Boolean LIBCALL VASTInit (void)
{
Char fname[PATH_MAX];
database[0] = gunzip[0] = '\0';
GetAppParam("vast", "VASTSRV", "Database", "", database, PATH_MAX);
if (database[0] == '\0')
{
ErrPostEx(SEV_FATAL,0,0, "MMDB config file / path to VAST data missing.\n");
return FALSE;
}
GetAppParam("vast", "VASTSRV", "Gunzip", "", gunzip, (size_t) 256 * (sizeof(char)));
if (gunzip[0] == '\0')
{
ErrPostEx(SEV_FATAL,0,0, "VASTInit failed: gunzip path missing.\n");
return FALSE;
}
GetAppParam("vast", "VASTSRV", "SubsetFile", "", fname, PATH_MAX);
if (fname[0] == '\0') {
ErrPostEx(SEV_FATAL, 0, 0, "VASTInit failed: no subset file name.\n");
return FALSE;
}
if (LoadSubsetTable(fname) != 1) {
ErrPostEx(SEV_FATAL, 0, 0, "VASTInit failed: can't load subset table.\n");
return FALSE;
}
return TRUE;
}
int main(int argc, char *argv[])
{
if (argc>=2 && strcmp(argv[1], "-help") &&
strcmp(argv[1], "--help") &&
strcmp(argv[1], "-h") ) { // recognize parameter file as argument
if (!lemur::api::ParamPushFile(argv[1]))
{
cerr << "Unable to load parameter file: " << argv[1] << endl;;
exit(1);
}
} else {
// handle "-help", display parameters
GetAppParam(); // called only to "register" parameters
cerr << "Parameters for " << argv[0] << endl;
lemur::api::ParamDisplay();
exit(0);
}
GetAppParam();
int result = 1;
try {
result = AppMain(argc,argv);
}
catch (lemur::api::Exception &ex) {
ex.writeMessage();
cerr << "Program aborted due to exception" << endl;;
exit(1);
}
// clean up
lemur::api::ParamClear();
return result;
}
static Int2 GetEntrezAppParam (CharPtr section, CharPtr type, CharPtr dflt, CharPtr buf, Int2 buflen)
{
Int2 rsult;
rsult = GetAppParam ("ENTREZCUSTOM", section, type, NULL, buf, buflen);
if (rsult) return rsult;
rsult = GetAppParam ("ENTREZ", section, type, dflt, buf, buflen);
return rsult;
}
extern Uint4 NI_GetEnvParamEx
(const Char *conf_file, const Char *conf_section,
const Char *env_name, const Char *conf_name,
Char *buf, Uint4 bufsize, const Char *dflt)
{
ASSERT ( (env_name && *env_name) || (conf_name && *conf_name) );
ASSERT ( buf && bufsize );
buf[0] = '\0';
#ifdef USE_GETENV
if (env_name && *env_name) {
const Char *str = getenv(env_name);
if (str && *str) {
Uint4 len = StrLen(str);
if (len >= bufsize)
return 0;
StrCpy(buf, str);
return len;
}
}
#endif
if (conf_name && *conf_name) {
if ( !conf_file )
conf_file = DEF_CONFIG_FILE;
if ( !conf_section )
conf_section = DEF_CONFIG_SECTION;
return GetAppParam
((CharPtr)conf_file, (CharPtr)conf_section, (CharPtr)conf_name,
(CharPtr)dflt, buf, (Int2)bufsize);
}
return 0;
}
static Boolean SetEntrezAppParam (CharPtr section, CharPtr type, CharPtr value)
{
Char tmp [32];
if (GetAppParam ("ENTREZCUSTOM", section, type, NULL, tmp, sizeof (tmp) - 1)) {
return SetAppParam ("ENTREZCUSTOM", section, type, value);
}
return SetAppParam ("ENTREZ", section, type, value);
}
/*****************************************************************************
Function: DDV_UseNetwork()
Purpose: Determines if DDV should use the network
Returns: TRUE if yes
*****************************************************************************/
static Boolean DDV_UseNetwork(void)
{
Char str[64];
if (GetAppParam
("DDV", "SETTINGS", "NETWORKAVAILABLE", NULL, str, sizeof(str))) {
if (StringICmp(str, "TRUE") == 0) return TRUE;
}
return FALSE;
}
static Boolean NoEntryExists (CharPtr sect, CharPtr type)
