static void determineCtab0(GtUword *Ctab, GtScoreHandler *scorehandler,
GtUchar vseq0, const GtUchar *useq, GtUword ustart)
{
GtUword rowindex, repl, mincost = GT_UWORD_MAX;
if (Ctab[1] == 0)
{
Ctab[0] = 0;
return;
}
for (rowindex = 0; rowindex < Ctab[1]; rowindex++)
{
repl = gt_scorehandler_get_replacement(scorehandler,
vseq0, useq[ustart+rowindex]);
if (repl == 0)
{
Ctab[0] = rowindex;
return;
}
if (repl <= mincost)
{
mincost = repl;
Ctab[0] = rowindex;
}
}
if (mincost > 2 * gt_scorehandler_get_gapscore(scorehandler))
{
Ctab[0] = (Ctab[1] > 0) ? Ctab[1]-1 : 0;
}
}
static void nextLStabcolumn(GtWord *Ltabcolumn,
GtUwordPair *Starttabcolumn,
GtScoreHandler *scorehandler,
const GtUchar *useq,
GtUword ustart, GtUword ulen,
const GtUchar b, GtUword colindex,
Gtmaxcoordvalue *max)
{
GtUword rowindex;
GtUwordPair northwestStarttabentry, westStarttabentry;
GtWord northwestLtabentry, westLtabentry, gapscore;
gt_assert(max != NULL);
gapscore = gt_scorehandler_get_gapscore(scorehandler);
westLtabentry = Ltabcolumn[0];
westStarttabentry = Starttabcolumn[0];
Ltabcolumn[0] = 0;
Starttabcolumn[0].a = 0;
Starttabcolumn[0].b = colindex;
for (rowindex = 1UL; rowindex <= ulen; rowindex++)
{
GtWord val;
northwestLtabentry = westLtabentry;
northwestStarttabentry = westStarttabentry;
westLtabentry = Ltabcolumn[rowindex];
westStarttabentry = Starttabcolumn[rowindex];
Ltabcolumn[rowindex] += gapscore;
val = northwestLtabentry + gt_scorehandler_get_replacement(scorehandler,
useq[ustart + rowindex-1], b);
if (val >= Ltabcolumn[rowindex])
{
Ltabcolumn[rowindex] = val;
Starttabcolumn[rowindex] = northwestStarttabentry;
}
if ((val = Ltabcolumn[rowindex-1]+gapscore) > Ltabcolumn[rowindex])
{
Ltabcolumn[rowindex] = val;
Starttabcolumn[rowindex]=Starttabcolumn[rowindex-1];
}
if (0 > Ltabcolumn[rowindex])
{
Ltabcolumn[rowindex] = 0;
Starttabcolumn[rowindex].a = rowindex;
Starttabcolumn[rowindex].b = colindex;
}
if (Ltabcolumn[rowindex] > gt_max_get_value(max))
{
gt_max_coord_update(max, Ltabcolumn[rowindex],
Starttabcolumn[rowindex],
rowindex, colindex);
}
}
}
static void nextEDtabRtabcolumn(GtUword *EDtabcolumn,
GtUword *Rtabcolumn,
GtUword colindex,
GtUword midcolumn,
GtUchar b,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
GtScoreHandler *scorehandler)
{
GtUword rowindex, val, gapcost,
northwestEDtabentry,
westEDtabentry,
northwestRtabentry,
westRtabentry = 0;
gt_assert(scorehandler);
gapcost = gt_scorehandler_get_gapscore(scorehandler);
westEDtabentry = EDtabcolumn[0];
EDtabcolumn[0] += gapcost;
if (colindex > midcolumn)
{
Rtabcolumn[0] = 0;
}
for (rowindex = 1UL; rowindex <= ulen; rowindex++) {
northwestEDtabentry = westEDtabentry;
northwestRtabentry = westRtabentry;
westEDtabentry = EDtabcolumn[rowindex];
westRtabentry = Rtabcolumn[rowindex];
EDtabcolumn[rowindex] += gapcost; /* 1. recurrence */
/* 2. recurrence: */
val = northwestEDtabentry + gt_scorehandler_get_replacement(scorehandler,
