static void s_CloseAsnConn(CONN conn, ECONN_Callback type, void* data)
{
struct SAsnConn_Cbdata* cbdata = (struct SAsnConn_Cbdata*) data;
assert(type == eCONN_OnClose && cbdata && cbdata->aip);
AsnIoFree(cbdata->aip, FALSE/*not a file - don't close*/);
if ( cbdata->cb.func )
(*cbdata->cb.func)(conn, type, cbdata->cb.data);
free(cbdata);
}
static void ProcessMultipleRecord (
CharPtr filename,
CSpeedFlagPtr cfp
)
{
AsnIoPtr aip;
AsnTypePtr atp;
BioseqPtr bsp;
Char buf [41];
Uint2 entityID;
FILE *fp;
SeqEntryPtr fsep;
Char longest [41];
Int4 numrecords, x;
SeqEntryPtr sep;
time_t starttime, stoptime, worsttime;
#ifdef OS_UNIX
Char cmmd [256];
CharPtr gzcatprog;
int ret;
Boolean usedPopen = FALSE;
#endif
if (cfp == NULL) return;
if (StringHasNoText (filename)) return;
#ifndef OS_UNIX
if (cfp->compressed) {
Message (MSG_POSTERR, "Can only decompress on-the-fly on UNIX machines");
return;
}
#endif
#ifdef OS_UNIX
if (cfp->compressed) {
gzcatprog = getenv ("NCBI_UNCOMPRESS_BINARY");
if (gzcatprog != NULL) {
sprintf (cmmd, "%s %s", gzcatprog, filename);
} else {
ret = system ("gzcat -h >/dev/null 2>&1");
if (ret == 0) {
sprintf (cmmd, "gzcat %s", filename);
} else if (ret == -1) {
Message (MSG_POSTERR, "Unable to fork or exec gzcat in ScanBioseqSetRelease");
return;
} else {
ret = system ("zcat -h >/dev/null 2>&1");
if (ret == 0) {
sprintf (cmmd, "zcat %s", filename);
} else if (ret == -1) {
Message (MSG_POSTERR, "Unable to fork or exec zcat in ScanBioseqSetRelease");
return;
} else {
Message (MSG_POSTERR, "Unable to find zcat or gzcat in ScanBioseqSetRelease - please edit your PATH environment variable");
return;
}
}
}
fp = popen (cmmd, /* cfp->binary? "rb" : */ "r");
usedPopen = TRUE;
} else {
fp = FileOpen (filename, cfp->binary? "rb" : "r");
}
#else
fp = FileOpen (filename, cfp->binary? "rb" : "r");
#endif
if (fp == NULL) {
Message (MSG_POSTERR, "FileOpen failed for input file '%s'", filename);
return;
}
aip = AsnIoNew (cfp->binary? ASNIO_BIN_IN : ASNIO_TEXT_IN, fp, NULL, NULL, NULL);
if (aip == NULL) {
Message (MSG_ERROR, "AsnIoNew failed for input file '%s'", filename);
return;
}
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "%s\n\n", filename);
fflush (cfp->logfp);
}
longest [0] = '\0';
worsttime = 0;
numrecords = 0;
atp = cfp->atp_bss;
while ((atp = AsnReadId (aip, cfp->amp, atp)) != NULL) {
if (atp == cfp->atp_se) {
sep = SeqEntryAsnRead (aip, atp);
if (sep != NULL) {
entityID = ObjMgrGetEntityIDForChoice (sep);
fsep = FindNthBioseq (sep, 1);
if (fsep != NULL && fsep->choice == 1) {
bsp = (BioseqPtr) fsep->data.ptrvalue;
if (bsp != NULL) {
SeqIdWrite (bsp->id, buf, PRINTID_FASTA_LONG, sizeof (buf));
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "%s\n", buf);
fflush (cfp->logfp);
}
}
}
starttime = GetSecs ();
for (x = 0; x < cfp->maxcount; x++) {
DoProcess (sep, entityID, cfp);
}
stoptime = GetSecs ();
if (stoptime - starttime > worsttime) {
worsttime = stoptime - starttime;
StringCpy (longest, buf);
}
numrecords++;
ObjMgrFreeByEntityID (entityID);
}
} else {
AsnReadVal (aip, atp, NULL);
}
}
AsnIoFree (aip, FALSE);
#ifdef OS_UNIX
if (usedPopen) {
pclose (fp);
} else {
FileClose (fp);
}
#else
FileClose (fp);
#endif
if (cfp->logfp != NULL && (! StringHasNoText (longest))) {
fprintf (cfp->logfp, "Longest processing time %ld seconds on %s\n",
(long) worsttime, longest);
fprintf (cfp->logfp, "Total number of records %ld\n", (long) numrecords);
fflush (cfp->logfp);
}
}
static void ProcessSingleRecord (
CharPtr filename,
CSpeedFlagPtr cfp
)
{
AsnIoPtr aip;
BioseqPtr bsp;
ValNodePtr bsplist = NULL;
BioseqSetPtr bssp;
Pointer dataptr = NULL;
Uint2 datatype, entityID = 0;
FileCache fc;
FILE *fp;
Int1 iotype;
Char line [512];
Int4 maxio = 1;
SeqEntryPtr sep;
time_t starttime, stoptime, worsttime;
CharPtr str;
Int4 x;
if (cfp == NULL) return;
if (StringHasNoText (filename)) return;
if (StringChr (cfp->io, 'r') != NULL) {
maxio = cfp->maxcount;
}
starttime = GetSecs ();
for (x = 0; x < maxio; x++) {
