Int2 Main ()
{
Int2 orient;
CharPtr txt=NULL;
Boolean Bool=TRUE;
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 (! 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;
}
if (!ID1BioseqFetchEnable("DotMatrix", FALSE))
{
ErrPostEx(SEV_FATAL, 1, 0, "Bad sequence offset values");
return -1;
}
LocalSeqFetchInit (FALSE);
DOT_StartupWindow();
LocalSeqFetchDisable ();
ID1BioseqFetchDisable();
}
Int2 Main (void)
{
AsnIoPtr aip;
Boolean convertgis;
Boolean extractmrnas;
CharPtr infile, outfile;
SeqEntryPtr sep;
/* 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 */
if (! GetArgs ("gi2accn", sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
infile = (CharPtr) myargs [i_argInputFile].strvalue;
outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
convertgis = (Boolean) myargs [c_argConvertGIs].intvalue;
extractmrnas = (Boolean) myargs [x_argExtractMrnas].intvalue;
aip = AsnIoOpen (infile, "r");
if (aip == NULL) {
Message (MSG_FATAL, "AsnIoOpen input file failed");
return 1;
}
sep = SeqEntryAsnRead (aip, NULL);
AsnIoClose (aip);
if (sep == NULL) {
Message (MSG_FATAL, "SeqEntryAsnRead failed");
return 1;
}
PubSeqFetchEnable ();
LookupFarSeqIDs (sep, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE);
/* Extract mRNA hits from BLAST against nr */
if (extractmrnas) {
VisitAnnotsInSep (sep, NULL, FindBlastNR);
DeleteMarkedObjects (0, OBJ_SEQENTRY, (Pointer) sep);
}
/* convert gi numbers to accession.version */
if (convertgis) {
VisitAlignmentsInSep (sep, NULL, UpdateAligns);
}
PubSeqFetchDisable ();
BasicSeqEntryCleanup (sep);
aip = AsnIoOpen (outfile, "w");
if (aip == NULL) {
Message (MSG_FATAL, "AsnIoOpen output file failed");
return 1;
}
SeqEntryAsnWrite (sep, aip, NULL);
AsnIoClose (aip);
return 0;
}
Int2 Main (void)
{
AsnIoPtr aop = NULL;
AsnModulePtr amp;
AsnTypePtr atp_bss, atp_ss, atp_se;
BioseqSet bss;
FILE *fp;
ValNodePtr head, vnp;
Char path [PATH_MAX];
CharPtr progname, str, subfile;
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;
}
MemSet ((Pointer) &bss, 0, sizeof (BioseqSet));
amp = AsnAllModPtr ();
if (amp == NULL) {
Message (MSG_FATAL, "Unable to load AsnAllModPtr");
return 1;
}
atp_bss = AsnFind ("Bioseq-set");
if (atp_bss == NULL) {
Message (MSG_FATAL, "Unable to find ASN.1 type Bioseq-set");
return 1;
}
atp_ss = AsnFind ("Bioseq-set.seq-set");
if (atp_ss == NULL) {
Message (MSG_FATAL, "Unable to find ASN.1 type Bioseq-set.seq-set");
return 1;
}
atp_se = AsnFind ("Bioseq-set.seq-set.E");
if (atp_se == NULL) {
Message (MSG_FATAL, "Unable to find ASN.1 type Bioseq-set.seq-set.E");
return 1;
}
ProgramPath (path, sizeof (path));
progname = StringRChr (path, DIRDELIMCHR);
if (progname != NULL) {
progname++;
} else {
progname = "idcleanscan";
}
if (! GetArgs (progname, sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
fp = FileOpen (myargs [o_argOutputFile].strvalue, "a");
if (fp == NULL) {
Message (MSG_FATAL, "FileOpen failed");
return 1;
}
if (StringHasNoText (myargs [p_argInputPath].strvalue)) {
str = myargs [i_argInputFile].strvalue;
if (! StringHasNoText (str)) {
DoReleaseFile (str, myargs [b_argBinaryFile].intvalue, myargs [c_argCompressed].intvalue, fp, aop, NULL);
}
} else {
head = DirCatalog (myargs [p_argInputPath].strvalue);
