static BioseqPtr DOT_GetBspFromGIOrAcc(CharPtr str)
{
BioseqPtr bsp;
Int4 gi;
Char ptr;
SeqIdPtr sip;
ValNode vn;
LinkSetPtr lsp;
Int4 uid;
str = TrimSpacesAroundString(str);
ptr = *str;
if (IS_ALPHA(ptr)) /* accession */
{
sip = SeqIdFromAccessionDotVersion(str);
bsp = BioseqLockById(sip);
} else /* it's a GI */
{
gi = atoi(str);
vn.choice = SEQID_GI;
vn.data.intvalue = gi;
vn.next = NULL;
bsp = BioseqLockById(&vn);
}
return bsp;
}
static BioseqPtr FetchOnlyBioseqFromID (CharPtr str)
{
BioseqPtr bsp = NULL;
Uint2 entityID;
SeqEntryPtr sep;
SeqIdPtr sip = NULL;
Int4 uid;
time_t t1, t2;
t1 = time (NULL);
uid = 0;
TrimSpacesAroundString (str);
if (IsAllDigits (str)) {
if (PvtStrToLong (str, &uid)) {
sip = ValNodeNew(NULL);
sip->choice = SEQID_GI;
sip->data.intvalue = uid;
} else {
uid = 0;
}
} else {
sip = SeqIdFromAccessionDotVersion (str);
uid = AccessionToGi (str);
}
sep = NULL;
if (uid > 0) {
sep = PubSeqSynchronousQuery (uid, 3, 0); /* retcode was 0 */
if (sep != NULL) {
bsp = BioseqFindInSeqEntry (sip, sep);
entityID = ObjMgrGetEntityIDForChoice (sep);
}
}
sip = SeqIdFree (sip);
if (debug_mode) {
t2 = time (NULL);
if (t2 - t1 > 1) {
printf ("Time to download %s from ID:%d\n", str, (int) (t2 - t1));
}
}
return bsp;
}
static void AddSpecMember (
ButtoN b
)
{
Char buf [128];
DollarAmountPtr dap;
Int2 days = 0;
MiscRatePtr mrp;
SscSpecPtr ssp;
SscTablesPtr stp;
Int2 which;
ssp = (SscSpecPtr) GetObjectExtra (b);
if (ssp == NULL) return;
stp = ssp->tables;
if (stp == NULL) return;
mrp = stp->miscrate_table;
if (mrp == NULL) return;
GetTitle (ssp->name, buf, sizeof (buf));
if (StringHasNoText (buf)) return;
TrimSpacesAroundString (buf);
if (! NormalizeAuthorCaps (buf)) return;
which = GetValue (ssp->whichspec);
if (which < 1) return;
switch (which) {
case 1 :
days = mrp->special_memb_days;
if (days < 0) {
days = 0;
}
if (AddToTempMemberList (stp, buf, days)) {
AddToContactList (stp->new_contacts, buf, VISITING_MEMBER);
if (GetStatus (ssp->visitfee)) {
dap = mrp->visiting_fee;
if (dap != NULL) {
AddFeeItem (stp->fees, buf, 0, NULL, dap->dollars, dap->cents,
VISITING_MEMB_FEE, NULL, NULL);
}
}
}
break;
case 2 :
days = mrp->special_memb_days;
if (days < 0) {
days = 0;
}
if (AddToTempMemberList (stp, buf, days)) {
AddToContactList (stp->new_contacts, buf, AFFIL_MEMBER);
if (GetStatus (ssp->affilfee)) {
dap = mrp->affiliated_fee;
if (dap != NULL) {
AddFeeItem (stp->fees, buf, 0, NULL, dap->dollars, dap->cents,
AFFIL_MEMB_FEE, NULL, NULL);
}
}
}
break;
case 3 :
if (AddToFullMemberList (stp, buf, ssp->jobs)) {
AddToContactList (stp->new_contacts, buf, TRANSIENT_MEMBER);
if (GetStatus (ssp->transfee)) {
dap = &(ssp->proratedtrans);
if (dap != NULL) {
AddFeeItem (stp->fees, buf, 0, NULL, dap->dollars, dap->cents,
TRANS_MEMB_FEE, NULL, NULL);
}
}
if (GetStatus (ssp->transssa)) {
dap = &(ssp->proratedssa);
if (dap != NULL) {
AddFeeItem (stp->fees, buf, 0, NULL, dap->dollars, dap->cents,
SSA_DUES_FEE, NULL, NULL);
}
}
}
break;
default :
break;
}
SafeHide (ssp->namegroup);
SafeHide (ssp->controls [ssp->currPage]);
SafeSetValue (ssp->whichspec, 0);
ssp->currPage = 0;
SetTitle (ssp->name, "");
