int gt_nextSequentiallcpvalue(GtUword *currentlcp,
Sequentialsuffixarrayreader *ssar,
GtError *err)
{
GtUchar tmpsmalllcpvalue;
int retval;
gt_assert(ssar != NULL);
if (ssar->scanfile)
{
retval = gt_readnextfromstream_GtUchar(&tmpsmalllcpvalue,
&ssar->suffixarray->lcptabstream);
if (retval > 0)
{
if (tmpsmalllcpvalue < (GtUchar) LCPOVERFLOW)
{
*currentlcp = (GtUword) tmpsmalllcpvalue;
} else
{
Largelcpvalue tmpexception;
retval = gt_readnextfromstream_Largelcpvalue(&tmpexception,
&ssar->suffixarray->llvtabstream);
if (retval == 0)
{
gt_error_set(err,"file %s: line %d: unexpected end of file when "
"reading llvtab",__FILE__,__LINE__);
return -1;
}
*currentlcp = tmpexception.value;
}
} else
{
return 0;
}
} else
{
if (ssar->nextlcptabindex < ssar->numberofsuffixes)
{
tmpsmalllcpvalue = ssar->suffixarray->lcptab[ssar->nextlcptabindex++];
if (tmpsmalllcpvalue < (GtUchar) LCPOVERFLOW)
{
*currentlcp = (GtUword) tmpsmalllcpvalue;
} else
{
gt_assert(ssar->suffixarray->llvtab[ssar->largelcpindex].position ==
ssar->nextlcptabindex-1);
*currentlcp = ssar->suffixarray->llvtab[ssar->largelcpindex++].value;
}
} else
{
return 0;
}
}
return 1;
}
int gt_emissionmergedesa_stepdeleteandinsertothersuffixes(
Emissionmergedesa *emmesa, GtError *err)
{
Mergertrienode *tmpsmallestleaf, *tmplcpnode;
Largelcpvalue tmpexception;
GtUchar tmpsmalllcpvalue;
int retval;
unsigned long tmpsuftabvalue,
tmplcpvalue,
tmplastbranchdepth;
unsigned int tmpidx;
gt_error_check(err);
for (emmesa->buf.nextstoreidx = 0;
emmesa->numofentries > 0 &&
emmesa->buf.nextstoreidx < (unsigned int) SIZEOFMERGERESULTBUFFER;
emmesa->buf.nextstoreidx++)
{
tmpsmallestleaf = gt_mergertrie_findsmallestnode(&emmesa->trierep);
tmplastbranchdepth = tmpsmallestleaf->parent->depth;
tmpidx = tmpsmallestleaf->suffixinfo.idx;
emmesa->buf.suftabstore[emmesa->buf.nextstoreidx].idx = tmpidx;
emmesa->buf.suftabstore[emmesa->buf.nextstoreidx].startpos
= tmpsmallestleaf->suffixinfo.startpos;
if (emmesa->nextpostable[tmpidx] >
gt_encseq_total_length(emmesa->suffixarraytable[tmpidx].encseq))
{
gt_mergertrie_deletesmallestpath(tmpsmallestleaf,&emmesa->trierep);
emmesa->numofentries--;
} else
{
retval = gt_readnextfromstream_GtUchar(&tmpsmalllcpvalue,
&emmesa->suffixarraytable[tmpidx].
lcptabstream);
if (retval < 0)
{
return -1;
}
if (retval == 0)
{
gt_error_set(err,"file %s: line %d: unexpected end of file when "
"reading lcptab",__FILE__,__LINE__);
return -2;
}
if (tmpsmalllcpvalue == LCPOVERFLOW)
{
retval = gt_readnextfromstream_Largelcpvalue(
&tmpexception,
&emmesa->suffixarraytable[tmpidx].llvtabstream);
if (retval < 0)
{
return -3;
}
if (retval == 0)
{
gt_error_set(err,"file %s: line %d: unexpected end of file when "
"reading llvtab",__FILE__,__LINE__);
return -4;
}
tmplcpvalue = tmpexception.value;
} else
{
tmplcpvalue = (unsigned long) tmpsmalllcpvalue;
}
if (tmplcpvalue > tmplastbranchdepth)
{
tmplastbranchdepth = tmplcpvalue;
}
tmplcpnode = findlargestnodeleqlcpvalue(tmpsmallestleaf,tmplcpvalue,err);
retval = gt_readnextfromstream_GtUlong(&tmpsuftabvalue,
&emmesa->suffixarraytable[tmpidx].
suftabstream_GtUlong);
if (retval == 0)
{
gt_error_set(err,"file %s: line %d: unexpected end of file when "
"reading suftab",__FILE__,__LINE__);
return -6;
}
emmesa->nextpostable[tmpidx]++;
fillandinsert(&emmesa->trierep,
tmpidx,
tmpsuftabvalue,
tmplcpnode,
emmesa->ident++);
tmpsmallestleaf = gt_mergertrie_findsmallestnode(&emmesa->trierep);
gt_mergertrie_deletesmallestpath(tmpsmallestleaf,&emmesa->trierep);
}
if (emmesa->numofentries > 0)
{
emmesa->buf.lcptabstore[emmesa->buf.nextstoreidx]
= tmplastbranchdepth;
emmesa->buf.lastpage = false;
} else
{
emmesa->buf.lastpage = true;
}
}
return 0;
}
