/*  Last edited: Apr 24 15:02 1997 (birney) */



%{
#include "complexsequence.h"
#include "genomic.h"



/*** ok, some types to works with ***/

#define AMINOACID CSEQ_PROTEIN_AMINOACID
#define CSEQ_PROTEIN_AMINOACID(cseq,index) (cseq->data[index])


/*** for genomic ***/

#define CSEQ_G_LEN 6

#define CSEQ_GENOMIC_BASE(cseq,index)      (cseq->data[(index)*CSEQ_G_LEN])
#define CSEQ_GENOMIC_CODON(cseq,index)     (cseq->data[(index)*CSEQ_G_LEN +1])
#define CSEQ_GENOMIC_5SS(cseq,index)       (cseq->data[(index)*CSEQ_G_LEN +2])
#define CSEQ_GENOMIC_3SS(cseq,index)       (cseq->data[(index)*CSEQ_G_LEN +3])
#define CSEQ_GENOMIC_REPEAT(cseq,index)    (cseq->data[(index)*CSEQ_G_LEN +4])
#define CSEQ_GENOMIC_CDSPOT(cseq,index)    (cseq->data[(index)*CSEQ_G_LEN +5])


/*** for cDNA  ***/

#define CSEQ_C_LEN 2

#define CSEQ_CDNA_BASE(cseq,index) (cseq->data[index*CSEQ_C_LEN])
#define CSEQ_CDNA_CODON(cseq,index) (cseq->data[index*CSEQ_C_LEN +1])

#define CSEQ_D_LEN 1

#define CSEQ_DNA_BASE(cseq,index) (cseq->data[index])

%}





%{
#include "complexevalset.h"


%func
makes a new ComplexSequence from a Genomic
sequence, using the repeat information to
structure the positives and negatives.
%%
ComplexSequence * evaluate_ComplexSequence_Genomic(Genomic * gen,ComplexSequenceEvalSet * cses,int score_for_repeat,int score_for_cds_in_repeat)
{
  int i,j;
  ComplexSequence * out;

  if( cses == NULL || cses->type != SEQUENCE_GENOMIC ) {
    warn("ComplexSequenceEvalSet is not valid for genomic!");
    return NULL;
  }

  assert(gen);
  assert(gen->baseseq);
  assert(gen->baseseq->seq);

  out = new_ComplexSequence(gen->baseseq,cses);


  if( out == NULL ) {
    return NULL;
  }
  
  for(i=0;i<gen->len;i++) {
    for(j=gen->repeat[i]->start;j<gen->repeat[i]->end;j++) {
      if( j >= gen->baseseq->len ) {
	warn("Overran sequence - j position %d, sequence length %d on repeat %d",j,gen->baseseq->len,i);
	break;
      }

      CSEQ_GENOMIC_REPEAT(out,j) = score_for_repeat;
      CSEQ_GENOMIC_CDSPOT(out,j) = score_for_cds_in_repeat;
    }
  }
  /*
  for(i=0;i<gen->baseseq->len;i++) 
    fprintf(stderr,"At position %6d %d\n",CSEQ_GENOMIC_CDSPOT(out,j));
  */

  return out;
}


%func
Makes a reasonably sensible genomic sequence
eval set. Has base and codon numbers (what
every good genomic sequence should do) and then
/stupid_5SS and /stupid_3SS. Finally the repeat/EST
regions modelled with the /flat_zero
%arg
%%
ComplexSequenceEvalSet * default_genomic_ComplexSequenceEvalSet(void)
{
  ComplexSequenceEvalSet * out;


  out = ComplexSequenceEvalSet_alloc_len(11);

  add_ComplexSequenceEvalSet(out,base_number_ComplexSequenceEval());
  add_ComplexSequenceEvalSet(out,codon_number_ComplexSequenceEval());
  add_ComplexSequenceEvalSet(out,stupid_5SS());
  add_ComplexSequenceEvalSet(out,stupid_3SS());
  add_ComplexSequenceEvalSet(out,flat_zero());
  add_ComplexSequenceEvalSet(out,flat_zero());


