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|
#!/usr/bin/env ruby
def getc_param(key)
if key == "PLAINSEQ" or key == "BARE_ENCSEQ"
return "const GtUchar *plainseq"
elsif key == "INTSEQ"
return "const GtUsainindextype *array"
else
return "const GtEncseq *encseq"
end
end
def getc_argument(key)
if key == "PLAINSEQ" or key == "BARE_ENCSEQ"
return "plainseq"
elsif key == "INTSEQ"
return "array"
else
return "encseq"
end
end
def getc_call(key,posexpr,seqaccess = false)
if key == "PLAINSEQ"
return "(GtUword)\nplainseq[#{posexpr}]"
elsif key == "INTSEQ"
return "(GtUword) array[#{posexpr}]"
elsif key == "BARE_ENCSEQ"
if seqaccess
return "(GtUword)\nGT_ISSPECIAL(tmpcc =\nplainseq[#{posexpr}])\n" +
" ? GT_UNIQUEINT(#{posexpr}) : (GtUword) tmpcc"
else
return "(GtUword)\nplainseq[#{posexpr}]"
end
elsif seqaccess
return "GT_ISSPECIAL(tmpcc =\ngt_encseq_reader_next_encoded_char(esr))\n" +
" ? GT_UNIQUEINT(#{posexpr}) : (GtUword) tmpcc"
else
return "(GtUword) gt_encseq_get_encoded_char(\n" +
"encseq,\n" +
"(GtUword) (#{posexpr}),\n" +
"sainseq->readmode)"
end
end
def special2unique(key,cc,start)
if key == "ENCSEQ" || key == "BARE_ENCSEQ"
return "if (GT_ISSPECIAL(#{cc})) { #{cc} = GT_UNIQUEINT(#{start}); }"
else
return ""
end
end
def declare_tmpvars(key,seqaccess = false)
if seqaccess and key == "ENCSEQ"
return "GtUchar tmpcc;\nGtEncseqReader *esr;"
elsif seqaccess and key == "BARE_ENCSEQ"
return "GtUchar tmpcc;"
else
return ""
end
end
def sstarfirstcharcount_bucketsize_assert_not_NULL(key,which)
if which.member?(key)
return "gt_assert(bucketsize != NULL && sstarfirstcharcount != NULL);"
else
return ""
end
end
def sstarfirstcharcount_update(key,struct,which)
if which.member?(key)
if struct
return "sainseq->sstarfirstcharcount[nextcc]++;"
else
return "sstarfirstcharcount[nextcc]++;"
end
else
return ""
end
end
def bucketsize_update(key,which)
if which.member?(key)
return "bucketsize[currentcc]++;"
else
return ""
end
end
def init_esr(key)
if key == "ENCSEQ"
return "esr = gt_encseq_create_reader_with_readmode(
encseq,
gt_readmode_inverse_direction(sainseq->readmode),
0);"
else
return ""
end
end
def delete_esr(key)
if key == "ENCSEQ"
return "gt_encseq_reader_delete(esr);"
else
return ""
end
end
begin
fo = File.open("src/match/sfx-sain.inc","w")
rescue => err
STDERR.puts "#{$0}: #{err}"
exit 1
end
fo.puts "/* Do not edit this file, as it is generated by #{__FILE__}.\n*/"
["PLAINSEQ","ENCSEQ","INTSEQ"].each do |key|
fo.puts <<CCODE
static void gt_sain_#{key}_fast_induceLtypesuffixes1(GtSainseq *sainseq,
#{getc_param(key)},
GtSsainindextype *suftab,
GtUword nonspecialentries)
{
GtUword lastupdatecc = 0;
GtSsainindextype *suftabptr, *bucketptr = NULL;
#{declare_tmpvars(key)}
GtUsainindextype *fillptr = sainseq->bucketfillptr;
gt_assert(sainseq->roundtable != NULL);
for (suftabptr = suftab, sainseq->currentround = 0;
suftabptr < suftab + nonspecialentries; suftabptr++)
{
GtSsainindextype position;
