extern void ArchiveBadgesDialog (
DialoG d,
FILE *fp
)
{
IntBadgPtr ibp;
Int2 k, n, numItems;
SscBadgPtr sbp;
sbp = (SscBadgPtr) GetObjectExtra (d);
if (sbp == NULL || fp == NULL) return;
GetDocParams (sbp->badglog, &numItems, NULL);
for (k = 1, n = 0; k <= numItems; k++) {
ibp = GetBadgInfo (sbp, k);
if (ibp == NULL) continue;
if (StringHasNoText (ibp->name)) continue;
n++;
}
if (n < 1) return;
fprintf (fp, "AWARDS -----\n\n%s\n\n", archiveBadgLabel);
for (k = 1; k <= numItems; k++) {
ibp = GetBadgInfo (sbp, k);
if (ibp == NULL) continue;
if (StringHasNoText (ibp->name)) continue;
SaveDocumentItem (sbp->badglog, fp, k);
}
fprintf (fp, "\n");
}
static void PrintMisMatches(FILE *out, CharPtr id_txt, ValNodePtr val, ValNodePtr col, ValNodePtr field)
{
CharPtr label = NULL;
while (field != NULL && (val != NULL || col != NULL)) {
if (val == NULL) {
if (!StringHasNoText (col->data.ptrvalue)) {
label = SummarizeFieldType (field);
fprintf (out, "%s\t%s\t\t%s\n", id_txt, label, (char *) col->data.ptrvalue);
}
} else if (col == NULL) {
if (!StringHasNoText (val->data.ptrvalue)) {
label = SummarizeFieldType (field);
fprintf (out, "%s\t%s\t%s\t\n", id_txt, label, (char *) val->data.ptrvalue);
}
} else if (!StringHasNoText (val->data.ptrvalue) && !StringHasNoText (col->data.ptrvalue)
&& StringCmp (val->data.ptrvalue, col->data.ptrvalue) != 0) {
label = SummarizeFieldType (field);
fprintf (out, "%s\t%s\t%s\t%s\n", id_txt, label, (char *) val->data.ptrvalue, (char *) col->data.ptrvalue);
}
label = MemFree (label);
if (val != NULL) {
val = val->next;
}
if (col != NULL) {
col = col->next;
}
field = field->next;
}
}
static void RecordThesis (ScanDataPtr sdp, CharPtr str)
{
StringSetPtr ssp;
ValNodePtr vnp;
if (sdp == NULL || StringHasNoText (str)) return;
for (vnp = sdp->lcList; vnp != NULL; vnp = vnp->next) {
ssp = (StringSetPtr) vnp->data.ptrvalue;
if (ssp == NULL) continue;
if (StringCmp (ssp->text, str) == 0) {
(ssp->count)++;
return;
}
}
ssp = MemNew (sizeof (StringSet));
if (ssp == NULL) return;
StringCpy (ssp->firstID, sdp->buf);
StringNCpy_0 (ssp->text, str, sizeof (ssp->text));
ssp->count = 1;
ValNodeAddPointer (&(sdp->lcList), 0, (Pointer) ssp);
}
static SeqIdPtr SmartGuessMakeId (CharPtr str)
{
CharPtr id_txt;
SeqIdPtr sip = NULL;
if (StringHasNoText (str)) {
return NULL;
} else if (StringChr (str, '|') != NULL) {
sip = MakeSeqID (str);
} else if (IsAllDigits (str)) {
id_txt = (CharPtr) MemNew (sizeof (Char) * (StringLen (str) + 4));
sprintf (id_txt, "gi|%s", str);
sip = MakeSeqID (id_txt);
id_txt = MemFree (id_txt);
} else if (StringChr (str, '_') != NULL) {
id_txt = (CharPtr) MemNew (sizeof (Char) * (StringLen (str) + 5));
sprintf (id_txt, "oth|%s", str);
sip = MakeSeqID (id_txt);
id_txt = MemFree (id_txt);
} else {
id_txt = (CharPtr) MemNew (sizeof (Char) * (StringLen (str) + 4));
sprintf (id_txt, "gb|%s", str);
sip = MakeSeqID (id_txt);
id_txt = MemFree (id_txt);
}
return sip;
}
extern void ExportBadgesDialog (
DialoG d,
ValNodePtr PNTR head
)
{
Char buf [128], tmp [32];
DoC doc;
IntBadgPtr ibp;
Int2 k, numItems;
