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#ifndef DYNAMITEestwrapHEADERFILE
#define DYNAMITEestwrapHEADERFILE
#ifdef _cplusplus
extern "C" {
#endif
#include "estwise3.h"
#include "estloop3.h"
#include "estfrag3.h"
#include "estslim3.h"
#include "estquick3.h"
#include "estslimloop.h"
typedef enum est_alg_type {
ESTWISE_3,
ESTLOOP_3,
ESTSLIM_3,
ESTQUICK_3,
ESTFRAG_3,
ESTSLIM_L
} est_alg_type;
/***************************************************/
/* Callable functions */
/* These are the functions you are expected to use */
/***************************************************/
/* Function: string_from_alg_estwrap(alg_type)
*
* Descrip: Returns the string form of the algorithm
*
*
* Arg: alg_type [UNKN ] Undocumented argument [int]
*
* Return [UNKN ] Undocumented return value [char *]
*
*/
char * Wise2_string_from_alg_estwrap(int alg_type);
#define string_from_alg_estwrap Wise2_string_from_alg_estwrap
/* Function: alg_estwrap_from_string(str)
*
* Descrip: This function returns the algorithm type
* for an est search from the string
*
*
* Arg: str [UNKN ] Undocumented argument [char *]
*
* Return [UNKN ] Undocumented return value [int]
*
*/
int Wise2_alg_estwrap_from_string(char * str);
#define alg_estwrap_from_string Wise2_alg_estwrap_from_string
/* Function: AlnBlock_from_Protein_estwise_wrap(pro,cdna,cp,cm,ct,comp,gap,ext,is_global,rmd,alg,rm,use_syn,allN,dpri,palpoi)
*
* Descrip: This function is the guts for the est single alignment
* mode.
*
* It uses /AlnBlock_from_TSM_estwise_wrap for the
* heavy part of the call
*
*
* Arg: pro [READ ] protein to be used in the comparison [Protein *]
* Arg: cdna [READ ] cdna to be compared to [cDNA *]
* Arg: cp [READ ] cdna parser indicating insertion deletion probabilities [cDNAParser *]
* Arg: cm [READ ] codon mapper indicating substitution errors etc [CodonMapper *]
* Arg: ct [READ ] codon table for the codon->amino acid mappings [CodonTable *]
* Arg: comp [READ ] comparison matrix to use [CompMat *]
* Arg: gap [UNKN ] gap penalty [int]
* Arg: ext [UNKN ] extension penalty [int]
* Arg: is_global [UNKN ] if true, global start-end in protein is used [boolean]
* Arg: rmd [UNKN ] random model of dna to use [RandomModelDNA *]
* Arg: alg [UNKN ] est algorithm type to use [int]
* Arg: rm [UNKN ] random protein model for use with compmat [RandomModel *]
* Arg: use_syn [UNKN ] if true, uses a synchronous coding model [boolean]
* Arg: allN [UNKN ] Undocumented argument [Probability]
* Arg: dpri [UNKN ] Undocumented argument [DPRunImpl *]
* Arg: palpoi [WRITE] the raw packed alignment output if wanted [PackAln **]
*
* Return [UNKN ] Undocumented return value [AlnBlock *]
*
*/
AlnBlock * Wise2_AlnBlock_from_Protein_estwise_wrap(Protein * pro,cDNA * cdna,cDNAParser * cp,CodonMapper * cm,CodonTable * ct,CompMat * comp,int gap,int ext,boolean is_global,RandomModelDNA * rmd,int alg,RandomModel * rm,boolean use_syn,Probability allN,DPRunImpl * dpri,PackAln ** palpoi);
#define AlnBlock_from_Protein_estwise_wrap Wise2_AlnBlock_from_Protein_estwise_wrap
/* Function: AlnBlock_from_TSM_estwise_wrap(tsm,cdna,cp,cm,ct,rmd,alg,use_syn,force_flat_insert,allN,dpri,palpoi)
*
* Descrip: This function is the basic wrap for Protein models
* vs cDNA sequences.
