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#include <objres.h>
#include <objseq.h>
#include <seqport.h>
#include <aacomp.h>
/* defines */
#define F7 7
#define F24 24
#define F42 42
#define PI 3.14159
/* functions - internal */
static FloatHiPtr AAC (SeqPortPtr spp, Int4 start, Int4 end,
Int4 numval, Int4 window,
FloatHiPtr scr, CharPtr res)
{
Int4 i, n, col;
Int4 stop;
Char aa;
Boolean flagMatch;
FloatHi temp, fmin = 0.0, fmax = 0.0, frange;
FloatHiPtr frealheadptr, fheadptr;
FloatHiPtr fptr;
fptr = (FloatHiPtr) MemNew ((sizeof (FloatHi)) * numval);
frealheadptr = fptr;
for (i = start; i < end+1; i++)
*fptr++ = 0.0;
fptr = frealheadptr;
for (i = 0; i < window/2; i++)
fptr++;
fheadptr = fptr;
stop = end + 1 - window + 1;
for (i = start; i < stop; i++)
{
temp = 0;
SeqPortSeek (spp, i, SEEK_SET);
for (col = 0; col < window; col++)
{
aa = SeqPortGetResidue (spp);
flagMatch = FALSE;
n = 0;
while (res[n] != '\0')
{
if (aa == res[n])
{
flagMatch = TRUE;
break;
}
n++;
}
if (flagMatch)
temp += scr[n];
}
temp /= window;
*fptr = temp;
fptr++;
}
fptr = fheadptr;
for (i = start; i < stop; i++)
{
if (*fptr > fmax)
fmax = *fptr;
fptr++;
}
fptr = fheadptr;
for (i = start; i < stop; i++)
{
if (*fptr < fmin)
fmin = *fptr;
fptr++;
}
frange = fmax-fmin;
fptr = fheadptr;
for (i = start; i < stop; i++)
{
*fptr = (*fptr - fmin)/frange*100;
fptr++;
}
return frealheadptr;
}
static SeqGraphPtr AACGraph (SeqPortPtr spp, Int4 start, Int4 end, Int4 window,
FloatHiPtr scr, CharPtr res)
{
SeqGraphPtr sgp;
Int4 gwidth = 500;
if ((sgp = SeqGraphNew ()) != NULL)
{
/* type and number of values and compression */
sgp->numval = end + 1;
sgp->compr = (Int4) (sgp->numval / gwidth);
if ((sgp->numval%gwidth) != 0)
sgp->compr += 1;
/* graph type */
sgp->flags[2] = 1;
sgp->values = (Pointer) MemNew ((sizeof (FloatHi)) * sgp->numval);
/* min/max */
sgp->max.realvalue = 100.0;
sgp->min.realvalue = 0.0;
sgp->axis.realvalue = 0.0;
/* scaling */
sgp->flags[1] = 1;
sgp->a = 2;
sgp->b = 0;
/* do it */
AAC (spp, start, end, end+1, window, scr, res);
}
return sgp;
}
/*
this stores a score for each of 24 resides
20 amino acids
2 ambiguous amino acids (ASX GLX)
1 unknown amino acid (the average score of the 20 generally)
1 stop codon (currently also the average score of the 20)
the scoring table should have the scores in a column
in order of the residues stored in static Char c[]
the caller must pass pointers to arrays that can hold
the 24 residues (res) and scores (scr)
a successful, tho not necessarily correct, read will return 24
*/
extern Int4 ReadAAC (CharPtr filename, FloatHiPtr scr, CharPtr res)
{
Int2 val, count;
Int4 type;
long int ltype;
FloatHi score;
Char buf[PATH_MAX], buff[PATH_MAX];
CharPtr bptr;
FILE *fio;
static Char c[] = {'A','B','C','D','E','F','G','H','I','K','L','M',
'N','P','Q','R','S','T','V','W','X','Y','Z','*'};
if (!FindPath ("ncbi", "ncbi", "data", buf, sizeof (buf)))
return 0;
FileBuildPath (buf, NULL, filename);
if ((fio = FileOpen (buf, "r")) == NULL)
{
if ((fio = FileOpen (filename, "r")) == NULL)
{
return 0;
}
}
val = 0;
type = -1;
while ((FileGets (buff, sizeof (buff), fio)) != NULL)
{
if (buff[0] == ';')
continue;
if (type == -1)
{
sscanf (buff, "%ld", <ype);
type = (Int4) ltype;
if (type != 1)
{
FileClose (fio);
return 0;
}
FileGets (buff, sizeof (buff), fio);
continue;
}
res[val] = c[val];
bptr = buff;
sscanf (bptr, "%lf", &score);
scr[val] = score;
val++;
if (val == F24)
break;
}
count = val;
FileClose (fio);
return (Int4) count;
}
/* functions - external */
extern FloatHiPtr AAComposition (SeqPortPtr spp,
Int4 start, Int4 end, Int4 numval,
FloatHiPtr scr, CharPtr res, Int4 window)
{
FloatHiPtr fptr;
fptr = AAC (spp, start, end, numval, window, scr, res);
return fptr;
}
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