static void ValidateOneFile (
CharPtr directory,
CharPtr base,
CharPtr suffix,
SeqEntryPtr sep
)
{
Char file [FILENAME_MAX], path [PATH_MAX];
ErrSev oldErrSev;
ValidStructPtr vsp;
StringNCpy_0 (path, directory, sizeof (path));
sprintf (file, "%s.%s", base, suffix);
FileBuildPath (path, NULL, file);
ErrSetOptFlags (EO_LOGTO_USRFILE);
ErrSetLogfile (path, ELOG_APPEND | ELOG_NOCREATE);
vsp = ValidStructNew ();
if (vsp != NULL) {
vsp->useSeqMgrIndexes = TRUE;
vsp->suppressContext = TRUE;
oldErrSev = ErrSetMessageLevel (SEV_NONE);
ValidateSeqEntry (sep, vsp);
ValidStructFree (vsp);
ErrSetMessageLevel (oldErrSev);
}
ErrSetLogfile (NULL, ELOG_APPEND | ELOG_NOCREATE);
ErrClearOptFlags (EO_LOGTO_USRFILE);
}
static void FlatfileOneFile (
CharPtr directory,
CharPtr base,
CharPtr suffix,
SeqEntryPtr sep
)
{
Char file [FILENAME_MAX], path [PATH_MAX];
FILE *fp;
ErrSev oldErrSev;
StringNCpy_0 (path, directory, sizeof (path));
sprintf (file, "%s.%s", base, suffix);
FileBuildPath (path, NULL, file);
fp = FileOpen (path, "w");
if (fp == NULL) return;
oldErrSev = ErrSetMessageLevel (SEV_MAX);
SeqEntryToFlat (sep, fp, GENBANK_FMT, SEQUIN_MODE);
ErrSetMessageLevel (oldErrSev);
FileClose (fp);
}
Int2 Nlm_Main(void) {
Boolean use_new_engine=FALSE;
char buf[256] = { '\0' };
StringCpy(buf, "mgblast ");
StringNCat(buf, BlastGetVersionNumber(), sizeof(buf)-StringLen(buf)-1);
if (! GetArgs (buf, NUMARG, myargs))
return (1);
UseLocalAsnloadDataAndErrMsg ();
if (! SeqEntryLoad())
return 1;
ErrSetMessageLevel(SEV_WARNING);
/*
if (myargs[ARG_FORCE_OLD].intvalue == 0 &&
myargs[ARG_OUTTYPE].intvalue > 1 &&
myargs[ARG_GILIST].strvalue == NULL)
use_new_engine = readdb_use_new_blast(myargs[ARG_DB].strvalue);
if (myargs[ARG_MASKEDQUERY].strvalue)
use_new_engine = FALSE;
*/
/*if (use_new_engine)
return Main_new();
else */
return Main_old();
}
Int2 Main (void)
{
Char buf[256] = { '\0' }; /* Used below for name and version. */
Int2 status = 0; /* return value of function. */
StringCpy(buf, "bl2seq ");
StringNCat(buf, BlastGetVersionNumber(), sizeof(buf)-StringLen(buf)-1);
if (! GetArgs (buf, NUMARG, myargs)) {
return (1);
}
UseLocalAsnloadDataAndErrMsg ();
if (! SeqEntryLoad())
return 1;
ErrSetMessageLevel(SEV_WARNING);
if (myargs[ARG_FORCE_OLD].intvalue != 0)
status = Main_old();
else
status = Main_new();
FreeArgs(NUMARG, myargs);
return status;
}
Int2 Main(void)
{
ValNodePtr vnp2 = NULL, vnp = NULL;
CharPtr pchar = NULL;
Int4 i = 0;
CharPtr pi = NULL;
ErrSetOptFlags(EO_LOG_SEVERITY | EO_LOG_CODES | EO_LOG_FILELINE | EO_LOG_USRFILE);
ErrSetLogfile("goquerylog", ELOG_BANNER);
ErrSetLogLevel(SEV_INFO);
ErrSetMessageLevel(SEV_MAX);
/*GODB_InitCodeBase();
GODB_OpenAllDBs();*/
if(!SHoundInit(FALSE, "goquery"))
{
printf("Cannot open SeqHound.\n");
return 1;
}
printf("Starting the query\n");
/*GODB_PrintAllRecords();*/
printf("Children of 7612\n");
vnp = SHoundGODBGetChildrenOf(7612);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Children of 4907\n");
vnp = SHoundGODBGetChildrenOf(4907);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Children of 5381\n");
vnp = SHoundGODBGetChildrenOf(5381);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Parent of 5381\n");
vnp = SHoundGODBGetParentOf(5381);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Parent of 5367\n");
vnp = SHoundGODBGetParentOf(5367);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Parent of 16883\n");
