/*  Last edited: Apr 24 14:51 1997 (birney) */


%{
#include "wisebase.h"
#include "probability.h"


enum cDNAParserTrans {
  PCD_INSERT_2_BASE = 0,
  PCD_INSERT_1_BASE,
  PCD_DELETE_2_BASE,
  PCD_DELETE_1_BASE,
  PCD_PARSER_TRANS_LEN };

%}


struct cDNAParser
Probability trans[PCD_PARSER_TRANS_LEN]
%info
This object holds the (very few) extra
transition information needed for the
estwise algorithm. It is sort of like
the 'gene model' part of sequencing
error (but very very simple)

%%

struct cDNAParserScore
Score trans[PCD_PARSER_TRANS_LEN]
%info
This object is the score counter
point to cDNAParser (which is
in probabilities). 
%%

api
object cDNAParser
des free_cDNAParser
endobject
func flat_cDNAParser
endapi

%{
#include "cdparser.h"

%func
Makes a convienient sum over all the transition
probabilities
%%
Probability removed_probability_from_cds_cdna(cDNAParser * cdp)
{
  return cdp->trans[PCD_INSERT_2_BASE] +
    cdp->trans[PCD_INSERT_1_BASE] +
      cdp->trans[PCD_DELETE_2_BASE] +
	cdp->trans[PCD_DELETE_1_BASE];
}
 
%func
Makes a new Score object from its probability
counterpart
%%
cDNAParserScore * cDNAParserScore_from_cDNAParser(cDNAParser * cdp)
{
  cDNAParserScore * out;

  out = cDNAParserScore_alloc();

  Probability2Score_move(cdp->trans,out->trans,PCD_PARSER_TRANS_LEN);

  return out;
}

%func
Makes a flat (ie, indels of 1 or 2 == p)
cDNA parser. This means that insertions
and deletions of both 1 or 2 bases are
all parameterised at the same probability

%arg
p r probability of an indel
%%
cDNAParser * flat_cDNAParser(Probability p)
{
  cDNAParser * out;

  out = cDNAParser_alloc();

  out->trans[PCD_INSERT_2_BASE] = p;
  out->trans[PCD_INSERT_1_BASE] = p;
  out->trans[PCD_DELETE_2_BASE] = p;
  out->trans[PCD_DELETE_1_BASE] = p;
    
  return out;
}


%}