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 scanfmafileviafileptr(Fmindex *fmindex,
GtSpecialcharinfo *specialcharinfo,
bool *storeindexpos,
const char *indexname,
FILE *fpin,
GtLogger *logger,
GtError *err)
{
bool haserr = false;
GtScannedprjkeytable *scannedprjkeytable;
unsigned int intstoreindexpos;
gt_error_check(err);
scannedprjkeytable = gt_scannedprjkeytable_new();
GT_SCANNEDPRJKEY_ADD("bwtlength",&fmindex->bwtlength,NULL);
GT_SCANNEDPRJKEY_ADD("longest",&fmindex->longestsuffixpos,NULL);
GT_SCANNEDPRJKEY_ADD("storeindexpos",&intstoreindexpos,NULL);
GT_SCANNEDPRJKEY_ADD("log2blocksize",&fmindex->log2bsize,NULL);
GT_SCANNEDPRJKEY_ADD("log2markdist",&fmindex->log2markdist,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("suffixlength",&fmindex->suffixlength,NULL);
if (!haserr)
{
GtStr *currentline;
unsigned int linenum;
currentline = gt_str_new();
for (linenum = 0; gt_str_read_next_line(currentline, fpin) != EOF;
linenum++)
{
if (gt_scannedprjkey_analyze(indexname,
FMASCIIFILESUFFIX,
linenum,
gt_str_get(currentline),
gt_str_length(currentline),
scannedprjkeytable,
err) != 0)
{
haserr = true;
break;
}
gt_str_reset(currentline);
}
gt_str_delete(currentline);
}
if (!haserr && gt_scannedprjkey_allkeysdefined(indexname,FMASCIIFILESUFFIX,
scannedprjkeytable,
logger,err) != 0)
{
haserr = true;
}
if (!haserr)
{
if (intstoreindexpos == 1U)
{
*storeindexpos = true;
} else
{
if (intstoreindexpos == 0)
{
*storeindexpos = false;
} else
{
gt_error_set(err,"illegal value in line matching \"storeindexpos=\"");
haserr = true;
}
}
}
gt_scannedprjkeytable_delete(scannedprjkeytable);
return haserr ? -1 : 0;
}