vnp = SHoundGODBGetParentOf(16883);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Name of 7625\n");
pchar = SHoundGODBGetNameByID(7625);
printf("%s\n", IsNullStr(pchar));
MemFree(pchar);
printf("Name of 16882\n");
pchar = SHoundGODBGetNameByID(16882);
printf("%s\n", IsNullStr(pchar));
MemFree(pchar);
printf("Name of 15412\n");
pchar = SHoundGODBGetNameByID(15412);
printf("%s\n", IsNullStr(pchar));
MemFree(pchar);
printf("All ancestors of 7627\n");
vnp2 = SHoundGODBGetAllAncestors(7627);
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("All ancestors of 5141\n");
vnp2 = SHoundGODBGetAllAncestors(5141);
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("All children of 7627\n");
vnp2 = SHoundGODBGetAllChildren(7627);
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("All children of 16787\n");
vnp2 = SHoundGODBGetAllChildren(16787);
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("Getting those records with EC\n");
vnp2 = SHoundGODBGetRecordByReference("EC");
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("Getting those records with ISBN\n");
vnp2 = SHoundGODBGetRecordByReference("ISBN");
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("Geting classification\n");
pi = SHoundGODBGetClassification(5935);
printf("%s\n", IsNullStr(pi));
ErrPostEx(SEV_INFO, 0, 0, "Done.");
/*GODB_InitUndoCodeBase();*/
SHoundFini();
return 0;
}
Int2 Main()
{
PMSD pmsdRoot = NULL;
static char valfilein[PATH_MAX];
Int2 iDotLen = 0;
AsnIoPtr aip=NULL;
NcbiMimeAsn1Ptr nmap=NULL;
BiostrucPtr bsp=NULL;
BiostrucSeqPtr bssp=NULL;
PDNMS pdnmsModelstruc = NULL;
ErrSev esMsg,esLog,esFatal;
PDNML pdnmlModel;
PMLD pmldThis;
Boolean isMime = FALSE;
Int4 iModels = 0, iNCBImodel = 0, iPDBmodel = 0, iAscii = 0;
/* Initialize MMDB-API */
ErrSetLogfile("error_strSummary.log", ELOG_APPEND|ELOG_BANNER);
ErrSetOptFlags(EO_SHOW_SEVERITY|EO_SHOW_CODES|EO_LOG_FILELINE|EO_SHOW_USERSTR|EO_SHOW_ERRTEXT|EO_BEEP|EO_WAIT_KEY|EO_LOGTO_USRFILE);
if (!GetArgs("strSummary reports on what is inside .val or .cn3 or .prt file to stdout.\nCaution - will not work on Biounits downloaded from NCBI, use Asymmetric Units\n",3,Rargs))
return 1;
/* we use exact filenames and extensions to avoid confusion */
StringCpy(valfilein, Rargs[0].strvalue);
if (FileLength(valfilein) == 0)
{
ErrPostEx(SEV_FATAL,13,1,"Unable to find input file %s",Rargs[0].strvalue);
return 13;
}
if (!OpenMMDBAPI(0,NULL)) {
ErrPostEx(SEV_FATAL,12,1,"Unable to open MMDBAPI, check for missing bstdt.val dictionary file.");
return 12;
}
/* load an ASN.1 file *.val or *.c3d or *.prt write out Biostruc only */
aip=AsnIoOpen(valfilein,"rb");
if (aip==NULL) {
ErrPostEx(SEV_FATAL,11,1,"Unable open ASN.1 stream in file %s",valfilein);
return 11;
}
/* first try biostruc load */
/* printf("try biostruc\n"); */
esMsg=ErrGetMessageLevel();
esLog=ErrGetLogLevel();
esFatal=ErrGetFatalLevel();
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
bsp=BiostrucAsnRead(aip,NULL);
AsnIoClose(aip);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
if (bsp == NULL) { /* try ascii */
aip = AsnIoOpen(valfilein,"r");
if (aip==NULL) {
ErrPostEx(SEV_FATAL,10,1,"Unable open binary or ascii ASN.1 from file %s",valfilein);
return 10;
}
esMsg=ErrGetMessageLevel();
esLog=ErrGetLogLevel();
esFatal=ErrGetFatalLevel();
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