{
Char str [256];
if (GetAppParam ("NCBI", sect, type, NULL, str, sizeof (str))) {
if (! StringHasNoText (str)) return FALSE;
}
return TRUE;
}
Boolean LIBCALL VASTInit (void)
{
GetAppParam("mmdb", "VAST", "Database", "", database, PATH_MAX);
if (database[0] == NULL)
{
ErrPostEx(SEV_FATAL,0,0, "MMDB config file / path to VAST data missing.\n");
return FALSE;
}
return TRUE;
}
/*Initialize codebase for the taxonomy database*/
void InitCodeBaseTax(void)
{
/*CHANGE : so the user name and database comes out of the seqhound
config files.*/
SQLCHAR db2alias[10];
SQLCHAR usr[10];
SQLCHAR passwd[10];
Char instance[10];
Char instancebuf[25];
GetAppParam("intrez", "datab", "username", NULL,(Char*) usr, (size_t)10 * (sizeof(Char)));
GetAppParam("intrez", "datab", "password", NULL, (Char*)passwd, (size_t)10 * (sizeof(Char)));
GetAppParam("intrez", "datab", "db2alias", NULL, (Char*)db2alias, (size_t)10 * (sizeof(Char)));
GetAppParam("intrez", "datab", "instance", NULL, (Char*)instance, (size_t)10 * (sizeof(Char)));
/*make sure the the dbeinst3 variable is defined--only for aix system*/
sprintf(instancebuf,"DB2INSTANCE=%s",IsNullStr(instance));
putenv(instancebuf);
/* allocate an envirnment handle */
if (SQLAllocHandle(SQL_HANDLE_ENV, SQL_NULL_HANDLE, &henv) != SQL_SUCCESS){
print_err(henv);
ErrPostEx(SEV_ERROR,0,0, "Unable to allocate envirnment handle.");
}
/* allocate a connection handle */
if (SQLAllocHandle(SQL_HANDLE_DBC, henv, &hdbc) == SQL_ERROR){
print_err(henv);
ErrPostEx(SEV_ERROR,0,0, "An error has occurred! Bastards!");
}
if(SQLConnect( hdbc, db2alias, SQL_NTS, usr, SQL_NTS, passwd, SQL_NTS) != SQL_SUCCESS){
ErrPostEx(SEV_ERROR,0,0, "could not connect to the database. ");
}
}
extern Pointer ReadFromTPASmart (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityID)
{
Char cmmd [256];
Pointer dataptr;
FILE* fp;
Char path [PATH_MAX];
Char err_path [PATH_MAX];
if (datatype != NULL) {
*datatype = 0;
}
if (entityID != NULL) {
*entityID = 0;
}
if (StringHasNoText (accn)) return NULL;
if (tpasmartfetchcmd == NULL) {
if (GetAppParam ("SEQUIN", "TPASMART", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
tpasmartfetchcmd = StringSaveNoNull (cmmd);
}
}
if (tpasmartfetchcmd == NULL) return NULL;
TmpNam (path);
#ifdef OS_UNIX
sprintf (err_path, "%s.err", path);
sprintf (cmmd, "csh %s %s > %s 2>%s", tpasmartfetchcmd, accn, path, err_path);
system (cmmd);
#endif
#ifdef OS_MSWIN
sprintf (cmmd, "%s %s -o %s", tpasmartfetchcmd, accn, path);
system (cmmd);
#endif
fp = FileOpen (path, "r");
if (fp == NULL) {
FileRemove (path);
return NULL;
}
dataptr = ReadAsnFastaOrFlatFile (fp, datatype, entityID, FALSE, FALSE, TRUE, FALSE);
FileClose (fp);
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
return dataptr;
}
Boolean MyOpenLL_GO(CharPtr name, Boolean Create)
{
Char pathdatab[PATH_MAX];
/*find path name of database (see NCBI toolkit corelib
and file "prebind.ini" in windows directory)*/
pathdatab[0] = '\0';
GetAppParam("dbxref", "databases", "path", NULL, pathdatab, (size_t)PATH_MAX * (sizeof(Char)));
StringCat(pathdatab, name);
/*printf("%s\n", pathdatab);*/
if (Create == FALSE)
{
/*open the datafile or return error*/
pD4LL_GO = d4open(&codeBase, pathdatab);
if (pD4LL_GO == NULL) return FALSE;
}
else
{
/*open the datafile or create the datafile or return error*/
pD4LL_GO = d4open(&codeBase, pathdatab);