if ((position = *suftabptr) > 0)
{
GtUword currentcc;
if (position >= (GtSsainindextype) sainseq->totallength)
{
sainseq->currentround++;
position -= (GtSsainindextype) sainseq->totallength;
}
currentcc = #{getc_call(key,"position")};
if (currentcc < sainseq->numofchars)
{
if (position > 0)
{
GtUword t, leftcontextcc;
position--;
leftcontextcc = #{getc_call(key,"position")};
t = (currentcc << 1) | (leftcontextcc < currentcc ? 1UL : 0);
gt_assert(currentcc > 0 &&
sainseq->roundtable[t] <= sainseq->currentround);
if (sainseq->roundtable[t] < sainseq->currentround)
{
position += (GtSsainindextype) sainseq->totallength;
sainseq->roundtable[t] = sainseq->currentround;
}
GT_SAINUPDATEBUCKETPTR(currentcc);
/* negative => position does not derive L-suffix
positive => position may derive L-suffix */
gt_assert(suftabptr < bucketptr);
*bucketptr++ = (t & 1UL) ? ~position : position;
*suftabptr = 0;
#ifdef SAINSHOWSTATE
gt_assert(bucketptr != NULL);
printf("L-induce: suftab[" GT_WU "]=" GT_WD "\\n",
(GtUword) (bucketptr-1-suftab),*(bucketptr-1));
#endif
}
} else
{
*suftabptr = 0;
}
} else
{
if (position < 0)
{
*suftabptr = ~position;
}
}
}
}
static void gt_sain_#{key}_induceLtypesuffixes1(GtSainseq *sainseq,
#{getc_param(key)},
GtSsainindextype *suftab,
GtUword nonspecialentries)
{
GtUword lastupdatecc = 0;
GtUsainindextype *fillptr = sainseq->bucketfillptr;
#{declare_tmpvars(key)}
GtSsainindextype *suftabptr, *bucketptr = NULL;
gt_assert(sainseq->roundtable == NULL);
for (suftabptr = suftab; suftabptr < suftab + nonspecialentries; suftabptr++)
{
GtSsainindextype position;
if ((position = *suftabptr) > 0)
{
GtUword currentcc = #{getc_call(key,"position")};
if (currentcc < sainseq->numofchars)
{
if (position > 0)
{
GtUword leftcontextcc;
position--;
leftcontextcc = #{getc_call(key,"position")};
GT_SAINUPDATEBUCKETPTR(currentcc);
/* negative => position does not derive L-suffix
positive => position may derive L-suffix */
gt_assert(suftabptr < bucketptr);
*bucketptr++ = (leftcontextcc < currentcc) ? ~position : position;
*suftabptr = 0;
#ifdef SAINSHOWSTATE
gt_assert(bucketptr != NULL);
printf("L-induce: suftab[" GT_WU "]=" GT_WD "\\n",
(GtUword) (bucketptr-1-suftab),*(bucketptr-1));
#endif
}
} else
{
*suftabptr = 0;
}
} else
{
if (position < 0)
{
*suftabptr = ~position;
}
}
}
}
static void gt_sain_#{key}_fast_induceStypesuffixes1(GtSainseq *sainseq,
#{getc_param(key)},
GtSsainindextype *suftab,
GtUword nonspecialentries)
{
GtUword lastupdatecc = 0;
GtUsainindextype *fillptr = sainseq->bucketfillptr;
#{declare_tmpvars(key)}
GtSsainindextype *suftabptr, *bucketptr = NULL;
gt_assert(sainseq->roundtable != NULL);
gt_sain_special_singleSinduction1(sainseq,
suftab,
(GtSsainindextype)
(sainseq->totallength-1));
if (sainseq->seqtype == GT_SAIN_ENCSEQ ||
sainseq->seqtype == GT_SAIN_BARE_ENCSEQ)
{
gt_sain_induceStypes1fromspecialranges(sainseq,suftab);
}
for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
suftabptr--)