useq[ustart+rowindex-1], b);
if (val <= EDtabcolumn[rowindex])
{
EDtabcolumn[rowindex] = val;
if (colindex > midcolumn)
{
Rtabcolumn[rowindex] = northwestRtabentry;
}
}
/* 3. recurrence: */
if ((val = EDtabcolumn[rowindex-1]+gapcost) < EDtabcolumn[rowindex])
{
EDtabcolumn[rowindex] = val;
if (colindex > midcolumn)
{
Rtabcolumn[rowindex] = Rtabcolumn[rowindex-1];
}
}
}
}
/*----------------------------local alignment---------------------------------*/
static GtWord fillDPtab_in_square_space_local(GtWord **Ltabcolumn,
GtMaxcoordvalue *max,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen,
const GtScoreHandler *scorehandler)
{
GtUword i, j;
GtWord gapscore, maxscore, overall_maxscore = 0;
gapscore = gt_scorehandler_get_gapscore(scorehandler);
Ltabcolumn[0][0] = 0;
for (i = 1; i <= ulen; i++)
{
Ltabcolumn[i][0] = 0;
}
for (j = 1; j <= vlen; j++)
{
Ltabcolumn[0][j] = 0;
for (i = 1; i <= ulen; i++)
{
GtWord val;
Ltabcolumn[i][j] = Ltabcolumn[i][j-1] + gapscore;
val = Ltabcolumn[i-1][j-1] +
gt_scorehandler_get_replacement(scorehandler,
useq[ustart+i-1], vseq[vstart+j-1]);
if (val >= Ltabcolumn[i][j])
{
Ltabcolumn[i][j] = val;
}
if ((val = Ltabcolumn[i-1][j] + gapscore) > Ltabcolumn[i][j])
{
Ltabcolumn[i][j] = val;
}
Ltabcolumn[i][j] = MAX(Ltabcolumn[i][j],0);
maxscore = Ltabcolumn[i][j];
if (maxscore > (GtWord) overall_maxscore)
{
overall_maxscore = maxscore;
gt_max_coord_update_without_start (max, maxscore,i,j);
}
}
}
return overall_maxscore;
}
static void evaluate_crosspoints_from_2dimtab(
GtUword **E,
GtUword *Ctab,
const GtScoreHandler *scorehandler,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen,
GtUword rowoffset)
{
GtUword gapcost, idx, jdx;
gt_assert(E && Ctab);
gapcost = gt_scorehandler_get_gapscore(scorehandler);
idx = ulen;
jdx = vlen;
while (jdx > 1 || idx > 0)
{
if (idx > 0 && jdx > 0 && E[idx][jdx] == E[idx-1][jdx-1] +
gt_scorehandler_get_replacement(scorehandler,
useq[ustart+idx-1],
vseq[vstart+jdx-1]))
{
idx--;
jdx--;
Ctab[jdx] = idx + rowoffset;
}
else if (idx > 0 && E[idx][jdx] == E[idx-1][jdx] + gapcost)
{
idx--;
/*continue*/
}
else if (jdx > 0 && E[idx][jdx] == E[idx][jdx-1] + gapcost)
{
jdx--;
Ctab[jdx] = idx + rowoffset;
}
else
gt_assert(false);
}
}
/*----------------------------global alignment--------------------------------*/
static void fillDPtab_in_square_space(GtUword **E,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen,
const GtScoreHandler *scorehandler)
{
GtUword i, j, gapcost;
gapcost = gt_scorehandler_get_gapscore(scorehandler);
E[0][0] = 0;
for (i = 1; i <= ulen; i++)
{
E[i][0] = E[i-1][0] + gapcost;
}
for (j = 1; j <= vlen; j++)
{
E[0][j] = E[0][j-1] + gapcost;
for (i = 1; i <= ulen; i++)
{
GtUword val;
E[i][j] = E[i][j-1] + gapcost;
val = E[i-1][j-1] + gt_scorehandler_get_replacement(scorehandler,
useq[ustart+i-1],
vseq[vstart+j-1]);
if (val <= E[i][j])
{
E[i][j] = val;
}
if ((val = E[i-1][j] + gapcost) < E[i][j])
{
E[i][j] = val;
}
}
}
}
