void gt_alignment_set_multieop_list(GtAlignment *alignment,
GtMultieoplist *eoplist)
{
gt_assert(alignment != NULL && eoplist != NULL);
gt_multieoplist_delete(alignment->eops);
alignment->eops = gt_multieoplist_ref(eoplist);
alignment->alilen = gt_multieoplist_get_length(eoplist);
}
GtWord gt_alignment_eval_with_score(const GtAlignment *alignment,
GtWord matchscore,
GtWord mismatchscore,
GtWord gapscore)
{
GtUword i, j, idx_u = 0, idx_v = 0, meoplen;
GtWord sumscore = 0;
GtMultieop *meop;
gt_assert(alignment != NULL);
gt_assert(gt_alignment_is_valid(alignment));
meoplen = gt_multieoplist_get_length(alignment->eops);
for (i = meoplen; i > 0; i--) {
meop = gt_multieoplist_get_entry(alignment->eops, i - 1);
switch (meop->type) {
case Mismatch:
case Match:
case Replacement:
for (j = 0; j < meop->steps; j++) {
if (alignment->u[idx_u] == alignment->v[idx_v] &&
ISNOTSPECIAL(alignment->u[idx_u])) {
sumscore += matchscore;
}
else {
sumscore += mismatchscore;
}
idx_u++;
idx_v++;
}
break;
case Deletion:
sumscore += gapscore * meop->steps;
idx_u += meop->steps;
break;
case Insertion:
sumscore += gapscore * meop->steps;
idx_v += meop->steps;
break;
}
}
return sumscore;
}
GtUword gt_alignment_eval(const GtAlignment *alignment)
{
GtUword i, j, idx_u = 0, idx_v = 0, sumcost = 0, meoplen;
GtMultieop *meop;
gt_assert(alignment != NULL);
gt_assert(gt_alignment_is_valid(alignment));
meoplen = gt_multieoplist_get_length(alignment->eops);
for (i = meoplen; i > 0; i--) {
meop = gt_multieoplist_get_entry(alignment->eops, i - 1);
switch (meop->type) {
case Mismatch:
for (j = 0; j < meop->steps; j++) {
sumcost++;
idx_u++;
idx_v++;
}
break;
case Match:
case Replacement:
for (j = 0; j < meop->steps; j++) {
if (tolower((int) alignment->u[idx_u]) !=
tolower((int) alignment->v[idx_v])) {
sumcost++;
}
idx_u++;
idx_v++;
}
break;
case Deletion:
sumcost += meop->steps;
idx_u += meop->steps;
break;
case Insertion:
sumcost += meop->steps;
idx_v += meop->steps;
break;
}
}
return sumcost;
}
void gt_alignment_show_with_mapped_chars(const GtAlignment *alignment,
const GtUchar *characters,
GtUchar wildcardshow,
FILE *fp)
{
GtUword i, j, idx_u, idx_v, meoplen;
GtMultieop *meop;
gt_assert(alignment);
gt_assert(gt_alignment_is_valid(alignment));
meoplen = gt_multieoplist_get_length(alignment->eops);
/* output first line */
idx_u = 0;
for (i = meoplen; i > 0; i--)
{
meop = gt_multieoplist_get_entry(alignment->eops, i - 1);
switch (meop->type)
{
case Mismatch:
case Match:
case Replacement:
case Deletion:
for (j = 0; j < meop->steps; j++)
{
gt_xfputc(ISSPECIAL(alignment->u[idx_u]) ?