{
GtSsainindextype position;
if ((position = *suftabptr) > 0)
{
if (position >= (GtSsainindextype) sainseq->totallength)
{
sainseq->currentround++;
position -= (GtSsainindextype) sainseq->totallength;
}
if (position > 0)
{
GtUword currentcc = #{getc_call(key,"position")};
if (currentcc < sainseq->numofchars)
{
GtUword t, leftcontextcc;
position--;
leftcontextcc = #{getc_call(key,"position")};
t = (currentcc << 1) | (leftcontextcc > currentcc ? 1UL : 0);
gt_assert(sainseq->roundtable[t] <= sainseq->currentround);
if (sainseq->roundtable[t] < sainseq->currentround)
{
position += (GtSsainindextype) sainseq->totallength;
sainseq->roundtable[t] = sainseq->currentround;
}
GT_SAINUPDATEBUCKETPTR(currentcc);
gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
*(--bucketptr) = (t & 1UL) ? ~(position+1) : position;
#ifdef SAINSHOWSTATE
printf("S-induce: suftab[" GT_WU "]=" GT_WD "\\n",
(GtUword) (bucketptr - suftab),*bucketptr);
#endif
}
}
*suftabptr = 0;
}
}
}
static void gt_sain_#{key}_induceStypesuffixes1(GtSainseq *sainseq,
#{getc_param(key)},
GtSsainindextype *suftab,
GtUword nonspecialentries)
{
GtUword lastupdatecc = 0;
GtUsainindextype *fillptr = sainseq->bucketfillptr;
#{declare_tmpvars(key)}
GtSsainindextype *suftabptr, *bucketptr = NULL;
gt_assert(sainseq->roundtable == NULL);
gt_sain_special_singleSinduction1(sainseq,
suftab,
(GtSsainindextype)
(sainseq->totallength-1));
if (sainseq->seqtype == GT_SAIN_ENCSEQ ||
sainseq->seqtype == GT_SAIN_BARE_ENCSEQ)
{
gt_sain_induceStypes1fromspecialranges(sainseq,suftab);
}
for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
suftabptr--)
{
GtSsainindextype position;
if ((position = *suftabptr) > 0)
{
GtUword currentcc = #{getc_call(key,"position")};
if (currentcc < sainseq->numofchars)
{
GtUword leftcontextcc;
position--;
leftcontextcc = #{getc_call(key,"position")};
GT_SAINUPDATEBUCKETPTR(currentcc);
gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
*(--bucketptr) = (leftcontextcc > currentcc)
? ~(position+1) : position;
#ifdef SAINSHOWSTATE
printf("S-induce: suftab[" GT_WU "]=" GT_WD "\\n",
(GtUword) (bucketptr - suftab),*bucketptr);
#endif
}
*suftabptr = 0;
}
}
}
static void gt_sain_#{key}_induceLtypesuffixes2(const GtSainseq *sainseq,
#{getc_param(key)},
GtSsainindextype *suftab,
GtUword nonspecialentries)
{
GtUword lastupdatecc = 0;
GtUsainindextype *fillptr = sainseq->bucketfillptr;
#{declare_tmpvars(key)}
GtSsainindextype *suftabptr, *bucketptr = NULL;
for (suftabptr = suftab; suftabptr < suftab + nonspecialentries; suftabptr++)
{
GtSsainindextype position = *suftabptr;
*suftabptr = ~position;
if (position > 0)
{
GtUword currentcc;
position--;
currentcc = #{getc_call(key,"position")};
if (currentcc < sainseq->numofchars)
{
gt_assert(currentcc > 0);
GT_SAINUPDATEBUCKETPTR(currentcc);
gt_assert(bucketptr != NULL && suftabptr < bucketptr);
*bucketptr++ = (position > 0 &&
(#{getc_call(key,"position-1")}) < currentcc)
? ~position : position;