if (pD4LL_GO == NULL)
pD4LL_GO = d4create(&codeBase, pathdatab, fieldInfo_GO, tagInfo_GO);
if (codeBase.errorCode) return FALSE;
}
/*assign the field pointers*/
pF4LL_NP_GO = d4field(pD4LL_GO, "NP_GO" );
pF4LL_GOID = d4field(pD4LL_GO, "GO_ID" );
pF4LL_PMID = d4field(pD4LL_GO, "PMID" );
pF4LL_EVICODE = d4field(pD4LL_GO, "EVICODE" );
/*assign the tag pointers*/
pT4LL_NP_GO = d4tag(pD4LL_GO, "NP_TAG_GO");
pT4LL_GOID = d4tag(pD4LL_GO, "GOID_TAG");
pT4LL_PMID = d4tag(pD4LL_GO, "PMID_TAG");
return TRUE;
}
/* create always true for this one */
Boolean LIBCALL OpenLL_GONoidx(CharPtr name)
{
Char pathdatab[PATH_MAX];
/*find path name of database (see NCBI toolkit corelib
and file "prebind.ini" in windows directory)*/
pathdatab[0] = '\0';
GetAppParam("dbxref", "databases", "path", NULL, pathdatab, (size_t)PATH_MAX * (sizeof(Char)));
StringCat(pathdatab, name);
/* open RESULT without index */
pD4LL_GO = d4open(&codeBase, pathdatab );
/*assign the field pointers*/
pF4LL_NP_GO = d4field(pD4LL_GO, "NP_GO" );
pF4LL_GOID = d4field(pD4LL_GO, "GO_ID" );
pF4LL_PMID = d4field(pD4LL_GO, "PMID" );
pF4LL_EVICODE = d4field(pD4LL_GO, "EVICODE" );
return TRUE;
}
static Int2 LIBCALLBACK TPASmartBioseqFetchFunc (Pointer data)
{
BioseqPtr bsp;
Char cmmd [256];
Pointer dataptr;
Uint2 datatype;
Uint2 entityID;
FILE* fp;
OMProcControlPtr ompcp;
ObjMgrProcPtr ompp;
Char path [PATH_MAX];
Char err_path [PATH_MAX];
SeqEntryPtr sep = NULL;
SeqIdPtr sip;
TextSeqIdPtr tsip;
ompcp = (OMProcControlPtr) data;
if (ompcp == NULL) return OM_MSG_RET_ERROR;
ompp = ompcp->proc;
if (ompp == NULL) return OM_MSG_RET_ERROR;
sip = (SeqIdPtr) ompcp->input_data;
if (sip == NULL) return OM_MSG_RET_ERROR;
if (sip->choice != SEQID_TPG) return OM_MSG_RET_ERROR;
tsip = (TextSeqIdPtr) sip->data.ptrvalue;
if (tsip == NULL || StringHasNoText (tsip->accession)) return OM_MSG_RET_ERROR;
if (tpasmartfetchcmd == NULL) {
if (GetAppParam ("SEQUIN", "TPASMART", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
tpasmartfetchcmd = StringSaveNoNull (cmmd);
}
}
if (tpasmartfetchcmd == NULL) return OM_MSG_RET_ERROR;
TmpNam (path);
#ifdef OS_UNIX
sprintf (err_path, "%s.err", path);
sprintf (cmmd, "csh %s %s > %s 2>%s", tpasmartfetchcmd, tsip->accession, path, err_path);
system (cmmd);
#endif
#ifdef OS_MSWIN
sprintf (cmmd, "%s %s -o %s", tpasmartfetchcmd, tsip->accession, path);
system (cmmd);
#endif
fp = FileOpen (path, "r");
if (fp == NULL) {
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
return OM_MSG_RET_ERROR;
}
dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, FALSE, FALSE, TRUE, FALSE);
FileClose (fp);
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
if (dataptr == NULL) return OM_MSG_RET_OK;
sep = GetTopSeqEntryForEntityID (entityID);
if (sep == NULL) return OM_MSG_RET_ERROR;
bsp = BioseqFindInSeqEntry (sip, sep);
ompcp->output_data = (Pointer) bsp;
ompcp->output_entityID = ObjMgrGetEntityIDForChoice (sep);
return OM_MSG_RET_DONE;
}
static BioseqPtr FetchBioseqFromSmartNotId (CharPtr accn, Uint2Ptr pEntityID)
{
BioseqPtr bsp;
Char cmmd [256];
Pointer dataptr;
Uint2 datatype;
Uint2 entityID;
FILE* fp;
OMProcControlPtr ompcp;
ObjMgrProcPtr ompp;
Char path [PATH_MAX];
Char err_path [PATH_MAX];
SeqEntryPtr sep = NULL;
SeqIdPtr sip;
TextSeqIdPtr tsip;
Int4 gi = 0;
ValNodePtr vnp;
time_t t1, t2;
if (srcchkfetchcmd == NULL) {