SetStatus (ssp->visitfee, TRUE);
SetStatus (ssp->affilfee, TRUE);
SetStatus (ssp->transfee, TRUE);
SetStatus (ssp->transssa, TRUE);
SetClubJobs (ssp->jobs, FALSE, FALSE, FALSE, FALSE);
Disable (b);
Update ();
}
Int2 Main (void)
{
Char app [64], type;
CSpeedFlagData cfd;
CharPtr directory, filter, infile, logfile, outfile, str, suffix;
Boolean remote;
time_t runtime, starttime, stoptime;
/* 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;
}
/* process command line arguments */
sprintf (app, "cspeedtest %s", CSPEEDTEST_APPLICATION);
if (! GetArgs (app, sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
MemSet ((Pointer) &cfd, 0, sizeof (CSpeedFlagData));
directory = (CharPtr) myargs [p_argInputPath].strvalue;
infile = (CharPtr) myargs [i_argInputFile].strvalue;
outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
filter = (CharPtr) myargs [f_argFilter].strvalue;
suffix = (CharPtr) myargs [x_argSuffix].strvalue;
cfd.batch = FALSE;
cfd.binary = (Boolean) myargs [b_argBinary].intvalue;
cfd.compressed = (Boolean) myargs [c_argCompressed].intvalue;
cfd.lock = (Boolean) myargs [l_argLockFar].intvalue;
cfd.type = 1;
str = myargs [a_argType].strvalue;
TrimSpacesAroundString (str);
if (StringDoesHaveText (str)) {
type = str [0];
} else {
type = 'a';
}
type = TO_LOWER (type);
switch (type) {
case 'a' :
cfd.type = 1;
break;
case 'e' :
cfd.type = 2;
break;
case 'b' :
cfd.type = 3;
break;
case 's' :
cfd.type = 4;
break;
case 'm' :
cfd.type = 5;
break;
case 't' :
cfd.type = 1;
cfd.batch = TRUE;
break;
case 'f' :
cfd.type = 6;
break;
case 'l' :
cfd.type = 7;
break;
default :
cfd.type = 1;
break;
}
remote = (Boolean) myargs [R_argRemote].intvalue;
cfd.maxcount = myargs [X_argMaxCount].intvalue;
if (cfd.maxcount < 1) {
cfd.maxcount = 1;
}
cfd.io = myargs [O_argInOut].strvalue;
cfd.clean = myargs [K_argClean].strvalue;
cfd.skip = myargs [P_argSkip].strvalue;
cfd.index = myargs [I_argIndex].strvalue;
cfd.seq = myargs [S_argSeq].strvalue;
cfd.feat = myargs [F_argFeat].strvalue;
cfd.desc = myargs [D_argDesc].strvalue;
cfd.verify = myargs [V_argVerify].strvalue;
cfd.amp = AsnAllModPtr ();
cfd.atp_bss = AsnFind ("Bioseq-set");
cfd.atp_bsss = AsnFind ("Bioseq-set.seq-set");
cfd.atp_se = AsnFind ("Bioseq-set.seq-set.E");
cfd.atp_bsc = AsnFind ("Bioseq-set.class");
cfd.bssp_atp = AsnLinkType (NULL, cfd.atp_bss);
logfile = (CharPtr) myargs [L_argLogFile].strvalue;
if (StringDoesHaveText (logfile)) {
cfd.logfp = FileOpen (logfile, "w");
}
if (remote) {
PubSeqFetchEnable ();
}
if (StringDoesHaveText (outfile)) {
cfd.ofp = FileOpen (outfile, "w");
}
starttime = GetSecs ();
if (StringDoesHaveText (directory)) {
DirExplore (directory, NULL, suffix, FALSE, ProcessOneRecord, (Pointer) &cfd);
} else if (StringDoesHaveText (infile)) {
ProcessOneRecord (infile, (Pointer) &cfd);
}
if (cfd.ofp != NULL) {
FileClose (cfd.ofp);
}
stoptime = GetSecs ();
runtime = stoptime - starttime;
if (cfd.logfp != NULL) {
fprintf (cfd.logfp, "Finished in %ld seconds\n", (long) runtime);
FileClose (cfd.logfp);
}
printf ("Finished in %ld seconds\n", (long) runtime);
if (remote) {
PubSeqFetchDisable ();
}
return 0;
}
