AsnIoPtr CreateAsnConn(CONN conn,
EAsnConn_Direction direction,
EAsnConn_Format fmt)
{
/* NB: Do not use ASNIO_{TEXT|BIN}_{IN|OUT} because they subsume FILE */
AsnIoPtr aip;
int type;
switch (fmt) {
case eAsnConn_Binary:
type = ASNIO_BIN;
break;
case eAsnConn_Text:
type = ASNIO_TEXT;
break;
default:
return 0;
}
switch (direction) {
case eAsnConn_Input:
aip = AsnIoNew(type | ASNIO_IN, 0, (void*) conn, s_AsnRead, 0);
break;
case eAsnConn_Output:
aip = AsnIoNew(type | ASNIO_OUT, 0, (void*) conn, 0, s_AsnWrite);
break;
default:
return 0;
}
if (aip)
s_SetAsnConn_CloseCb(conn, aip);
return aip;
}
NLM_EXTERN AsnIoConnPtr QUERY_AsnIoConnOpen (
const char* mode,
CONN conn
)
{
Int1 type;
AsnIoConnPtr aicp;
if (strcmp(mode, "r") == 0)
type = (ASNIO_IN | ASNIO_TEXT);
else if (strcmp(mode, "rb") == 0)
type = (ASNIO_IN | ASNIO_BIN);
else if (strcmp(mode, "w") == 0)
type = (ASNIO_OUT | ASNIO_TEXT);
else if (strcmp(mode, "wb") == 0)
type = (ASNIO_OUT | ASNIO_BIN);
else {
AsnIoErrorMsg (NULL, 81, mode);
return NULL;
}
aicp = (AsnIoConnPtr) MemNew (sizeof (AsnIoConn));
aicp->aip = AsnIoNew (type, NULL, (Pointer) aicp, AsnIoConnRead, AsnIoConnWrite);
aicp->conn = conn;
return aicp;
}
static void SeqEntryToFeat (SeqEntryPtr sep, FILE *fp)
{
AsnExpOptPtr aeop;
AsnIoPtr aip;
ExpStructPtr esp;
if (sep != NULL && fp != NULL) {
esp = MemNew (sizeof (ExpStruct));
if (esp != NULL) {
aip = AsnIoNullOpen ();
if (aip != NULL) {
esp->fp = fp;
esp->aip = AsnIoNew (ASNIO_TEXT_OUT, fp, NULL, NULL, NULL);
esp->is_na = is_na;
esp->feat = 3; /* look for CdRegion SeqFeat */
aeop = AsnExpOptNew (aip, "Seq-feat", (Pointer) esp, GetSeqFeat);
if (aeop != NULL) {
SeqEntryAsnWrite (sep, aip, NULL);
fflush (fp);
AsnExpOptFree (aip, aeop);
}
AsnIoClose (aip);
}
MemFree (esp);
}
}
}
BiostrucAnnotSetPtr LIBCALL VASTBsAnnotSetGet (Int4 uid)
{
AsnIoPtr aip = NULL;
AsnTypePtr atp = NULL;
Char path[PATH_MAX];
Char compath[PATH_MAX];
Char tempfile[PATH_MAX];
Char pcId[20];
Int2 iFileExists = 0;
BiostrucAnnotSetPtr pbsa = NULL;
int iAvail = 1;
FILE *pipe;
sprintf(pcId, "%ld", (long) uid);
path[0] = '\0';
StringCpy(path, database);
StringCat(path, pcId);
StringCat(path, ".bas");
#ifdef MMDB_UNIXCOMPRESSED
compath[0] = '\0';
sprintf(compath, "%s -d -c %s.gz ", gunzip, path);
pipe = popen(compath, "rb");
if (pipe == NULL) {
ErrPostEx(SEV_FATAL,0,0, "VASTBsAnnotSetGet failed: Can't find gunzip in path.\n");
return NULL;
}
aip = AsnIoNew(ASNIO_BIN_IN, pipe, NULL, NULL, NULL);
#else
iFileExists = FileLength(path);
if (iFileExists == 0)
{
return NULL;
}
aip = AsnIoOpen(path, "rb");
#endif
if (aip)
{
pbsa = BiostrucAnnotSetAsnRead(aip, NULL);
AsnIoClose (aip);
}
#ifdef MMDB_UNIXCOMPRESSED
pclose(pipe);
#endif
if (!pbsa) return NULL;
return pbsa;
}
static
int mfmt_init_output( void *handle, char *file_name, FILE *fd )
{
/* Open the file using the AsnIoOpen routine */
asn_hand->ioptr = AsnIoNew( (asn_hand->mode == binary) ?