#ifdef SAINSHOWSTATE
gt_assert(bucketptr != NULL);
printf("L-induce: suftab[" GT_WU "]=" GT_WD "\\n",
(GtUword) (bucketptr-1-suftab),*(bucketptr-1));
#endif
}
}
}
}
static void gt_sain_#{key}_induceStypesuffixes2(const GtSainseq *sainseq,
#{getc_param(key)},
GtSsainindextype *suftab,
GtUword nonspecialentries)
{
GtUword lastupdatecc = 0;
GtUsainindextype *fillptr = sainseq->bucketfillptr;
#{declare_tmpvars(key)}
GtSsainindextype *suftabptr, *bucketptr = NULL;
gt_sain_special_singleSinduction2(sainseq,
suftab,
(GtSsainindextype) sainseq->totallength,
nonspecialentries);
if (sainseq->seqtype == GT_SAIN_ENCSEQ ||
sainseq->seqtype == GT_SAIN_BARE_ENCSEQ)
{
gt_sain_induceStypes2fromspecialranges(sainseq,suftab,nonspecialentries);
}
for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
suftabptr--)
{
GtSsainindextype position;
if ((position = *suftabptr) > 0)
{
GtUword currentcc;
position--;
currentcc = #{getc_call(key,"position")};
if (currentcc < sainseq->numofchars)
{
GT_SAINUPDATEBUCKETPTR(currentcc);
gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
*(--bucketptr) = (position == 0 ||
(#{getc_call(key,"position-1")}) > currentcc)
? ~position : position;
#ifdef SAINSHOWSTATE
gt_assert(bucketptr != NULL);
printf("S-induce: suftab[" GT_WU "]=" GT_WD "\\n",
(GtUword) (bucketptr-suftab),*bucketptr);
#endif
}
} else
{
*suftabptr = ~position;
}
}
}
CCODE
end
["PLAINSEQ","ENCSEQ","BARE_ENCSEQ","INTSEQ"].each do |key|
fo.puts <<CCODE
static int gt_sain_#{key}_compare_Sstarstrings(const GtSainseq *sainseq,
#{getc_param(key)},
GtUword start1,
GtUword start2,
GtUword len)
{
GtUword end1 = start1 + len;
gt_assert(start1 <= sainseq->totallength &&
start2 <= sainseq->totallength &&
start1 != start2);
while (start1 < end1)
{
GtUword cc1, cc2;
if (start1 == sainseq->totallength)
{
gt_assert(start1 > start2);
return 1;
}
if (start2 == sainseq->totallength)
{
gt_assert(start1 < start2);
return -1;
}
cc1 = #{getc_call(key,"start1")};#{special2unique(key,"cc1","start1")};
cc2 = #{getc_call(key,"start2")};#{special2unique(key,"cc2","start2")};
if (cc1 < cc2)
{
return -1;
}
if (cc1 > cc2)
{
return 1;
}
start1++;
start2++;
}
return 0;
}
static void gt_sain_#{key}_expandorder2original(GtSainseq *sainseq,
#{getc_param(key)},
GtUword numberofsuffixes,
GtUsainindextype *suftab)
{
GtUsainindextype *suftabptr,
position,
*sstarsuffixes = suftab + GT_MULT2(numberofsuffixes),
*sstarfirstcharcount = NULL,
*bucketsize = NULL;
GtUword nextcc = GT_UNIQUEINT(sainseq->totallength);
#{declare_tmpvars(key,true)}
bool nextisStype = true;
if (sainseq->seqtype == GT_SAIN_INTSEQ)
{
GtUword charidx;
gt_assert(sainseq->sstarfirstcharcount == NULL);
sstarfirstcharcount = sainseq->sstarfirstcharcount
= sainseq->bucketfillptr;
bucketsize = sainseq->bucketsize;
for (charidx = 0; charidx < sainseq->numofchars; charidx++)
{
sstarfirstcharcount[charidx] = 0;
bucketsize[charidx] = 0;
}
}
#{sstarfirstcharcount_bucketsize_assert_not_NULL(key,["INTSEQ"])}#{init_esr(key)}