if (! StringHasNoText (myargs [s_argSubset].strvalue)) {
aop = AsnIoOpen (myargs [s_argSubset].strvalue, /* "wb" */ "w");
AsnOpenStruct (aop, atp_bss, (Pointer) &bss);
AsnOpenStruct (aop, atp_ss, (Pointer) bss.seq_set);
/*
av.intvalue = BioseqseqSet_class_genbank;
AsnWrite (aop, atp_cls, &av);
*/
}
for (vnp = head; vnp != NULL; vnp = vnp->next) {
if (vnp->choice == 0) {
str = (CharPtr) vnp->data.ptrvalue;
if (! StringHasNoText (str)) {
subfile = myargs [x_argFileSelect].strvalue;
if (StringHasNoText (subfile) || StringStr (str, subfile) != NULL) {
#ifdef OS_UNIX
/* printf ("%s\n", str); */
#endif
DoReleaseFile (str, myargs [b_argBinaryFile].intvalue, myargs [c_argCompressed].intvalue, fp, aop, atp_se);
}
}
}
}
if (aop != NULL) {
AsnCloseStruct (aop, atp_ss, (Pointer) bss.seq_set);
AsnCloseStruct (aop, atp_bss, (Pointer) &bss);
AsnIoClose (aop);
}
ValNodeFreeData (head);
}
FileClose (fp);
return 0;
}
Int2 Main (void)
{
CharPtr base, directory, organism, ptr;
Boolean altstart, findorf, flatfile, validate;
ValNodePtr head, vnp;
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 (! FeatDefSetLoad ()) {
Message (MSG_FATAL, "FeatDefSetLoad failed");
return 1;
}
if (! GetArgs ("sgd2asn", sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
directory = (CharPtr) myargs [0].strvalue;
base = (CharPtr) myargs [1].strvalue;
organism = (CharPtr) myargs [2].strvalue;
findorf = (Boolean) myargs [3].intvalue;
altstart = (Boolean) myargs [4].intvalue;
validate = (Boolean) myargs [5].intvalue;
flatfile = (Boolean) myargs [6].intvalue;
if (! StringHasNoText (base)) {
ptr = StringStr (base, ".fsa");
if (ptr != NULL) {
*ptr = '\0';
ProcessOneRecord (directory, base, organism, findorf, altstart, validate, flatfile);
}
} else {
head = DirCatalog (directory);
for (vnp = head; vnp != NULL; vnp = vnp->next) {
if (vnp->choice == 0) {
base = (CharPtr) vnp->data.ptrvalue;
if (! StringHasNoText (base)) {
ptr = StringStr (base, ".fsa");
if (ptr != NULL) {
*ptr = '\0';
ProcessOneRecord (directory, base, organism, findorf, altstart, validate, flatfile);
}
}
}
}
ValNodeFreeData (head);
}
return 0;
}
Int2 Main(void)
{
Char app [64];
Int4 rval = 0;
CharPtr id_file;
ValNodePtr fetch_list = NULL;
ValNodePtr field_list = NULL;
ValNodePtr table;
Boolean meta_mode = FALSE;
FILE *fp;
/* 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;
}
#ifdef INTERNAL_NCBI_TBL_CHK
SmartFetchEnable ();
TPASmartFetchEnable ();
if (! PUBSEQBioseqFetchEnable ("tbl_chk", FALSE)) {
Message (MSG_POSTERR, "PUBSEQBioseqFetchEnable failed");
return 1;
}
#else
PubSeqFetchEnable ();
#endif
/* process command line arguments */
sprintf (app, "tbl_chk %s", TBL_CHK_APPLICATION);
if (! GetArgs (app, sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
id_file = (CharPtr) myargs [i_argInputFile].strvalue;
debug_mode = (Boolean) myargs [D_argDebugMode].intvalue;
meta_mode = (Boolean) myargs [m_argMetaMode].intvalue;
fp = FileOpen (id_file, "r");
if (fp == NULL) {
Message (MSG_ERROR, "Unable to open %s", id_file);
return 1;
}
table = ReadTabTableFromFile (fp);
FileClose (fp);
if (table == NULL || table->next == NULL) {
Message (MSG_ERROR, "Table must have at least two rows, one header and one data");
return 1;
}