bsp=BiostrucAsnRead(aip,NULL);
AsnIoClose(aip);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
if (bsp) iAscii = 1;
}
if (bsp==NULL) {
/* printf("try mime binary\n"); */
/* then try NCBIMime load */
aip=NULL;
aip=AsnIoOpen(valfilein,"rb");
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
nmap=NcbiMimeAsn1AsnRead(aip,NULL);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
AsnIoClose(aip);
if (nmap == NULL) {
/* printf("try mime ascii\n"); */
aip=AsnIoOpen(valfilein,"r");
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
nmap=NcbiMimeAsn1AsnRead(aip,NULL);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
AsnIoClose(aip);
if (nmap) iAscii = 1;
}
if (nmap!=NULL) {
/* got an NCBI mime */
if (nmap->choice!=NcbiMimeAsn1_strucseq && nmap->choice!=NcbiMimeAsn1_strucseqs) {
/* wrong MIME type */
nmap=NcbiMimeAsn1Free(nmap);
ErrPostEx(SEV_ERROR,9,1,"MIME-type wrapper is not a strucseq or strucseqs - no Biostruc to report in: %s",valfilein);
return 9;
}
isMime = TRUE;
/* unwrap the mime and leave the bsp for PDB conversion */
bssp=(BiostrucSeqPtr)(nmap->data.ptrvalue);
bsp=bssp->structure;
bssp->structure = NULL;
/* may want to report on contents of wrapper ... */
nmap=NcbiMimeAsn1Free(nmap); /* discard the wrapper */
nmap = NULL;
bssp = NULL;
}
}
if (bsp == NULL) {
ErrPostEx(SEV_ERROR,8,1,"No Biostruc in files to report in: %s",valfilein);
return 8;
}
pdnmsModelstruc=MakeAModelstruc(bsp);
if (pdnmsModelstruc==NULL) {
ErrPostEx(SEV_ERROR,7,1,"Unable to convert Biostruc to Modelstruc");
return 7;
}
pmsdRoot=(PMSD)(pdnmsModelstruc->data.ptrvalue);
if (pmsdRoot==NULL) {
ErrPostEx(SEV_ERROR,6,1,"Internal error.");
return 6;
}
/* OK, Ready to Start Reporting */
printf("Filename: %s\n", valfilein);
if (Rargs[1].intvalue == FALSE) {
if (iAscii) printf("ASCII Asn.1 (.prt) ");
else printf("Binary Asn.1 (.val) ");
if (isMime) printf("Entry Point: NCBIMime\n");
else printf("Entry Point: Biostruc\n");
if (pmsdRoot->pcPDBName != NULL) printf("PDB code: %s\n",pmsdRoot->pcPDBName);
printf("MMDB Id: %d\n", (int) pmsdRoot->iMMDBid);
printf("Name: %s\n",GetStrucStrings(pdnmsModelstruc, LONG_NAME));
printf("PDB Class: %s\n",GetStrucStrings(pdnmsModelstruc, PDB_CLASS));
printf("PDB Source: %s\n",GetStrucStrings(pdnmsModelstruc, PDB_SOURCE));
pdnmlModel=pmsdRoot->pdnmlModels;
while (pdnmlModel) {
iModels++;
pmldThis=(PMLD)(pdnmlModel->data.ptrvalue);
if (pmldThis->iType==Model_type_ncbi_all_atom) {
iNCBImodel = pdnmlModel->choice;
}
if (pmldThis->iType==Model_type_pdb_model) {
iPDBmodel = pdnmlModel->choice;
}
pdnmlModel=pdnmlModel->next;
}
printf("Number of Models: %d\n",iModels);
if(iNCBImodel) printf("NCBI All Atom Model: %d\n",iNCBImodel);
if (iPDBmodel) printf("PDB All Atom Model: %d\n",iPDBmodel);
if (pmsdRoot->pDictLocal) printf("Has Local Chemical Graph Dictionary\n");
printf("Number of Molecules: %d\n", (int) pmsdRoot->iMolCount); /* number of molecules */
printf("Number of Objects: %d\n",(int) pmsdRoot->iObjCount); /* number of objects */
printf("Number of Density Sets: %d\n",(int) pmsdRoot->iDensCount); /* number of densities */
printf("Number of Inter-Molecule Bonds: %d\n", (int) pmsdRoot->iIMBCount);
if (Rargs[2].intvalue == TRUE) {
printf("\n\nRAMACHANDRAN Angles for all Proteins:\n");
if (iNCBImodel) {
printf("NCBI All Atom Coordinate Model Number %d\n\nChain, AA, Num, Phi, Psi\n",iNCBImodel);
