GtScoreHandler *gt_scorehandler2costhandler(const GtScoreHandler *scorehandler)
{
GtScoreHandler *costhandler;
gt_assert(scorehandler != NULL);
if (scorehandler->scorematrix == NULL)
{
GtWord matchscore, mismatchscore, gap_extension, gap_opening,
maxscore = MAX(MAX(GT_DIV2(scorehandler->matchscore+1),
GT_DIV2(scorehandler->mismatchscore+1)),
MAX(1 + scorehandler->gap_extension,0));
matchscore = 2 * maxscore - scorehandler->matchscore;
mismatchscore = 2 * maxscore - scorehandler->mismatchscore;
gap_extension = maxscore - scorehandler->gap_extension;
gap_opening = -scorehandler->gap_opening;
costhandler = gt_scorehandler_new(matchscore,
mismatchscore,
gap_opening,
gap_extension);
if (!scorehandler->mappedsequence)
{
gt_scorehandler_plain(costhandler);
}
} else
{
int maxscore;
GtWord gap_extension, gap_opening;
unsigned int i, j,
dim = gt_score_matrix_get_dimension(scorehandler->scorematrix);
GtScoreMatrix *costmatrix
= gt_score_matrix_clone_empty(scorehandler->scorematrix);
for (maxscore = 0, i = 0; i < dim; i++)
{
for (j = 0; j < dim; j++)
{
int val = gt_score_matrix_get_score(scorehandler->scorematrix, i, j);
if (val > maxscore)
{
maxscore = val;
}
}
}
maxscore = MAX(GT_DIV2(maxscore+1), 1 + scorehandler->gap_extension);
for (i = 0; i < dim; i++)
{
for (j = 0; j < dim; j++)
{
/* translate */
int score = gt_score_matrix_get_score(scorehandler->scorematrix,i,j);
gt_score_matrix_set_score(costmatrix, i, j, 2 * maxscore - score);
}
}
gap_extension = maxscore - scorehandler->gap_extension;
gap_opening = -scorehandler->gap_opening;
costhandler = gt_scorehandler_new( 0,0, gap_opening, gap_extension);
gt_scorehandler_add_scorematrix(costhandler,costmatrix);
}
return costhandler;
}
/* handle score and cost values */
static GtScoreHandler *gt_arguments2scorehandler(
const GtLinspaceArguments *arguments,
GtError *err)
{
GtWord matchscore, mismatchscore, gap_open, gap_extension;
GtScoreHandler *scorehandler = NULL;
GtScoreMatrix *scorematrix = NULL;
int had_err = 0;
gt_error_check(err);
if (gt_str_array_size(arguments->linearcosts) > 0)
{
GtUword wordindex = 0;
if (arguments->protein)
{
scorematrix
= gt_score_matrix_new_read_protein(
gt_str_array_get(arguments->linearcosts,wordindex++),
err);
if (scorematrix == NULL)
{
had_err = -1;
}
matchscore = 0;
mismatchscore = 0;
} else
{
had_err = gt_parse_score_value(__LINE__,&matchscore,
gt_str_array_get(arguments->linearcosts,
wordindex++),
arguments->global,err);
if (!had_err)
{
had_err = gt_parse_score_value(__LINE__,&mismatchscore,
gt_str_array_get(arguments->linearcosts,
wordindex++),
arguments->global,err);
}
}
if (!had_err)
{
gap_open = 0;
had_err = gt_parse_score_value(__LINE__,&gap_extension,
gt_str_array_get(arguments->linearcosts,
wordindex++),
false,err);
}
} else /*if (gt_str_array_size(arguments->affinecosts) > 0)*/
{
GtUword wordindex = 0;
if (arguments->protein)
{
scorematrix = gt_score_matrix_new_read_protein(
gt_str_array_get(arguments->affinecosts,
wordindex++), err);
if (scorematrix == NULL)
{
had_err = -1;
}
matchscore = mismatchscore = 0;
} else
{
had_err = gt_parse_score_value(__LINE__,&matchscore,
gt_str_array_get(arguments->affinecosts,
wordindex++),
arguments->global,err);
if (!had_err)
{
had_err = gt_parse_score_value(__LINE__,&mismatchscore,
gt_str_array_get(arguments->affinecosts,
wordindex++),
arguments->global,err);
}
}
if (!had_err)
{
had_err = gt_parse_score_value(__LINE__,&gap_open,
gt_str_array_get(arguments->affinecosts,
wordindex++),
false,err);
}
if (!had_err)
{
had_err = gt_parse_score_value(__LINE__,&gap_extension,
gt_str_array_get(arguments->affinecosts,
wordindex),
false,err);
}
}
if (!had_err)
{
scorehandler = gt_scorehandler_new(matchscore, mismatchscore,
gap_open, gap_extension);
if (scorematrix != NULL)
{
gt_scorehandler_add_scorematrix(scorehandler,scorematrix);
}
}
return scorehandler;
}
