extern DustRegionPtr DustBioseq (BioseqPtr bsp,
Int4 start, Int4 stop,
DustDataPtr ddp)
{
DustRegionPtr drp;
SeqPortPtr spp;
if (bsp == NULL || ddp == NULL)
return NULL;
if (!ISA_na (bsp->mol))
{
ErrPostEx (SEV_WARNING, 1, 2, "Not nucleic acid");
ErrShow ();
return NULL;
}
/* error msg stuff */
ErrSetOptFlags (EO_MSG_CODES);
spp = SeqPortNew (bsp, start, stop, 0, Seq_code_ncbi2na);
if (spp == NULL)
{
ErrPostEx (SEV_ERROR, 1, 4, "SeqPort open failed");
ErrShow ();
return NULL;
}
drp = DustSeqPort (spp, start, stop, ddp);
SeqPortFree (spp);
return drp;
}
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);
}
Int2 Main()
{
static Char pcUname[2000]="";
/* Arg -l to keep the log file */
Int2 retval = 0;
#ifdef OS_UNIX
struct utsname utsbuf;
#endif
#define NUMARGS 1
static Nlm_Arg myargs[NUMARGS] = {
/*0*/ { "Keep error.log file?", "F", NULL, NULL, TRUE, 'l', ARG_BOOLEAN, 0.0, 0, NULL} };
if ( !Nlm_GetArgs("Benchtraj", NUMARGS, myargs) ) return 1;
ErrSetOptFlags(EO_SHOW_SEVERITY|EO_SHOW_CODES|EO_LOG_FILELINE|EO_SHOW_USERSTR|EO_SHOW_ERRTEXT|EO_BEEP|EO_WAIT_KEY|EO_LOGTO_USRFILE);
#ifdef OS_UNIX
/* use uname to get sysinfo */
if (uname(&utsbuf)>=0) {
sprintf(pcUname,"%s %s %s %s %s\n",utsbuf.sysname,utsbuf.nodename,utsbuf.release,utsbuf.version,utsbuf.machine);
}
#else
#ifdef OS_MSWIN
/* assume ver is available */
if (GetMSWinVerInfo(pcUname)!=ERR_SUCCESS) {
StringCpy(pcUname,"Not Available\n");
}
#endif
#endif
printf("OS Reported:\n%s\n",pcUname);
retval = TRADESBenchmark();
if (!myargs[0].intvalue) FileRemove("error.log");
return retval;
}
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);
}
SeqLocPtr SeqLocDust (SeqLocPtr this_slp,
Int2 level, Int2 window, Int2 minwin, Int2 linker)
{
SeqLocPtr next_slp, slp = NULL;
ValNodePtr vnp = NULL;
SeqIdPtr id;
BioseqPtr bsp;
SeqPortPtr spp;
DREGION PNTR reg, PNTR regold;
Int4 nreg;
Int4 start, end, l;
Int2 loopDustMax = 0;
/* error msg stuff */
ErrSetOptFlags (EO_MSG_CODES);
if (!this_slp)
{
ErrPostEx (SEV_ERROR, 2, 1,
"no sequence location given for dusting");
ErrShow ();
return slp;
}
/* place for dusted regions */
regold = reg = MemNew (sizeof (DREGION));
if (!reg)
{
ErrPostEx (SEV_FATAL, 2, 2,
"memory allocation error");
ErrShow ();
return slp;
}
reg->from = 0;
reg->to = 0;
reg->next = NULL;
/* count seqlocs */
next_slp = NULL;
while ((next_slp = SeqLocFindNext (this_slp, next_slp)) != NULL)
loopDustMax++;
if (!loopDustMax)
{
ErrPostEx (SEV_ERROR, 2, 3,
"can not find next seq loc");
ErrShow ();
}
/* loop for dusting as needed */
next_slp = NULL;
while ((next_slp = SeqLocFindNext (this_slp, next_slp)) != NULL)
{
/* offsets into actual sequence */
start = SeqLocStart (next_slp);
end = SeqLocStop (next_slp);
/* if all goes okay should get a seqport pointer */
id = SeqLocId (next_slp);
if (!id)
{
ErrPostEx (SEV_ERROR, 2, 4,
"no bioseq id");
ErrShow ();
continue;
}
bsp = BioseqLockById (id);
if (!bsp)
{
ErrPostEx (SEV_ERROR, 2, 5,
"no bioseq");
ErrShow ();
continue;
}
if (!ISA_na (bsp->mol))
{
ErrPostEx (SEV_WARNING, 2, 6,
"not nucleic acid");
ErrShow ();
BioseqUnlock (bsp);
continue;
}
spp = SeqPortNew (bsp, start, end, 0, Seq_code_ncbi2na);
BioseqUnlock (bsp);
if (!spp)
{
ErrPostEx (SEV_ERROR, 2, 7,
"sequence port open failed");
ErrShow ();
continue;
}
l = spp->totlen;
nreg = dust_segs (l, spp, start, reg,
(Int4)level, (Int4)window, (Int4)minwin, (Int4)linker);
slp = slpDust (spp, slp, id, &vnp,
reg, nreg, loopDustMax);
/* find tail - this way avoids referencing the pointer */
while (reg->next) reg = reg->next;
SeqPortFree (spp);
}
/* clean up memory */
reg = regold;
while (reg)
{
regold = reg;
reg = reg->next;
MemFree (regold);
}
return slp;
}
SeqLocPtr BioseqDust (BioseqPtr bsp, Int4 start, Int4 end,
Int2 level, Int2 window, Int2 minwin, Int2 linker)
{
SeqLocPtr slp = NULL; /* initialize */
ValNodePtr vnp = NULL;
SeqPortPtr spp;
DREGION PNTR reg, PNTR regold;
Int4 nreg;
Int4 l;
Int4 loopDustMax = 1;
/* error msg stuff */
/* ErrSetOptFlags (EO_MSG_CODES | EO_SHOW_FILELINE | EO_BEEP); */
ErrSetOptFlags (EO_MSG_CODES);
/* make sure bioseq is there */
if (!bsp)
{
ErrPostEx (SEV_ERROR, 1, 1,
"no bioseq");
ErrShow ();
return slp;
}
if (!ISA_na (bsp->mol))
{
ErrPostEx (SEV_WARNING, 1, 2,
"not nucleic acid");
ErrShow ();
return slp;
}
/* place for dusted regions */
reg = MemNew (sizeof (DREGION));
if (!reg)
{
ErrPostEx (SEV_FATAL, 1, 3,
"memory allocation error");
ErrShow ();
return slp;
}
reg->from = 0;
reg->to = 0;
reg->next = NULL;
/* do it */
spp = SeqPortNew (bsp, start, end, 0, Seq_code_ncbi2na);
if (!spp)
{
ErrPostEx (SEV_ERROR, 1, 4,
"sequence port open failed");
ErrShow ();
MemFree (reg);
return slp;
}
l = spp->totlen;
nreg = dust_segs (l, spp, start, reg, (Int4)level, (Int4)window, (Int4)minwin, (Int4)linker);
slp = slpDust (spp, NULL, bsp->id, &vnp, reg, nreg, loopDustMax);
/* clean up memory */
SeqPortFree (spp);
while (reg)
{
regold = reg;
reg = reg->next;
MemFree (regold);
}
return slp;
}