if (GetAppParam ("SEQUIN", "TBL_CHK", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
srcchkfetchcmd = StringSaveNoNull (cmmd);
}
}
if (srcchkfetchcmd == NULL) {
if (GetAppParam ("SEQUIN", "SMART", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
srcchkfetchcmd = StringSaveNoNull (cmmd);
}
}
if (srcchkfetchcmd == NULL) return NULL;
TmpNam (path);
t1 = time(NULL);
#ifdef OS_UNIX
sprintf (err_path, "%s.err", path);
sprintf (cmmd, "csh %s %s > %s 2>%s", srcchkfetchcmd, accn, path, err_path);
system (cmmd);
#endif
#ifdef OS_MSWIN
sprintf (cmmd, "%s %s -o %s", srcchkfetchcmd, accn, path);
system (cmmd);
#endif
fp = FileOpen (path, "r");
if (fp == NULL) {
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
return OM_MSG_RET_ERROR;
}
dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, FALSE, FALSE, TRUE, FALSE);
FileClose (fp);
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
if (dataptr == NULL) return NULL;
sep = GetTopSeqEntryForEntityID (entityID);
if (sep == NULL) return NULL;
sip = SmartGuessMakeId (accn);
bsp = BioseqFindInSeqEntry (sip, sep);
sip = SeqIdFree (sip);
if (debug_mode) {
t2 = time(NULL);
if (t2 - t1 > 1) {
printf("Time to download %s from SMART:%d\n", accn, t2 - t1);
}
}
if (pEntityID != NULL) {
*pEntityID = entityID;
}
return bsp;
}
Int2 Main (void)
{
AsnIoPtr aip;
AsnTypePtr atp;
FILE *dfp = NULL;
Boolean do_nuc = FALSE;
Boolean do_prot = FALSE;
XtraPtr extra;
FILE *fp;
GBSeq gbsq;
GBSet gbst;
Boolean get_var;
Char line [256];
Boolean only_new;
CharPtr str;
Char xmlbuf [128];
XtraBlock xtra;
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
UseLocalAsnloadDataAndErrMsg ();
ErrPathReset ();
if (! AllObjLoad ()) {
Message (MSG_FATAL, "AllObjLoad failed");
return 1;
}
if (! SubmitAsnLoad ()) {
Message (MSG_FATAL, "SubmitAsnLoad failed");
return 1;
}
if (! SeqCodeSetLoad ()) {
Message (MSG_FATAL, "SeqCodeSetLoad failed");
return 1;
}
if (! GeneticCodeTableLoad ()) {
Message (MSG_FATAL, "GeneticCodeTableLoad failed");
return 1;
}
if (! objgbseqAsnLoad ()) {
Message (MSG_POSTERR, "objgbseqAsnLoad failed");
return 1;
}
if (! GetArgs ("gbseqget", sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
fp = FileOpen (myargs [i_argInputFile].strvalue, "r");
if (fp == NULL) {
return 1;
}
if (! StringHasNoText (myargs [d_argDateFile].strvalue)) {
dfp = FileOpen (myargs [d_argDateFile].strvalue, "r");
if (dfp == NULL) {
return 1;
}
}
if (GetAppParam ("NCBI", "SETTINGS", "XMLPREFIX", NULL, xmlbuf, sizeof (xmlbuf))) {
AsnSetXMLmodulePrefix (StringSave (xmlbuf));
}
MemSet ((Pointer) &xtra, 0, sizeof (XtraBlock));
MemSet ((Pointer) &gbsq, 0, sizeof (GBSeq));
xtra.gbseq = &gbsq;
aip = AsnIoOpen (myargs [o_argOutputFile].strvalue, "wx");
if (aip == NULL) {
Message (MSG_POSTERR, "AsnIoOpen failed");
FileClose (fp);
return 1;
}
only_new = (Boolean) myargs [n_argNewRecords].intvalue;
get_var = (Boolean) myargs [v_argVariations].intvalue;
str = myargs [m_argMolecule].strvalue;
if (StringICmp (str, "n") == 0) {
do_nuc = TRUE;
} else if (StringICmp (str, "p") == 0) {
do_prot = TRUE;
} else if (StringICmp (str, "b") == 0) {
do_nuc = TRUE;
do_prot = TRUE;
} else {
do_nuc = TRUE;
}
PubSeqFetchEnable ();
xtra.aip = aip;
atp = AsnLinkType (NULL, AsnFind ("GBSet"));
xtra.atp = AsnLinkType (NULL, AsnFind ("GBSet.E"));
if (atp == NULL || xtra.atp == NULL) {