WriteStdoutRamaOneModel(pmsdRoot, iNCBImodel );
}
else if (iPDBmodel) {
printf("PDB All Atom Coordinate Model Number %d:\n\nChain, AA, Num, Phi, Psi\n",iPDBmodel);
WriteStdoutRamaOneModel(pmsdRoot, iPDBmodel );
}
}
}
printf("\n\n");
/* Output FASTA for each chain and dump het list - oldie but goodie code ! */
WriteFASTASeqHet(pdnmsModelstruc, stdout);
/* Shut Down MMDB-API */
/* All Modelstrucs remaining are freed in CloseMMDB-API() */
CloseMMDBAPI();
return 0;
}
Int2 Main(void)
{
UDVLogoDataPtr ldp;
Boolean UseNetwork;
WindoW w;
DdvMainWinPtr mWin_d;/*main window data*/
ObjMgrPtr omp = NULL;
Boolean NoGaps;
if ( !Nlm_GetArgsSilent("DDV 1.0", NUMARGS, DDV_myargs) ) return 1;
ErrSetMessageLevel(SEV_WARNING);
ErrSetOptFlags(EO_SHOW_CODES);
ErrSetOptFlags(EO_XLATE_CODES);
/*init some important stuffs*/
UseLocalAsnloadDataAndErrMsg();
if (! AllObjLoad()){
Message (MSG_ERROR, "AsnObjLoad() failed.");
return(1);
}
if (! SubmitAsnLoad()){
Message (MSG_ERROR, "SeqSubmitLoad() failed.");
return(1);
}
if (!SeqCodeSetLoad ()){
Message (MSG_ERROR, "SeqCodeSetLoad () failed.");
return(1);
}
if (!GeneticCodeTableLoad()){
Message (MSG_ERROR, "GeneticCodeTableLoad() failed.");
return(1);
}
if (!FeatDefSetLoad()){
Message (MSG_ERROR, "FeatDefSeqLoad() failed.");
return(1);
}
/*init data blocks*/
mWin_d=(DdvMainWinPtr)MemNew(sizeof(DdvMainWin));
if (!mWin_d){
Message (MSG_ERROR, "Viewer creation failed.");
return(1);
}
/* look for "nogaps" runtime parameter */
NoGaps = (Boolean)DDV_myargs[0].intvalue;
SetAppProperty("dde_nogaps",(void*)&NoGaps);
mWin_d->EditAllowed = (Boolean)DDV_myargs[1].intvalue;
/*init data blocks*/
ldp=(UDVLogoDataPtr)MemNew(sizeof(UDVLogoData));
if (ldp){
MemSet(ldp,0,sizeof(UDVLogoData));
}
else{
Message (MSG_ERROR, "Viewer creation failed.");
return(1);
}
/*OBjMgr Callback Function declaration*/
/* REG_DDV_AUTO_EDIT; */
REG_DDV_AUTO_VIEW;
REGISTER_UDV_AUTONOMOUS;
REG_DDV_SLA_EDIT;
/* increment maximum # of objects held in memory */
omp = ObjMgrWriteLock();
if(omp != NULL ) omp->maxtemp = DDV_MAXTEMP;
ObjMgrUnlock();
w=DDV_StartMainWin_Master(mWin_d,ldp);
if (w==NULL) goto fin;
ProcessUpdatesFirst(FALSE);
UseNetwork=mWin_d->UseNetwork;
/*display main window*/
RealizeWindow(w);
Show(w);
/*enter loop events*/
ProcessEvents();
fin:
/*close network connection, if needed*/
if (UseNetwork && EntrezIsInited()) EntrezBioseqFetchDisable();
/*clean up*/
if (ldp) MemFree(ldp);
RemoveAppProperty("UDVLogoData");
return(0);
}
Int2 Main (void)
{
Int2 m_argModuleIn=0, f_arg_moduleOut=1,
X_argDTDModuleOut=2, T_argTreeDumpOut=3,
v_argPrintFileIn = 4, p_argPrintFileOut = 5,
x_argXMLDataOut=6, d_argBinaryFileIn = 7
, t_argAsnTypeName = 8, e_argBinaryFileOut = 9
, o_argHeadFile = 10, l_argLoadFile = 11
, b_argBufferSize = 12, w_argTokenMax = 13
/*--- args below here are capitilized and for code generation, only--*/
/*-- Except for the 'M' arg, which will also affect normal use ---*/
, G_argGenerateCode = 14, M_argMoreModuleFiles = 15
, B_argCodeFileName = 16, D_argCodeGenDebugLevel = 17
, S_argDebugFileName = 18, I_argExtraIncludeName = 19
, Z_argBitTwiddle = 20, K_argLoadName = 21
, J_objMgrEntry = 22, L_objMgrLabel = 23, P_argXMLmodulePrefix = 24
, V_argChoiceStruct = 25;
AsnIoPtr aip = NULL,
aipout = NULL,
xaipout = NULL,
aipencode = NULL;
FILE * fp;
AsnModulePtr amp = NULL,
currentmod = NULL,
nextmod, thisamp;
AsnTypePtr atp;
Boolean print_each_module = FALSE;
