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/*----------------------------------------------------------------------------
*
* smithwatermangotoh.c
*
* Copyright (c) 2008-2018, Euler Taveira de Oliveira
*
*----------------------------------------------------------------------------
*/
#include "similarity.h"
double pgs_swg_threshold = 0.7f;
bool pgs_swg_is_normalized = true;
/*
* TODO move this function to similarity.c
*/
static double _smithwatermangotoh(char *a, char *b)
{
float **matrix; /* dynamic programming matrix */
int alen, blen;
int i, j;
double maxvalue;
alen = strlen(a);
blen = strlen(b);
elog(DEBUG2, "alen: %d; blen: %d", alen, blen);
if (alen == 0)
return blen;
if (blen == 0)
return alen;
matrix = (float **) malloc((alen + 1) * sizeof(float *));
if (matrix == NULL)
elog(ERROR, "memory exaushted for array size %d", alen);
for (i = 0; i <= alen; i++)
{
matrix[i] = (float *) malloc((blen + 1) * sizeof(float));
if (matrix[i] == NULL)
elog(ERROR, "memory exaushted for array size %d", blen);
}
#ifdef PGS_IGNORE_CASE
elog(DEBUG2, "case-sensitive turns off");
for (i = 0; i < alen; i++)
a[i] = tolower(a[i]);
for (j = 0; j < blen; j++)
b[j] = tolower(b[j]);
#endif
maxvalue = 0.0;
/* initial values */
for (i = 0; i <= alen; i++)
{
float c = megapcost(a, b, i, 0);
if (i == 0)
{
matrix[0][0] = max2(0.0, c);
}
else
{
float maxgapcost = 0.0;
int wstart = i - PGS_SWG_WINDOW_SIZE;
int k;
if (wstart < 1)
wstart = 1;
for (k = wstart; k < i; k++)
maxgapcost = max2(maxgapcost, matrix[i - k][0] - swggapcost(i - k, i));
matrix[i][0] = max3(0.0, maxgapcost, c);
}
if (matrix[i][0] > maxvalue)
maxvalue = matrix[i][0];
}
for (j = 0; j <= blen; j++)
{
float c = megapcost(a, b, 0, j);
if (j == 0)
{
matrix[0][0] = max2(0.0, c);
}
else
{
float maxgapcost = 0.0;
int wstart = j - PGS_SWG_WINDOW_SIZE;
int k;
if (wstart < 1)
wstart = 1;
for (k = wstart; k < j; k++)
maxgapcost = max2(maxgapcost, matrix[0][j - k] - swggapcost(j - k, j));
matrix[0][j] = max3(0.0, maxgapcost, c);
}
if (matrix[0][j] > maxvalue)
maxvalue = matrix[0][j];
}
for (i = 1; i <= alen; i++)
{
for (j = 1; j <= blen; j++)
{
int wstart;
int k;
float maxgapcost1 = 0.0,
maxgapcost2 = 0.0;
/* get operation cost */
float c = megapcost(a, b, i, j);
wstart = i - PGS_SWG_WINDOW_SIZE;
if (wstart < 1)
wstart = 1;
for (k = wstart; k < i; k++)
maxgapcost1 = max2(maxgapcost1, matrix[i - k][0] - swggapcost(i - k, i));
wstart = j - PGS_SWG_WINDOW_SIZE;
if (wstart < 1)
wstart = 1;
for (k = wstart; k < j; k++)
maxgapcost2 = max2(maxgapcost2, matrix[0][j - k] - swggapcost(j - k, j));
matrix[i][j] = max4(0.0,
maxgapcost1,
maxgapcost2,
matrix[i-1][j-1] + c);
elog(DEBUG2, "(i, j) = (%d, %d); cost(%c, %c): %.3f; max(zero, top, left, diag) = (0.0, %.3f, %.3f, %.3f) = %.3f",
i, j, a[i-1], b[j-1], c,
maxgapcost1,
maxgapcost2,
matrix[i-1][j-1] + c, matrix[i][j]);
if (matrix[i][j] > maxvalue)
maxvalue = matrix[i][j];
}
}
for (i = 0; i <= alen; i++)
free(matrix[i]);
free(matrix);
return maxvalue;
}
PG_FUNCTION_INFO_V1(smithwatermangotoh);
Datum
smithwatermangotoh(PG_FUNCTION_ARGS)
{
char *a, *b;
double maxvalue;
float8 res;
a = DatumGetPointer(DirectFunctionCall1(textout, PointerGetDatum(PG_GETARG_TEXT_P(0))));
b = DatumGetPointer(DirectFunctionCall1(textout, PointerGetDatum(PG_GETARG_TEXT_P(1))));
if (strlen(a) > PGS_MAX_STR_LEN || strlen(b) > PGS_MAX_STR_LEN)
ereport(ERROR,
(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("argument exceeds the maximum length of %d bytes",
PGS_MAX_STR_LEN)));
maxvalue = (float8) min2(strlen(a), strlen(b));
res = _smithwatermangotoh(a, b);
elog(DEBUG1, "is normalized: %d", pgs_swg_is_normalized);
elog(DEBUG1, "maximum length: %.3f", maxvalue);
elog(DEBUG1, "swgdistance(%s, %s) = %.3f", a, b, res);
if (maxvalue == 0)
{
res = 1.0;
}
if (pgs_swg_is_normalized)
{
if (PGS_SW_MAX_COST > (-1 * PGS_SW_GAP_COST))
maxvalue *= PGS_SW_MAX_COST;
else
maxvalue *= -1 * PGS_SW_GAP_COST;
/* paranoia ? */
if (maxvalue == 0.0)
res = 1.0;
else
res = (res / maxvalue);
}
elog(DEBUG1, "swg(%s, %s) = %.3f", a, b, res);
PG_RETURN_FLOAT8(res);
}
PG_FUNCTION_INFO_V1(smithwatermangotoh_op);
Datum smithwatermangotoh_op(PG_FUNCTION_ARGS)
{
float8 res;
/*
* store *_is_normalized value temporarily 'cause
* threshold (we're comparing against) is normalized
*/
bool tmp = pgs_swg_is_normalized;
pgs_swg_is_normalized = true;
res = DatumGetFloat8(DirectFunctionCall2(
smithwatermangotoh,
PG_GETARG_DATUM(0),
PG_GETARG_DATUM(1)));
/* we're done; back to the previous value */
pgs_swg_is_normalized = tmp;
PG_RETURN_BOOL(res >= pgs_swg_threshold);
}
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