Message (MSG_POSTERR, "AsnLinkType or AsnFind failed");
return 1;
}
extra = &xtra;
MemSet ((Pointer) &gbst, 0, sizeof (GBSet));
AsnOpenStruct (aip, atp, (Pointer) &gbst);
if (dfp != NULL) {
DoQuery (fp, dfp, extra, get_var, do_nuc, do_prot);
} else {
str = ReadALine (line, sizeof (line), fp);
while (str != NULL) {
if (! StringHasNoText (str)) {
ProcessAccession (str, extra, only_new, get_var, do_nuc, do_prot);
}
str = ReadALine (line, sizeof (line), fp);
}
}
AsnCloseStruct (aip, atp, NULL);
AsnPrintNewLine (aip);
AsnIoClose (aip);
FileClose (dfp);
FileClose (fp);
PubSeqFetchDisable ();
return 0;
}
extern void ShowNetConfigForm (WndActnProc activate, FormMessageFunc messages,
VoidProc accepted, VoidProc cancelled,
VoidProc turnedOff, Boolean netCurrentlyOn)
{
ButtoN b;
GrouP c;
GrouP g;
GrouP h;
GrouP j;
Int2 len;
NetConfigPtr ncp;
PrompT ppt0, ppt1;
ButtoN rb;
Char str [256];
WindoW w;
GrouP x;
GrouP z;
w = NULL;
ncp = (NetConfigPtr) MemNew (sizeof (NetConfigData));
if (ncp != NULL) {
w = FixedWindow (-50, -33, -10, -10, "Network Configuration",
StdSendCloseWindowMessageProc);
SetObjectExtra (w, ncp, StdCleanupFormProc);
ncp->form = (ForM) w;
ncp->formmessage = ConfigMessageProc;
ncp->appmessage = messages;
ncp->activate = activate;
SetActivate (w, ConfigFormActivate);
ncp->accepted = accepted;
ncp->cancelled = cancelled;
ncp->turnedOff = turnedOff;
h = HiddenGroup (w, -1, 0, NULL);
SetGroupSpacing (h, 5, 10);
j = HiddenGroup (h, 2, 0, NULL);
ppt0 = StaticPrompt (j, "Connection", 0, 0, programFont, 'l');
ncp->srvConnMode = HiddenGroup (j, 4, 0, ChangeConnection);
SetObjectExtra (ncp->srvConnMode, ncp, NULL);
rb = RadioButton (ncp->srvConnMode, "None");
RadioButton (ncp->srvConnMode, "Normal");
RadioButton (ncp->srvConnMode, "Firewall");
/* RadioButton (ncp->srvConnMode, "Stateless"); */
SetValue (ncp->srvConnMode, 2);
if (turnedOff == NULL) {
Disable (rb);
}
AlignObjects (ALIGN_MIDDLE, (HANDLE) ppt0, (HANDLE) ncp->srvConnMode, NULL);
ncp->netGroup = HiddenGroup (h, -1, 0, NULL);
SetGroupSpacing (ncp->netGroup, 5, 10);
SelectFont (programFont);
len = StringWidth ("HTTP Proxy Server ") + 2;
SelectFont (systemFont);
z = HiddenGroup (ncp->netGroup, -2, 0, NULL);
StaticPrompt (z, "HTTP Proxy Server", len, dialogTextHeight, programFont, 'l');
ncp->proxyHost = DialogText (z, "", 12, ChangeProxy);
SetObjectExtra (ncp->proxyHost, ncp, NULL);
/*
StaticPrompt (z, "", 0, 0, programFont, 'l');
StaticPrompt (z, "", 0, 0, programFont, 'l');
*/
ppt0 = StaticPrompt (z, "HTTP Proxy Port ", len, dialogTextHeight, programFont, 'l');
ncp->proxyPort = DialogText (z, "", 3, NULL);
x = MultiLinePrompt (z, "Non-transparent Proxy Server", len, programFont);
ncp->firewallProxy = DialogText (z, "", 12, NULL);
AlignObjects (ALIGN_MIDDLE, (HANDLE) x, (HANDLE) ncp->firewallProxy, NULL);
/*
AlignObjects (ALIGN_MIDDLE, (HANDLE) ppt0, (HANDLE) ncp->proxyPort,
(HANDLE) ncp->firewallProxy, NULL);
*/
AlignObjects (ALIGN_RIGHT, (HANDLE) ncp->proxyHost, (HANDLE) ncp->firewallProxy, NULL);
AlignObjects (ALIGN_LEFT, (HANDLE) ncp->proxyHost, (HANDLE) ncp->firewallProxy, NULL);
g = HiddenGroup (ncp->netGroup, 5, 0, NULL);
/*
ppt0 = StaticPrompt (g, "Domain name server", 0, 0, programFont, 'l');
ncp->dnsAvailable = CheckBox (g, "Available", NULL);
*/
ncp->dnsAvailable = CheckBox (g, "Domain Name Server", NULL);
SetStatus (ncp->dnsAvailable, TRUE);
