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#include <objres.h>
#include <objseq.h>
#include <seqport.h>
#include <seqpcc.h>
/* defines */
#define F7 7
#define F24 24
#define F42 42
#define PI 3.14159
/* functions - internal */
static FloatHi PPCC (FloatHi score)
{
FloatHi meang = 0.77;
FloatHi stdg = 0.20;
FloatHi meanc = 1.63;
FloatHi stdc = 0.24;
FloatHi constg, constc;
FloatHi evalg, evalc;
FloatHi Gg, Gc;
FloatHi prob;
constg = 1 / (stdg * 2 * PI);
constc = 1 / (stdc * 2 * PI);
evalg = (((score - meang) / stdg) * ((score - meang) / stdg)) / 2;
evalc = (((score - meanc) / stdc) * ((score - meanc) / stdc)) / 2;
evalg = exp (evalg);
evalc = exp (evalc);
Gg = constg / evalg;
Gc = constc / evalc;
prob = Gc / ((30 * Gg) + Gc);
return prob;
}
static FloatHi nroot (FloatHi fv, Int4 wv)
{
FloatHi fi = 1.0;
fi = fi / (FloatHi) wv;
fv = pow (fv, fi);
return fv;
}
static void PCC (SeqPortPtr spp, Int4 start, Int4 end, Int4 window,
FloatHi scr[F24][F42], Char res[F24], FloatHiPtr fptr)
{
Int4 i, n, col;
Int4 stop;
Char aa;
Boolean flagMatch;
FloatHi temp;
FloatHiPtr fheadptr;
fheadptr = fptr;
for (i = start; i < end; i++)
*fptr++ = 0.0;
fptr = fheadptr;
stop = end - window;
for (i = start; i < stop; i++)
{
SeqPortSeek (spp, i, SEEK_SET);
temp = 1.0;
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][col];
}
temp = nroot (temp, window);
temp = PPCC (temp);
if (temp < 0.0)
temp = 0.0;
temp *= 100.0;
fheadptr = fptr;
for (n = 0; n < window; n++)
{
if (temp > *fptr)
*fptr = temp;
fptr++;
}
fptr = fheadptr;
fptr++;
}
return;
}
static SeqGraphPtr PCCGraph (SeqPortPtr spp, Int4 start, Int4 end, Int4 window,
FloatHi scr[F24][F42], Char res[F24])
{
SeqGraphPtr sgp;
Int4 gwidth = 500;
FloatHiPtr fptr;
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 */
fptr = (FloatHiPtr) sgp->values;
PCC (spp, start, end, window, scr, res, fptr);
}
return sgp;
}
static Int4 ReadPCC (CharPtr res, FloatHi scr[F24][F42], Int4 window)
{
FILE *fin;
Int2 i, n, val, count;
Int2 numcol;
FloatHi score;
Char buf[PATH_MAX], buff[PATH_MAX];
CharPtr bptr;
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','*'};
numcol = F7;
if (!FindPath ("ncbi", "ncbi", "data", buf, sizeof (buf)))
return 0;
FileBuildPath (buf, NULL, "KSpcc.dat");
if ((fin = FileOpen (buf, "r")) == NULL)
{
if ((fin = FileOpen ("KSpcc.dat", "r")) == NULL)
{
return 0;
}
}
val = 0;
while ((FileGets (buff, sizeof (buff), fin)) != NULL)
{
if (buff[0] == ';')
continue;
res[val] = c[val];
bptr = buff;
for (n = 0; n < numcol; n++)
{
sscanf (bptr, "%lf", &score);
scr[val][n] = score;
bptr += 7;
}
val++;
if (val == F24)
break;
}
count = val;
for (n = numcol; n < window; n++)
{
if (n == F42)
break;
val = (Int2) (n % numcol);
for (i = 0; i < F24; i++)
{
scr[i][n] = scr[i][val];
}
}
FileClose (fin);
return (Int4) count;
}
/* functions - external */
extern SeqGraphPtr PCCProc (BioseqPtr bsp, SeqFeatPtr sfp, Int4 window)
{
SeqIdPtr psip;
BioseqPtr pbsp;
Int4 start, end;
FloatHi scr[F24][F42];
Char res[F24];
SeqPortPtr spp;
SeqGraphPtr sgp = NULL;
if (bsp != NULL)
{
pbsp = bsp;
if (!ISA_aa (pbsp->mol))
return sgp;
}
else if (sfp != NULL)
{
if (sfp->data.choice != SEQFEAT_CDREGION)
return sgp;
psip = SeqLocId (sfp->product);
pbsp = BioseqFind (psip);
if (pbsp == NULL)
return sgp;
if (!ISA_aa (pbsp->mol))
return sgp;
}
if (ReadPCC (res, scr, window) != F24)
return sgp;
start = 0;
end = pbsp->length-1;
if ((spp = SeqPortNew (pbsp, start, end, 0, Seq_code_iupacaa)) != NULL)
{
end -= window;
sgp = PCCGraph (spp, start, end, window, scr, res);
SeqPortFree (spp);
}
return sgp;
}
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