static void showprjinfo(FILE *outprj,
GtReadmode readmode,
const GtEncseq *encseq,
GtUword numberofallsortedsuffixes,
unsigned int prefixlength,
GtUword numoflargelcpvalues,
double averagelcp,
GtUword maxbranchdepth,
const Definedunsignedlong *longest)
{
GtUword totallength;
GtUword numofsequences;
totallength = gt_encseq_total_length(encseq);
fprintf(outprj,"totallength="GT_WU"\n",totallength);
PRJSPECIALOUT(specialcharacters);
PRJSPECIALOUT(specialranges);
PRJSPECIALOUT(realspecialranges);
PRJSPECIALOUT(lengthofspecialprefix);
PRJSPECIALOUT(lengthofspecialsuffix);
PRJSPECIALOUT(wildcards);
PRJSPECIALOUT(wildcardranges);
PRJSPECIALOUT(realwildcardranges);
PRJSPECIALOUT(lengthofwildcardprefix);
PRJSPECIALOUT(lengthofwildcardsuffix);
numofsequences = gt_encseq_num_of_sequences(encseq);
fprintf(outprj,"numofsequences="GT_WU"\n",numofsequences);
fprintf(outprj,"numofdbsequences="GT_WU"\n",numofsequences);
fprintf(outprj,"numofquerysequences=0\n");
fprintf(outprj,"numberofallsortedsuffixes="GT_WU"\n",
numberofallsortedsuffixes);
if (longest->defined)
{
fprintf(outprj,"longest="GT_WU"\n",longest->valueunsignedlong);
}
fprintf(outprj,"prefixlength=%u\n",prefixlength);
fprintf(outprj,"largelcpvalues="GT_WU"\n",numoflargelcpvalues);
fprintf(outprj,"averagelcp=%.2f\n",averagelcp);
fprintf(outprj,"maxbranchdepth="GT_WU"\n",maxbranchdepth);
fprintf(outprj,"integersize=%u\n",
(unsigned int) (sizeof (GtUword) * CHAR_BIT));
fprintf(outprj,"littleendian=%c\n",gt_is_little_endian() ? '1' : '0');
fprintf(outprj,"readmode=%u\n",(unsigned int) readmode);
fprintf(outprj,"mirrored=%c\n", gt_encseq_is_mirrored(encseq) ? '1' : '0');
}
static int scanprjfileuintkeysviafileptr(Suffixarray *suffixarray,
const char *indexname,
GtLogger *logger,
FILE *fpin,
GtError *err)
{
uint32_t integersize, littleendian, readmodeint, mirrored;
unsigned int linenum;
GtUword currentlinelength;
size_t dbfilelen = strlen(DBFILEKEY);
bool haserr = false;
GtScannedprjkeytable *scannedprjkeytable;
GtStr *currentline;
/* the following five variables are local as the parsed values are
not required: they are determined by reading the encseq */
GtSpecialcharinfo specialcharinfo;
GtUword totallength,
numofsequences,
numofdbsequences,
numofquerysequences;
gt_error_check(err);
scannedprjkeytable = gt_scannedprjkeytable_new();
GT_SCANNEDPRJKEY_ADD("totallength",&totallength,NULL);
GT_SCANNEDPRJKEY_ADD("specialcharacters",
&specialcharinfo.specialcharacters,NULL);
GT_SCANNEDPRJKEY_ADD("specialranges",
&specialcharinfo.specialranges,NULL);
GT_SCANNEDPRJKEY_ADD("realspecialranges",
&specialcharinfo.realspecialranges,NULL);
GT_SCANNEDPRJKEY_ADD("lengthofspecialprefix",
&specialcharinfo.lengthofspecialprefix,NULL);
GT_SCANNEDPRJKEY_ADD("lengthofspecialsuffix",
&specialcharinfo.lengthofspecialsuffix,NULL);
GT_SCANNEDPRJKEY_ADD("wildcards",
&specialcharinfo.wildcards,NULL);
GT_SCANNEDPRJKEY_ADD("wildcardranges",
&specialcharinfo.wildcardranges,NULL);
GT_SCANNEDPRJKEY_ADD("realwildcardranges",
&specialcharinfo.realwildcardranges,NULL);
GT_SCANNEDPRJKEY_ADD("lengthofwildcardprefix",
&specialcharinfo.lengthofwildcardprefix,NULL);
GT_SCANNEDPRJKEY_ADD("lengthofwildcardsuffix",
&specialcharinfo.lengthofwildcardsuffix,NULL);
GT_SCANNEDPRJKEY_ADD("numofsequences",&numofsequences,NULL);
GT_SCANNEDPRJKEY_ADD("numofdbsequences",&numofdbsequences,NULL);
