/****************************************************************************
* ConvertEmbedQual:
* -- convert the '/' characters at the start of the embedded-qualifier
* token to '_'
* 12-20-93
*****************************************************************************/
NLM_EXTERN void ConvertEmbedQual(CharPtr value)
{
CharPtr bptr, ptr, qualname, slash;
Int2 val;
if (value != NULL) {
for (bptr = value; *bptr != '\0';) {
for (;*bptr != '/' && *bptr != '\0'; bptr++)
continue;
if (*bptr == '/') {
for (slash = bptr, ++bptr, ptr = bptr; *bptr != '=' && *bptr != ' '
&& *bptr != '\0'; bptr++)
continue;
qualname = TextSave(ptr, bptr-ptr);
val = GBQualNameValid(qualname);
if (val >= 0)
*slash = '_';
MemFree(qualname);
}
} /* for */
}
} /* ConvertEmbedQual */
/****************************************************************************
* ScanEmbedQual:
* -- retun NULL if no embedded qualifiers found; otherwise, return the
* embedded qualifier.
* -- scan embedded valid qualifier
* 6-29-93
*****************************************************************************/
NLM_EXTERN CharPtr ScanEmbedQual(CharPtr value)
{
CharPtr bptr, ptr, qual;
Int2 val;
if (value != NULL) {
for (bptr = value; *bptr != '\0';) {
for (;*bptr != '/' && *bptr != '\0'; bptr++)
continue;
if (*bptr == '/') {
for (++bptr, ptr = bptr; *bptr != '=' && *bptr != ' '
&& *bptr != '\0'; bptr++)
continue;
qual = TextSave(ptr, bptr-ptr);
val = GBQualNameValid(qual);
if (val >= 0)
return (qual);
MemFree(qual);
}
} /* for */
}
return (NULL);
} /* ScanEmbedQual */
/*****************************************************************************
* CkQualMatchToken:
* 6-29-93
*****************************************************************************/
NLM_EXTERN int CkQualMatchToken
(GBQualPtr PNTR head_gbqp, GBQualPtr gbqp,
GBQualPtr preq,
Boolean error_msgs, Boolean perform_corrections, CharPtr array_string[],
Int2 totalstr)
{
CharPtr msg=NULL, bptr, eptr, str;
int retval = GB_FEAT_ERR_NONE;
if(gbqp->val == NULL) {
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_InvalidDataFormat,
"NULL value for (%s)", gbqp->qual);
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
return retval;
}
str = gbqp->val;
for (bptr = str; *str != '\0' && *str != ' '; str++)
continue;
eptr = str;
while (*str != '\0' && *str == ' ')
str++;
if (*str == '\0') {
msg = TextSave(bptr, eptr-bptr);
if (MatchArrayStringIcase(array_string, totalstr, msg) == -1) {
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_InvalidDataFormat,
"Value not in list of legal values /%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_Too_many_tokens,
"/%s=%s", gbqp->qual,gbqp->val);
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
MemFree(msg);
return retval;
} /* CkQualMatchToken */
/***************************************************************************
* 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 */
/***************************************************************************
* CkQualText:
* -- return error severity
* -- also check if embedded qualifier
* -- format "text"
* if called from /note, ="" will cause qualifier to be dropped.
