DocUid LIBCALL MMDBEvalPDB(CharPtr str)
{
Entrez2BooleanReplyPtr e2br;
Entrez2IdListPtr e2id;
Entrez2RequestPtr e2rq;
Entrez2ReplyPtr e2ry;
Char tmp [61];
Uint4 uid = 0;
if (str == NULL) return 0;
StringNCpy_0 (tmp, str, sizeof (tmp) - 10);
if (StringStr (tmp, "[ACCN]") == NULL) {
StringCat (tmp, " [ACCN]");
}
e2rq = EntrezCreateBooleanRequest (TRUE, FALSE, "Structure", tmp,
0, 0, NULL, 1, 0);
if (e2rq == NULL) return 0;
e2ry = EntrezSynchronousQuery (e2rq);
e2rq = Entrez2RequestFree (e2rq);
if (e2ry == NULL) return 0;
e2br = EntrezExtractBooleanReply (e2ry);
if (e2br == NULL) return 0;
if (e2br->count > 0) {
e2id = e2br->uids;
if (e2id != NULL && e2id->num > 0 && e2id->uids != NULL) {
BSSeek (e2id->uids, 0, SEEK_SET);
uid = Nlm_BSGetUint4 (e2id->uids);
}
}
Entrez2BooleanReplyFree (e2br);
return uid;
/*
LinkSetPtr plsLink = NULL;
DocUid duUID = 0;
if ((!str)) return (DocUid) 0;
plsLink = EntrezTLEvalString(str, (DocType) TYP_ST,
(DocField) FLD_ACCN, NULL, NULL);
if (plsLink != NULL && plsLink->num > 0 && plsLink->uids != NULL)
{
duUID = plsLink->uids[0];
}
LinkSetFree(plsLink);
return duUID;
*/
}
static NI_DispatcherPtr s_GenericInit
(CharPtr configFile, CharPtr configSection, Boolean showMonitor,
CharPtr lastDispatcher, Int2 lastDispLen)
{
NI_DispatcherPtr disp = (NI_DispatcherPtr)MemNew(sizeof(NI_Dispatcher));
disp->interface = eNII_Debug;
if ( lastDispatcher )
StringNCpy_0(lastDispatcher, "Debug NCBI Network Client", lastDispLen);
disp->motd = StringSave("Makes a direct connection to the specified server");
disp->adminInfo = StringSave("Denis V. Vakatov "
"([email protected])");
disp->referenceCount = 1;
return disp;
}
static void Cn3D_PNGSaveProc(IteM i)
{
Char fname[PATH_MAX];
Char defname[32];
PDNMS pdnmsThis = GetSelectedModelstruc();
fname[0] = '\0';
defname[0] = '\0';
if (pdnmsThis == NULL)
StringNCpy_0(defname,
pdnmsThis ? GetStrucStrings(pdnmsThis,
PDB_ACC) : "cn3d",
sizeof(defname) - 4);
StringCat(defname, ".png");
if (GetOutputFileName(fname, sizeof(fname), defname)) {
Nlm_SaveImagePNG(fname);
}
}
static void Cn3D_GifSaveProc(IteM i)
{
Char fname[PATH_MAX];
Char defname[32];
PDNMS pdnmsThis = GetSelectedModelstruc();
fname[0] = '\0';
defname[0] = '\0';
if (pdnmsThis == NULL)
StringNCpy_0(defname,
pdnmsThis ? GetStrucStrings(pdnmsThis,
PDB_ACC) : "cn3d",
sizeof(defname) - 4);
StringCat(defname, ".gif");
if (GetOutputFileName(fname, sizeof(fname), defname)) {
SaveImageGIF(Nlm_GetViewerImage3D(Cn3D_v3d), fname);
}
}
static Boolean PvtStrToLong (CharPtr str, Int4Ptr longval)
{
Char ch;
Int2 i;
Int2 len;
Char local [64];
Boolean nodigits;
Boolean rsult;
long int val;
rsult = FALSE;
if (longval != NULL) {
*longval = (Int4) 0;
}
len = (Int2) StringLen (str);
if (len != 0) {
rsult = TRUE;
nodigits = TRUE;
for (i = 0; i < len; i++) {
ch = str [i];
if (ch == ' ' || ch == '+' || ch == '-') {
} else if (ch < '0' || ch > '9') {
rsult = FALSE;
} else {
nodigits = FALSE;
}
}
if (nodigits) {
rsult = FALSE;
}
if (rsult && longval != NULL) {
StringNCpy_0 (local, str, sizeof (local));
if (sscanf (local, "%ld", &val) == 1) {
*longval = val;
}
}
}
return rsult;
}
static FILE* OpenOneFile (
CharPtr directory,
CharPtr base,
CharPtr suffix
)
{
Char file [FILENAME_MAX], path [PATH_MAX];
if (base == NULL) {
base = "";
}
if (suffix == NULL) {
suffix = "";
}
StringNCpy_0 (path, directory, sizeof (path));
