Undocumented return value [GeneWiseSegment *]
*
*/
GeneWiseSegment * Wise2_hard_link_GeneWiseSegment(GeneWiseSegment * obj);
#define hard_link_GeneWiseSegment Wise2_hard_link_GeneWiseSegment
/* Function: GeneWiseSegment_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [GeneWiseSegment *]
*
*/
GeneWiseSegment * Wise2_GeneWiseSegment_alloc(void);
#define GeneWiseSegment_alloc Wise2_GeneWiseSegment_alloc
/* Function: free_GeneWiseSegment(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 [GeneWiseSegment *]
*
* Return [UNKN ] Undocumented return value [GeneWiseSegment *]
*
*/
GeneWiseSegment * Wise2_free_GeneWiseSegment(GeneWiseSegment * obj);
#define free_GeneWiseSegment Wise2_free_GeneWiseSegment
/* Function: add_GeneWise(obj,add)
*
* Descrip: Adds another object to the list. It will expand the list if necessary
*
*
* Arg: obj [UNKN ] Object which contains the list [GeneWise *]
* Arg: add [OWNER] Object to add to the list [GeneWiseSegment *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_add_GeneWise(GeneWise * obj,GeneWiseSegment * add);
#define add_GeneWise Wise2_add_GeneWise
/* Function: flush_GeneWise(obj)
*
* Descrip: Frees the list elements, sets length to 0
* If you want to save some elements, use hard_link_xxx
* to protect them from being actually destroyed in the free
*
*
* Arg: obj [UNKN ] Object which contains the list [GeneWise *]
*
* Return [UNKN ] Undocumented return value [int]
*
*/
int Wise2_flush_GeneWise(GeneWise * obj);
#define flush_GeneWise Wise2_flush_GeneWise
/* Function: GeneWise_alloc_std(void)
*
* Descrip: Equivalent to GeneWise_alloc_len(GeneWiseLISTLENGTH)
*
*
*
* Return [UNKN ] Undocumented return value [GeneWise *]
*
*/
GeneWise * Wise2_GeneWise_alloc_std(void);
#define GeneWise_alloc_std Wise2_GeneWise_alloc_std
/* Function: GeneWise_alloc_len(len)
*
* Descrip: Allocates len length to all lists
*
*
* Arg: len [UNKN ] Length of lists to allocate [int]
*
* Return [UNKN ] Undocumented return value [GeneWise *]
*
*/
GeneWise * Wise2_GeneWise_alloc_len(int len);
#define GeneWise_alloc_len Wise2_GeneWise_alloc_len
/* Function: hard_link_GeneWise(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 [GeneWise *]
*
* Return [UNKN ] Undocumented return value [GeneWise *]
*
*/
GeneWise * Wise2_hard_link_GeneWise(GeneWise * obj);
#define hard_link_GeneWise Wise2_hard_link_GeneWise
/* Function: GeneWise_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [GeneWise *]
*
*/
GeneWise * Wise2_GeneWise_alloc(void);
#define GeneWise_alloc Wise2_GeneWise_alloc
/* Function: free_GeneWise(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 [GeneWise *]
*
* Return [UNKN ] Undocumented return value [GeneWise *]
*
*/
GeneWise * Wise2_free_GeneWise(GeneWise * obj);
#define free_GeneWise Wise2_free_GeneWise
/* Function: hard_link_GeneWiseScoreSegment(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 [GeneWiseScoreSegment *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScoreSegment *]
*
*/
GeneWiseScoreSegment * Wise2_hard_link_GeneWiseScoreSegment(GeneWiseScoreSegment * obj);
#define hard_link_GeneWiseScoreSegment Wise2_hard_link_GeneWiseScoreSegment
/* Function: GeneWiseScoreSegment_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [GeneWiseScoreSegment *]
*
*/
GeneWiseScoreSegment * Wise2_GeneWiseScoreSegment_alloc(void);
#define GeneWiseScoreSegment_alloc Wise2_GeneWiseScoreSegment_alloc
/* Function: free_GeneWiseScoreSegment(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 [GeneWiseScoreSegment *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScoreSegment *]
*
*/
GeneWiseScoreSegment * Wise2_free_GeneWiseScoreSegment(GeneWiseScoreSegment * obj);
#define free_GeneWiseScoreSegment Wise2_free_GeneWiseScoreSegment
/* Function: add_GeneWiseScore(obj,add)
*
* Descrip: Adds another object to the list. It will expand the list if necessary
*
*
* Arg: obj [UNKN ] Object which contains the list [GeneWiseScore *]
* Arg: add [OWNER] Object to add to the list [GeneWiseScoreSegment *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_add_GeneWiseScore(GeneWiseScore * obj,GeneWiseScoreSegment * add);
#define add_GeneWiseScore Wise2_add_GeneWiseScore
/* Function: flush_GeneWiseScore(obj)
*
* Descrip: Frees the list elements, sets length to 0
* If you want to save some elements, use hard_link_xxx
* to protect them from being actually destroyed in the free
*
*
* Arg: obj [UNKN ] Object which contains the list [GeneWiseScore *]
*
* Return [UNKN ] Undocumented return value [int]
*
*/
int Wise2_flush_GeneWiseScore(GeneWiseScore * obj);