gt_scannedprjkey_add(scannedprjkeytable,"numofquerysequences",
&numofquerysequences,0,false,NULL);
GT_SCANNEDPRJKEY_ADD("numberofallsortedsuffixes",
&suffixarray->numberofallsortedsuffixes,NULL);
GT_SCANNEDPRJKEY_ADD("longest",&suffixarray->longest.valueunsignedlong,
&suffixarray->longest.defined);
GT_SCANNEDPRJKEY_ADD("prefixlength",&suffixarray->prefixlength,NULL);
GT_SCANNEDPRJKEY_ADD("largelcpvalues",
&suffixarray->numoflargelcpvalues.valueunsignedlong,
&suffixarray->numoflargelcpvalues.defined);
gt_scannedprjkey_add(scannedprjkeytable,"averagelcp",
&suffixarray->averagelcp.valuedouble,
sizeof (suffixarray->averagelcp.valuedouble),
true,
&suffixarray->averagelcp.defined);
GT_SCANNEDPRJKEY_ADD("maxbranchdepth",
&suffixarray->maxbranchdepth.valueunsignedlong,
&suffixarray->maxbranchdepth.defined);
GT_SCANNEDPRJKEY_ADD("integersize",&integersize,NULL);
GT_SCANNEDPRJKEY_ADD("littleendian",&littleendian,NULL);
GT_SCANNEDPRJKEY_ADD("readmode",&readmodeint,NULL);
GT_SCANNEDPRJKEY_ADD("mirrored",&mirrored,NULL);
currentline = gt_str_new();
for (linenum = 0; gt_str_read_next_line(currentline, fpin) != EOF; linenum++)
{
currentlinelength = gt_str_length(currentline);
if (dbfilelen <= (size_t) currentlinelength &&
memcmp(DBFILEKEY,gt_str_get(currentline),dbfilelen) == 0)
{
/* Nothing */
} else
{
if (gt_scannedprjkey_analyze(indexname,
GT_PROJECTFILESUFFIX,
linenum,
gt_str_get(currentline),
currentlinelength,
scannedprjkeytable,
err) != 0)
{
haserr = true;
break;
}
}
gt_str_reset(currentline);
}
gt_str_delete(currentline);
if (!haserr && gt_scannedprjkey_allkeysdefined(indexname,GT_PROJECTFILESUFFIX,
scannedprjkeytable,
logger,err) != 0)
{
haserr = true;
}
if (!haserr && integersize != (uint32_t) 32 && integersize != (uint32_t) 64)
{
gt_error_set(err,"%s%s contains illegal line defining the integer size",
indexname,GT_PROJECTFILESUFFIX);
haserr = true;
}
if (!haserr && integersize != (uint32_t) (sizeof (GtUword) * CHAR_BIT))
{
gt_error_set(err,"index was generated for %u-bit integers while "
"this program uses %u-bit integers",
(unsigned int) integersize,
(unsigned int) (sizeof (GtUword) * CHAR_BIT));
haserr = true;
}
if (!haserr)
{
if (gt_is_little_endian())
{
if (littleendian != (uint32_t) 1)
{
gt_error_set(err,"computer has little endian byte order, while index "
"was built on computer with big endian byte order");
haserr = true;
}
} else
{
if (littleendian == (uint32_t) 1)
{
gt_error_set(err,"computer has big endian byte order, while index "
"was built on computer with little endian byte "
"order");
haserr = true;
}
}
}
if (!haserr)
{
if (readmodeint > (uint32_t) 3)
{
gt_error_set(err,"illegal readmode %u",(unsigned int) readmodeint);
haserr = true;
}
suffixarray->readmode = (GtReadmode) readmodeint;
}
if (!haserr)
{
if (mirrored > (uint32_t) 1)
{
gt_error_set(err,"illegal mirroring flag: only 0(=no mirroring) and "
"1 (=mirroring) is supported, but read %u",
(unsigned int) mirrored);
haserr = true;
}
suffixarray->mirroredencseq = (mirrored == (uint32_t) 1);
}
gt_scannedprjkeytable_delete(scannedprjkeytable);
return haserr ? -1 : 0;
}
static int scanprjfileuintkeysviafileptr(Suffixarray *suffixarray,
const GtStr *indexname,
Verboseinfo *verboseinfo,
FILE *fpin,
GtError *err)
{
uint32_t integersize, littleendian, readmodeint;
unsigned int linenum;
unsigned long currentlinelength;