SscBadgPtr sbp;
sbp = (SscBadgPtr) GetObjectExtra (d);
if (sbp == NULL || head == NULL) return;
doc = sbp->badglog;
GetDocParams (doc, &numItems, NULL);
for (k = 1; k <= numItems; k++) {
ibp = GetBadgInfo (sbp, k);
if (ibp == NULL) continue;
if (StringHasNoText (ibp->name)) continue;
buf [0] = '\0';
ExportDocCell (doc, k, 1, buf);
TabToCol (buf, 22);
ExportDocCell (doc, k, 3, tmp);
StringCat (buf, tmp);
ValNodeCopyStr (head, k + 100, buf);
}
}
static void ExciseProteinIDLine (CharPtr line)
{
CharPtr protein_id_line_start = NULL, protein_id_line_end;
if (StringHasNoText (line))
{
return;
}
protein_id_line_start = StringStr (line, "\n\t\t\tprotein_id\t");
if (protein_id_line_start == NULL)
{
return;
}
protein_id_line_end = StringChr (protein_id_line_start + 1, '\n');
if (protein_id_line_end == NULL)
{
return;
}
while (*protein_id_line_end != 0)
{
*protein_id_line_start = *protein_id_line_end;
protein_id_line_start ++;
protein_id_line_end ++;
}
*protein_id_line_start = 0;
}
NLM_EXTERN Int4 VecScreenCheckQueue (
VQUEUE* queue
)
{
CONN conn;
Nlm_Int4 count = 0;
VQueuePtr curr;
time_t currtime;
VQueuePtr next;
VQueuePtr PNTR qptr;
Char str [128];
qptr = (VQueuePtr PNTR) queue;
if (qptr == NULL || *qptr == NULL) return 0;
curr = *qptr;
while (curr != NULL) {
next = curr->next;
/* check for return of rID, WAITING, of SUCCESS message */
QUERY_CheckQueue (&(curr->connqueue));
if (curr->done) {
VecScreen_RemoveFromQueue (queue, curr);
} else {
if (curr->connqueue == NULL) {
currtime = GetSecs ();
if (currtime - curr->postedTime < curr->secondsToWait) {
} else if (! StringHasNoText (curr->rid)) {
/* estimated wait time has expired, so queue another check */
if (curr->secondsToWait < 300) {
curr->secondsToWait *= 2;
if (curr->secondsToWait > 300) {
curr->secondsToWait = 300;
}
}
curr->postedTime = GetSecs ();
sprintf (str, "req=%s", curr->rid);
conn = VecScreenOpenConnection (str);
QUERY_SendQuery (conn);
QUERY_AddToQueue (&(curr->connqueue), conn, SecondVecScreenCallback, (Pointer) curr, TRUE);
}
}
count++;
}
curr = next;
}
return count;
}
static Boolean NoEntryExists (CharPtr sect, CharPtr type)
{
Char str [256];
if (GetAppParam ("NCBI", sect, type, NULL, str, sizeof (str))) {
if (! StringHasNoText (str)) return FALSE;
}
return TRUE;
}
static Boolean HasMismatch
(ValNodePtr values,
ValNodePtr col)
{
Boolean rval = FALSE;
while (!rval && values != NULL && col != NULL) {
if (StringHasNoText (values->data.ptrvalue)
&& StringHasNoText (col->data.ptrvalue)) {
/* both empty, ignore */
} else if (StringCmp (values->data.ptrvalue, col->data.ptrvalue)) {
rval = TRUE;
}
values = values->next;
col = col->next;
}
if (values != NULL || col != NULL) {
rval = TRUE;
}
return rval;
}
static void DoTitle (SeqDescrPtr vnp, Pointer userdata)
{
Char ch;
CharPtr ptr, str, tmp;
ScanDataPtr sdp;
if (vnp->choice != Seq_descr_title) return;
str = (CharPtr) vnp->data.ptrvalue;
if (StringHasNoText (str)) return;
sdp = (ScanDataPtr) userdata;
tmp = str;
ptr = StringStr (tmp, "complete ");
while (ptr != NULL) {
tmp = ptr + 9;
ch = *tmp;
