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;
}
}
/***************************************************************************
* CkQualSeqaa:
* -- format (seq:"codon-sequence", aa:amino_acid)
* -- example /codon=(seq:"ttt",aa:Leu)
* /codon=(seq: "ttt", aa: Leu )
* 6-29-93
***************************************************************************/
NLM_EXTERN int CkQualSeqaa (GBQualPtr PNTR head_gbqp, GBQualPtr gbqp,
GBQualPtr preq,
Boolean error_msgs, Boolean perform_corrections)
{
CharPtr eptr, str, aa;
int retval = GB_FEAT_ERR_NONE;
str = gbqp->val;
if (StringNICmp(str, "(seq:", 5) == 0) {
str += 5;
while (*str == ' ')
++str;
if ((eptr = StringChr(str, ',')) != NULL) {
while (str != eptr)
str++;
while (*str != '\0' && (*str == ',' || *str == ' '))
str++;
if (StringNICmp(str, "aa:", 3) == 0) {
str += 3;
while (*str == ' ')
++str;
if ((eptr = StringChr(str, ')')) != NULL) {
aa = TextSave(str, eptr-str);
retval = CkQualPosSeqaa(head_gbqp, gbqp, preq,
error_msgs, perform_corrections, aa, eptr);
}
} /* if, aa: */ else{
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_AA,
"Missing aa: /%s=%s",gbqp->qual,gbqp->val);
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
}else{
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_SeqPosComma,
"Missing \',\' /%s=%s",gbqp->qual,gbqp->val);
/* ) match */
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
} /* if, (seq: */ else {
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_Seq,
"Missing (seq: /%s=%s",gbqp->qual,gbqp->val);
/* ) match */
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
return retval;
} /* CkQualSeqaa */
/***************************************************************************
* CkQualPosaa:
*
* -- format (pos:base_range, aa:amino_acid)
* -- example /anticodon=(pos:34..36,aa:Phe)
* /anticodon=(pos: 34..36, aa: Phe)
* 10-12-93
****************************************************************************/
NLM_EXTERN int CkQualPosaa(GBQualPtr PNTR head_gbqp, GBQualPtr gbqp,
GBQualPtr preq,
Boolean error_msgs, Boolean perform_corrections)
{
CharPtr eptr, str, aa = NULL;
int retval = GB_FEAT_ERR_NONE;
str = gbqp->val;
if (StringNICmp(str, "(pos:", 5) == 0) {
str += 5;
while (*str == ' ')
++str;
/*---I expect that we maight need to allow blanks here,
but not now... -Karl 1/28/94 */
if ((eptr = StringChr(str, ',')) != NULL) {
while (str != eptr && (IS_DIGIT(*str) || *str == '.'))
str++;
if (str == eptr) {
while (*str != '\0' && (*str == ',' || *str == ' '))
str++;
if (StringNICmp(str, "aa:", 3) == 0) {
str += 3;
while (*str == ' ')
++str;
if ((eptr = StringChr(str, ')')) != NULL) {
aa = TextSave(str, eptr-str);
retval = CkQualPosSeqaa(head_gbqp, gbqp, preq,
error_msgs, perform_corrections, aa, eptr);
}
} /* if, aa: */ else{
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_AA,
"Missing aa: /%s=%s",gbqp->qual,gbqp->val);
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
}
}else{
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_SeqPosComma,
"Missing \',\' /%s=%s",gbqp->qual,gbqp->val);
/* ) match */
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
} /* if, (pos: */ else{
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_Pos,
"Missing (pos: /%s=%s",gbqp->qual,gbqp->val);
/* ) match */
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
return retval;
} /* CkQualPosaa */
/***************************************************************************
* CkQualSite:
* -- format (5'site:boolean, 3'site:boolean)
* -- example /cons_splice=(5'site:YES, 3'site:NO)
* 6-29-93
***************************************************************************/
NLM_EXTERN int CkQualSite ( GBQualPtr PNTR head_gbqp, GBQualPtr gbqp,
GBQualPtr preq,
Boolean error_msgs, Boolean perform_corrections )
{
int retval = GB_FEAT_ERR_NONE;
CharPtr bptr, str;
Boolean ok=FALSE;
CharPtr yes_or_no = "not \'YES\', \'NO\' or \'ABSENT\'";
str = gbqp->val;
if (StringNICmp(str, "(5'site:", 8) == 0) {
bptr = str;
str += 8;
if (StringNICmp(str, "YES", 3) == 0 || StringNICmp(str, "NO", 2) == 0 ||
StringNICmp(str, "ABSENT", 6) == 0) {
if (StringNICmp(str, "YES", 3) == 0)
str += 3;
else if (StringNICmp(str, "NO", 2) == 0)
str += 2;
else
str += 6;
for (; *str == ' '; str++);
for (; *str == ','; str++);
for (; *str == ' '; str++);
if (StringNICmp(str, "3'site:", 7) == 0) {