AsnCodeInfoPtr acip = (AsnCodeInfoPtr)MemNew(sizeof(AsnCodeInfo));
CharPtr filename = NULL, p, last_comma, objmgrentry = NULL;
int len;
/* never abort on error, but show it */
ErrSetFatalLevel(SEV_MAX);
ErrSetMessageLevel(SEV_MIN);
asnargs[P_argXMLmodulePrefix].defaultvalue = (const char *)AsnGetXMLmodulePrefix();
if (! GetArgs("AsnTool 4", NUMARGS, asnargs))
return 1;
ErrClear();
AsnSetXMLmodulePrefix((CharPtr)(asnargs[P_argXMLmodulePrefix].strvalue));
/*
if (! GetArgs("AsnTool 4", NUMARGS, asnargs))
return 1;
ErrClear();
*/
if (! AsnIoSetBufsize(NULL, (Int2)asnargs[b_argBufferSize].intvalue))
return 1;
if ((aip = AsnIoOpen(asnargs[m_argModuleIn].strvalue, "r")) == NULL)
{
ErrShow();
return 1;
}
acip -> loadname = asnargs[m_argModuleIn].strvalue;
if (asnargs[K_argLoadName].strvalue != NULL) {
acip -> loadname = asnargs[K_argLoadName].strvalue; /* overrides m_argModuleIn, if set */
}
if (asnargs[e_argBinaryFileOut].strvalue != NULL) /* output a binary value file */
if ((aipencode = AsnIoOpen(asnargs[e_argBinaryFileOut].strvalue, "wb")) == NULL)
{
ErrShow();
return 1;
}
/** parse the module(s) ***/
if (asnargs[f_arg_moduleOut].strvalue != NULL)
{
if ((aipout = AsnIoOpen(asnargs[f_arg_moduleOut].strvalue, "w")) == NULL)
{
ErrShow();
return 1;
}
}
thisamp = NULL;
while ((nextmod = AsnLexTReadModule(aip)) != NULL )
{
if (thisamp == NULL)
thisamp = nextmod;
if (amp == NULL)
amp = nextmod;
else
currentmod->next = nextmod;
currentmod = nextmod;
}
acip -> last_amp = currentmod; /* last module of main file */
AsnStoreTree(acip->loadname, thisamp); /* store and link tree */
/*--- read additional module files that will be used for everything
but code generation.
---*/
if (asnargs[M_argMoreModuleFiles].strvalue != NULL)
for (p = asnargs[M_argMoreModuleFiles].strvalue; *p; p = last_comma + 1) {
/*--- extract next filename for reading ASN.1 definitions ---*/
for (last_comma = p; *last_comma; last_comma++) {
if (*last_comma == ',')
break;
}
len = last_comma - p;
filename = (char *)MemFree (filename);
filename = (char *)MemNew (len + 1);
StringNCpy (filename, p, len);
filename[len] = '\0';
#ifdef WIN_DUMB
printf ("Loading %s \n", filename);
#endif
if ((aip = AsnIoOpen(filename, "r")) == NULL)
{
ErrShow();
return 1;
}
/*--- read the modules in this current file ---*/
thisamp = NULL;
while ((nextmod = AsnLexTReadModule(aip)) != NULL )
{
if (thisamp == NULL)
thisamp = nextmod;
if (amp == NULL)
amp = nextmod;
else
currentmod->next = nextmod;
currentmod = nextmod;
}
AsnStoreTree(filename, thisamp); /* store and link tree */
if (!*last_comma)
break;
aip = AsnIoClose(aip);
}
aip = AsnIoClose(aip);
if (amp == NULL)
{
ErrPostEx(SEV_FATAL,0,0, "Unable to continue due to bad ASN.1 module");
ErrShow();
return 1;
}
if (asnargs[f_arg_moduleOut].strvalue != NULL)
{
if ((aipout = AsnIoOpen(asnargs[f_arg_moduleOut].strvalue, "w")) == NULL)
{
ErrShow();
return 1;
}
currentmod = amp;
do
{
AsnPrintModule(currentmod, aipout);
if (currentmod == acip->last_amp) /* last main module */
currentmod = NULL;
else
currentmod = currentmod->next;
} while (currentmod != NULL);
aipout = AsnIoClose(aipout);
}
if (asnargs[X_argDTDModuleOut].strvalue != NULL)
{
Char tbuf[250];
CharPtr ptr;
if (! StringCmp(asnargs[X_argDTDModuleOut].strvalue, "m"))
{
print_each_module = TRUE;
}
else
{
if ((aipout = AsnIoOpen(asnargs[X_argDTDModuleOut].strvalue, "wx")) == NULL)