(int) wildcardshow :
(int) characters[alignment->u[idx_u]], fp);
idx_u++;
}
break;
case Insertion:
for (j = 0; j < meop->steps; j++)
{
gt_xfputc(GAPSYMBOL, fp);
}
break;
}
}
gt_xfputc('\n', fp);
/* output middle line */
idx_u = idx_v = 0;
for (i = meoplen; i > 0; i--)
{
meop = gt_multieoplist_get_entry(alignment->eops, i - 1);
switch (meop->type)
{
case Mismatch:
case Match:
case Replacement:
for (j = 0; j < meop->steps; j++)
{
if (alignment->u[idx_u] == alignment->v[idx_v] &&
ISNOTSPECIAL(alignment->u[idx_u]))
{
gt_xfputc(MATCHSYMBOL, fp);
} else
{
gt_xfputc(MISMATCHSYMBOL, fp);
}
idx_u++;
idx_v++;
}
break;
case Deletion:
for (j = 0; j < meop->steps; j++)
{
gt_xfputc(MISMATCHSYMBOL, fp);
idx_u++;
}
break;
case Insertion:
for (j = 0; j < meop->steps; j++)
{
gt_xfputc(MISMATCHSYMBOL, fp);
idx_v++;
}
break;
}
}
gt_xfputc('\n', fp);
/* ouput last line */
idx_v = 0;
for (i = meoplen; i > 0; i--)
{
meop = gt_multieoplist_get_entry(alignment->eops, i - 1);
switch (meop->type)
{
case Mismatch:
case Match:
case Replacement:
case Insertion:
for (j = 0; j < meop->steps; j++)
{
gt_xfputc(ISSPECIAL(alignment->v[idx_v]) ?
(int) wildcardshow :
(int) characters[alignment->v[idx_v]], fp);
idx_v++;
}
break;
case Deletion:
for (j = 0; j < meop->steps; j++)
{
gt_xfputc(GAPSYMBOL, fp);
}
break;
}
}
gt_xfputc('\n', fp);
}
/* XXX: add width parameter and format the GtAlignment accordingly */
void gt_alignment_show(const GtAlignment *alignment, FILE *fp)
{
GtUword i, j, idx_u, idx_v, meoplen;
GtMultieop *meop;
gt_assert(alignment);
gt_assert(gt_alignment_is_valid(alignment));
meoplen = gt_multieoplist_get_length(alignment->eops);
/* output first line */
idx_u = 0;
for (i = meoplen; i > 0; i--) {
meop = gt_multieoplist_get_entry(alignment->eops, i - 1);
switch (meop->type) {
case Mismatch:
case Match:
case Replacement:
case Deletion:
for (j = 0; j < meop->steps; j++)
gt_xfputc((int) alignment->u[idx_u++], fp);
break;
case Insertion:
for (j = 0; j < meop->steps; j++)
gt_xfputc(GAPSYMBOL, fp);
break;
}
}
gt_xfputc('\n', fp);
/* output middle line */
idx_u = idx_v = 0;
for (i = meoplen; i > 0; i--) {
meop = gt_multieoplist_get_entry(alignment->eops, i - 1);
switch (meop->type) {
case Mismatch:
case Match:
case Replacement:
for (j = 0; j < meop->steps; j++) {
if (tolower((int) alignment->u[idx_u++]) ==
tolower((int) alignment->v[idx_v++]))
gt_xfputc(MATCHSYMBOL, fp);
else
gt_xfputc(MISMATCHSYMBOL, fp);
}
break;
case Deletion:
for (j = 0; j < meop->steps; j++) {
gt_xfputc(MISMATCHSYMBOL, fp);
idx_u++;
}
break;
case Insertion:
for (j = 0; j < meop->steps; j++) {
gt_xfputc(MISMATCHSYMBOL, fp);
idx_v++;
}
break;
}
}
gt_xfputc('\n', fp);
/* ouput last line */
idx_v = 0;
for (i = meoplen; i > 0; i--) {
meop = gt_multieoplist_get_entry(alignment->eops, i - 1);
switch (meop->type) {
case Mismatch:
case Match:
case Replacement:
case Insertion:
for (j = 0; j < meop->steps; j++)
gt_xfputc((int) alignment->v[idx_v++], fp);
break;
case Deletion:
for (j = 0; j < meop->steps; j++)
gt_xfputc(GAPSYMBOL, fp);
break;
}
}
gt_xfputc('\n', fp);
}
GtUword gt_alignment_get_length(const GtAlignment *alignment)
{
gt_assert(alignment != NULL);
return gt_multieoplist_get_length(alignment->eops);
}