while (ch != '\0' && (! (IS_WHITESP (ch)))) {
tmp++;
ch = *tmp;
}
if (ch == '\0') return;
if (StringNICmp (tmp, " genome", 7) == 0) {
tmp [7] = '\0';
RecordTitle (sdp, ptr);
return;
} else if (StringNICmp (tmp, " DNA", 4) == 0) {
tmp [4] = '\0';
RecordTitle (sdp, ptr);
return;
} else if (StringNICmp (tmp, " sequence", 9) == 0) {
tmp [9] = '\0';
RecordTitle (sdp, ptr);
return;
}
ptr = StringStr (tmp, "complete ");
}
if (StringStr (str, "genome DNA") != NULL) {
RecordTitle (sdp, "genome DNA");
return;
}
if (sdp->bulk) return;
if (StringStr (str, "genomic DNA") != NULL) {
RecordTitle (sdp, "genomic DNA");
return;
}
}
static Boolean SaveSetsInOneSelectedSet (GatherObjectPtr gop)
{
SetSavePtr ssp;
SelStructPtr sel;
BioseqSetPtr bssp;
CharPtr filename, file_fmt = "%s_%d.sqn";
SeqEntryPtr sep;
AsnIoPtr aip;
#ifdef WIN_MAC
FILE *fp;
#endif
if (gop == NULL || gop->dataptr == NULL || gop->itemtype != OBJ_BIOSEQSET) return TRUE;
ssp = (SetSavePtr) gop->userdata;
if (ssp == NULL || StringHasNoText (ssp->file_base)) return TRUE;
sel = ssp->sel;
while (sel != NULL
&& (sel->entityID != gop->entityID
|| sel->itemtype != gop->itemtype
|| sel->itemID != gop->itemID))
{
sel = sel->next;
}
if (sel == NULL) return TRUE;
bssp = gop->dataptr;
filename = (CharPtr) MemNew (sizeof (Char) + (StringLen (ssp->file_base) + StringLen (file_fmt) + 15));
for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
sprintf (filename, file_fmt, ssp->file_base, ssp->file_num);
ssp->file_num++;
#ifdef WIN_MAC
fp = FileOpen (filename, "r");
if (fp != NULL) {
FileClose (fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
aip = AsnIoOpen(filename, "w");
SeqEntryAsnWrite (sep, aip, NULL);
AsnIoClose (aip);
}
filename = MemFree (filename);
return TRUE;
}
extern Pointer ReadFromTPASmart (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityID)
{
Char cmmd [256];
Pointer dataptr;
FILE* fp;
Char path [PATH_MAX];
Char err_path [PATH_MAX];
if (datatype != NULL) {
*datatype = 0;
}
if (entityID != NULL) {
*entityID = 0;
}
if (StringHasNoText (accn)) return NULL;
if (tpasmartfetchcmd == NULL) {
if (GetAppParam ("SEQUIN", "TPASMART", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
tpasmartfetchcmd = StringSaveNoNull (cmmd);
}
}
if (tpasmartfetchcmd == NULL) return NULL;
TmpNam (path);
#ifdef OS_UNIX
sprintf (err_path, "%s.err", path);
sprintf (cmmd, "csh %s %s > %s 2>%s", tpasmartfetchcmd, accn, path, err_path);
system (cmmd);
#endif
#ifdef OS_MSWIN
sprintf (cmmd, "%s %s -o %s", tpasmartfetchcmd, accn, path);
system (cmmd);
#endif
fp = FileOpen (path, "r");
if (fp == NULL) {
FileRemove (path);
return NULL;
}
dataptr = ReadAsnFastaOrFlatFile (fp, datatype, entityID, FALSE, FALSE, TRUE, FALSE);
FileClose (fp);
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
return dataptr;
}
/* Set HTTP user header */
static void x_SetupUserHeader (
SConnNetInfo* net_info,
const char* appName,
EMIME_Type type,
EMIME_SubType subtype,
EMIME_Encoding encoding
)
{
const char* userAgentName = NULL;
char user_header [MAX_CONTENT_TYPE_LEN + 80];
/* content-type if specified */