ASNIO_BIN_OUT : ASNIO_TEXT_OUT, fd, NULL, NULL, NULL );
if( asn_hand->ioptr == NULL ) {
asn_hand->have_error = ErrFetch( &asn_hand->error );
} else {
asn_hand->have_error = FALSE;
asn_hand->open_state = init_output;
asn_hand->count = 0;
}
return( asn_hand->ioptr != NULL );
}
static void s_TestIdFormatting(const char* s)
{
size_t len = strlen(s);
CObjectIStreamAsn ois(s, len);
CSeq_id cxx_id;
AsnIoMemPtr aimp = AsnIoMemOpen
(const_cast<char*>("r"),
reinterpret_cast<BytePtr>(const_cast<char*>(s)), len);
AsnIoPtr aip = AsnIoNew((ASNIO_IN | ASNIO_TEXT), NULL, aimp,
AsnIoMemRead, AsnIoMemWrite);
TAutoSeqId c_id;
ois.Read(&cxx_id, CSeq_id::GetTypeInfo(), CObjectIStream::eNoFileHeader);
aip->read_id = TRUE;
c_id = SeqIdAsnRead(aip, s_SeqIdATP);
BOOST_CHECK_EQUAL(s_IdLabel(c_id, eFastaShort),
s_IdLabel(cxx_id, eFastaShort));
BOOST_CHECK_EQUAL(s_IdLabel(c_id, eTextAccVer),
s_IdLabel(cxx_id, eTextAccVer));
BOOST_CHECK_EQUAL(s_IdLabel(c_id, eTextAccOnly),
s_IdLabel(cxx_id, eTextAccOnly));
BOOST_CHECK_EQUAL(s_IdLabel(c_id, eReport), s_IdLabel(cxx_id, eReport));
}
void BEPrintIds(BEDataPtr pBdata, Uint4 *ids, int count)
{
Int4 i;
SeqEntryPtr sep, sep_all;
Boolean retvalue = TRUE;
SeqIdPtr sip = NULL;
BioseqPtr bsp;
BGenBankPtr bgbp;
AsnIoPtr aip;
Boolean is_na = FALSE;
if(pBdata->format == F_GILIST) {
for(i = 0; i < count; i++)
fprintf(stdout, "%d\n", (int) ids[i]);
return;
}
if(pBdata->database == 0)
is_na = TRUE;
if(pBdata->format == F_ASN1_GENB)
bgbp = BGenBankInit();
for(i = 0; i < count; i++) {
sep_all = BESeqEntryGet(ids[i]);
if(sep_all == NULL) {
ErrPostEx(SEV_ERROR, 88, 67, "Retrieving of blob for the "
"gi=%d failed", (int)ids[i]);
continue;
}
if(!pBdata->allset) {
ObjMgrRegister(OBJ_SEQENTRY, sep_all);
sip = ValNodeNew(NULL);
sip->choice = SEQID_GI;
sip->data.intvalue = ids[i];
if((bsp = BioseqFind(sip)) == NULL) {
ErrPostEx(SEV_ERROR, 88, 67,
"Error finding bioseq for gi=%d\n", (int)ids[i]);
continue;
}
sep = SeqEntryNew();
sep->choice = 1; /* Bioseq */
sep->data.ptrvalue = bsp;
} else {
sep = sep_all;
}
switch(pBdata->format) {
case F_FASTA: /* 1 */
if(!SeqEntryToFasta(sep, stdout, is_na)) {
if(!SeqEntryToFasta(sep, stdout, !is_na)) {
ErrPostEx(SEV_ERROR, 88, 67, "Printing of FASTA format "
"(gi=%d) failed\r\n", (int)ids[i]);
}
}
break;
case F_ASN1: /* 2 */
aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
SeqEntryAsnWrite(sep, aip, NULL);
AsnIoClose(aip);
break;
case F_GILIST: /* 3 */
for(i = 0; i < count; i++)
fprintf(stdout, "%d\n", (int) ids[i]);
break;
case F_DLIST: /* 4 */
if (IS_Bioseq(sep))
retvalue = SeqEntrysToDefline(sep, stdout, is_na, 3);
else
retvalue = SeqEntrysToDefline(sep, stdout, is_na, 0);
if(retvalue == FALSE) {
if (IS_Bioseq(sep))
retvalue = SeqEntrysToDefline(sep, stdout, !is_na, 3);
else
retvalue = SeqEntrysToDefline(sep, stdout, !is_na, 0);
}
break;
case F_ASN1_GENB: /* 5 */
retvalue = SeqEntryAsnWrite(sep, bgbp->aip, bgbp->atp);
break;
default:
case F_GEN: /* 0 */
if(!SeqEntryToFlatEx(sep_all, stdout,
is_na ? GENBANK_FMT : GENPEPT_FMT,
RELEASE_MODE, sip, FF_REGULAR)) {
if(!SeqEntryToFlatEx(sep_all, stdout,