field_list = GetFieldListFromHeader(table->data.ptrvalue);
if (field_list == NULL) {
Message (MSG_ERROR, "Unable to read table header");
table = FreeTabTable (table);
return 1;
}
fetch_list = FetchItemListFromTable (table);
MakeFetchItemIndex(fetch_list);
fp = FileOpen ((CharPtr) myargs [o_argOutputFile].strvalue, "w");
if (fp == NULL) {
Message (MSG_ERROR, "Unable to open %s", (CharPtr) myargs [o_argOutputFile].strvalue);
rval = 1;
} else {
if (meta_mode) {
fprintf (fp, "Accession\tField\tOld Value\tNew Value\n");
}
ProcessBioseqsWithCaching (fetch_list, field_list, table, meta_mode, fp);
}
FileClose (fp);
field_list = FieldTypeListFree (field_list);
fetch_list = FetchItemListFree (fetch_list);
MakeFetchItemIndex(NULL);
return rval;
}
Int2 Main (void)
{
EntrezInfoPtr eip;
PaneL p;
RecT r;
Char str [16];
Int2 val;
WindoW w;
/*
#if defined(WIN16)
#else
PRGD prgdDict;
#endif
*/
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
ProcessUpdatesFirst (FALSE);
/*
if (! GetAppParam ("NCBI", "NCBI", NULL, NULL, str, sizeof (str) - 1)) {
if (Message (MSG_YN, configMessage) == ANS_YES) {
ShowNetConfigForm (ConfigFormActivated, ConfigFormMessage,
ConfigAccepted, ConfigCancelled);
ProcessEvents ();
return 0;
} else {
Message (MSG_FATAL, "Entrez cannot run without ncbi configuration file");
}
return 0;
}
if (! GetAppParam ("NCBI", "NCBI", NULL, NULL, str, sizeof (str) - 1)) {
Message (MSG_FATAL, "Entrez cannot find ncbi configuration file");
return 0;
}
*/
UseLocalAsnloadDataAndErrMsg ();
SetupAppProperties ();
SetupCommonFonts ();
entrezRelease [0] = '\0';
sprintf (entrezVersion, "Entrez Application Version %s", ENTREZ_APP_VERSION);
w = FixedWindow (-50, -33, -10, -10, "Entrez", NULL);
p = SimplePanel (w, AboutBoxWidth (), 14 * stdLineHeight, DrawAbout);
Show (w);
#ifdef WIN_MOTIF
Select (w);
ObjectRect (p, &r);
Select (p);
InsetRect (&r, 3, 3);
InvalRect (&r);
#endif
Update ();
WatchCursor ();
SetTitle (w, "Finding Entrez Data");
if (! EntrezBioseqFetchEnable ("Entrez", TRUE)) {
ArrowCursor ();
/* Message (MSG_FATAL, "Unable to connect to Entrez databases"); */
if (Message (MSG_YN, configMessage) == ANS_YES) {
ShowNetConfigForm (ConfigFormActivated, ConfigFormMessage,
ConfigAccepted, ConfigCancelled, NULL, TRUE);
ProcessEvents ();
return 0;
} else {
Message (MSG_FATAL, "Entrez cannot run connection to the data server");
}
return 0;
}
ID1BioseqFetchEnable ("Entrez", TRUE);
LocalSeqFetchInit (FALSE);
#ifdef WIN_MAC
SetDeactivate (NULL, MacDeactProc);
SetupMacMenus ();
#endif
eip = EntrezGetInfo ();
if (eip != NULL) {
/*
{
AsnIoPtr aip;
aip = AsnIoOpen ("eip", "w");
if (aip != NULL) {
EntrezInfoAsnWrite (eip, aip, NULL);
AsnIoClose (aip);
}
}
*/
sprintf (entrezRelease, "Entrez Data Release %d.%d", (int) eip->version, (int) eip->issue);
Select (p);
ObjectRect (p, &r);
InsetRect (&r, 3, 3);
InvalRect (&r);
Update ();
}
SetTitle (w, "Loading parse tables");
if (! AllObjLoad ()) {
ArrowCursor ();
Message (MSG_FATAL, "AllObjLoad failed");
return 0;
}
if (! SubmitAsnLoad ()) {
ArrowCursor ();
Message (MSG_FATAL, "SubmitAsnLoad failed");
return 0;
}
SetTitle (w, "Loading print templates");
if (! PrintTemplateSetLoad ("objprt.prt")) {
ArrowCursor ();
Message (MSG_FATAL, "PrintTemplateSetLoad objprt.prt failed");