*
*
* Arg: tsm [READ ] threestatemodel to be compared to the dna [ThreeStateModel *]
* Arg: cdna [READ ] cdna to be compared to [cDNA *]
* Arg: cp [READ ] cdna parser indicating insertion deletion probabilities [cDNAParser *]
* Arg: cm [READ ] codon mapper indicating substitution errors etc [CodonMapper *]
* Arg: ct [READ ] codon table for the codon->amino acid mappings [CodonTable *]
* Arg: rmd [UNKN ] random model of dna to use [RandomModelDNA *]
* Arg: alg [UNKN ] est algorithm type to use [int]
* Arg: use_syn [UNKN ] if true, uses a synchronous coding model [boolean]
* Arg: force_flat_insert [UNKN ] Undocumented argument [boolean]
* Arg: allN [UNKN ] Undocumented argument [Probability]
* Arg: dpri [UNKN ] Undocumented argument [DPRunImpl *]
* Arg: palpoi [WRITE] the raw packed alignment output if wanted [PackAln **]
*
* Return [UNKN ] Undocumented return value [AlnBlock *]
*
*/
AlnBlock * Wise2_AlnBlock_from_TSM_estwise_wrap(ThreeStateModel * tsm,cDNA * cdna,cDNAParser * cp,CodonMapper * cm,CodonTable * ct,RandomModelDNA * rmd,int alg,boolean use_syn,boolean force_flat_insert,Probability allN,DPRunImpl * dpri,PackAln ** palpoi);
#define AlnBlock_from_TSM_estwise_wrap Wise2_AlnBlock_from_TSM_estwise_wrap
/* Function: Hscore_from_TSM_estwise(tdb,cdb,cp,cm,rmd,use_syn,alg,bits_cutoff,allN,flat_insert,report_level,die_on_error,dbsi)
*
* Descrip: Runs a database search for the estwise set
* of algorithms
*
*
* Arg: tdb [READ ] a three state model database [ThreeStateDB *]
* Arg: cdb [READ ] a dna sequence database [cDNADB *]
* Arg: cp [READ ] the codon parser for this comparison [cDNAParser *]
* Arg: cm [READ ] the codon mapper for this comparison [CodonMapper *]
* Arg: rmd [READ ] random model used for the dna sequence comparison [RandomModelDNA *]
* Arg: use_syn [UNKN ] whether a synchronous coding model should be used or not [boolean]
* Arg: alg [UNKN ] algorithm to use [int]
* Arg: bits_cutoff [UNKN ] Undocumented argument [double]
* Arg: allN [UNKN ] Undocumented argument [Probability]
* Arg: flat_insert [UNKN ] Undocumented argument [boolean]
* Arg: report_level [UNKN ] Undocumented argument [int]
* Arg: die_on_error [UNKN ] if true, dies if there is an error [boolean]
* Arg: dbsi [UNKN ] Undocumented argument [DBSearchImpl *]
*
* Return [OWNER] a newly allocated Hscore structure of the search [Hscore *]
*
*/
Hscore * Wise2_Hscore_from_TSM_estwise(ThreeStateDB * tdb,cDNADB * cdb,cDNAParser * cp,CodonMapper * cm,RandomModelDNA * rmd,boolean use_syn,int alg,double bits_cutoff,Probability allN,boolean flat_insert,int report_level,boolean die_on_error,DBSearchImpl * dbsi);
#define Hscore_from_TSM_estwise Wise2_Hscore_from_TSM_estwise
/* Function: write_mul_estwise_AlnBlock(alb,ct,ofp)
*
* Descrip: writes an mul format protein multiple
* alignment from an AlnBlock with the first
* sequence an HMM/protein and ignored, and
* the second and subsequent sequences cdna sequences
* which are then translated into proteins
*
* This relies considerably on the alb being made
* correctly, and if it is not, then god help you.
*
* the estwisedb programs makes the alb correctly
*
*
* Arg: alb [UNKN ] Undocumented argument [AlnBlock *]
* Arg: ct [UNKN ] Undocumented argument [CodonTable *]
* Arg: ofp [UNKN ] Undocumented argument [FILE *]
*
*/
void Wise2_write_mul_estwise_AlnBlock(AlnBlock * alb,CodonTable * ct,FILE * ofp);
#define write_mul_estwise_AlnBlock Wise2_write_mul_estwise_AlnBlock
/* 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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