  out->type = SEQUENCE_GENOMIC;

  prepare_ComplexSequenceEvalSet(out);

  return out;
}

%func
Makes a ComplexSequenceEval that puts NEGI everywhere
%%
ComplexSequenceEval * flat_negi(void)
{
  ComplexSequenceEval * out;
  out= ComplexSequenceEval_alloc();

  out->left_window   = 0;
  out->right_window  = 0;
  out->outside_score = NEGI;
  out->eval_func     = flat_negi_eval;

  return out;
}

%func
used by flat negi
%type internal
%%
int flat_negi_eval(int type,void *data,char * seq)
{
  return NEGI;
}
    

%func
Makes a ComplexSequenceEval that puts 0 everywhere
%arg
%%
ComplexSequenceEval * flat_zero(void)
{
  ComplexSequenceEval * out;
  
  out= ComplexSequenceEval_alloc();

  out->left_window   = 0;
  out->right_window  = 0;
  out->outside_score = NEGI;
  out->eval_func     = flat_zero_eval;

  return out;
}

%func
Used by /flat_zero as function actually called
%type internal
%arg
%%
int flat_zero_eval(int type,void *data,char * seq)
{
  return 0;
}


%func
Reasonably stupid 5'SS, of 0 at GT's
and NEGI elsewhere. Pretends to have a longer
footprint than it needs to satisify the lookbacks
of more proper genomic models
%arg
%%
ComplexSequenceEval * stupid_5SS(void)
{
  ComplexSequenceEval * out;
  
  out= ComplexSequenceEval_alloc();

  out->left_window   = 3;
  out->right_window  = 7;
  out->left_lookback = 8;
  out->outside_score = NEGI;
  out->eval_func     = stupid_5SS_eval;

  return out;
}

%func
Function which actually does the evaluation for
5'SS
%type internal
%arg
%%
int stupid_5SS_eval(int type,void *data,char * seq)
{
  if( *(seq) == 'G' && *(seq+1) == 'T' ) 
    return 0;
  else return NEGI;
}


%func
Reasonably stupid 3'SS, of 0 at AG's
and NEGI elsewhere. Pretends to have a longer
footprint than it needs to satisify the lookbacks
of more proper genomic models
%arg
%%
ComplexSequenceEval * stupid_3SS(void)
{
  ComplexSequenceEval * out;
  
  out= ComplexSequenceEval_alloc();

  out->left_window   = 3;
  out->right_window  = 3;
  out->left_lookback = 5;
  out->outside_score = NEGI;
  out->eval_func     = stupid_3SS_eval;

  return out;
}


%func
Function which actually does the evaluation for
3'SS
%type internal
%arg
%%
int stupid_3SS_eval(int type,void *data,char * seq)
{
  if( *(seq-1) == 'A' && *(seq) == 'G' ) 
    return 0;
  else return NEGI;
}



   /********************************/
   /* cDNA and base stuff          */
   /********************************/

%func
Makes a very sensible DNA sequence
eval set. You shouldn't need your own
%arg
%%
ComplexSequenceEvalSet * default_DNA_ComplexSequenceEvalSet(void)
{
  ComplexSequenceEvalSet * out;


  out = ComplexSequenceEvalSet_alloc_len(1);

  add_ComplexSequenceEvalSet(out,base_number_ComplexSequenceEval());
  out->type = SEQUENCE_DNA;

  prepare_ComplexSequenceEvalSet(out);

  return out;
}


%func
Makes a very sensible cDNA sequence
eval set. You shouldn't need your own
%arg
%%
ComplexSequenceEvalSet * default_cDNA_ComplexSequenceEvalSet(void)
{
  ComplexSequenceEvalSet * out;


  out = ComplexSequenceEvalSet_alloc_len(2);

  add_ComplexSequenceEvalSet(out,base_number_ComplexSequenceEval());
  add_ComplexSequenceEvalSet(out,codon_number_ComplexSequenceEval());
  out->type = SEQUENCE_CDNA;