/* StaticPrompt (g, " ", 0, 0, programFont, 'l'); */
ppt1 = StaticPrompt (g, "Timeout", 0, popupMenuHeight, programFont, 'l');
ncp->timeOut = PopupList (g, TRUE, NULL);
PopupItem (ncp->timeOut, "10 seconds");
PopupItem (ncp->timeOut, "30 seconds");
PopupItem (ncp->timeOut, "60 seconds");
PopupItem (ncp->timeOut, " 5 minutes");
SetValue (ncp->timeOut, 2);
AlignObjects (ALIGN_MIDDLE, /* (HANDLE) ppt0, */ (HANDLE) ncp->dnsAvailable,
(HANDLE) ppt1, (HANDLE) ncp->timeOut, NULL);
c = HiddenGroup (w, 4, 0, NULL);
SetGroupSpacing (c, 10, 2);
ncp->accept = PushButton (c, "Accept", AcceptNetConfigForm);
SetObjectExtra (ncp->accept, ncp, NULL);
b = PushButton (c, "Cancel", StdSendCancelButtonMessageProc);
SetObjectExtra (b, ncp, NULL);
/*
AlignObjects (ALIGN_CENTER, (HANDLE) h, (HANDLE) c, NULL);
*/
AlignObjects (ALIGN_CENTER, (HANDLE) j, (HANDLE) z, (HANDLE) g, (HANDLE) c, NULL);
RealizeWindow (w);
if (! netCurrentlyOn) {
SafeSetValue (ncp->srvConnMode, 1);
Hide (ncp->netGroup);
} else if (GetAppParam ("NCBI", "CONN", "FIREWALL", NULL, str, sizeof (str))) {
if (StringICmp (str, "TRUE") == 0) {
SafeSetValue (ncp->srvConnMode, 3);
}
}
if (GetAppParam ("NCBI", "CONN", "HTTP_PROXY_HOST", NULL, str, sizeof (str))) {
if (! StringHasNoText (str)) {
SafeSetTitle (ncp->proxyHost, str);
if (GetValue (ncp->srvConnMode) == 2) {
SafeSetValue (ncp->srvConnMode, 3);
}
}
}
if (GetAppParam ("NCBI", "CONN", "HTTP_PROXY_PORT", NULL, str, sizeof (str))) {
if (! StringHasNoText (str)) {
SafeSetTitle (ncp->proxyPort, str);
}
}
if (GetAppParam ("NCBI", "CONN", "PROXY_HOST", NULL, str, sizeof (str))) {
if (! StringHasNoText (str)) {
SafeSetTitle (ncp->firewallProxy, str);
}
}
if (GetAppParam ("NCBI", "CONN", "HOST", NULL, str, sizeof (str))) {
if (StringICmp (str, "130.14.29.110") == 0) {
SafeSetStatus (ncp->dnsAvailable, FALSE);
}
}
if (GetAppParam ("NCBI", "CONN", "TIMEOUT", "30", str, sizeof (str))) {
if (StringICmp (str, "10") == 0) {
SafeSetValue (ncp->timeOut, 1);
} else if (StringICmp (str, "60") == 0) {
SafeSetValue (ncp->timeOut, 3);
} else if (StringICmp (str, "300") == 0) {
SafeSetValue (ncp->timeOut, 4);
} else {
SafeSetValue (ncp->timeOut, 2);
}
}
ChangeConfigControls (ncp);
Show (w);
Select (w);
Select (ncp->proxyHost);
}
}
static void SetupAppProperties (void)
{
Char str [32];
Int2 val;
showAsnPage = TRUE;
if (GetEntrezAppParam ("PREFERENCES", "SHOWASNPAGE", "", str, sizeof (str) - 1)) {
if (StringICmp (str, "FALSE") == 0) {
showAsnPage = FALSE;
}
}
MemSet ((Pointer) (&medviewprocs), 0, sizeof (MedlineViewProcs));
medviewprocs.cleanupObjectPtr = FALSE;
medviewprocs.activateForm = MedlineViewFormActivated;
medviewprocs.closeForm = NULL;
medviewprocs.useFolderTabs = CHANGE_VIEW_POPUP;
/*
medviewprocs.initPage = CITATION_PAGE;
*/
#ifndef WIN_MAC
medviewprocs.createMenus = MedlineViewFormMenus;
#endif
medviewprocs.showAsnPage = showAsnPage;
medviewprocs.useScrollText = FALSE;
medviewprocs.handleMessages = EntrezMedlineFormMessage;
medviewprocs.makeControls = DoMakeViewerLinkControls;
SetAppProperty ("MedlineDisplayForm", &medviewprocs);
MemSet ((Pointer) (&seqviewprocs), 0, sizeof (SeqViewProcs));
seqviewprocs.hasTargetControl = TRUE;
seqviewprocs.hasDoneButton = FALSE;
seqviewprocs.hasDuplicateButton = FALSE;
seqviewprocs.launchEditors = FALSE;
seqviewprocs.launchSubviewers = TRUE;
seqviewprocs.sendSelectMessages = TRUE;