is_na ? GENPEPT_FMT : GENBANK_FMT,
RELEASE_MODE, sip, FF_REGULAR)) {
}
}
break;
}
SeqEntryFree(sep_all);
ValNodeFree(sip);
}
if(pBdata->format == F_ASN1_GENB)
BGenBankClose(bgbp);
return;
}
BGenBankPtr BGenBankInit(void)
{
BGenBankPtr bgbp;
AsnModulePtr amp;
AsnTypePtr atp_bioseq_set;
AsnTypePtr atp_bioseq_set_level;
AsnTypePtr atp_bioseq_set_class;
AsnTypePtr atp_bioseq_set_release;
AsnTypePtr atp_bioseq_set_date;
AsnTypePtr atp_bioseq_set_seq_set;
AsnTypePtr atp_bioseq_set_seq_set_E;
Char release[] = "Q-server Production";
Char date_time[128];
NCBI_Date date;
DataVal dv;
DateClean(&date);
bgbp = (BGenBankPtr)MemNew(sizeof(BGenBank));
bgbp->aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
amp = AsnAllModPtr();
MACRO_atp_find(atp_bioseq_set,Bioseq-set);
MACRO_atp_find(atp_bioseq_set_level,Bioseq-set.level);
MACRO_atp_find(atp_bioseq_set_class,Bioseq-set.class);
MACRO_atp_find(atp_bioseq_set_release,Bioseq-set.release);
MACRO_atp_find(atp_bioseq_set_date,Bioseq-set.date);
MACRO_atp_find(atp_bioseq_set_seq_set,Bioseq-set.seq-set);
MACRO_atp_find(atp_bioseq_set_seq_set_E,Bioseq-set.seq-set.E);
if(!AsnOpenStruct(bgbp->aip,atp_bioseq_set,NULL))
return NULL;
dv.intvalue = 0;
if(!AsnWrite(bgbp->aip,atp_bioseq_set_level,&dv))
return NULL;
dv.intvalue = 7;
if(!AsnWrite(bgbp->aip,atp_bioseq_set_class,&dv))
return NULL;
dv.ptrvalue = &release;
if(!AsnWrite(bgbp->aip,atp_bioseq_set_release,&dv))
return NULL;
Nlm_DayTimeStr(date_time,TRUE,TRUE);
date.str=date_time;
if(!DateAsnWrite(&date,bgbp->aip,atp_bioseq_set_date))
return NULL;
if(!AsnOpenStruct(bgbp->aip,atp_bioseq_set_seq_set,NULL))
return NULL;
AsnIoFlush(bgbp->aip);
bgbp->atp =atp_bioseq_set_seq_set_E;
bgbp->atp_bioseq_set_seq_set = atp_bioseq_set_seq_set;
bgbp->atp_bioseq_set = atp_bioseq_set;
return bgbp;
}
static NI_HandPtr s_GenericGetService
(NI_DispatcherPtr disp, CharPtr configFile, CharPtr configSection,
CharPtr defService, Boolean hasResource)
{
NI_HandPtr result;
SOCK sock;
Char srv_host[64];
Uint2 srv_port;
Uint4 conn_try;
/* get the server host name */
NI_GetEnvParam(configFile, configSection, ENV_DEBUG_HOST,
srv_host, sizeof(srv_host), "");
if ( !srv_host[0] ) {
ErrPostEx(SEV_ERROR, 0, 0, ENV_DEBUG_HOST ": undefined");
return 0;
}
{{ /* get the server port */
Char str[32];
int val;
NI_GetEnvParam(configFile, configSection, ENV_DEBUG_PORT,
str, sizeof(str), "");
val = atoi(str);
if (val <= 0) {
ErrPostEx(SEV_ERROR, 0, 0, ENV_DEBUG_PORT ": bad(%d) or undefined", val);
return 0;
}
srv_port = (Uint2)val;
}}
{{ /* alternate the max. number of attemts to establish a connection */
Char str[32];
int val;
NI_GetEnvParam(configFile, configSection, ENV_DEBUG_TRY,
str, sizeof(str), "");
val = atoi(str);
conn_try = (Uint4)((val > 0) ? val : DEF_DEBUG_TRY);
}}
/* establish connection to the server */
for (sock = 0; !sock && conn_try; conn_try--) {
if (SOCK_Create(srv_host, srv_port, 0, &sock) != eIO_Success) {
ErrPostEx(SEV_WARNING, 0, 1,
"[Debug NI Client] Cannot connect to host \"%s\", port %d;",
srv_host, (int)srv_port);
}
}
if ( !sock ) {
ErrPostEx(SEV_ERROR, 0, 1,
"[Debug NI Client] Failed to connect to host \"%s\", port %d;",