return 0;
}
if (! PrintTemplateSetLoad ("asn2ff.prt")) {
ArrowCursor ();
Message (MSG_FATAL, "PrintTemplateSetLoad asn2ff.prt failed");
return 0;
}
/*
if (! PrintTemplateSetLoad ("makerpt.prt")) {
ArrowCursor ();
Message (MSG_FATAL, "PrintTemplateSetLoad makerpt.prt failed");
return 0;
}
*/
SetTitle (w, "Loading sequence alphabet converter");
if (! SeqCodeSetLoad ()) {
ArrowCursor ();
Message (MSG_FATAL, "SeqCodeSetLoad failed");
return 0;
}
SetTitle (w, "Loading feature definitions");
if (! FeatDefSetLoad ()) {
ArrowCursor ();
Message (MSG_FATAL, "FeatDefSetLoad failed");
return 0;
}
if (! SetupPrintOptions ()) {
ArrowCursor ();
Message (MSG_FATAL, "StdPrintOptionsNew failed");
return 0;
}
/*
#ifndef WIN16
SetTitle (w, "Loading structure dictionary");
if (OpenMMDBAPI ((POWER_VIEW ^ FETCH_ENTREZ), NULL)) {
prgdDict = GetPRGDDictionary ();
Cn3DWin_Entrez(NULL, TRUE);
}
#endif
*/
SetTitle (w, "Creating menus");
REGISTER_MEDLINE_VIEW;
REGISTER_NEW_SEQENTRY_VIEW;
VSMFileInit ();
VSeqMgrInit (FALSE);
SetTitle (w, "Creating window");
InitMuskStyles ();
if (GetEntrezAppParam ("PREFERENCES", "DEFAULTSTYLE", "", str, sizeof (str))) {
if (StrToInt (str, &val) && val >= 0) {
SetMuskCurrentSt (GetMuskStyleName (val));
}
}
/*
SetTitle (w, "Creating help window");
if (helpForm == NULL) {
helpForm = CreateHelpForm (-95, -5, "Entrez Help", "entrez.hlp",
HideHelpForm, HelpActivateProc);
}
*/
SetTitle (w, "Creating initial window");
termListForm = CreateTermListForm (-70, -70, "Entrez1 Query",
TermSelectionActivateProc,
TermSelectionFormMessage);
Remove (w);
ArrowCursor ();
if (termListForm != NULL) {
Show (termListForm);
Select (termListForm);
Update ();
docSumForm = CreateDocSumForm (-90, -10, "Entrez1 Document",
DocumentSummaryActivateProc,
DocumentSummaryFormMessage);
UseDelayedNeighbor (docSumForm, TRUE);
if (docSumForm != NULL) {
ProcessEvents ();
} else {
Message (MSG_FATAL, "Unable to create document window");
}
} else {
Message (MSG_FATAL, "Unable to create term list window");
}
WatchCursor ();
val = GetMuskCurrentSt ();
if (val < 0) {
val = 0;
}
if (val >= GetMuskTotalSt ()) {
val = 0;
}
if (val > 0) {
sprintf (str, "%d", (int) val);
SetEntrezAppParam ("PREFERENCES", "DEFAULTSTYLE", str);
} else {
SetEntrezAppParam ("PREFERENCES", "DEFAULTSTYLE", "0");
}
CleanupEntrez ();
ArrowCursor ();
return 0;
}
Int2 Main()
{
AsnIoPtr aip;
BioseqPtr bsp;
Pointer dataptr;
Uint2 datatype;
Boolean found;
SPI_mRNAToHerdPtr h_head;
SPI_mRNAToHerdPtr h_prev;
SPI_mRNAToHerdPtr hptr;
FILE *ifp;
Boolean isGIlist;
Char line[60];
Boolean lowercase;
SeqLocPtr lcaseloc;
FILE *ofp;
FILE *ofp2;
SeqAlignPtr sap;
SeqAnnotPtr sanp;
SeqEntryPtr sep;
FILE *sfp;
SeqIdPtr sip;
SeqLocPtr slp;
SPI_bsinfoPtr spig;
SPI_bsinfoPtr spig_head;
SPI_bsinfoPtr spig_prev;
SPI_bsinfoPtr spim;
SPI_bsinfoPtr spim_head;
SPI_bsinfoPtr spim_prev;
SPI_OptionsPtr spot;
SPI_RegionInfoPtr srip = NULL;
SPI_RegionInfoPtr srip_head;
SPI_RegionInfoPtr srip_prev;
CharPtr str;
CharPtr txt;
ID1BioseqFetchEnable("spidey", FALSE);
LocalSeqFetchInit(FALSE);
/* standard setup */
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 (! 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;
}