sprintf (file, "%s%s", base, suffix);
FileBuildPath (path, NULL, file);
return FileOpen (path, "r");
}
static void WriteOneFile (
CharPtr directory,
CharPtr base,
CharPtr suffix,
SeqEntryPtr sep
)
{
AsnIoPtr aip;
Char file [FILENAME_MAX], path [PATH_MAX];
StringNCpy_0 (path, directory, sizeof (path));
sprintf (file, "%s.%s", base, suffix);
FileBuildPath (path, NULL, file);
aip = AsnIoOpen (path, "w");
if (aip == NULL) return;
SeqEntryAsnWrite (sep, aip, NULL);
AsnIoFlush (aip);
AsnIoClose (aip);
}
Int2 Main(void)
{
Char app [64];
CharPtr directory;
CharPtr ptr;
Char sfx [32];
OutputStreamData osd;
InputStreamData isd;
AsnStreamData asd;
Int4 gap_sizes[2];
Int4 rval = 0;
Int4 u_eq = 0, u_gteq = -1, k_eq = 0, k_gteq = -1;
/* standard setup */
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
UseLocalAsnloadDataAndErrMsg ();
ErrPathReset ();
/* finish resolving internal connections in ASN.1 parse tables */
if (! AllObjLoad ()) {
Message (MSG_FATAL, "AllObjLoad failed");
return 1;
}
if (! SubmitAsnLoad ()) {
Message (MSG_FATAL, "SubmitAsnLoad failed");
return 1;
}
if (! FeatDefSetLoad ()) {
Message (MSG_FATAL, "FeatDefSetLoad failed");
return 1;
}
if (! SeqCodeSetLoad ()) {
Message (MSG_FATAL, "SeqCodeSetLoad failed");
return 1;
}
if (! GeneticCodeTableLoad ()) {
Message (MSG_FATAL, "GeneticCodeTableLoad failed");
return 1;
}
SetUpAsnStreamData (&asd);
/* initialize OuputStreamData */
MemSet (&osd, 0, sizeof (osd));
/* initialize InputStreamData */
MemSet (&isd, 0, sizeof (isd));
/* initialize gap_sizes */
gap_sizes[0] = 0;
gap_sizes[1] = 0;
/* process command line arguments */
sprintf (app, "raw2delt %s", RAW2DELT_APPLICATION);
if (! GetArgs (app, sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
u_eq = (Int4) myargs [u_argEqUnknownGap].intvalue;
u_gteq = (Int4) myargs [U_argGTEqUnknownGap].intvalue;
k_eq = (Int4) myargs [k_argEqUnknownGap].intvalue;
k_gteq = (Int4) myargs [K_argGtEqUnknownGap].intvalue;
if (u_eq < 1 && u_gteq < 1 && k_eq < 1 && k_gteq < 1) {
Message (MSG_FATAL, "Must specify values for at least one of -u, -U, -k, -K");
return 1;
} else if (u_eq > -1 && u_gteq > -1) {
Message (MSG_FATAL, "May only specify value for -u or -U, not both");
return 1;
} else if (k_eq > -1 && k_gteq > -1) {
Message (MSG_FATAL, "May only specify value for -k or -K, not both");
return 1;
}
if (u_eq > 0) {
gap_sizes[0] = u_eq;
} else if (u_gteq > 0) {
gap_sizes[0] = 0 - u_gteq;
}
if (k_eq > 0) {
gap_sizes[1] = k_eq;
} else if (k_gteq > 0) {
gap_sizes[1] = 0 - k_gteq;
}
if (gap_sizes[0] == gap_sizes[1]) {
Message (MSG_FATAL, "Cannot specify the same size for known and unknown length gaps");
return 1;
}
directory = (CharPtr) myargs [p_argInputPath].strvalue;
osd.results_dir = (CharPtr) myargs [r_argOutputPath].strvalue;
if (StringHasNoText (osd.results_dir)) {
osd.results_dir = NULL;
}
osd.suffix = (CharPtr) myargs [x_argSuffix].strvalue;
osd.outsuffix = (CharPtr) myargs [s_argOutSuffix].strvalue;
osd.base = (CharPtr) myargs [i_argInputFile].strvalue;
osd.outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
if (StringHasNoText (osd.outfile)) {
osd.outfile = NULL;
}
osd.is_binary = (Boolean) myargs [d_argOutputBinary].intvalue;
if (osd.base == "stdin") {
osd.base = NULL;
}
/* if we don't have an output directory or an output file, and the user hasn't provided an
* output suffix, add a default.