srv_host, (int)srv_port);
return 0;
}
/* open ASN i/o, etc. */
result = (NI_HandPtr)MemNew(sizeof(NI_Handle));
result->extra_proc_info = sock;
result->raip = AsnIoNew((ASNIO_BIN | ASNIO_IN), (FILE *)0,
(void *)sock, s_AsnRead, (IoFuncType)0);
result->waip = AsnIoNew((ASNIO_BIN | ASNIO_OUT), (FILE *)0,
(void *)sock, (IoFuncType)0, s_AsnWrite);
AsnIoSetErrorMsg(result->raip, s_AsnErrorFunc);
AsnIoSetErrorMsg(result->waip, s_AsnErrorFunc);
result->hostname = StringSave("");
result->disp = disp;
disp->referenceCount++;
return result;
}
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);
}
}
BiostrucPtr LIBCALL
MMDBBiostrucGet (DocUid uid, Int4 mdlLvl, Int4 maxModels)
{
AsnIoPtr aip = NULL;
BiostrucPtr pbs = NULL;
int index;
Int4 acc;
#ifdef MMDB_PUBSTRUCT
extern WWWInfoPtr info;
if(!file_db)
{
Int4 state = 0;
char *dbserver = (database[0]?database:NULL);
acc = uid;
if(WWWFindName(info, "ps_acc") >=0)
aip = PubStruct_readasn(dbserver, acc);
else
{
index = WWWFindName(info, "ps_state");
if (index >= 0)
{
char * item;
item = WWWGetValueByIndex(info,index);
if (!StrToInt4(item,&state))
ErrPostEx(SEV_ERROR,0,0, "cant convert Pubstruct_state<%s> into integer",item);
}
if (state == 0 )
aip = PubStruct_viewasn(dbserver, uid);
else
{
acc = PubStruct_lookup(dbserver,uid, state);
/*
fprintf(stderr,"%s:%d: acc=%d <<- %s(mmdb=%d,state=%d)\n",
__FILE__,__LINE__,acc,dbserver,uid,state);
*/
if (acc>0)
aip = PubStruct_readasn(dbserver, acc);
}
}
}
else
#endif
{
Char path[PATH_MAX];
sprintf(path, "%s%ld.val", database, (long) uid);
#ifdef MMDB_UNIXCOMPRESSED
{
FILE *pipe;
Char compath[PATH_MAX];
sprintf(compath,"%s -c %s.gz ", gunzip, path);
pipe=popen(compath,"rb");
if (pipe == 0)
{
ErrPostEx(SEV_FATAL,0,0, "MMDBBiostrucGet failed: Can't find gunzip in path.\n");
return NULL;
}
aip = AsnIoNew(ASNIO_BIN_IN, pipe , NULL, NULL, NULL);
}
#else
if (FileLength(path) == 0)
return NULL;
aip = AsnIoOpen(path, "rb");
#endif
}
if (!aip)
return NULL;
pbs = BiostrucAsnGet(aip, NULL, mdlLvl, maxModels);
#ifdef MMDB_PUBSTRUCT
if(!file_db)
PubStruct_closeasn (aip,1);
else
#endif
AsnIoClose (aip);
return pbs;
}
Boolean LIBCALL VastToCn3D(WWWInfoPtr www_info)
{
FILE *pFile = NULL;
FILE *pIn = NULL;
Char pcBuf[100], pcLine[256], giBuf[20], URL[200];
CharPtr pcTest, pcL1 = NULL, Name, www_arg;
Int4 GetGi, Fid, Fsid, iFileExists = 0, indx;
BiostrucAnnotSetPtr pbsa = NULL;
BiostrucAnnotSetPtr pbsaShort = NULL;
BiostrucFeatureSetPtr pbsfs = NULL;
BiostrucFeaturePtr pbsf = NULL;
BiostrucResidueGraphSetPtr stdDictionary;
ValNodePtr pvnFids = NULL, pvnFid = NULL;
Int2 iTest = 0, iPDB = 0, iColor;
AsnIoPtr aip = NULL;
Byte bRender;
Char *IPAddress = getenv("REMOTE_HOST");
Int4 NumLabels, iMMDBId;
ValNode * pbsidThis;
BiostrucPtr pbsMaster, pbsSlave, pbsSlaveHead = NULL, pbsSlaveTail, pbsTemp;
Char szName[5], chain[2];
Char * szTemp;
SeqAnnotPtr psaAlignHead = NULL, psaAlignTail;
SeqAlignPtr salpHead, salpTail;
SeqIdPtr sip;
DenseSegPtr dsp;
BioseqPtr bsp;
SeqEntryPtr sep;
char str [52];
NcbiMimeAsn1Ptr pvnNcbi;
BiostrucAlignPtr pbsaStruct;
AsnIoPtr paiFile, aipr;