if (!GetArgs("SPIDEY", NUMARGS, myargs))
return 0;
/* set the error message level high to suppress warnings from BLAST */
isGIlist = (Boolean)myargs[MYARGGILIST].intvalue;
txt = myargs[MYARGGENFILE].strvalue;
ifp = FileOpen(txt, "r");
spig_head = NULL;
if (ifp == NULL)
{
bsp = SPI_GetBspFromGIOrAcc(txt);
if (bsp == NULL)
{
ErrPostEx(SEV_ERROR, 0, 0, "Can't open genomic input file\n");
return -1;
} else
{
spig_head = (SPI_bsinfoPtr)MemNew(sizeof(SPI_bsinfo));
spig_head->bsp = bsp;
}
}
if (spig_head == NULL)
{
spig_prev = NULL;
/* read in the genomic sequence(s) first and put them into bsinfo structures */
while ((dataptr = ReadAsnFastaOrFlatFile (ifp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE)) != NULL)
{
if (datatype == OBJ_BIOSEQ)
{
spig = (SPI_bsinfoPtr)MemNew(sizeof(SPI_bsinfo));
spig->bsp = (BioseqPtr)dataptr;
if (spig_head == NULL)
spig_head = spig_prev = spig;
else
{
spig_prev->next = spig;
spig_prev = spig;
}
} else if (datatype == OBJ_SEQENTRY)
{
sep = (SeqEntryPtr)dataptr;
SeqEntryExplore(sep, &spig_head, SPI_FindAllNuc);
}
}
FileClose(ifp);
}
if (spig_head == NULL)
{
ErrPostEx(SEV_ERROR, 0, 0, "No valid bioseqs in genomic file\n");
return -1;
} else if (ISA_aa(spig_head->bsp->mol))
{
ErrPostEx(SEV_ERROR, 0, 0, "At least one of the genomic sequences appears to be a protein.\n");
return -1;
}
if (spig_head->next != NULL)
{
ErrPostEx(SEV_ERROR, 0, 0, "This version can only process one genomic sequence at a time. Only the first sequence in this file will be used.\n");
spig_head->next = NULL;
}
spim_head = spim_prev = NULL;
txt = myargs[MYARGMRNAFILE].strvalue;
ifp = FileOpen(txt, "r");
if (ifp == NULL)
{
bsp = SPI_GetBspFromGIOrAcc(txt);
if (bsp == NULL)
{
ErrPostEx(SEV_ERROR, 0, 0, "Can't open mRNA input file\n");
return -1;
} else
{
spim_head = (SPI_bsinfoPtr)MemNew(sizeof(SPI_bsinfo));
spim_head->bsp = bsp;
}
}
if (spim_head == NULL)
{
lowercase = (Boolean)myargs[MYARGMASKED].intvalue;
lcaseloc = NULL;
/* if the mRNA has lowercase masking, read it in carefully to record the masking */
if (lowercase == TRUE)
{
while ((sep = FastaToSeqEntryForDb(ifp, TRUE, NULL, TRUE, NULL, NULL, &lcaseloc)) != NULL)
{
SeqEntryExplore(sep, &spim_head, SPI_FindAllNuc);
if (lcaseloc != NULL) /* put masking info into the bsinfo structure */
{
spim = spim_head;
sip = SeqLocId(lcaseloc);
found = FALSE;
while (spim != NULL && !found)
{
if (SeqIdComp(sip, spim->bsp->id) == SIC_YES)
{
found = TRUE;
spim->lcaseloc = lcaseloc;
}
spim = spim->next;
}
lcaseloc = NULL;
}
}
} else if (isGIlist) /* mRNA file is a list of GIs, must fetch the bioseqs */
{
str = ReadALine(line, sizeof(line), ifp);
while (str != NULL)
{
bsp = SPI_GetBspFromGIOrAcc(str);
if (bsp != NULL)
{
spim = (SPI_bsinfoPtr)MemNew(sizeof(SPI_bsinfo));
spim->bsp = bsp;
if (spim_head == NULL)
spim_head = spim_prev = spim;
else
{
spim_prev->next = spim;
spim_prev = spim;
}
}
str = ReadALine(line, sizeof(line), ifp);
}
} else /* mRNAs are FASTA or ASN.1, read them all in */
{
while ((dataptr = ReadAsnFastaOrFlatFile (ifp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE)) != NULL)
{
if (datatype == OBJ_BIOSEQ)
{
spim = (SPI_bsinfoPtr)MemNew(sizeof(SPI_bsinfo));
spim->bsp = (BioseqPtr)dataptr;
if (spim_head == NULL)