* all others no error, all other, if no qualifier, will add "" value
****************************************************************************/
NLM_EXTERN int CkQualText (GBQualPtr PNTR head_gbqp, GBQualPtr gbqp,
GBQualPtr preq,
Boolean PNTR has_embedded, Boolean from_note, Boolean error_msgs,
Boolean perform_corrections)
{
CharPtr value=NULL, bptr, eptr, str;
int retval = GB_FEAT_ERR_NONE;
if (has_embedded != NULL){
*has_embedded = FALSE;
}
if (gbqp->val == NULL) {
if (from_note){
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_EmptyNote,
"/note with no text ");
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
return retval;
} else {
retval = GB_FEAT_ERR_SILENT;
if (perform_corrections){
gbqp ->val = StringSave("\"\""); /* yup, a "" string is legal */
} else {
return retval;
}
}
}
str = gbqp->val;
while (*str != '\0' && (*str == ' ' || *str == '\"')){
/* open double quote */
str++;
if (*(str-1) == '\"'){
break; /* so does not continue through a "" string */
}
}
/* find first close double quote */
for (bptr = str; *str != '\0' && *str != '\"'; str++)
continue;
eptr = str;
while (*str != '\0' && (*str == ' ' || *str == '\"'))
str++;
if (*str != '\0'){
/* extra stuff is already rm in ParseQualifiers(). Tatiana*/
/* extra stuff, if perform corrections, remove it */
/* ERROR here sets retval*/
}
value = TextSave(bptr, eptr-bptr);
/* Some check must be done for illegal characters in gbpq->val
for (s = value; *s != '\0'; s++) {
if (!IS_WHITESP(*s) && !IS_ALPHANUM(*s) && *s != '\"') {
if (error_msgs){
ErrPostEx(SEV_WARNING, ERR_QUALIFIER_IllegalCharacter,
"illegal char [%c] used in qualifier %s", s, gbqp ->qual);
}
return (retval > GB_FEAT_ERR_REPAIRABLE) ? retval :
GB_FEAT_ERR_REPAIRABLE;
}
}
*/
/* only finds first embedded qualifier */
if (value != NULL && ((bptr = ScanEmbedQual(value)) != NULL)) {
if (has_embedded != NULL) {
*has_embedded = TRUE;
}
MemFree(value);
MemFree(bptr);
if (from_note){
if (error_msgs){
ErrPostEx(SEV_WARNING, ERR_QUALIFIER_NoteEmbeddedQual,
"/note with embedded qualifiers %s", gbqp ->val);
}
return (retval > GB_FEAT_ERR_REPAIRABLE) ? retval :
GB_FEAT_ERR_REPAIRABLE;
}else{
if (error_msgs){
ErrPostEx(SEV_WARNING, ERR_QUALIFIER_EmbeddedQual,
"/%s with embedded qualifiers %s",
gbqp -> qual, gbqp ->val);
}
return retval;
}
/* This needs to be discussed some!, not sure -Karl 1/28/94 */
}
MemFree(value);
return retval;
} /* CkQualText */
/***************************************************************************
* 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 */
/***************************************************************************
* SplitMultiValQual:
*
*
****************************************************************************/
NLM_EXTERN int SplitMultiValQual(GBQualPtr PNTR gbqp,
Boolean error_msgs, Boolean perform_corrections)
{
Int2 val/*, len -- UNUSED */;
GBQualPtr next_q, curq, preq = NULL, first_q, tmp;
int retval = GB_FEAT_ERR_NONE;
CharPtr bptr, ptr, buf;
for (first_q = curq = *gbqp; curq != NULL; curq = next_q) {
next_q = curq -> next; /* in case deleted */
val = GBQualSplit(curq->qual);
/* len = StringLen(curq->qual); -- NO EFFECT */
if (val == -1) {
preq = curq;
continue;
}
bptr = curq->val;
if (bptr == NULL) {
preq = curq;
continue;
}
if (*bptr != '(') {
preq = curq;
continue;
}
if (*(bptr+StringLen(bptr)-1) != ')') {
preq = curq;
continue;
}
*(bptr+StringLen(bptr)-1) = '\0';
if ((ptr = StringChr(bptr, ',')) == NULL) {
StringCpy(bptr, bptr+1);
preq = curq;
continue;
}
ErrPostEx(SEV_WARNING, ERR_QUALIFIER_MultiValue,
"Splited qualifier %s", curq->qual);
buf = bptr;
bptr++;
curq->val = TextSave(bptr, ptr-bptr);
bptr = ptr + 1;
curq->next = NULL;
while ((ptr = StringChr(bptr, ',')) != NULL) {
tmp = GBQualNew();
tmp->qual = StringSave(curq->qual);
tmp->val = TextSave(bptr, ptr-bptr);
curq = tie_qual(curq, tmp);
bptr = ptr + 1;
}
tmp = GBQualNew();
tmp->qual = StringSave(curq->qual);
tmp->val = StringSave(bptr);
curq = tie_qual(curq, tmp);
tmp->next = next_q;
curq = tmp;
MemFree(buf);
if (preq){
/*---- we have retained a qualifier, previously ----*/
