extern EISeq *
createEncIdxSeq(const GtStr *projectName,
const struct seqBaseParam *params,
size_t numExtHeaders, const uint16_t *headerIDs,
const uint32_t *extHeaderSizes,
headerWriteFunc *extHeaderCallbacks, void **headerCBData,
bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
varExtBitsEstimator biVarBits, void *cbState,
Verboseinfo *verbosity, GtError *err)
{
Suffixarray suffixArray;
struct encIdxSeq *newSeqIdx;
Seqpos length;
gt_assert(projectName);
/* map and interpret index project file */
if (streamsuffixarray(&suffixArray,
SARR_SUFTAB | SARR_BWTTAB, projectName, verbosity, err))
return NULL;
length = getencseqtotallength(suffixArray.encseq) + 1;
newSeqIdx = createEncIdxSeqFromSA(&suffixArray, length,
projectName, params,
numExtHeaders, headerIDs,
extHeaderSizes, extHeaderCallbacks,
headerCBData, biFunc, cwExtBitsPerPos,
biVarBits, cbState, err);
freesuffixarray(&suffixArray);
return newSeqIdx;
}
static int inputthesequences(unsigned int *numofchars,
unsigned long *nextpostable,
Suffixarray *suffixarraytable,
const GtStrArray *indexnametab,
unsigned int demand,
GtLogger *logger,
GtError *err)
{
unsigned long idx;
const char *indexname;
gt_error_check(err);
for (idx=0; idx<gt_str_array_size(indexnametab); idx++)
{
indexname = gt_str_array_get(indexnametab,idx);
if (streamsuffixarray(&suffixarraytable[idx],
demand,
indexname,
logger,
err) != 0)
{
return -1;
}
if (idx == 0)
{
*numofchars =
gt_alphabet_num_of_chars(
gt_encseq_alphabet(suffixarraytable[idx].encseq));
}
nextpostable[idx] = 0;
}
return 0;
}
int gt_test_trieins(bool onlyins,const char *indexname,GtError *err)
{
Suffixarray suffixarray;
bool haserr = false;
unsigned long totallength = 0;
gt_error_check(err);
if (streamsuffixarray(&suffixarray,
SARR_ESQTAB,
indexname,
NULL,
err) != 0)
{
haserr = true;
} else
{
totallength = gt_encseq_total_length(suffixarray.encseq);
}
if (!haserr)
{
Mergertrierep trierep;
const GtUchar *characters;
trierep.encseqreadinfo = gt_malloc(sizeof *trierep.encseqreadinfo);
trierep.encseqreadinfo->encseqptr = suffixarray.encseq;
trierep.encseqreadinfo->readmode = suffixarray.readmode;
characters
= gt_alphabet_characters(gt_encseq_alphabet(suffixarray.encseq));
gt_mergertrie_initnodetable(&trierep,totallength,1U);
maketrie(&trierep,characters,totallength);
if (onlyins)
{
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
showtrie(&trierep,characters);
#endif
checktrie(&trierep,totallength+1,totallength,err);
#endif
} else
{
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
showallnoderelations(trierep.root);
#endif
#endif
successivelydeletesmallest(&trierep,totallength,characters,err);
}
gt_mergertrie_delete(&trierep);
}
gt_freesuffixarray(&suffixarray);
return haserr ? -1 : 0;
}
int test_trieins(bool onlyins,const GtStr *indexname,GtError *err)
{
Suffixarray suffixarray;
bool haserr = false;
Seqpos totallength = 0;
gt_error_check(err);
if (streamsuffixarray(&suffixarray,
SARR_ESQTAB,
indexname,
NULL,
err) != 0)
{
haserr = true;
} else
{
totallength = getencseqtotallength(suffixarray.encseq);
}
if (!haserr)
{
Mergertrierep trierep;
const GtUchar *characters;
ALLOCASSIGNSPACE(trierep.encseqreadinfo,NULL,Encseqreadinfo,1);
trierep.encseqreadinfo[0].encseqptr = suffixarray.encseq;
trierep.encseqreadinfo[0].readmode = suffixarray.readmode;
characters = getencseqAlphabetcharacters(suffixarray.encseq);
mergertrie_initnodetable(&trierep,totallength,1U);
maketrie(&trierep,characters,totallength);
if (onlyins)
{
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
showtrie(&trierep,characters);
#endif
checktrie(&trierep,totallength+1,totallength,err);
#endif
} else
{
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
showallnoderelations(trierep.root);
#endif
#endif
successivelydeletesmallest(&trierep,totallength,characters,err);
}
mergertrie_delete(&trierep);
}
freesuffixarray(&suffixarray);
return haserr ? -1 : 0;
}
extern EISeq *
loadEncIdxSeq(const GtStr *projectName,
enum seqBaseEncoding encType, int features,
Verboseinfo *verbosity, GtError *err)
{
struct encIdxSeq *newSeqIdx = NULL;
Suffixarray suffixArray;
Seqpos len;
do
{
if (streamsuffixarray(&suffixArray, 0, projectName, verbosity, err))
break;
len = getencseqtotallength(suffixArray.encseq) + 1;
newSeqIdx = loadEncIdxSeqForSA(&suffixArray, len, projectName,
encType, features, err);
freesuffixarray(&suffixArray);
} while (0);
return newSeqIdx;
}