spim_head = spim_prev = spim;
else
{
spim_prev->next = spim;
spim_prev = spim;
}
} else if (datatype == OBJ_SEQENTRY)
{
sep = (SeqEntryPtr)dataptr;
SeqEntryExplore(sep, &spim_head, SPI_FindAllNuc);
}
}
}
FileClose(ifp);
}
if (spim_head == NULL)
{
ErrPostEx(SEV_ERROR, 0, 0, "No valid bioseqs in mRNA file\n");
return -1;
} else if (ISA_aa(spim_head->bsp->mol))
{
ErrPostEx(SEV_ERROR, 0, 0, "At least one of the mRNA sequences appears to be a protein\n");
return -1;
}
txt = myargs[MYARGTABLE].strvalue;
if (txt != NULL)
{
ifp = FileOpen(txt, "r");
if (ifp == NULL)
{
ErrPostEx(SEV_ERROR, 0, 0, "Unable to open table file\n");
return -1;
}
SPI_ReadFeatureTable(ifp, spim_head);
spim = spim_head;
while (spim != NULL)
{
if (spim->lcaseloc != NULL)
{
slp = (SeqLocPtr)ValNodeNew(NULL);
slp->choice = SEQLOC_MIX;
slp->data.ptrvalue = (Pointer)spim->lcaseloc;
spim->lcaseloc = slp;
}
spim = spim->next;
}
}
spim = spim_head;
spot = (SPI_OptionsPtr)MemNew(sizeof(SPI_Options));
spot->printaln = myargs[MYARGPRALIGN].intvalue;
txt = myargs[MYARGOUTFILE].strvalue;
ofp = FileOpen(txt, "w");
if (ofp == NULL && spot->printaln != 3)
{
ErrPostEx(SEV_ERROR, 0, 0, "Unable to open output file\n");
return -1;
}
if (spot->printaln >= 2)
{
txt = myargs[MYARGALNFILE].strvalue;
ofp2 = FileOpen(txt, "a");
if (ofp2 == NULL)
{
ErrPostEx(SEV_ERROR, 0, 0, "Unable to open output file 2\n");
return -1;
}
} else
ofp2 = NULL;
/** ErrSetMessageLevel(SEV_MAX); **/
spot->firstpasseval = myargs[MYARG1STEVAL].floatvalue;
spot->secpasseval = myargs[MYARG2NDEVAL].floatvalue;
spot->thirdpasseval = myargs[MYARG3RDEVAL].floatvalue;
spot->numreturns = myargs[MYARGNUMMOD].intvalue;
spot->idcutoff = myargs[MYARGIDCUT].intvalue;
spot->lencutoff = myargs[MYARGLENCUT].intvalue;
spot->interspecies = (Boolean)myargs[MYARGSPEC].intvalue;
spot->printasn = (Boolean)myargs[MYARGASN].intvalue;
spot->fetchcds = (Boolean)myargs[MYARGGETCDS].intvalue;
/*spot->ace = (Boolean)myargs[MYARGACEDB].intvalue;*/
spot->from = myargs[MYARGFROM].intvalue;
spot->to = myargs[MYARGTO].intvalue;
spot->makemult = (Boolean)myargs[MYARGMULT].intvalue;
/*KSK*/
spot->bigintron = (Boolean)myargs[MYARGXL].intvalue;
spot->bigintron_size = myargs[MYARGXL_SIZE].intvalue;
spot->repeat_db_file = myargs[MYARGREPDB].strvalue;
txt = myargs[MYARGORG].strvalue;
if (!StringICmp(txt, "d") || !StringICmp(txt, "D")){
spot->organism = SPI_FLY;
}
else if (!StringICmp(txt, "p") || !StringICmp(txt, "P")){
spot->organism = SPI_PLANT;
}
else if (!StringICmp(txt, "c") || !StringICmp(txt, "C")){
spot->organism = SPI_CELEGANS;
}
else if (!StringICmp(txt, "m") || !StringICmp(txt, "M")){
spot->organism = SPI_DICTY;
}
else {
spot->organism = SPI_VERTEBRATE;
}
sap = NULL;
if (spot->printasn)
spot->sap_head = &sap;
txt = myargs[MYARGSTRAND].strvalue;
if (txt != NULL)
{
if (StrChr(txt, 'p') || StrChr(txt, 'P'))
spot->strand = Seq_strand_plus;
else
spot->strand = Seq_strand_minus;
} else
spot->strand = Seq_strand_both;
/*txt = myargs[MYARGDRAFTFILE].strvalue;
if (txt != NULL)
spot->draftfile = StringSave(txt);*/
txt = myargs[MYARGDSPLICE].strvalue;
if (txt != NULL)
{
sfp = FileOpen(txt, "r");
SPI_GetSpliceInfo(spot, sfp, TRUE);
FileClose(sfp);
}
txt = myargs[MYARGASPLICE].strvalue;
if (txt != NULL)
