void gt_eoplist_match_add(GtEoplist *eoplist,GtUword length)
{
gt_assert(eoplist != NULL && length > 0);
eoplist->countmatches += length;
while (true)
{
if (length <= FT_EOPCODE_MAXMATCHES)
{
gt_assert(length > 0);
GT_EOPLIST_PUSH(eoplist,(uint8_t) (length - 1)); /* R length */
break;
}
GT_EOPLIST_PUSH(eoplist,FT_EOPCODE_MAXMATCHES - 1); /* R max */
length -= FT_EOPCODE_MAXMATCHES;
}
}
void front_trace_multireplacement(GtEoplist *eoplist,GtUword repnum)
{
gt_assert(eoplist != NULL && repnum > 0);
eoplist->countmatches += repnum;
while (true)
{
if (repnum <= FT_EOPCODE_MAXREPLACEMENT)
{
gt_assert(repnum > 0);
GT_EOPLIST_PUSH(eoplist,(uint8_t) (repnum - 1)); /* R repnum */
break;
}
GT_EOPLIST_PUSH(eoplist,FT_EOPCODE_MAXREPLACEMENT - 1); /* R max */
repnum -= FT_EOPCODE_MAXREPLACEMENT;
}
}
void gt_eoplist_insertion_add(GtEoplist *eoplist)
{
gt_assert(eoplist != NULL);
GT_EOPLIST_PUSH(eoplist,FT_EOPCODE_INSERTION);
eoplist->countinsertions++;
}
void gt_eoplist_deletion_add(GtEoplist *eoplist)
{
GT_EOPLIST_PUSH(eoplist,FT_EOPCODE_DELETION);
eoplist->countdeletions++;
}
void gt_eoplist_mismatch_add(GtEoplist *eoplist)
{
GT_EOPLIST_PUSH(eoplist,FT_EOPCODE_MISMATCH); /* R 1 */
eoplist->countmismatches++;
}
static void gt_front_trace_backtracepath2eoplist(GtEoplist *eoplist,
unsigned int lastlcs,
const GtBacktraceFrontpath
*backtracepath,
GtUword elementsinbacktracepath,
GT_UNUSED GtUword ulen,
GT_UNUSED GtUword vlen)
{
GtUword idx, deletions = 0, insertions = 0, mismatches = 0, matches = 0;
if (lastlcs > 0)
{
front_trace_multireplacement(eoplist,lastlcs);
matches += lastlcs;
}
gt_assert(eoplist != NULL);
for (idx = 0; idx < elementsinbacktracepath; idx++)
{
if (backtracepath[idx].eopcode == FT_EOPCODE_DELETION)
{
eoplist->countdeletions++;
deletions++;
} else
{
if (backtracepath[idx].eopcode == FT_EOPCODE_INSERTION)
{
eoplist->countinsertions++;
insertions++;
} else
{
eoplist->countmismatches++;
mismatches++;
}
}
GT_EOPLIST_PUSH(eoplist,backtracepath[idx].eopcode);
if (backtracepath[idx].lcs > 0)
{
front_trace_multireplacement(eoplist,backtracepath[idx].lcs);
matches += backtracepath[idx].lcs;
}
}
/*
if (matches + mismatches + deletions != ulen)
{
fprintf(stderr,
"matches=" GT_WU ",mismatches=" GT_WU ",deletions=" GT_WU ","
"sum=" GT_WU " != " GT_WU " = ulen\n",
matches,mismatches,deletions,
matches+mismatches+deletions,
ulen);
}
if (matches + mismatches + insertions != vlen)
{
fprintf(stderr,
"matches=" GT_WU ",mismatches=" GT_WU ",insertions=" GT_WU ","
"sum=" GT_WU " " != " GT_WU " = vlen\n",
matches,mismatches,insertions,
matches+mismatches+insertions,
vlen);
}
*/
}
static void front_trace2eoplist_directed(GtEoplist *eoplist,
GtFronttrace *front_trace,
const Polished_point *pp,
const GtUchar *useq,
GT_UNUSED GtUword ulen,
const GtUchar *vseq,
GT_UNUSED GtUword vlen)
{
GtUword distance, localoffset, globaloffset, remainingvalidfronts,
totalrunlength = 0, trimleft;
GtWord diagonal;
unsigned int row, lcs;
