/*  Last edited: Dec  5 19:45 1996 (birney) */


%{

#include "wisebase.h"
#include "probability.h"


#define PackAlnLISTLENGTH 64

%}

api
object PackAln
des  free_PackAln
func show_simple_PackAln
func show_bits_and_cumlative_PackAln
endobject
object PackAlnUnit
des  free_PackAlnUnit
endobject
endapi

struct PackAlnUnit
int i // position in query 
int j // position in target
int state // state in FSM
int score !def="0" // score of the transition that reached this state
%info
Internal object for /PackAln:
A single position of an alignment
as the (i,j,state) triple
%%

struct PackAln
PackAlnUnit ** pau !list // list of PackAlnUnits from start to end
int score; // score over the entire alignment
%info
This is the lowest-level of representation
of a DP alignment, being the list of 
(i,j,state) triples taken through the
DP matrix. The score for the transition to
this point is held as well.

This object is very low level and often a
much better choice for representation is
in /AlnBlock objects 
%%

%{
#include "packaln.h"

%func
shows packalnunit very simply ;)
%type internal
%%
void show_simple_PackAlnUnit(PackAlnUnit * pau,FILE * ofp)
{
  fprintf(ofp,"Position i:[%d] j:[%d] State:[%d] Score: %d\n",pau->i,pau->j,pau->state,pau->score);
}

%func
shows packalnunit with the text mapping
%type internal
%%
void show_text_PackAlnUnit(PackAlnUnit * pau,char * (*state_to_char)(int),FILE * ofp)
{
  fprintf(ofp,"Position i:[%4d] j:[%4d] State:[%2d] Score:[%3d] [%s]\n",pau->i,pau->j,pau->state,pau->score,(*state_to_char)(pau->state));
}

%func
Shows packaln as: 

i,j,state,score,bits,cumlative-score,cumlative-bits

cumlative score and cumlative bits are useful sometimes
%%
void show_bits_and_cumlative_PackAln(PackAln * pal,FILE * ofp)
{
  int i;
  int cs = 0;
  double cb = 0.0;


  fprintf(ofp,"Score %d\n",pal->score);
  for(i=0;i<pal->len;i++) {
    auto PackAlnUnit * pau;
    pau = pal->pau[i];

    cs += pal->pau[i]->score;
    cb += Score2Bits(pal->pau[i]->score);
    fprintf(ofp,"i [%4d] j [%4d] state [%2d] score [%4d] bits [%2.2f] Score-CF [%6d] Bits-CF[%4.2f]\n",pau->i,pau->j,pau->state,pau->score,Score2Bits(pau->score),cs,cb);
  }

} 

 
%func
shows packaln with a pretty verbose debugging 
format
%%
void show_simple_PackAln(PackAln * pal,FILE * ofp)
{
  register int i;

  fprintf(ofp,"Score %d\n",pal->score);
  for(i=0;i<pal->len;i++)
    show_simple_PackAlnUnit(pal->pau[i],ofp);
}

%func
shows packaln with a pretty verbose debugging 
format, but with a conversion function from state number to
a string
%%
void show_text_PackAln(PackAln * pal,char * (*state_to_char)(int),FILE * ofp)
{
  register int i;

  fprintf(ofp,"Score %d\n",pal->score);
  for(i=0;i<pal->len;i++)
    show_text_PackAlnUnit(pal->pau[i],state_to_char,ofp);
}

%func
inverts the packaln so that the last unit is the first
etc. Because most alignments are read backwards this
is useful
%arg
pal PackAln to be inverted 
%%
void invert_PackAln(PackAln * pal) 
{
  PackAlnUnit ** temp;
  register int i;

  /*** there are better ways to do this! ***/

  temp = (PackAlnUnit **) ckcalloc(pal->len,sizeof(PackAlnUnit *));
  
  for(i=0;i<pal->len;i++) 
    temp[i] = pal->pau[pal->len-1-i];
  for(i=0;i<pal->len;i++)
    pal->pau[i] = temp[i];

  ckfree(temp);
}



%}