{
ErrShow();
return 1;
}
}
currentmod = amp;
do
{
if (print_each_module)
{
StringMove(tbuf, currentmod->modulename);
for (ptr = tbuf; *ptr != '\0'; ptr++)
{
if (*ptr == '-')
*ptr = '_';
}
StringMove(ptr, ".dtd");
AsnPrintModuleXMLInc(currentmod, tbuf);
StringMove(ptr, ".mod");
aipout = AsnIoOpen(tbuf, "wx");
}
AsnPrintModuleXML(currentmod, aipout);
if (print_each_module)
aipout = AsnIoClose(aipout);
if (currentmod == acip->last_amp) /* last main module */
currentmod = NULL;
else
currentmod = currentmod->next;
} while (currentmod != NULL);
if (! print_each_module)
aipout = AsnIoClose(aipout);
}
if (asnargs[T_argTreeDumpOut].strvalue != NULL)
{
if ((fp = FileOpen(asnargs[T_argTreeDumpOut].strvalue, "w")) == NULL)
{
ErrShow();
return 1;
}
currentmod = amp;
do
{
AsnPrintTreeModule(currentmod, fp);
if (currentmod == acip->last_amp) /* last main module */
currentmod = NULL;
else
currentmod = currentmod->next;
} while (currentmod != NULL);
FileClose(fp);
}
acip -> amp = amp;
/* print a value file */
if (asnargs[p_argPrintFileOut].strvalue != NULL)
{
if ((aipout = AsnIoOpen(asnargs[p_argPrintFileOut].strvalue, "w")) == NULL)
{
ErrShow();
return 1;
}
}
/* print an XML file */
if (asnargs[x_argXMLDataOut].strvalue != NULL)
{
if ((xaipout = AsnIoOpen(asnargs[x_argXMLDataOut].strvalue, "wx")) == NULL)
{
ErrShow();
return 1;
}
}
if (asnargs[v_argPrintFileIn].strvalue != NULL) /* read a printvalue file */
{
if ((aip = AsnIoOpen(asnargs[v_argPrintFileIn].strvalue, "r")) == NULL)
{
ErrShow();
return 1;
}
AsnTxtReadValFile(amp, aip, aipout, aipencode, xaipout);
ErrShow();
}
aip = AsnIoClose(aip);
if (asnargs[d_argBinaryFileIn].strvalue != NULL) /* read a ber file */
{
if ((asnargs[t_argAsnTypeName].strvalue == NULL) || (! TO_UPPER(*asnargs[t_argAsnTypeName].strvalue)))
{
ErrPostEx(SEV_FATAL,0,0, "Must use -t Type to define contents of decode file");
ErrShow();
return 1;
}
atp = AsnTypeFind(amp, asnargs[t_argAsnTypeName].strvalue);
if (atp == NULL)
{
#ifdef WIN_MSWIN
ErrPostEx(SEV_FATAL,0,0, "Couldn't find Type %Fs", asnargs[t_argAsnTypeName].strvalue);
#else
ErrPostEx(SEV_FATAL,0,0, "Couldn't find Type %s", asnargs[t_argAsnTypeName].strvalue);
#endif
ErrShow();
return 1;
}
if ((aip = AsnIoOpen(asnargs[d_argBinaryFileIn].strvalue, "rb")) == NULL)
{
ErrShow();
return 1;
}
AsnBinReadValFile(atp, aip, aipout, aipencode, xaipout);
ErrShow();
}
AsnIoClose(xaipout);
AsnIoClose(aipout);
AsnIoClose(aip);
AsnIoClose(aipencode);
if (asnargs[o_argHeadFile].strvalue != NULL) /* produce header file */
AsnOutput(asnargs[o_argHeadFile].strvalue, amp, FALSE, (Int2)asnargs[w_argTokenMax].intvalue);
if (asnargs[l_argLoadFile].strvalue != NULL) /* produce loader file */
AsnOutput(asnargs[l_argLoadFile].strvalue, amp, TRUE, (Int2)asnargs[w_argTokenMax].intvalue);
if (asnargs[G_argGenerateCode ].intvalue != 0)
{
acip -> filename = asnargs[B_argCodeFileName].strvalue;
acip -> do_bit_twiddle = asnargs[Z_argBitTwiddle].intvalue;
acip -> force_choice_struct = asnargs[V_argChoiceStruct].intvalue;
acip -> include_filename = asnargs[I_argExtraIncludeName].strvalue;
acip -> maxDefineLength = asnargs[w_argTokenMax].intvalue;
acip -> debug_level = asnargs[D_argCodeGenDebugLevel ].intvalue;
acip -> object_manager_entry = asnargs[J_objMgrEntry].strvalue;
acip -> object_label = asnargs[L_objMgrLabel].strvalue;
if (asnargs[S_argDebugFileName].strvalue != NULL) {