if (entityID != 0) {
ObjMgrFreeByEntityID (entityID);
entityID = 0;
dataptr = NULL;
}
if (cfp->type == 1) {
fp = FileOpen (filename, "r");
if (fp == NULL) {
Message (MSG_POSTERR, "Failed to open '%s'", filename);
return;
}
dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, FALSE, FALSE, FALSE);
FileClose (fp);
entityID = ObjMgrRegister (datatype, dataptr);
} else if (cfp->type >= 2 && cfp->type <= 5) {
aip = AsnIoOpen (filename, cfp->binary? "rb" : "r");
if (aip == NULL) {
Message (MSG_POSTERR, "AsnIoOpen failed for input file '%s'", filename);
return;
}
switch (cfp->type) {
case 2 :
dataptr = (Pointer) SeqEntryAsnRead (aip, NULL);
datatype = OBJ_SEQENTRY;
break;
case 3 :
dataptr = (Pointer) BioseqAsnRead (aip, NULL);
datatype = OBJ_BIOSEQ;
break;
case 4 :
dataptr = (Pointer) BioseqSetAsnRead (aip, NULL);
datatype = OBJ_BIOSEQSET;
break;
case 5 :
dataptr = (Pointer) SeqSubmitAsnRead (aip, NULL);
datatype = OBJ_SEQSUB;
break;
default :
break;
}
AsnIoClose (aip);
entityID = ObjMgrRegister (datatype, dataptr);
} else if (cfp->type == 6) {
fp = FileOpen (filename, "r");
if (fp == NULL) {
Message (MSG_POSTERR, "Failed to open '%s'", filename);
return;
}
dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, FALSE, FALSE, FALSE);
FileClose (fp);
entityID = ObjMgrRegister (datatype, dataptr);
} else if (cfp->type == 7) {
fp = FileOpen (filename, "r");
if (fp == NULL) {
Message (MSG_POSTERR, "Failed to open '%s'", filename);
return;
}
FileCacheSetup (&fc, fp);
str = FileCacheReadLine (&fc, line, sizeof (line), NULL);
while (str != NULL) {
str = FileCacheReadLine (&fc, line, sizeof (line), NULL);
}
FileClose (fp);
return;
} else {
Message (MSG_POSTERR, "Input format type '%d' unrecognized", (int) cfp->type);
return;
}
}
if (entityID < 1 || dataptr == NULL) {
Message (MSG_POSTERR, "Data read failed for input file '%s'", filename);
return;
}
if (datatype == OBJ_SEQSUB || datatype == OBJ_SEQENTRY ||
datatype == OBJ_BIOSEQ || datatype == OBJ_BIOSEQSET) {
stoptime = GetSecs ();
worsttime = stoptime - starttime;
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "ASN reading time %ld seconds\n", (long) worsttime);
fflush (cfp->logfp);
}
sep = GetTopSeqEntryForEntityID (entityID);
if (sep == NULL) {
sep = SeqEntryNew ();
if (sep != NULL) {
if (datatype == OBJ_BIOSEQ) {
bsp = (BioseqPtr) dataptr;
sep->choice = 1;
sep->data.ptrvalue = bsp;
SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep);
} else if (datatype == OBJ_BIOSEQSET) {
bssp = (BioseqSetPtr) dataptr;
sep->choice = 2;
sep->data.ptrvalue = bssp;
SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) bssp, sep);
} else {
sep = SeqEntryFree (sep);
}
}
sep = GetTopSeqEntryForEntityID (entityID);
}
if (sep != NULL) {
if (cfp->lock) {
starttime = GetSecs ();
bsplist = LockFarComponents (sep);
stoptime = GetSecs ();
worsttime = stoptime - starttime;
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "Far component locking time %ld seconds\n", (long) worsttime);
fflush (cfp->logfp);
}
}
if (StringChr (cfp->io, 'w') != NULL) {
starttime = GetSecs ();
iotype = ASNIO_TEXT_OUT;
if (StringChr (cfp->io, 'b') != NULL) {
iotype = ASNIO_BIN_OUT;
}
for (x = 0; x < cfp->maxcount; x++) {
aip = AsnIoNew (iotype, cfp->ofp, NULL, NULL, NULL);
if (aip != NULL) {
SeqEntryAsnWrite (sep, aip, NULL);
AsnIoFree (aip, FALSE);
}
}
stoptime = GetSecs ();
worsttime = stoptime - starttime;
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "ASN writing time %ld seconds\n", (long) worsttime);
fflush (cfp->logfp);
}
}
starttime = GetSecs ();
for (x = 0; x < cfp->maxcount; x++) {
DoProcess (sep, entityID, cfp);
}
stoptime = GetSecs ();
worsttime = stoptime - starttime;
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "Internal processing time %ld seconds\n", (long) worsttime);
fflush (cfp->logfp);
}
ObjMgrFreeByEntityID (entityID);
bsplist = UnlockFarComponents (bsplist);
}
} else {
Message (MSG_POSTERR, "Datatype %d not recognized", (int) datatype);
}
}