if (preq -> next != next_q){
/*-- did not delete curq ----*/
preq = curq;
}
}else {
/* ---- no qualifier previously retained, is there a new head pointer? */
if (first_q == *gbqp){
/* ---- we have kept our first qualifier */
preq = curq;
}else{
/*--- we deleted the head of the queue, record current first qualifier */
first_q = *gbqp;
}
}
if (*gbqp == NULL){
break; /* was one, is gone */
}
}
return retval;
} /* SplitMultiValQual */
/***************************************************************************
* CkQualTokenType:
* -- format single token
* -- example ParFlat_Stoken_type /label=Albl_exonl /mod_base=m5c
* ParFlat_BracketInt_type /citation=[3] or /citation= ([1],[3])
* ParFlat_Integer_type /transl_table=4
* ParFlat_Number_type /number=4b
* -- not implemented yet, treat as ParFlat_Stoken_type:
* -- feature_label or base_range
* /rpt_unit=Alu_rpt1 /rpt_unit=202..245
* -- Accession-number:feature-name or
* Database_name:Acc_number:feature_label
* /usedin=X10087:proteinx
* 10-12-93
***************************************************************************/
NLM_EXTERN int CkQualTokenType (GBQualPtr PNTR head_gbqp, GBQualPtr gbqp,
GBQualPtr preq,
Boolean error_msgs, Boolean perform_corrections, Uint1 type)
{
CharPtr token = NULL, bptr, eptr, str;
Boolean token_there = FALSE;
int retval = GB_FEAT_ERR_NONE;
str = gbqp->val;
if (str != NULL)
if (*str != '\0'){
token_there = TRUE;
}
if (! token_there) {
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_InvalidDataFormat,
"Missing value /%s=...",gbqp->qual);
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}else{
/* token there */
for (bptr = str; *str != '\0' && *str != ' '; str++)
continue;
eptr = str;
while (*str != '\0' && *str == ' ')
str++;
if (*str == '\0') {
/*------single token found ----*/
token = TextSave(bptr, eptr-bptr);
bptr = token;
switch (type) {
case ParFlat_BracketInt_type:
/*-------this can be made to be much more rigorous --Karl ---*/
str = CkBracketType(token);
break;
case ParFlat_Integer_type:
for (str = token; *str != '\0' && IS_DIGIT(*str); str++)
continue;
if (*str == '\0') {
str = NULL;
}
break;
case ParFlat_Stoken_type:
str = CkLabelType(token);
break;
case ParFlat_Number_type:
str = CkNumberType(token);
break;
default:
str = NULL;
break;
}
if (str != NULL) {
switch (type) {
case ParFlat_BracketInt_type:
bptr = "Invalid [integer] format";
break;
case ParFlat_Integer_type:
bptr = "Not an integer number";
break;
case ParFlat_Stoken_type:
bptr = "Invalid format";
break;
/*-- logically can not happen, as coded now -Karl 1/31/94 --*/
default: bptr = "Bad qualifier value";
break;
}
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_InvalidDataFormat,
"%s=%s, at %s", gbqp->qual,gbqp->val, str);
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
} else{
/*-- more than a single token found ---*/
if (error_msgs){
ErrPostEx(SEV_ERROR, ERR_QUALIFIER_Xtratext,
"extra text found /%s=%s, at %s",gbqp->qual,gbqp->val, str);
}
retval = GB_FEAT_ERR_DROP;
if (perform_corrections){
DeleteGBQualFromList(head_gbqp, gbqp, preq);
}
}
} /* token there */
MemFree(token);
return retval;
} /* CkQualTokenType */
void menu()
{
exit_menu = 0;
uint8_t menu,regreso,opcion=0,continue_menu=0;
while(exit_menu ==0)
{
regreso =0;
clrscr();
gotoxy(0x01,0x01);
UART0_putsf(MenuOp);
menu = UART0_getch();
switch (menu)
{
case 'a': /*Mensaje de marquesina */
{
clrscr();
UART0_putsf(SubMenuOp1);
gotoxy(6,10);
TextSave(TEXT_ADDRESS);
exit_menu =0;
break;
}
case 'b': /*Ajuste de Reloj*/
{
clrscr();
gotoxy(0x01,0x01);
UART0_putsf(SubMenuOp2);
opcion = 0;
while(opcion == 0)
{
if( Timer2_Flag ())
{
gotoxy(0x06,0x06);
Clock_Update();
Clock_Display();
}
if(UART0_kbhit() == 0x0D)
{
clrscr();
gotoxy(0x01,0x01);
UART0_putsf(SubMenuOp2a);
gotoxy(0x06,0x06);
config_clock();
clrscr();
gotoxy(0x01,0x01);
UART0_putsf(SubMenuOp2);
opcion = 0;
}
if(UART0_kbhit() == 0x1B)
{
opcion = 1;
}
} /* ajuste(hr:min) (mostrar reloj actual) */
exit_menu =0;
break;
}
case 'c':
{
exit_menu =1;
clrscr();
break;/*Salir */
}
default:
{
exit_menu =0;
break;
}
}
}
if(continue_menu == 1)
{
clrscr();
}
}