DefinedSeqpos maxbranchdepth;
size_t dbfilelen = strlen(DBFILEKEY);
bool haserr = false;
GtArray *riktab;
GtStr *currentline;
/* the following five variables are local as the parsed values are
not required: they are determined by reading the encodedsequence */
Seqpos totallength;
Specialcharinfo specialcharinfo;
unsigned long numofsequences,
numofdbsequences,
numofquerysequences;
gt_error_check(err);
riktab = gt_array_new(sizeofReadintkeys());
SETREADINTKEYS("totallength",&totallength,NULL);
SETREADINTKEYS("specialcharacters",
&specialcharinfo.specialcharacters,NULL);
SETREADINTKEYS("specialranges",
&specialcharinfo.specialranges,NULL);
SETREADINTKEYS("realspecialranges",
&specialcharinfo.realspecialranges,NULL);
SETREADINTKEYS("lengthofspecialprefix",
&specialcharinfo.lengthofspecialprefix,NULL);
SETREADINTKEYS("lengthofspecialsuffix",
&specialcharinfo.lengthofspecialsuffix,NULL);
SETREADINTKEYS("numofsequences",&numofsequences,NULL);
SETREADINTKEYS("numofdbsequences",&numofdbsequences,NULL);
setreadintkeys(riktab,"numofquerysequences",&numofquerysequences,0,NULL);
SETREADINTKEYS("longest",&suffixarray->longest.valueseqpos,
&suffixarray->longest.defined);
SETREADINTKEYS("prefixlength",&suffixarray->prefixlength,NULL);
SETREADINTKEYS("largelcpvalues",
&suffixarray->numoflargelcpvalues.valueseqpos,
&suffixarray->numoflargelcpvalues.defined);
SETREADINTKEYS("maxbranchdepth",&maxbranchdepth.valueseqpos,
&maxbranchdepth.defined);
SETREADINTKEYS("integersize",&integersize,NULL);
SETREADINTKEYS("littleendian",&littleendian,NULL);
SETREADINTKEYS("readmode",&readmodeint,NULL);
currentline = gt_str_new();
for (linenum = 0; gt_str_read_next_line(currentline, fpin) != EOF; linenum++)
{
currentlinelength = gt_str_length(currentline);
if (dbfilelen <= (size_t) currentlinelength &&
memcmp(DBFILEKEY,gt_str_get(currentline),dbfilelen) == 0)
{
/* Nothing */
} else
{
if (analyzeuintline(indexname,
PROJECTFILESUFFIX,
linenum,
gt_str_get(currentline),
currentlinelength,
riktab,
err) != 0)
{
haserr = true;
break;
}
}
gt_str_reset(currentline);
}
gt_str_delete(currentline);
if (!haserr && allkeysdefined(indexname,PROJECTFILESUFFIX,riktab,
verboseinfo,err) != 0)
{
haserr = true;
}
if (!haserr &&
integersize != (uint32_t) 32 &&
integersize != (uint32_t) 64)
{
gt_error_set(err,"%s%s contains illegal line defining the integer size",
gt_str_get(indexname),PROJECTFILESUFFIX);
haserr = true;
}
if (!haserr && integersize != (uint32_t) (sizeof (Seqpos) * CHAR_BIT))
{
gt_error_set(err,"index was generated for %u-bit integers while "
"this program uses %u-bit integers",
(unsigned int) integersize,
(unsigned int) (sizeof (Seqpos) * CHAR_BIT));
haserr = true;
}
if (!haserr)
{
if (gt_is_little_endian())
{
if (littleendian != (uint32_t) 1)
{
gt_error_set(err,"computer has little endian byte order, while index "
"was build on computer with big endian byte order");
haserr = true;
}
} else
{
if (littleendian == (uint32_t) 1)
{
gt_error_set(err,"computer has big endian byte order, while index "
"was build on computer with little endian byte "
"order");
haserr = true;
}
}
}
if (!haserr)
{
if (readmodeint > (uint32_t) 3)
{
gt_error_set(err,"illegal readmode %u",(unsigned int) readmodeint);
haserr = true;
}
suffixarray->readmode = (Readmode) readmodeint;
}
gt_array_delete(riktab);
return haserr ? -1 : 0;
}