{
sfp = FileOpen(txt, "r");
SPI_GetSpliceInfo(spot, sfp, FALSE);
FileClose(sfp);
}
h_head = h_prev = NULL;
srip_head = srip_prev = NULL;
while (spim != NULL)
{
spot->lcaseloc = spim->lcaseloc;
if (spot->draftfile == NULL)
srip = SPI_AlnSinglemRNAToGen(spig_head, spim, ofp, ofp2, spot);
else
{
hptr = SPI_AlnSinglemRNAToPieces(spig_head, spim, ofp, ofp2, spot);
if (h_head != NULL)
{
h_prev->next = hptr;
h_prev = hptr;
} else
h_head = h_prev = hptr;
}
if (srip != NULL)
{
if (srip_head != NULL)
{
srip_prev->next = srip;
srip_prev = srip;
} else
srip_head = srip_prev = srip;
}
spim = spim->next;
}
if (spot->makemult)
{
SPI_MakeMultipleAlignment(srip_head);
SPI_PrintMultipleAlignment(srip_head, FALSE, spig_head->bsp, ofp);
SPI_RegionListFree(srip_head);
} else
SPI_RegionListFree(srip_head);
/* create the ASN.1 output, if requested; need to use the continuous alignment */
/* that was generated */
if (spot->printasn && *(spot->sap_head) != NULL && spot->draftfile == NULL)
{
sanp = SeqAnnotForSeqAlign(*(spot->sap_head));
txt = myargs[MYARGASNFILE].strvalue;
aip = AsnIoOpen(txt, "w");
SeqAnnotAsnWrite(sanp, aip, NULL);
AsnIoClose(aip);
SeqAlignSetFree(*(spot->sap_head));
}
FileClose(ofp);
FileClose(ofp2);
SPI_OptionsFree(spot);
SPI_bsinfoFreeList(spim_head);
SPI_bsinfoFreeList(spig_head);
LocalSeqFetchDisable();
ID1BioseqFetchDisable();
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)
{
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;
}
Nlm_Int2 Main ()
{
Int2 iTest;
Byte bRender;
Int2 iColor;
PDNMS pdnmsModelstruc;
BiostrucPtr pbsBiostruc;
Char cOut[254];
FILE *pFile;
ErrSetFatalLevel(SEV_MAX);
if (! GetArgs("GetMMDB",NUMARGS,myargs))
return 1;
/* Initialize MMDBAPI */
if (! OpenMMDBAPI(0, NULL))
{
printf("Have not opened mmdbapi");
return 2;
}
/* load an ASN.1 Biostruc */
/* Any other method of obtaining a Biostruc is fine... */
/* This one does a built-in lookup of PDB accesion numbers */
/* then fetches the file using the Entrez clinet-server interface */
pbsBiostruc = FetchBiostrucPDB(myargs[0].strvalue, myargs[3].intvalue, 100);
if (pbsBiostruc == NULL)
{
printf("Have not fetched Biostruc");
return 3;
}
/* convert it into a Modelstruc pointed to by pdnmsModelstruc */
pdnmsModelstruc= MakeAModelstruc(pbsBiostruc);
if ( pdnmsModelstruc == NULL )
{
printf("Have not converted Biostruc");
return 4;
}
if (myargs[1].intvalue == 0) /* Summary */
{
if (!myargs[2].strvalue)
{
sprintf(cOut,"%s.sum", myargs[0].strvalue);
pFile = fopen(cOut, "w");
}
else
pFile = fopen(myargs[2].strvalue,"w");
iTest = WriteStructSummary(pdnmsModelstruc,pFile);
}
if (myargs[1].intvalue == 2) /* Kinemage */
{
bRender = (Byte) myargs[5].intvalue;
iColor = (Int2) myargs[4].intvalue;
if (!myargs[2].strvalue)
{
sprintf(cOut,"%s.kin", myargs[0].strvalue);
pFile = fopen(cOut, "w");
}
else
pFile = fopen(myargs[2].strvalue,"w");
iTest = WriteKinAllModel(pdnmsModelstruc,pFile,
iColor,bRender);
}
if (myargs[1].intvalue == 1) /* PDB */
{
if (!myargs[2].strvalue)
{
sprintf(cOut,"%s.pdb", myargs[0].strvalue);
pFile = fopen(cOut, "w");
}
else
pFile = fopen(myargs[2].strvalue,"w");
iTest = WritePDBAllModel(pdnmsModelstruc,pFile);
}
/* Free the Modelstruc (and its enclosed Biostruc) */