if (type < eMIME_T_Unknown) {
VERIFY( MIME_ComposeContentTypeEx (type, subtype, encoding,
user_header, MAX_CONTENT_TYPE_LEN) );
ConnNetInfo_OverrideUserHeader (net_info, user_header);
}
/* allow the user to specify a prog. name, otherwise get it from elsewhere */
if (StringHasNoText (appName)) {
const char* progName = GetProgramName();
if (StringHasNoText (progName)) {
char path [PATH_MAX];
Nlm_ProgramPath (path, sizeof (path));
userAgentName = StringRChr (path, DIRDELIMCHR);
if (userAgentName)
++userAgentName;
} else
userAgentName = progName;
} else
userAgentName = appName;
if (StringDoesHaveText (userAgentName)) {
sprintf (user_header, "User-Agent: %.80s\r\n", userAgentName);
ConnNetInfo_ExtendUserHeader (net_info, user_header);
}
}
static void DOT_AcceptNetworkProc(ButtoN b)
{
DOTStartDataPtr sdata;
WindoW w;
Char str1[50]={""}, str2[50]={""};
BioseqPtr qbsp=NULL, sbsp=NULL;
SeqEntryPtr qsep, ssep;
Uint2 entityID1, entityID2;
Int2 rtn=0;
DOTMainDataPtr mip;
SeqLocPtr slp1=NULL, slp2=NULL;
w=ParentWindow(b);
Hide(w);
sdata=(DOTStartDataPtr)GetObjectExtra(w);
GetTitle(sdata->id1, str1, sizeof(str1));
GetTitle(sdata->id2, str2, sizeof(str2));
if (StringHasNoText (str1) || StringHasNoText(str2)) {
Message (MSG_ERROR, "enter GI or Accession number");
Show (w);
Select (w);
Select (sdata->id1);
return;
}
qbsp = DOT_FetchBioseqGivenString(str1, &rtn);
sbsp = DOT_FetchBioseqGivenString(str2, &rtn);
if (rtn <0 || !qbsp || !sbsp){
DOT_RespondtoFetch(rtn, w, sdata);
return;
}
DOT_RunRequest(w, qbsp, sbsp, sdata);
}
static void PrintGraphMessage (BioseqPtr bsp, ScanDataPtr sdp,
CharPtr prefix, CharPtr suffix)
{
Char buf [41];
if (bsp == NULL || sdp == NULL || prefix == NULL) return;
SeqIdWrite (bsp->id, buf, PRINTID_FASTA_LONG, sizeof (buf));
fprintf (sdp->fp, "QA - %s - %s", buf, prefix);
if (! StringHasNoText (suffix)) {
fprintf (sdp->fp, " - %s", suffix);
}
fprintf (sdp->fp, "\n");
}
static Boolean UpdateContigReadId (TContigReadPtr read, SeqIdReplaceListPtr pair_list, Boolean no_lookup, Boolean is_srr, char *has_errors)
{
SeqIdPairPtr pair;
SeqIdPtr sip_find;
Char id_buf[255];
Boolean rval = TRUE;
if (read == NULL || StringHasNoText (read->read_id)) {
rval = FALSE;
} else {
sip_find = MakeSeqID (read->read_id);
pair = FindReplacementInSeqIdReplaceList (sip_find, pair_list);
if (pair != NULL && (no_lookup || OkToReplaceId (pair, read->read_seq, has_errors))) {
if (pair->is_complement) {
if (read->is_complement) {
read->is_complement = FALSE;
} else {
read->is_complement = TRUE;
}
}
if (pair->ti > 0) {
read->ti = pair->ti;
} else {
if (pair->sip_replace->choice == SEQID_LOCAL) {
SeqIdWrite (pair->sip_replace, id_buf, PRINTID_REPORT, sizeof (id_buf) - 1);
} else {
SeqIdWrite (pair->sip_replace, id_buf, PRINTID_FASTA_LONG, sizeof (id_buf) - 1);
}
if (is_srr) {
if (read->srr != NULL) {
free (read->srr);
}
read->srr = malloc (sizeof (Char) * (StringLen (id_buf) + 1));
sprintf (read->srr, "%s", id_buf);
free (read->read_id);
read->read_id = NULL;
} else {
free (read->read_id);
read->read_id = malloc (sizeof (Char) * (StringLen (id_buf) + 1));