for (position = (GtUsainindextype) (sainseq->totallength-1); /* Nothing */;
position--)
{
GtUword currentcc = #{getc_call(key,"position",true)};
bool currentisStype = (currentcc < nextcc ||
(currentcc == nextcc && nextisStype)) ? true : false;
if (!currentisStype && nextisStype)
{
#{sstarfirstcharcount_update(key,false,["INTSEQ"])}
*--sstarsuffixes = position+1;
}
#{bucketsize_update(key,["INTSEQ"])}
nextisStype = currentisStype;
nextcc = currentcc;
if (position == 0)
{
break;
}
}
#{delete_esr(key)}
for (suftabptr = suftab; suftabptr < suftab + numberofsuffixes; suftabptr++)
{
*suftabptr = sstarsuffixes[*suftabptr];
}
}
static GtUword gt_sain_#{key}_insertSstarsuffixes(GtSainseq *sainseq,
#{getc_param(key)},
GtUsainindextype *suftab,
GtLogger *logger)
{
GtUword nextcc = GT_UNIQUEINT(sainseq->totallength),
countSstartype = 0;
GtUsainindextype position, *fillptr = sainseq->bucketfillptr;
GtSainbuffer *sainbuffer = gt_sainbuffer_new(suftab,fillptr,
sainseq->numofchars,
sainseq->totallength,logger);
#{declare_tmpvars(key,true)}
bool nextisStype = true;
gt_sain_endbuckets(sainseq);
#{init_esr(key)}
for (position = (GtUsainindextype) (sainseq->totallength-1); /* Nothing */;
position--)
{
GtUword currentcc = #{getc_call(key,"position",true)};
bool currentisStype = (currentcc < nextcc ||
(currentcc == nextcc && nextisStype)) ? true : false;
if (!currentisStype && nextisStype)
{
countSstartype++;
#{sstarfirstcharcount_update(key,true,["PLAINSEQ","ENCSEQ","BARE_ENCSEQ"])}
if (sainbuffer != NULL)
{
gt_sainbuffer_update(sainbuffer,nextcc,position);
} else
{
suftab[--fillptr[nextcc]] = position;
}
#undef SAINSHOWSTATE
#ifdef SAINSHOWSTATE
printf("Sstar.suftab[" GT_WU "]=" GT_WU "\\n",fillptr[nextcc],position+1);
#endif
}
nextisStype = currentisStype;
nextcc = currentcc;
if (position == 0)
{
break;
}
}
#{delete_esr(key)}
gt_sainbuffer_flushall(sainbuffer);
gt_sainbuffer_delete(sainbuffer);
gt_assert(GT_MULT2(countSstartype) <= sainseq->totallength);
return countSstartype;
}
static void gt_sain_#{key}_assignSstarlength(GtSainseq *sainseq,
#{getc_param(key)},
GtUsainindextype *lentab)
{
bool nextisStype = true;
GtUsainindextype position,
nextSstartypepos = (GtUsainindextype) sainseq->totallength;
#{declare_tmpvars(key,true)}
GtUword nextcc = GT_UNIQUEINT(sainseq->totallength);
#{init_esr(key)}
for (position = (GtUsainindextype) (sainseq->totallength-1); /* Nothing */;
position--)
{
GtUword currentcc = #{getc_call(key,"position",true)};
bool currentisStype = (currentcc < nextcc ||
(currentcc == nextcc && nextisStype)) ? true : false;
if (!currentisStype && nextisStype)
{
gt_assert(position < nextSstartypepos);
lentab[GT_DIV2(position+1)] = nextSstartypepos - position;
nextSstartypepos = position + 1;
}
nextisStype = currentisStype;
nextcc = currentcc;
if (position == 0)
{
break;
}
}
#{delete_esr(key)}
}
CCODE
end
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