/* FreeAModelstruc(PDNMS pdnmsThis); not necessary */
/* This can be done individually - but all Modelstrucs */
/* remaining are freed in CloseMMDBAPI() */
/* Shut Down MMDBAPI */
CloseMMDBAPI();
return TRUE;
}
Int2 Main (void)
{
CharPtr base, directory, outfile, suffix, ptr;
BioseqSetPtr bssp;
ValNodePtr head, vnp;
SeqEntryPtr sep;
SeqSubmitPtr ssp;
/* 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 */
if (! GetArgs ("subfuse", sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
directory = (CharPtr) myargs [p_argInputPath].strvalue;
outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
suffix = (CharPtr) myargs [x_argSuffix].strvalue;
bssp = BioseqSetNew ();
if (bssp == NULL) return 0;
bssp->_class = BioseqseqSet_class_genbank;
sep = SeqEntryNew ();
if (sep == NULL) return 0;
sep->choice = 2;
sep->data.ptrvalue = (Pointer) bssp;
ssp = SeqSubmitNew ();
if (ssp == NULL) return 0;
ssp->datatype = 1;
ssp->data = (Pointer) sep;
/* get list of all files in source directory */
head = DirCatalog (directory);
for (vnp = head; vnp != NULL; vnp = vnp->next) {
if (vnp->choice == 0) {
base = (CharPtr) vnp->data.ptrvalue;
if (! StringHasNoText (base)) {
ptr = StringStr (base, suffix);
if (ptr != NULL) {
*ptr = '\0';
Message (MSG_POST, "Processing %s\n", base);
ProcessOneRecord (ssp, bssp, directory, base, suffix);
}
}
}
}
/* clean up file list */
ValNodeFreeData (head);
/* write output file */
WriteOneSubmission (outfile, ssp);
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;
}
Int2 Main (void)
{
Int2 db = -1;
Int2 i;
Boolean makeCDS;
Char path [PATH_MAX];
CharPtr progname;
FILE *fp;
Int2 rsult;
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
UseLocalAsnloadDataAndErrMsg ();
ErrPathReset ();
if (! AllObjLoad ()) {
Message (MSG_FATAL, "AllObjLoad failed");
return 1;
}
if (! SeqCodeSetLoad ()) {
Message (MSG_FATAL, "SeqCodeSetLoad failed");
return 1;
}
if (! GeneticCodeTableLoad ()) {
Message (MSG_FATAL, "GeneticCodeTableLoad failed");
return 1;
}
ProgramPath (path, sizeof (path));
progname = StringRChr (path, DIRDELIMCHR);
if (progname != NULL) {
progname++;
} else {
progname = "fetchent";
}
/* GetArgs is a portable way of obtaining arguments */
if (! GetArgs (progname, NUMARG, myargs)) {
Message (MSG_FATAL, "GetArgs failed");
return 1;
}
/* Map database argument to TYP_XX value */
for (i = 0; databases [i] != NULL; i++) {
if (StringICmp (myargs [0].strvalue, databases [i]) == 0) {
db = i;
}
}
/* Convert M, P, or N alternative database symbols to proper code */
if (db >= 3 && db <= 5) {
db -= 3;
}
if (db < 0 || db > 2) {
Message (MSG_FATAL, "Database must be ML, AA, or NT");
return 1;
}
if (! EntrezInit (progname, FALSE, NULL)) {
Message (MSG_FATAL, "EntrezInit failed");
return 1;
}
fp = FileOpen (myargs [2].strvalue, "w");
if (fp == NULL) {
Message (MSG_FATAL, "FileOpen failed");
return 1;
}
makeCDS = (Boolean) myargs [3].intvalue;
if (makeCDS && db != TYP_NT) {
Message (MSG_ERROR, "Coding region extraction inappropriate");
makeCDS = FALSE;
}
rsult = ProcessQuery (db, myargs [1].strvalue, makeCDS, fp);
FileClose (fp);
EntrezFini ();
return rsult;
}
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;
}
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;
}