  prepare_ComplexSequenceEvalSet(out);

  return out;
}




%func
ComplexSequenceEval that puts a codon
number in there (0-125 inc, 125 = impossible codon).
%arg
%%
ComplexSequenceEval * codon_number_ComplexSequenceEval(void)
{
  ComplexSequenceEval * out;


  out = ComplexSequenceEval_alloc();

  if (out == NULL ) {
    return NULL;
  }
  
  out->left_window = 2;
  out->right_window = 0;
  out->outside_score = 125;
  out->eval_func = codon_number_func;


  return out;
}

%func
Function which actually does the codon evaluation
%type internal
%arg
%%
int codon_number_func(int type,void * data,char * seq)
{
  return codon_from_seq(seq-2);
} 

  
%func
Function which puts a 64 base codon...
%%
ComplexSequenceEval * codon64_number_ComplexSequenceEval(void)
{
  ComplexSequenceEval * out;


  out = ComplexSequenceEval_alloc();

  if (out == NULL ) {
    return NULL;
  }
  
  out->left_window = 2;
  out->right_window = 0;
  out->outside_score = 65;
  out->eval_func = codon64_number_func;


  return out;
}

%func
Function which actually does the codon64 evaluation
%type internal
%arg
%%
int codon64_number_func(int type,void * data,char * seq)
{
  int codon;

  if( !is_non_ambiguous_codon_seq(seq-2) ) {
      	return 64;
  }
  codon = codon_from_seq(seq-2);

  return base4_codon_from_codon(codon);
} 



%func
ComplexSequenceEval that puts a base
number (0-5 inc)
%arg
%%
ComplexSequenceEval * base_number_ComplexSequenceEval(void)
{
  ComplexSequenceEval * out;


  out = ComplexSequenceEval_alloc();

  if (out == NULL ) {
    return NULL;
  }
  
  out->left_window = out->right_window = 0;
  out->eval_func = base_number_func;

  return out;
}
  

%func
Function which actually does the evaluation bases
%type internal
%arg
%%
int base_number_func(int type,void * data,char * seq)
{
  return base_from_char(*seq);
} 



  /***************************/
  /* amino acid stuff        */
  /***************************/


%func
Makes a very sensible protein sequence
eval set. You shouldn't need your own
%arg
%%
ComplexSequenceEvalSet * default_aminoacid_ComplexSequenceEvalSet(void)
{
  ComplexSequenceEvalSet * out;


  out = ComplexSequenceEvalSet_alloc_len(1);

  add_ComplexSequenceEvalSet(out,aminoacid_number_ComplexSequenceEval());

  out->type = SEQUENCE_PROTEIN;

  prepare_ComplexSequenceEvalSet(out);

  return out;
}



%func
ComplexSequenceEval that puts a amino acid
number in there (0-26)
%arg
%%
ComplexSequenceEval * aminoacid_number_ComplexSequenceEval(void)
{
  ComplexSequenceEval * out;


  out = ComplexSequenceEval_alloc();

  if (out == NULL ) {
    return NULL;
  }
  
  out->left_window = out->right_window = 0;
  out->eval_func = aminoacid_number_func;

  return out;
}
  

%func
Function which actually does the evaluation for aminoacids
%type internal
%arg
%%
int aminoacid_number_func(int type,void * data,char * seq)
{
  return (int)(toupper((int)*seq)-'A');
} 


  /***************************/
  /* dna stuff               */
  /***************************/


%func
Makes a very sensible dna sequence
eval set. You shouldn't need your own
%arg
%%
ComplexSequenceEvalSet * default_dna_ComplexSequenceEvalSet(void)
{
  ComplexSequenceEvalSet * out;

  out = ComplexSequenceEvalSet_alloc_len(1);

  add_ComplexSequenceEvalSet(out,base_number_ComplexSequenceEval());

  out->type = SEQUENCE_DNA;

  prepare_ComplexSequenceEvalSet(out);

  return out;
}

%}