*/
if (osd.results_dir == NULL && osd.outfile == NULL && StringHasNoText (osd.outsuffix)) {
osd.outsuffix = ".delta";
}
isd.is_binary = (Boolean) myargs [b_argInputBinary].intvalue;
isd.is_seqentry = (Boolean) myargs [e_argInputSeqEntry].intvalue;
isd.directory = directory;
isd.base = osd.base;
isd.suffix = osd.suffix;
if (StringDoesHaveText (osd.outfile)) {
osd.aip = AsnIoOpen (osd.outfile, "w");
if (osd.aip == NULL) {
Message (MSG_FATAL, "Unable to open output file");
return 1;
}
} else {
if (StringHasNoText (osd.results_dir)) {
osd.results_dir = directory;
}
/* if we're putting the results in a separate directory, strip the directory name from the output base */
if (!StringHasNoText (osd.results_dir) && !StringHasNoText (osd.base)) {
#ifdef OS_MSWIN
ptr = StringRChr (osd.base, '\\');
#else
ptr = StringRChr (osd.base, '/');
#endif;
if (ptr != NULL) {
osd.base = ptr + 1;
}
}
}
if (StringHasNoText(directory) && StringHasNoText(osd.base)) {
rval = ProcessStream (&isd, &osd, &asd, gap_sizes);
} else if (StringDoesHaveText (osd.base)) {
ptr = StringRChr (osd.base, '.');
sfx[0] = '\0';
if (ptr != NULL) {
StringNCpy_0 (sfx, ptr, sizeof (sfx));
*ptr = '\0';
}
osd.suffix = sfx;
isd.suffix = sfx;
if (isd.is_binary) {
rval = ProcessStream (&isd, &osd, &asd, gap_sizes);
} else {
rval = ProcessOneRecord (directory, &osd, gap_sizes);
}
} else {
rval = FileRecurse (directory, &isd, &osd, &asd, gap_sizes);
}
if (osd.aip != NULL) {
AsnIoFlush (osd.aip);
AsnIoClose (osd.aip);
}
return rval;
}
/* return -1 on failure, 0 on success */
static Int4 FileRecurse (
CharPtr directory,
InputStreamPtr isp,
OutputStreamPtr osp,
AsnStreamPtr asp,
Int4Ptr gap_sizes
)
{
Char path [PATH_MAX];
CharPtr ptr;
CharPtr str;
ValNodePtr head, vnp;
CharPtr orig_dir, orig_base;
Int4 rval = 0;
/* get list of all files in source directory */
head = DirCatalog (directory);
for (vnp = head; vnp != NULL; vnp = vnp->next) {
if (vnp->choice == 0) {
str = (CharPtr) vnp->data.ptrvalue;
if (StringDoesHaveText (str)) {
/* does filename have desired substring? */
ptr = StringStr (str, osp->suffix);
if (ptr != NULL) {
/* make sure detected suffix is really at end of filename */
if (StringCmp (ptr, osp->suffix) == 0) {
*ptr = '\0';
/* process file that has desired suffix (usually .fsa) */
osp->base = str;
orig_dir = isp->directory;
isp->directory = directory;
orig_base = isp->base;
isp->base = str;
if (isp->is_binary) {
rval |= ProcessStream (isp, osp, asp, gap_sizes);
} else {
rval |= ProcessOneRecord (directory, osp, gap_sizes);
}
isp->directory = orig_dir;
isp->base = orig_base;
osp->base = NULL;
}
}
}
} else if (vnp->choice == 1) {
/* recurse into subdirectory */
StringNCpy_0 (path, directory, sizeof (path));
str = (CharPtr) vnp->data.ptrvalue;
FileBuildPath (path, str, NULL);
rval |= FileRecurse (path, isp, osp, asp, gap_sizes);
}
}
/* clean up file list */
ValNodeFreeData (head);
return rval;
}
static Boolean LIBCALLBACK FirstVecScreenCallback (
CONN conn,
Nlm_VoidPtr userdata,
EIO_Status status
)
{
VQueuePtr cqp;