sprintf (read->read_id, "%s", id_buf);
}
}
read->local = FALSE;
}
sip_find = SeqIdFree (sip_find);
}
return rval;
}
static Boolean IsAllDigits (CharPtr str)
{
CharPtr cp;
if (StringHasNoText (str)) return FALSE;
cp = str;
while (*cp != 0 && isdigit (*cp)) {
cp++;
}
if (*cp == 0) {
return TRUE;
} else {
return FALSE;
}
}
static void ProcessOneRecord (
CharPtr filename,
Pointer userdata
)
{
CSpeedFlagPtr cfp;
if (StringHasNoText (filename)) return;
cfp = (CSpeedFlagPtr) userdata;
if (cfp == NULL) return;
if (cfp->batch) {
ProcessMultipleRecord (filename, cfp);
} else {
ProcessSingleRecord (filename, cfp);
}
}
static Pointer AdjPageToAwardDataPtr(DialoG d)
{
AwardDataPtr badges, bdp, lastbdp;
IntBadgPtr ibp;
Int2 k, numItems;
SscBadgPtr sbp;
SscTablesPtr stp;
sbp = (SscBadgPtr) GetObjectExtra (d);
if (sbp == NULL) return NULL;
stp = sbp->tables;
if (stp == NULL) return NULL;
badges = NULL;
lastbdp = NULL;
GetDocParams (sbp->badglog, &numItems, NULL);
for (k = 1; k <= numItems; k++) {
ibp = GetBadgInfo (sbp, k);
if (ibp == NULL) continue;
if (StringHasNoText (ibp->name)) continue;
bdp = AwardDataNew ();
if (bdp == NULL) continue;
bdp->name = StringSaveNotEmpty (ibp->name);
bdp->type = ibp->type;
bdp->comment = StringSaveNotEmpty (ibp->comment);
bdp->reason = ibp->reason;
if (badges == NULL) {
badges = bdp;
}
if (lastbdp != NULL) {
lastbdp->next = bdp;
}
lastbdp = bdp;
}
return (Pointer) badges;
}
NLM_EXTERN Boolean VecScreenAsynchronousRequest (
CharPtr database,
BioseqPtr bsp,
VQUEUE* queue,
VecScreenResultProc resultproc,
VecScreenAnnounceProc announceproc,
VoidPtr userdata
)
{
CONN conn;
FILE *fp;
Char path [PATH_MAX];
Char str [128];
if (bsp == NULL || queue == NULL || resultproc == NULL) return FALSE;
if (StringHasNoText (database)) {
database = "UniVec";
}
sprintf (str, "db=%s", database);
conn = VecScreenOpenConnection (str);
if (conn == NULL) return FALSE;
TmpNam (path);
fp = FileOpen (path, "w");
BioseqToFasta (bsp, fp, ISA_na (bsp->mol));
FileClose (fp);
fp = FileOpen (path, "r");
QUERY_CopyFileToQuery (conn, fp);
FileClose (fp);
QUERY_SendQuery (conn);
VecScreen_AddToQueue (queue, resultproc, announceproc, userdata, conn, bsp);
FileRemove (path);
return TRUE;
}
static ValNodePtr FieldsFromFieldListString (CharPtr str)
{
CharPtr cpy, val, comma;
Int4 qual;
ValNodePtr field_list = NULL, qc;
if (StringHasNoText (str)) {
return NULL;
}
cpy = StringSave (str);
val = cpy;
comma = StringChr(val, ',');
while (comma != NULL) {
*comma = 0;
qual = GetSourceQualTypeByName(val);
if (qual < 0) {
Message (MSG_ERROR, "%s is not a recognized source field name", val);
} else {
qc = ValNodeNew (NULL);
qc->choice = SourceQualChoice_textqual;
qc->data.intvalue = qual;
ValNodeAddPointer (&field_list, FieldType_source_qual, qc);
}
*comma = ',';
val = comma + 1;
comma = StringChr (val, ',');
}
qual = GetSourceQualTypeByName(val);
if (qual < 0) {
Message (MSG_ERROR, "%s is not a recognized source field name", val);
} else {
qc = ValNodeNew (NULL);
qc->choice = SourceQualChoice_textqual;
qc->data.intvalue = qual;