Boolean is_network;
Int4 uid, uidmaster = 0;
Int2 retcode = 3;
CharPtr JobID = NULL, pcPass;
Char AsnPath[PATH_MAX];
Char AsnName[10];
Int2 ret, complexity;
Int4 iFidCount = 0;
Boolean Chain;
/* SeqAsnLoad();
objmmdb1AsnLoad();
objmmdb2AsnLoad();
objmmdb3AsnLoad();
SeqAlignAsnLoad();
objmimeAsnLoad();
*/
if ((indx = WWWFindName(www_info, "uid")) < 0) {
printf("Content-type: text/html\n\n");
printf("<h3>No accession (PDB ID) was input - nothing to report.</h3>\n");
return 0;
}
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
GetGi = (Int4) atoi(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Non-numeric MMDB-id input - no results.</h3>\n");
return 0;
}
/* vsid and pass are to look at alignments from VAST Search */
if ((indx = WWWFindName(www_info, "vsid")) >= 0) {
www_arg = WWWGetValueByIndex(www_info, indx);
JobID = StringSave(www_arg);
if ((indx = WWWFindName(www_info, "pass")) < 0) {
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<h2>VAST SEARCH</h2>\n");
printf("<h3>Password required.</h3>\n");
return 0;
}
else {
www_arg = WWWGetValueByIndex(www_info, indx);
pcPass = StringSave(www_arg);
if ((ret = Check_VastSearch_Password(pcPass, JobID)) != 1) {
if (ret == 2) return 0;
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<h2>VAST SEARCH</h2>\n");
printf("<h3>Incorrect password.</h3>\n");
return 0;
}
}
}
if ((indx = WWWFindName(www_info, "hit")) < 0) {
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<br>\n<h2>No alignment was selected!</h2>\n");
printf("<h3>Please click on up to 5 boxes in the leftmost column of the table.</h3>\n");
return 0;
}
/* loop over all the "hit" values in the list */
NumLabels = WWWGetNumEntries(www_info);
for (indx = 0; indx < NumLabels; indx++) {
Name = WWWGetNameByIndex(www_info, indx);
if (StrICmp(Name, "hit") == 0) {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
Fid = (Int4) atol(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Non-numeric slave alignment code - no results.</h3>\n");
return 0;
}
if (++iFidCount > 5) break;
pvnFid = ValNodeAddInt(&pvnFids, 0, Fid);
}
}
if ((indx = WWWFindName(www_info, "chaindom")) < 0) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>No feature set ID (master alignment code) - nothing to report.</h3>\n");
return 0;
}
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
Fsid = (Int4) atoi(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Non-numeric master alignment code - no results.</h3>\n");
return 0;
}
if ((indx = WWWFindName(www_info, "chn_complexity")) < 0)
Chain = TRUE;
else
{
www_arg = WWWGetValueByIndex(www_info, indx);
complexity =(Int2)atoi(www_arg);
if (complexity) Chain = TRUE;
else Chain = FALSE;
}
if ((indx = WWWFindName(www_info, "atm_complexity")) < 0)
/* select alpha Carbons only by default */
complexity = ONECOORDRES;
else {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
complexity = (Int2) atoi(www_arg);
else
complexity = ONECOORDRES;
}
if ((complexity != ONECOORDRES) && (complexity != ONECOORDATOM))
/* bizarre value, but default to alpha-Carbons only */
complexity = ONECOORDRES;