FILE *fp;
Char line [256];
Char path [PATH_MAX];
CharPtr rid;
CharPtr rtoe;
CharPtr str;
long int val;
/* read rID or failure message */
cqp = (VQueuePtr) userdata;
TmpNam (path);
fp = FileOpen (path, "w");
QUERY_CopyResultsToFile (conn, fp);
FileClose (fp);
fp = FileOpen (path, "r");
str = ReadALine (line, sizeof (line), fp);
while (str != NULL) {
if (! StringHasNoText (line)) {
if (line [0] == '>') {
if (StringNICmp (line, ">Vector", 7) == 0) {
rid = StringStr (line, "RID: ");
if (rid != NULL) {
rid += 5;
rtoe = StringStr (rid, " RTOE: ");
if (rtoe != NULL) {
*rtoe = '\0';
rtoe += 7;
StringNCpy_0 (cqp->rid, rid, sizeof (cqp->rid));
if (sscanf (rtoe, "%ld", &val) == 1) {
cqp->estTime = (time_t) val;
cqp->secondsToWait = (Int2) val + 2;
} else {
cqp->secondsToWait = 15;
}
if (cqp->secondsToWait > 15) {
cqp->secondsToWait = 15;
}
if (cqp->announceproc != NULL) {
cqp->announceproc (rid, cqp->seqid, (Int2) val);
}
}
} else if (StringStr (line, "FAILED") != NULL) {
cqp->done = TRUE;
if (cqp->resultproc != NULL) {
cqp->resultproc (NULL, cqp->userdata, cqp->rid, cqp->seqid, FALSE);
}
}
} else if (StringNICmp (line, ">Message", 8) == 0) {
str = ReadALine (line, sizeof (line), fp);
while (str != NULL && StringNCmp (line, "//", 2) != 0) {
Message (MSG_POST, "%s\n", str);
if (StringStr (line, "FAILURE") != NULL) {
cqp->done = TRUE;
}
str = ReadALine (line, sizeof (line), fp);
}
}
}
}
str = ReadALine (line, sizeof (line), fp);
}
FileClose (fp);
FileRemove (path);
return TRUE;
}
NLM_EXTERN CONN QUERY_OpenUrlQuery (
const char* host_machine,
Nlm_Uint2 host_port,
const char* host_path,
const char* arguments,
const char* appName,
Nlm_Uint4 timeoutsec,
EMIME_Type type,
EMIME_SubType subtype,
EMIME_Encoding encoding,
THCC_Flags flags
)
{
CONN conn;
CONNECTOR connector;
SConnNetInfo* net_info;
EIO_Status status;
if (StringHasNoText (host_path))
return NULL;
/* fill in connection info fields and create the connection */
net_info = ConnNetInfo_Create(0);
ASSERT ( net_info );
x_SetupUserHeader (net_info, appName, type, subtype, encoding);
if (StringDoesHaveText (host_machine)) {
StringNCpy_0 (net_info->host, host_machine, sizeof (net_info->host));
}
if ( host_port ) {
net_info->port = host_port;
}
StringNCpy_0 (net_info->path, host_path, sizeof (net_info->path));
if (StringDoesHaveText (arguments)) {
StringNCpy_0 (net_info->args, arguments, sizeof (net_info->args));
}
if (timeoutsec == (Nlm_Uint4)(-1L)) {
net_info->timeout = kInfiniteTimeout;
} else if ( timeoutsec ) {
net_info->tmo.sec = timeoutsec;
net_info->tmo.usec = timeoutsec;
net_info->timeout = &net_info->tmo;
}
connector = HTTP_CreateConnector (net_info, NULL, flags);
ConnNetInfo_Destroy (net_info);
if (connector == NULL) {
ErrPostEx (SEV_ERROR, 0, 0, "QUERY_OpenUrlQuery failed in HTTP_CreateConnector");
conn = NULL;
} else if ((status = CONN_Create (connector, &conn)) != eIO_Success) {
ErrPostEx (SEV_ERROR, 0, 0, "QUERY_OpenUrlQuery failed in CONN_Create: %s",
IO_StatusStr (status));
ASSERT (conn == NULL);
}
return conn;
}