static EmbPEntry dbiblast_nextblastentry(PBlastDb db, ajint ifile,
const AjPStr idformat,
AjBool systemsort,
AjPStr const * fields,
ajint * maxFieldLen,
ajuint* maxidlen, ajuint* countfield,
AjPFile elistfile,
AjPFile * alistfile)
{
ajint i;
static ajint lastfile = -1;
static ajint iparser = -1;
static ajint called = 0;
static ajuint tabhdr[TABLESIZE];
static ajint iload = TABLESIZE-1;
static ajint irest = 0;
static ajint ipos = 0;
static ajint jpos = 0;
ajint ir;
ajint j;
static ajint is = 0;
char* token;
static ajint nfields;
ajint ifield;
if(!called)
{
for(i=0; parser[i].Name; i++)
if(ajStrMatchC(idformat, parser[i].Name))
{
iparser = i;
break;
}
if(iparser < 0)
ajFatal("idformat '%S' unknown", idformat);
ajDebug("idformat '%S' Parser %d\n", idformat, iparser);
ajStrSetRes(&id, HDRSIZE);
ajStrSetRes(&acc, HDRSIZE);
ajStrSetRes(&hline, HDRSIZE);
called = 1;
}
if(!fdl)
{
nfields=0;
while(fields[nfields])
nfields++;
if(nfields)
AJCNEW(fdl, nfields);
for(i=0; i < nfields; i++)
fdl[i] = ajListNew();
}
if(lastfile != ifile)
{
lastfile = ifile;
ipos = 1;
/* isize = 0;*/
irest = 0;
iload = TABLESIZE-1;
}
if(!dbiblastEntry || !systemsort)
dbiblastEntry = embDbiEntryNew(nfields);
/* pick up the next entry, parse it and dump it */
if(ipos > db->Size)
return NULL;
if( ipos >= irest)
{
ajDebug("ipos: %d iload: %d irest: %d\n", ipos, iload, irest);
irest = ipos + TABLESIZE - 2;
if(irest > db->Size)
{
iload = db->Size - ipos + 1;
irest = db->Size;
}
jpos=0;
j = dbiblast_loadtable(tabhdr, iload, db, db->TopHdr, ipos-1);
if(!j)
ajDebug("No elements read");
}
j = dbiblast_ncblreadhdr(&hline, db, tabhdr[jpos], tabhdr[jpos+1]);
if(!parser[iparser].Parser(hline, alistfile, systemsort, fields,
maxFieldLen, countfield, &id, fdl))
ajFatal("failed to parse '%S'", hline);
ir = ipos;
if(ajStrGetLen(id) > *maxidlen)
*maxidlen = ajStrGetLen(id);
if(systemsort)
ajFmtPrintF(elistfile, "%S %d %d %d\n", id, ir, is, ifile+1);
else
{
dbiblastEntry->entry = ajCharNewS(id);
dbiblastEntry->rpos = ir;
dbiblastEntry->spos = is;
dbiblastEntry->filenum = ifile+1;
/* field tokens as list, then move to dbiblastEntry->field */
for(ifield=0; ifield < nfields; ifield++)
{
dbiblastEntry->nfield[ifield] = ajListGetLength(fdl[ifield]);
if(dbiblastEntry->nfield[ifield])
{
AJCNEW(dbiblastEntry->field[ifield],
dbiblastEntry->nfield[ifield]);
i = 0;
while(ajListPop(fdl[ifield], (void**) &token))
dbiblastEntry->field[ifield][i++] = token;
}
else
dbiblastEntry->field[ifield] = NULL;
}
}
ipos++;
jpos++;
return dbiblastEntry;
}
static EmbPEntry dbifasta_NextFlatEntry(AjPFile libr, ajint ifile,
AjPRegexp idexp,
ajuint type, AjBool systemsort,
AjPStr const * fields,
ajint* maxFieldLen,
ajuint* maxidlen, ajuint* countfield,
AjPFile elistfile, AjPFile* alistfile)
{
ajint ir;
ajint is = 0;
char* token;
ajint i;
static ajint nfields;
ajint ifield;
if(!dbifastaGFdl)
{
nfields = 0;
while(fields[nfields])
nfields++;
if(nfields)
AJCNEW(dbifastaGFdl, nfields);
for(i=0; i < nfields; i++)
{
dbifastaGFdl[i] = ajListNew();
}
}
if(!dbifastaGEntry || !systemsort)
dbifastaGEntry = embDbiEntryNew(nfields);
if(!dbifasta_ParseFasta(libr, &ir, maxFieldLen,
countfield, idexp, type,
alistfile, systemsort, fields))
return NULL;
/* id to dbifastaGEntry->entry */
if(ajStrGetLen(dbifastaGTmpId) > *maxidlen)
*maxidlen = ajStrGetLen(dbifastaGTmpId);
if(systemsort)
ajFmtPrintF(elistfile, "%S %d %d %d\n",
dbifastaGTmpId, ir, is, ifile+1);
else
{
dbifastaGEntry->entry = ajCharNewS(dbifastaGTmpId);
dbifastaGEntry->rpos = ir;
dbifastaGEntry->spos = is;
dbifastaGEntry->filenum = ifile+1;
/* field tokens as list, then move to ret->field */
for(ifield=0; ifield < nfields; ifield++)
{
dbifastaGEntry->nfield[ifield] =
(ajuint) ajListGetLength(dbifastaGFdl[ifield]);
if(dbifastaGEntry->nfield[ifield])
{
AJCNEW(dbifastaGEntry->field[ifield],
dbifastaGEntry->nfield[ifield]);
i = 0;
while(ajListPop(dbifastaGFdl[ifield], (void**) &token))
dbifastaGEntry->field[ifield][i++] = token;
}
else
dbifastaGEntry->field[ifield] = NULL;
}
}
return dbifastaGEntry;
}