/* action == 0 indicates MIME; action == 1 is text; action == 2 is save */
if ((indx = WWWFindName(www_info, "action")) < 0)
iPDB = 0;
else {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
iPDB = (Int4) atoi(www_arg);
else
iPDB = 0;
}
if (VASTInit() != TRUE) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Can't find VAST data on server.\n");
printf("Contact [email protected]</h3>\n");
return 0;
}
OpenMMDBAPI((POWER_VIEW /* ^ FETCH_ENTREZ */), NULL);
pbsa = LocalGetFeatureSet(GetGi, Fsid, JobID);
if (pbsa == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>No master alignment record exists for %ld.</h3>\n", (long) GetGi);
return 0;
}
if (iFidCount == 1)
pbsaShort = BiostrucAnnotSetGetByFid(pbsa, Fid, Fsid);
else
pbsaShort = PruneBiostrucAnnotHits(pbsa, Fsid, pvnFids);
if (pbsaShort == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Can't find alignment record.</h3>\n");
return 0;
}
if (MMDBInit() == FALSE) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>MMDBInit failed.</h3>\n");
return 0;
}
pbsfs = pbsaShort->features;
pbsaStruct = BiostrucAlignNew();
if (pbsfs)
{
pbsf = pbsfs->features;
szTemp = pbsf->name;
szName[0] = szTemp[0];
szName[1] = szTemp[1];
szName[2] = szTemp[2];
szName[3] = szTemp[3];
szName[4] = '\0';
}
if (JobID == NULL)
pbsMaster = FetchBiostrucPDB(szName, complexity, 1);
else
{
AsnName[0]='\0';
StringCpy(AsnName, "/b");
StringCat(AsnName, szName);
AsnPath[0]='\0';
StringCpy(AsnPath, VSPATH);
StringCat(AsnPath, JobID);
StringCat(AsnPath, AsnName);
pbsMaster = FetchBS(AsnPath, 0, complexity, 1, POWER_VIEW);
}
if (pbsMaster == NULL)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3> Unable to load master structure.</h3>\n");
return 0;
}
/* Load in Standard Dictionary to make sequences - Ken */
aipr = NULL;
aipr = AsnIoOpen("bstdt", "rb");
if (aipr == NULL)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Can't find standard dictionary.</h3>\n");
return 0;
}
stdDictionary = BiostrucResidueGraphSetAsnRead(aipr, NULL);
AsnIoFlush(aipr);
aipr = AsnIoClose(aipr);
/* retrieve the bioseq for master and put in ValNode */
sep = (SeqEntryPtr) MakeBioseqs(pbsMaster, stdDictionary);
if ( sep == NULL )
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to get SeqEntry.</h3>\n");
return 0;
}
ValNodeLink(&(pbsaStruct->sequences), sep);
/* PruneBiostruc if Aligned Chain Options has been chosen */
if (Chain)
{
if (szTemp[4] != ' ')
{
chain[0] = szTemp[4];
chain[1] = '\0';
pbsTemp = (BiostrucPtr)PruneBiostruc(pbsMaster, chain);
pbsMaster = NULL;
pbsMaster = pbsTemp;
}
}
/* Make a linked list of Biostrucs of the slave structures*/
while (pbsf)
{
szTemp = pbsf->name;
szName[0] = szTemp[7];
szName[1] = szTemp[8];
szName[2] = szTemp[9];
szName[3] = szTemp[10];
szName[4] = '\0';
if (!pbsSlaveHead)
{
pbsSlaveHead = FetchBiostrucPDB(szName, complexity, 1);
if (!pbsSlaveHead)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3> Unable to load slave structure.</h3>\n");
return 0;
}
/* Make Bioseq for Slaves */
sep = (SeqEntryPtr) MakeBioseqs(pbsSlaveHead, stdDictionary);
if ( sep == NULL )
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to get SeqEntry.</h3>\n");