seqviewprocs.highlightSelections = TRUE;
seqviewprocs.cleanupObjectPtr = FALSE;
seqviewprocs.activateForm = BioseqViewFormActivated;
seqviewprocs.closeForm = NULL;
seqviewprocs.useFolderTabs = CHANGE_VIEW_POPUP;
/*
seqviewprocs.initNucPage = NUCASN2FF_PAGE_1;
seqviewprocs.initProtPage = PROTGENPEPT_PAGE;
*/
#ifndef WIN_MAC
seqviewprocs.createMenus = BioseqViewFormMenus;
#endif
seqviewprocs.allowScrollText = FALSE;
seqviewprocs.startInScrollText = FALSE;
seqviewprocs.handleMessages = EntrezSeqViewFormMessage;
seqviewprocs.makeControls = DoMakeViewerLinkControls;
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &mapPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &sumPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &gphPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &alnPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &seqPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &gbgnPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &gnbkPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &emblPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &gnptPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &fstaPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &qualPageData);
if (showAsnPage) {
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &asnPageData);
AddBioseqPageToList (&(seqviewprocs.pageSpecs), &dskPageData);
}
SetAppProperty ("SeqDisplayForm", &seqviewprocs);
if (GetAppParam ("ENTREZ", "PREFERENCES", "TEXTEDITDISPLAYS", "", str, sizeof (str))) {
if (StringICmp (str, "TRUE") == 0) {
medviewprocs.useScrollText = TRUE;
seqviewprocs.allowScrollText = TRUE;
seqviewprocs.startInScrollText = TRUE;
}
}
if (GetEntrezAppParam ("PREFERENCES", "MINPIXELWIDTH", "", str, sizeof (str))) {
if (StrToInt (str, &val) && val > 0) {
val = MIN (val, screenRect.right);
medviewprocs.minPixelWidth = val;
seqviewprocs.minPixelWidth = val;
}
}
if (GetEntrezAppParam ("PREFERENCES", "MINPIXELHEIGHT", "", str, sizeof (str))) {
if (StrToInt (str, &val) && val > 0) {
val = MIN (val, screenRect.bottom);
medviewprocs.minPixelHeight = val;
seqviewprocs.minPixelHeight = val;
}
}
if (GetEntrezAppParam ("PREFERENCES", "TEXTPIXELWIDTH", "", str, sizeof (str))) {
if (StrToInt (str, &val) && val > 0) {
val = MIN (val, screenRect.right);
txtviewprocs.minPixelWidth = val;
}
}
if (GetEntrezAppParam ("PREFERENCES", "TEXTPIXELHEIGHT", "", str, sizeof (str))) {
if (StrToInt (str, &val) && val > 0) {
val = MIN (val, screenRect.bottom);
txtviewprocs.minPixelHeight = val;
}
}
if (GetEntrezAppParam ("SETTINGS", "MEDPAGE", "Abstract", str, sizeof (str))) {
medviewprocs.initMedLabel = StringSaveNoNull (str);
}
if (GetEntrezAppParam ("SETTINGS", "NUCPAGE", "GenBank", str, sizeof (str))) {
seqviewprocs.initNucLabel = StringSaveNoNull (str);
}
if (GetEntrezAppParam ("SETTINGS", "PRTPAGE", "GenPept", str, sizeof (str))) {
seqviewprocs.initProtLabel = StringSaveNoNull (str);
}
if (GetEntrezAppParam ("SETTINGS", "GENMPAGE", "Map", str, sizeof (str))) {
seqviewprocs.initGenomeLabel = StringSaveNoNull (str);
}
MemSet ((Pointer) (&entrezglobals), 0, sizeof (EntrezGlobals));
entrezglobals.retrieveDocsProc = DoRetrieveDocuments;
entrezglobals.loadNamedUidProc = DoLoadNamedUidList;
entrezglobals.launchViewerProc = DoLaunchRecordViewer;
#ifndef WIN_MAC
entrezglobals.createTrmLstMenus = TermListFormMenus;