ValNodeAddPointer (&field_list, FieldType_source_qual, qc);
}
cpy = MemFree (cpy);
return field_list;
}
static void DoNewFastaDefline (
BioseqPtr bsp,
Pointer userdata
)
{
BioseqSetPtr bssp;
CSpeedFlagPtr cfp;
Char id [128];
CharPtr title;
if (bsp == NULL) return;
cfp = (CSpeedFlagPtr) userdata;
if (cfp == NULL) return;
if (StringChr (cfp->skip, 's') != NULL) {
if (bsp->idx.parenttype == OBJ_BIOSEQSET) {
bssp = (BioseqSetPtr) bsp->idx.parentptr;
if (bssp != NULL) {
if (bssp->_class == BioseqseqSet_class_segset ||
bssp->_class == BioseqseqSet_class_parts) return;
}
}
}
if (StringChr (cfp->skip, 'v') != NULL) {
if (bsp->repr == Seq_repr_virtual) return;
}
id [0] = '\0';
SeqIdWrite (bsp->id, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
title = NewCreateDefLine (NULL, bsp, FALSE, FALSE);
if (StringHasNoText (title)) {
title = StringSave ("?");
}
if (cfp->ofp != NULL) {
fprintf (cfp->ofp, ">%s %s\n", id, title);
}
MemFree (title);
}
static void PrintFeatureMessage (SeqFeatPtr sfp, ScanDataPtr sdp,
CharPtr prefix, CharPtr suffix)
{
BioseqPtr bsp;
Char buf [41];
if (sfp == NULL || sdp == NULL || prefix == NULL) return;
bsp = BioseqFindFromSeqLoc (sfp->location);
if (bsp != NULL) {
SeqIdWrite (bsp->id, buf, PRINTID_FASTA_LONG, sizeof (buf));
fprintf (sdp->fp, "%s - %s", prefix, buf);
} else {
fprintf (sdp->fp, "%s - %s", prefix, sdp->buf);
}
if (! StringHasNoText (suffix)) {
fprintf (sdp->fp, " - %s", suffix);
}
fprintf (sdp->fp, "\n");
}
static Boolean OkToReplaceId (SeqIdPairPtr pair, CharPtr seq_str, char *has_errors)
{
Boolean rval = FALSE;
SeqEntryPtr fetched_sep, old_scope;
BioseqPtr bsp_replace;
if (StringHasNoText (seq_str)) {
rval = FALSE;
}
if (pair == NULL || pair->sip_replace == NULL) {
rval = FALSE;
} else if ((fetched_sep = FetchRead (pair->sip_replace)) == NULL) {
rval = FALSE;
ReportInvalidReplacement (pair->sip_replace, "Unable to fetch far sequence", has_errors);
} else {
old_scope = SeqEntrySetScope (fetched_sep);
bsp_replace = BioseqFind (pair->sip_replace);
SeqEntrySetScope (old_scope);
if (bsp_replace == NULL) {
rval = FALSE;
ReportInvalidReplacement (pair->sip_replace, "Unable to locate far sequence after fetch", has_errors);
} else if (DoesSeqStringMatchBsp (seq_str, bsp_replace, Seq_strand_plus)) {
/* matches */
rval = TRUE;
pair->ti = GetTraceIDFromIdList (bsp_replace->id);
} else if (DoesSeqStringMatchBsp (seq_str, bsp_replace, Seq_strand_minus)) {
/* matches on complement */
pair->is_complement = TRUE;
rval = TRUE;
pair->ti = GetTraceIDFromIdList (bsp_replace->id);
} else {
/* later, are we going to try to find trim lengths? */
rval = FALSE;
ReportInvalidReplacement (pair->sip_replace, "Replacement does not match local", has_errors);
}
SeqEntryFree (fetched_sep);
}
return rval;
}
static void DoThesis (PubdescPtr pdp, Pointer userdata)
{
CitBookPtr cbp;
Char ch;
ScanDataPtr sdp;
CharPtr title, tmp;
ValNodePtr ttl, vnp;
if (pdp == NULL) return;
for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
if (vnp->choice == PUB_Man) {
cbp = (CitBookPtr) vnp->data.ptrvalue;
if (cbp != NULL) {