return 0;
}
ValNodeLink(&(pbsaStruct->sequences), sep);
/* PruneBiostruc if Aligned Chain Options has been chosen */
if (Chain)
{
if (szTemp[11] != ' ')
{
chain[0] = szTemp[11];
chain[1] = '\0';
pbsTemp = (BiostrucPtr)PruneBiostruc(pbsSlaveHead, chain);
pbsSlaveHead = NULL;
pbsSlaveHead = pbsTemp;
}
}
pbsSlaveTail = pbsSlaveHead;
}
else
{
pbsSlave = FetchBiostrucPDB(szName, complexity, 1);
if (!pbsSlave)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3> Unable to load slave structure.</h3>\n");
return 0;
}
/* Make Bioseq for Slaves */
sep = (SeqEntryPtr) MakeBioseqs(pbsSlave, stdDictionary);
if ( sep == NULL )
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to get SeqEntry.</h3>\n");
return 0;
}
ValNodeLink(&(pbsaStruct->sequences), sep);
/* PruneBiostruc if Aligned Chain Options has been chosen */
if (Chain)
{
if (szTemp[11] != ' ')
{
chain[0] = szTemp[11];
chain[1] = '\0';
pbsTemp = (BiostrucPtr)PruneBiostruc(pbsSlave, chain);
pbsSlave = NULL;
pbsSlave = pbsTemp;
}
}
pbsSlaveTail->next = pbsSlave;
pbsSlaveTail = pbsSlaveTail->next;
pbsSlaveTail->next = NULL;
}
pbsf = pbsf->next;
}
/* Make a linked list of sequence alignments of master and slaves */
pbsf=pbsfs->features;
while (pbsf) {
if (!psaAlignHead) {
psaAlignHead = fnPBSFtoPSA (pbsf); /* get the sequence alignments */
if (psaAlignHead == NULL || psaAlignHead->data == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to create SeqAnnot.</h3>\n");
return 0;
}
salpHead = (SeqAlignPtr)(psaAlignHead->data);
salpTail = salpHead;
}
else {
psaAlignTail = fnPBSFtoPSA (pbsf);
salpTail->next = (SeqAlignPtr)(psaAlignTail->data);
if (psaAlignTail == NULL || psaAlignTail->data == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to create SeqAnnot.</h3>\n");
return 0;
}
salpTail = salpTail->next;
salpTail->next = NULL;
}
pbsf = pbsf->next;
}
pbsaStruct->master = pbsMaster;
pbsaStruct->slaves = pbsSlaveHead;
pbsaStruct->alignments = pbsaShort;
pbsaStruct->seqalign = psaAlignHead;
pvnNcbi = ValNodeNew(NULL);
pvnNcbi->choice = NcbiMimeAsn1_alignstruc;
pvnNcbi->data.ptrvalue = pbsaStruct;
pvnNcbi = (NcbiMimeAsn1Ptr) CheckId(pvnNcbi, JobID); /* to check identity, yanli */
OutputFile = stdout;
if (iPDB == 0) /* cn3d MIME */
printf ("Content-type: chemical/ncbi-asn1-binary\n\n");
else if (iPDB == 1) { /* "See File" */
printf ("Content-type: text/html\n\n");
printf ("<HTML><body><pre>\n");
}
else /* "Save File" */
printf ("Content-type: application/octet-stream\n\n");
if (iPDB != 1)
paiFile = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
else
paiFile = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
NcbiMimeAsn1AsnWrite(pvnNcbi, paiFile, NULL);
AsnIoFlush(paiFile);
AsnIoClose(paiFile);
CloseMMDBAPI();
MMDBFini();
VASTFini();
return 0;
} /* end of VastToCn3D */
AsnMemoryWrite::AsnMemoryWrite(Uint2 mode)
: m_Data(new char[512]), m_Size(512), m_Ptr(0)
{
m_Out = AsnIoNew(mode | ASNIO_OUT, 0, this,
0, reinterpret_cast<IoFuncType>(WriteAsn));
}
void AsnMemoryRead::Init(void)
{
m_Ptr = 0;
m_In = AsnIoNew(m_mode | ASNIO_IN, 0, this,
reinterpret_cast<IoFuncType>(ReadAsn), 0);
}