str += 7;
if (StringNICmp(str, "YES", 3) == 0 ||
StringNICmp(str, "NO", 2) == 0 ||
StringNICmp(str, "ABSENT", 6) == 0) {
if (StringNICmp(str, "YES", 3) == 0)
str += 3;
else if (StringNICmp(str, "NO", 2) == 0)
str += 2;
else
str += 6;
if (*str == ')') {
while (*str != '\0' && (*str == ' ' || *str == ')'))
str++;
if (*str == '\0')
ok=TRUE;
else {
bptr = "extra characters";
}
} /* if, ")" */ else{
}
} /* if, yes or no */ else{
bptr = yes_or_no;
}
} /* if, 3'site */ else{
bptr="3\' site";
}
} /* if, yes or no */else {
bptr = yes_or_no;
}
} /* if, 5'site */else {
bptr="5\' site";
}
if (! ok){
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_Cons_splice,
"%s /%s=%s", bptr, gbqp->qual,gbqp->val);
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
return retval;
} /* CkQualSite */
static Boolean LIBCALLBACK FirstVecScreenCallback (
CONN conn,
Nlm_VoidPtr userdata,
EIO_Status status
)
{
VQueuePtr cqp;
FILE *fp;
Char line [256];
Char path [PATH_MAX];
CharPtr rid;
CharPtr rtoe;
CharPtr str;
long int val;
/* read rID or failure message */
cqp = (VQueuePtr) userdata;
TmpNam (path);
fp = FileOpen (path, "w");
QUERY_CopyResultsToFile (conn, fp);
FileClose (fp);
fp = FileOpen (path, "r");
str = ReadALine (line, sizeof (line), fp);
while (str != NULL) {
if (! StringHasNoText (line)) {
if (line [0] == '>') {
if (StringNICmp (line, ">Vector", 7) == 0) {
rid = StringStr (line, "RID: ");
if (rid != NULL) {
rid += 5;
rtoe = StringStr (rid, " RTOE: ");
if (rtoe != NULL) {
*rtoe = '\0';
rtoe += 7;
StringNCpy_0 (cqp->rid, rid, sizeof (cqp->rid));
if (sscanf (rtoe, "%ld", &val) == 1) {
cqp->estTime = (time_t) val;
cqp->secondsToWait = (Int2) val + 2;
} else {
cqp->secondsToWait = 15;
}
if (cqp->secondsToWait > 15) {
cqp->secondsToWait = 15;
}
if (cqp->announceproc != NULL) {
cqp->announceproc (rid, cqp->seqid, (Int2) val);
}
}
} else if (StringStr (line, "FAILED") != NULL) {
cqp->done = TRUE;
if (cqp->resultproc != NULL) {
cqp->resultproc (NULL, cqp->userdata, cqp->rid, cqp->seqid, FALSE);
}
}
} else if (StringNICmp (line, ">Message", 8) == 0) {
str = ReadALine (line, sizeof (line), fp);
while (str != NULL && StringNCmp (line, "//", 2) != 0) {
Message (MSG_POST, "%s\n", str);
if (StringStr (line, "FAILURE") != NULL) {
cqp->done = TRUE;
}
str = ReadALine (line, sizeof (line), fp);
}
}
}
}
str = ReadALine (line, sizeof (line), fp);
}
FileClose (fp);
FileRemove (path);
return TRUE;
}
static Boolean LIBCALLBACK SecondVecScreenCallback (
CONN conn,
Nlm_VoidPtr userdata,
EIO_Status status
)
{
VQueuePtr cqp;
FILE *fp;
Char line [256];
Char path [PATH_MAX];
CharPtr rid;
CharPtr sttus;
CharPtr str;
Boolean success = FALSE;
Boolean waiting = FALSE;
/* look for waiting, failure, or success */
cqp = (VQueuePtr) userdata;
TmpNam (path);
fp = FileOpen (path, "w");
QUERY_CopyResultsToFile (conn, fp);
FileClose (fp);
fp = FileOpen (path, "r");
str = ReadALine (line, sizeof (line), fp);
while (str != NULL) {
if (! StringHasNoText (line)) {
if (line [0] == '>') {
if (StringNICmp (line, ">Vector", 7) == 0) {
rid = StringStr (line, "RID: ");
if (rid != NULL) {
rid += 5;
sttus = StringStr (rid, " Status: ");
if (sttus != NULL) {
*sttus = '\0';
sttus += 9;
if (StringCmp (cqp->rid, rid) != 0) {
ErrPostEx (SEV_ERROR, 0, 0, "RID mismatch '%s' vs '%s'", cqp->rid, rid);
cqp->done = TRUE;
} else if (StringStr (sttus, "FAILED") != NULL) {
cqp->done = TRUE;
} else if (StringStr (sttus, "unknown") != NULL) {
ErrPostEx (SEV_ERROR, 0, 0, "RID unknown '%s'", rid);
cqp->done = TRUE;
} else if (StringStr (sttus, "SUCCESS") != NULL) {
success = TRUE;
} else if (StringStr (sttus, "WAITING") != NULL) {
waiting = TRUE;
/*
Message (MSG_POST, "WAITING");
*/
}
}
}
} else if (StringNICmp (line, ">Message", 8) == 0) {
str = ReadALine (line, sizeof (line), fp);
while (str != NULL && StringNCmp (line, "//", 2) != 0) {
Message (MSG_POST, "%s\n", str);
if (StringStr (line, "FAILURE") != NULL) {
if (! waiting) {
cqp->done = TRUE;
}
}
str = ReadALine (line, sizeof (line), fp);
}
}
}
}
str = ReadALine (line, sizeof (line), fp);
}
FileClose (fp);
if (success) {
cqp->resultproc (path, cqp->userdata, cqp->rid, cqp->seqid, success);
cqp->done = TRUE;
} else if (cqp->done) {
cqp->resultproc (NULL, cqp->userdata, cqp->rid, cqp->seqid, success);
}
FileRemove (path);
return TRUE;
}