ttl = cbp->title;
if (ttl != NULL) {
title = (CharPtr) ttl->data.ptrvalue;
if (! StringHasNoText (title)) {
if (StringLen (title) > 3) {
ch = *title;
if (IS_LOWER (ch)) {
tmp = title;
ch = *tmp;
while (ch != '\0' && (! (IS_WHITESP (ch)))) {
tmp++;
ch = *tmp;
}
*tmp = '\0';
sdp = (ScanDataPtr) userdata;
RecordThesis (sdp, title);
}
}
}
}
}
}
}
}
static FieldRulePtr FieldRuleFromTagString (CharPtr str)
{
FieldRulePtr rule;
CharPtr tmp;
if (StringHasNoText (str)) {
return NULL;
}
rule = FieldRuleNew ();
rule->field_name = ExtractTagListColumn (str, COMMENTRULEEDIT_FIELDNAME_COLUMN);
rule->match_expression = ExtractTagListColumn (str, COMMENTRULEEDIT_MATCH_COLUMN);
tmp = ExtractTagListColumn (str, COMMENTRULEEDIT_REQUIRED_COLUMN);
if (tmp != NULL && atoi (tmp) > 0) {
rule->required = TRUE;
} else {
rule->required = FALSE;
}
tmp = MemFree (tmp);
return rule;
}
static void DoFastaComp (
BioseqPtr bsp,
Pointer userdata,
Boolean ignoreExisting
)
{
Char buf [4096];
CSpeedFlagPtr cfp;
Char id [128];
CharPtr title;
if (bsp == NULL) return;
cfp = (CSpeedFlagPtr) userdata;
if (cfp == NULL) return;
id [0] = '\0';
SeqIdWrite (bsp->id, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
buf [0] = '\0';
CreateDefLineExEx (NULL, bsp, buf, sizeof (buf) - 1, 0,
NULL, NULL, ignoreExisting, FALSE);
title = NewCreateDefLine (NULL, bsp, ignoreExisting, FALSE);
if (StringHasNoText (title)) {
title = StringSave ("?");
}
if (StringCmp (buf, title) != 0) {
if (cfp->ofp != NULL) {
fprintf (cfp->ofp, "< %s %s\n", id, buf);
fprintf (cfp->ofp, "> %s %s\n", id, title);
}
printf ("< %s %s\n", id, buf);
printf ("> %s %s\n", id, title);
fflush (stdout);
}
MemFree (title);
}
static Boolean ValidateContigReadId (TContigReadPtr read, char *has_errors)
{
SeqIdPairData pair;
Char id_buf[255];
Boolean rval = TRUE;
if (read == NULL || StringHasNoText (read->read_id)) {
rval = FALSE;
} else if (!read->local) {
rval = TRUE;
} else {
pair.sip_find = NULL;
pair.is_complement = FALSE;
pair.is_consensus = FALSE;
pair.trim3 = 0;
pair.trim5 = 0;
pair.sip_replace = MakeSeqID (read->read_id);
pair.ti = 0;
if (OkToReplaceId (&pair, read->read_seq, has_errors)) {
if (pair.is_complement && !read->is_complement) {
read->is_complement = TRUE;
} else if (!pair.is_complement && read->is_complement) {
read->is_complement = FALSE;
}
if (pair.ti > 0) {
read->ti = pair.ti;
} else {
SeqIdWrite (pair.sip_replace, id_buf, PRINTID_FASTA_LONG, sizeof (id_buf) - 1);
free (read->read_id);
read->read_id = malloc (sizeof (Char) * (StringLen (id_buf) + 1));
sprintf (read->read_id, "%s", id_buf);
}
read->local = FALSE;
}
pair.sip_replace = SeqIdFree (pair.sip_replace);
}
return rval;
}
extern void PopulateHelpDoc (
DoC d,
CharPtr filename
)
{
FonT fnt;
FILE *fp;
Char path [PATH_MAX];
if (d == NULL || StringHasNoText (filename)) return;
fp = OpenAFile (filename, path);
if (fp == NULL) return;
FileClose (fp);
#ifdef WIN_MSWIN
fnt = systemFont;
#else
fnt = programFont;
#endif
DisplayFancy (d, path, &helpParFmt, &helpColFmt, fnt, 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;
}