(acip -> bug_fp) = FileOpen (asnargs[S_argDebugFileName].strvalue, "w");
} else {
(acip -> bug_fp) = FileOpen ("stderr", "w");
}
AsnCode(acip);
}
MemFree(acip);
MemFree(filename);
return 0;
}
/*****************************************************************************
*
* PrintTemplateSetPtr PrintTemplateSetLoad()
* loads PrintTemplates
* If path== NULL, looks for "prt.prt" in the "data" directory
*
*****************************************************************************/
static Boolean PrintTemplateSetLoadInt ( CharPtr path, Boolean verbose )
{
AsnIoPtr aip;
FILE *f;
Boolean retval;
Char filename [80];
Char fullpath [PATH_MAX];
CharPtr ptr;
ErrSev lastLevel;
aip = NULL;
if (path != NULL && *path != '\0' && StringRChr (path, DIRDELIMCHR) != NULL) {
StringNCpy (fullpath, path, sizeof (fullpath) - 1);
if ((aip = AsnIoOpen (fullpath, "r")) == NULL) {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", fullpath);
}
return FALSE;
}
} else {
if (path != NULL && *path != '\0') {
StringNCpy (filename, path, sizeof (filename) - 1);
} else {
StringCpy (filename, "prt.prt");
}
ProgramPath (fullpath, sizeof (fullpath) - 1);
ptr = StringRChr (fullpath, DIRDELIMCHR);
if (ptr != NULL) {
*ptr = '\0';
}
FileBuildPath (fullpath, NULL, filename);
/* silence SEV_INFO errors from FileOpen() */
if ((lastLevel = ErrGetMessageLevel()) < SEV_WARNING)
ErrSetMessageLevel (SEV_WARNING);
if ((f = FileOpen (fullpath, "r")) == NULL) {
ErrSetMessageLevel (lastLevel);
if (FindPath ("NCBI", "NCBI", "DATA", fullpath, sizeof (fullpath) - 1)) {
FileBuildPath (fullpath, NULL, filename);
if ((aip = AsnIoOpen (fullpath, "r")) == NULL) {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", fullpath);
}
return FALSE;
}
} else {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "FindPath failed in PrintTemplateSetLoad - ncbi configuration file missing or incorrect");
}
return FALSE;
}
} else {
ErrSetMessageLevel (lastLevel);
FileClose (f);
if ((aip = AsnIoOpen(fullpath, "r")) == NULL) {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", fullpath);
}
return FALSE;
}
}
}
retval = PrintTemplateSetAsnRead(aip);
AsnIoClose(aip);
return retval;
}
static void DoProcess (
SeqEntryPtr sep,
Uint2 entityID,
CSpeedFlagPtr cfp
)
{
Char id [64];
ErrSev oldErrSev;
ValidStructPtr vsp;
if (sep == NULL || cfp == NULL) return;
if (StringChr (cfp->clean, 't') != NULL) {
VisitDescriptorsInSep (sep, NULL, MarkTitles);
DeleteMarkedObjects (entityID, 0, NULL);
}
if (StringChr (cfp->clean, 'a') != NULL) {
AssignIDsInEntity (entityID, 0, NULL);
}
if (StringChr (cfp->clean, 'b') != NULL) {
BasicSeqEntryCleanup (sep);
}
if (StringChr (cfp->clean, 's') != NULL) {
SeriousSeqEntryCleanup (sep, NULL, NULL);
}
if (StringChr (cfp->index, 'f') != NULL) {
SeqMgrIndexFeatures (entityID, 0);
}
if (StringChr (cfp->seq, 'c') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaExist);
}
if (StringChr (cfp->seq, 'C') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaRegen);
}
if (StringChr (cfp->seq, 's') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaSeq);
}
if (StringChr (cfp->seq, 'S') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaSeq);
}
if (StringChr (cfp->seq, 'r') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaRaw);
}
if (StringChr (cfp->seq, 'd') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaDefline);
}