#define flush_GeneWiseScore Wise2_flush_GeneWiseScore
/* Function: GeneWiseScore_alloc_std(void)
*
* Descrip: Equivalent to GeneWiseScore_alloc_len(GeneWiseScoreLISTLENGTH)
*
*
*
* Return [UNKN ] Undocumented return value [GeneWiseScore *]
*
*/
GeneWiseScore * Wise2_GeneWiseScore_alloc_std(void);
#define GeneWiseScore_alloc_std Wise2_GeneWiseScore_alloc_std
/* Function: GeneWiseScore_alloc_len(len)
*
* Descrip: Allocates len length to all lists
*
*
* Arg: len [UNKN ] Length of lists to allocate [int]
*
* Return [UNKN ] Undocumented return value [GeneWiseScore *]
*
*/
GeneWiseScore * Wise2_GeneWiseScore_alloc_len(int len);
#define GeneWiseScore_alloc_len Wise2_GeneWiseScore_alloc_len
/* Function: hard_link_GeneWiseScore(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 [GeneWiseScore *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScore *]
*
*/
GeneWiseScore * Wise2_hard_link_GeneWiseScore(GeneWiseScore * obj);
#define hard_link_GeneWiseScore Wise2_hard_link_GeneWiseScore
/* Function: GeneWiseScore_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [GeneWiseScore *]
*
*/
GeneWiseScore * Wise2_GeneWiseScore_alloc(void);
#define GeneWiseScore_alloc Wise2_GeneWiseScore_alloc
/* Function: free_GeneWiseScore(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 [GeneWiseScore *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScore *]
*
*/
GeneWiseScore * Wise2_free_GeneWiseScore(GeneWiseScore * obj);
#define free_GeneWiseScore Wise2_free_GeneWiseScore
/* Function: hard_link_GeneWiseScoreFlat(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 [GeneWiseScoreFlat *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScoreFlat *]
*
*/
GeneWiseScoreFlat * Wise2_hard_link_GeneWiseScoreFlat(GeneWiseScoreFlat * obj);
#define hard_link_GeneWiseScoreFlat Wise2_hard_link_GeneWiseScoreFlat
/* Function: GeneWiseScoreFlat_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [GeneWiseScoreFlat *]
*
*/
GeneWiseScoreFlat * Wise2_GeneWiseScoreFlat_alloc(void);
#define GeneWiseScoreFlat_alloc Wise2_GeneWiseScoreFlat_alloc
/* Unplaced functions */
/* There has been no indication of the use of these functions */
/***************************************************/
/* Internal functions */
/* you are not expected to have to call these */
/***************************************************/
Probability Wise2_probability_of_this_codon(int codon,RandomModelDNA * rmd);
#define probability_of_this_codon Wise2_probability_of_this_codon
void Wise2_show_GeneWise(GeneWise * gw,FILE * ofp);
#define show_GeneWise Wise2_show_GeneWise
void Wise2_show_GeneWiseSegment(GeneWiseSegment * seg,FILE * ofp);
#define show_GeneWiseSegment Wise2_show_GeneWiseSegment
GeneWiseSegment * Wise2_GeneWiseSegment_from_ThreeStateUnit(ThreeStateUnit * tsu,Probability factor,CodonMapper * cm,GeneWiseCodonModel * gwcm,Probability allN);
#define GeneWiseSegment_from_ThreeStateUnit Wise2_GeneWiseSegment_from_ThreeStateUnit
Probability Wise2_Probability_of_codon(int codon,CodonTable * ct,Probability * aminoacid_26_array,Probability stop);
#define Probability_of_codon Wise2_Probability_of_codon
GeneWiseScoreSegment * Wise2_GeneWiseScoreSegment_from_GeneWiseSegment(GeneWiseSegment * prev,GeneWiseSegment * seg);
#define GeneWiseScoreSegment_from_GeneWiseSegment Wise2_GeneWiseScoreSegment_from_GeneWiseSegment
void Wise2_swap_GeneWise(GeneWiseSegment ** list,int i,int j) ;
#define swap_GeneWise Wise2_swap_GeneWise
void Wise2_qsort_GeneWise(GeneWiseSegment ** list,int left,int right,int (*comp)(GeneWiseSegment * ,GeneWiseSegment * ));
#define qsort_GeneWise Wise2_qsort_GeneWise
void Wise2_sort_GeneWise(GeneWise * obj,int (*comp)(GeneWiseSegment *, GeneWiseSegment *));
#define sort_GeneWise Wise2_sort_GeneWise
boolean Wise2_expand_GeneWise(GeneWise * obj,int len);
#define expand_GeneWise Wise2_expand_GeneWise
void Wise2_swap_GeneWiseScore(GeneWiseScoreSegment ** list,int i,int j) ;
#define swap_GeneWiseScore Wise2_swap_GeneWiseScore
void Wise2_qsort_GeneWiseScore(GeneWiseScoreSegment ** list,int left,int right,int (*comp)(GeneWiseScoreSegment * ,GeneWiseScoreSegment * ));
#define qsort_GeneWiseScore Wise2_qsort_GeneWiseScore
void Wise2_sort_GeneWiseScore(GeneWiseScore * obj,int (*comp)(GeneWiseScoreSegment *, GeneWiseScoreSegment *));
#define sort_GeneWiseScore Wise2_sort_GeneWiseScore
boolean Wise2_expand_GeneWiseScore(GeneWiseScore * obj,int len);
#define expand_GeneWiseScore Wise2_expand_GeneWiseScore
#ifdef _cplusplus
}
#endif
#endif
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