entrezglobals.createDocSumMenus = DocSumFormMenus;
#endif
SetAppProperty ("EntrezGlobals", &entrezglobals);
entrezglobals.showAsn = showAsnPage;
entrezglobals.persistDefault = TRUE;
if (GetEntrezAppParam ("PREFERENCES", "PARENTSPERSIST", "", str, sizeof (str) - 1)) {
if (StringICmp (str, "FALSE") == 0) {
entrezglobals.persistDefault = FALSE;
}
}
entrezglobals.alignDefault = TRUE;
if (GetEntrezAppParam ("PREFERENCES", "ALIGNCHECKED", NULL, str, sizeof (str) - 1)) {
if (StringICmp (str, "FALSE") == 0) {
entrezglobals.alignDefault = FALSE;
}
}
if (GetAppParam ("ENTREZ", "PREFERENCES", "POPDOWN", "", str, sizeof (str) - 1)) {
if (StringICmp (str, "TRUE") == 0) {
entrezglobals.popdownBehavior = TRUE;
}
}
if (GetEntrezAppParam ("PREFERENCES", "LOOKUPDIRECT", "", str, sizeof (str) - 1)) {
if (StringICmp (str, "TRUE") == 0) {
entrezglobals.lookupDirect = TRUE;
}
}
entrezglobals.sortFields = TRUE;
if (GetAppParam ("ENTREZ", "PREFERENCES", "SORTFIELDS", "", str, sizeof (str) - 1)) {
if (StringICmp (str, "FALSE") == 0) {
entrezglobals.sortFields = FALSE;
}
}
if (GetEntrezAppParam ("SETTINGS", "DATABASE", "MEDLINE", str, sizeof (str))) {
entrezglobals.initDatabase = StringSaveNoNull (str);
}
if (GetEntrezAppParam ("SETTINGS", "FIELD", "All Fields", str, sizeof (str))) {
entrezglobals.initField = StringSaveNoNull (str);
}
if (GetEntrezAppParam ("SETTINGS", "MODE", "Automatic", str, sizeof (str))) {
entrezglobals.initMode = StringSaveNoNull (str);
}
if (GetEntrezAppParam ("SETTINGS", "BROWSER", NULL, str, sizeof (str))) {
SetAppProperty ("MedviewBrowserPath", (void *) StringSave (str));
}
MemSet ((Pointer) (&stdedprocs), 0, sizeof (StdEditorProcs));
#ifdef WIN_MAC
stdedprocs.activateForm = StdEditorFormActivated;
#endif
stdedprocs.handleMessages = EntrezStdEditorFormMessage;
SetAppProperty ("StdEditorForm", &stdedprocs);
MemSet ((Pointer) (&txtviewprocs), 0, sizeof (TextViewProcs));
txtviewprocs.useScrollText = FALSE;
SetAppProperty ("TextDisplayForm", &txtviewprocs);
}
Boolean LIBCALL MMDBInit (void)
{
char *msg;
char path[PATH_MAX];
FILE *f;
#define ERROR(err_msg) { msg = err_msg; goto errexit; }
#ifdef MMDB_PUBSTRUCT
GetAppParam("mmdb", "MMDB", "PubStruct", "", path, sizeof(path));
if (strcmp(path,"yes")==0)
file_db = 0;
else
file_db = 1;
if (!file_db) /* if database reading */
{
GetAppParam("mmdb", "MMDB", "Database", "", database, sizeof(database));
return TRUE;
}
#endif
/* filebased mmdbsrv */
GetAppParam("mmdb", "MMDB", "Database", "", database, sizeof(database));
GetAppParam("mmdb", "MMDB", "Index" , "", indexname, sizeof(indexname));
if (database[0] == 0)
ERROR("MMDBInit failed: config file / path to data missing.\n");
if (indexname[0] == 0)
ERROR("MMDBInit failed: config file / index file missing.\n");
assert(sizeof(path) > strlen(database) + strlen(indexname));
sprintf(path,"%s%s",database,indexname);
f = fopen(path,"r");
if(f)
fclose(f);
else
ERROR("MMDBInit failed: incorrect mmdb.idx path.\n");
#ifdef MMDB_UNIXCOMPRESSED
GetAppParam("mmdb", "MMDBSRV", "Gunzip", "", gunzip, sizeof(gunzip));
if (gunzip[0] == 0)
ERROR("MMDBInit failed: gunzip path missing.\n");
f = fopen(gunzip,"r");
if(f)
fclose(f);
else
ERROR("MMDBInit failed: incorrect gunzip path .\n");
#endif
return LoadMMDBIdx(database, indexname);
#undef ERROR
errexit:
ErrPostEx(SEV_FATAL,0,0, msg);
return FALSE;
}