uint8_t trace, preferred_eop = FT_EOP_REPLACEMENT;
gt_assert(front_trace != NULL && front_trace->gen_nextfree > 0 && pp != NULL);
localoffset = polished_point2offset(front_trace,pp);
remainingvalidfronts = valid_total_fronts(front_trace->gen_table,
pp->distance,
front_trace->gen_nextfree);
gt_assert(remainingvalidfronts <= front_trace->backref_nextfree);
globaloffset = front_trace->backref_nextfree - remainingvalidfronts;
distance = pp->distance;
diagonal = (GtWord) pp->alignedlen - (GtWord) GT_MULT2(pp->row);
trace = front_trace->backref_table[globaloffset + localoffset].bits;
lcs = front_trace->backref_table[globaloffset + localoffset].lcs;
row = pp->row;
trimleft = pp->trimleft;
gt_assert(distance < front_trace->gen_nextfree);
while (distance > 0)
{
GtUword nextrowadd;
GtWord base_diagonal;
if (eoplist != NULL)
{
if (lcs > 0)
{
front_trace_multireplacement(eoplist,lcs);
}
} else
{
gt_check_diagonal_run(useq, vseq, diagonal, row - lcs, row);
}
if (trace & preferred_eop)
{
totalrunlength++;
if (preferred_eop == FT_EOP_REPLACEMENT)
{
nextrowadd = 1;
} else
{
if (preferred_eop == FT_EOP_INSERTION)
{
gt_assert(-(GtWord) ulen < diagonal);
diagonal--;
nextrowadd = 0;
} else
{
gt_assert(preferred_eop == FT_EOP_DELETION);
gt_assert(diagonal < (GtWord) vlen);
diagonal++;
nextrowadd = 1;
}
}
} else
{
if (trace & FT_EOP_REPLACEMENT)
{
preferred_eop = FT_EOP_REPLACEMENT;
nextrowadd = 1;
} else
{
if (trace & FT_EOP_INSERTION)
{
gt_assert(-(GtWord) ulen < diagonal);
diagonal--;
preferred_eop = FT_EOP_INSERTION;
nextrowadd = 0;
} else
{
gt_assert(trace & FT_EOP_DELETION);
gt_assert(diagonal < (GtWord) vlen);
diagonal++;
preferred_eop = FT_EOP_DELETION;
nextrowadd = 1;
}
}
}
if (eoplist != NULL)
{
if (preferred_eop == FT_EOP_DELETION)
{
GT_EOPLIST_PUSH(eoplist,FT_EOPCODE_DELETION);
eoplist->countdeletions++;
} else
{
if (preferred_eop == FT_EOP_INSERTION)
{
GT_EOPLIST_PUSH(eoplist,FT_EOPCODE_INSERTION);
eoplist->countinsertions++;
} else
{
GT_EOPLIST_PUSH(eoplist,0); /* R 1 */
eoplist->countmismatches++;
}
}
}
gt_assert(trimleft >=
(GtUword) front_trace->gen_table[distance].trimleft_diff);
trimleft -= (GtUword) front_trace->gen_table[distance].trimleft_diff;
distance--;
base_diagonal = (GtWord) trimleft - (GtWord) distance;
gt_assert(base_diagonal <= diagonal);
gt_assert(diagonal <
base_diagonal + (GtWord) front_trace->gen_table[distance].valid);
localoffset = (GtUword) (diagonal - base_diagonal);
gt_assert((GtUword) front_trace->gen_table[distance].valid
<= globaloffset);
globaloffset -= (GtUword) front_trace->gen_table[distance].valid;
gt_assert(row >= lcs + nextrowadd);
row -= lcs + nextrowadd;
trace = front_trace->backref_table[globaloffset + localoffset].bits;
lcs = front_trace->backref_table[globaloffset + localoffset].lcs;
}
/*printf("avg runlength=%.2f\n",(double) pp->distance/totalrunlength);*/
gt_assert(globaloffset + localoffset == 0 && trace == 0);
if (eoplist != NULL && lcs > 0)
{
front_trace_multireplacement(eoplist,lcs);
}
}