if (StringChr (cfp->seq, 'D') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaDefline);
}
if (StringChr (cfp->seq, 'T') != NULL) {
VisitDescriptorsInSep (sep, NULL, MarkTitles);
DeleteMarkedObjects (entityID, 0, NULL);
SeqMgrIndexFeatures (entityID, 0);
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaDefline);
}
if (StringChr (cfp->seq, 'x') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoNewFastaDefline);
}
if (StringChr (cfp->seq, 'X') != NULL) {
VisitDescriptorsInSep (sep, NULL, MarkTitles);
DeleteMarkedObjects (entityID, 0, NULL);
SeqMgrIndexFeatures (entityID, 0);
VisitBioseqsInSep (sep, (Pointer) cfp, DoNewFastaDefline);
}
if (StringChr (cfp->seq, 'f') != NULL) {
VisitFeaturesInSep (sep, (Pointer) cfp, DoFastaFeat);
}
if (StringChr (cfp->seq, 't') != NULL) {
VisitFeaturesInSep (sep, (Pointer) cfp, DoFastaTrans);
}
if (StringChr (cfp->feat, 'v') != NULL) {
VisitFeaturesInSep (sep, NULL, DoVisitFeaturesTest);
}
if (StringChr (cfp->feat, 'g') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
VisitFeaturesInSep (sep, (Pointer) cfp, DoGeneOverlapPrintTest);
}
if (StringChr (cfp->feat, 'h') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
VisitFeaturesInSep (sep, (Pointer) cfp, DoGeneOverlapSpeedTest);
}
if (StringChr (cfp->feat, 'x') != NULL) {
}
if (StringChr (cfp->feat, 'o') != NULL) {
}
if (StringChr (cfp->feat, 'd') != NULL) {
}
if (StringChr (cfp->feat, 't') != NULL) {
SeqEntryToGnbk (sep, NULL, FTABLE_FMT, SEQUIN_MODE, NORMAL_STYLE,
0, 0, SHOW_PROT_FTABLE, NULL, cfp->ofp);
}
if (StringChr (cfp->feat, 's') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
cfp->nucbsp = FindNucBioseq (sep);
if (cfp->nucbsp != NULL) {
BioseqToGeneticCode (cfp->nucbsp, &(cfp->genCode), NULL, NULL, NULL, 0, NULL);
SeqIdWrite (cfp->nucbsp->id, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
fprintf (cfp->ofp, "%s\n", id);
VisitBioseqsInSep (sep, (Pointer) cfp, DoSuggestIntervals);
cfp->nucbsp = NULL;
cfp->genCode = 0;
}
}
if (StringChr (cfp->feat, 'S') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
cfp->nucbsp = FindNucBioseq (sep);
if (cfp->nucbsp != NULL) {
BioseqToGeneticCode (cfp->nucbsp, &(cfp->genCode), NULL, NULL, NULL, 0, NULL);
SetBatchSuggestNucleotide (cfp->nucbsp, cfp->genCode);
SeqIdWrite (cfp->nucbsp->id, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
fprintf (cfp->ofp, "%s\n", id);
VisitBioseqsInSep (sep, (Pointer) cfp, DoSuggestIntervals);
ClearBatchSuggestNucleotide ();
cfp->nucbsp = NULL;
cfp->genCode = 0;
}
}
if (StringChr (cfp->feat, 'c') != NULL) {
VisitFeaturesInSep (sep, (Pointer) cfp, DoVisitCodingRegions);
}
if (StringChr (cfp->desc, 'b') != NULL) {
}
if (StringChr (cfp->desc, 't') != NULL) {
}
if (StringChr (cfp->verify, 'v') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
vsp = ValidStructNew ();
if (vsp != NULL) {
vsp->useSeqMgrIndexes = TRUE;
vsp->suppressContext = TRUE;
vsp->seqSubmitParent = TRUE;
vsp->testLatLonSubregion = TRUE;
oldErrSev = ErrSetMessageLevel (SEV_NONE);
vsp->errfunc = ValidCallback;
vsp->userdata = (Pointer) cfp->ofp;
/* vsp->convertGiToAccn = FALSE; */
ValidateSeqEntry (sep, vsp);
ValidStructFree (vsp);
ErrSetMessageLevel (oldErrSev);
}
}
if (StringChr (cfp->verify, 'b') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
SeqEntryToGnbk (sep, NULL, GENBANK_FMT, SEQUIN_MODE, NORMAL_STYLE,
0, 0, 0, NULL, cfp->ofp);
}
if (cfp->ofp != NULL) {
fflush (cfp->ofp);
}
}
