/*****************************************************************************
*
* int AsnBufGetWordBreak(str, maxlen)
* return length (<= maxlen) of str to next white space
*
*****************************************************************************/
static size_t LIBCALL AsnBufGetWordBreak (CharPtr str, size_t stringlen, size_t maxlen)
{
register CharPtr tmp;
register size_t len;
if (stringlen <= maxlen)
return stringlen;
tmp = str + maxlen; /* point just PAST the end of region */
len = maxlen + 1;
while ((len) && (! IS_WHITESP(*tmp)))
{
len--;
tmp--;
}
while ((len) && (IS_WHITESP(*tmp)))
{
len--; /* move past white space */
tmp--;
}
if (len < 1) /* never found any whitespace or only 1 space */
len = maxlen; /* have to break a word */
return len;
}
static CharPtr get_token(CharPtr str, CharPtr token)
{
int i;
token[2]= '\0';
while(IS_WHITESP(*str)) {
if(*str == '\0') return NULL;
++str;
}
if(*str == '\0') return NULL;
for(i= 1; i < 250; i++) {
if(IS_WHITESP(*str)) {
token[i]= ' ';
token[i+1]= '\0';
return str;
}
if(*str == '\0') {
token[i]= ' ';
token[i+1]= '\0';
return NULL;
}
token[i]= TO_UPPER(*str);
str++;
}
token[i]= ' ';
token[i+1]= '*';
token[i+2]= '\0';
return str;
}
NLM_EXTERN size_t Nlm_stream2text(const Nlm_Char FAR PNTR str, size_t max_col,
int PNTR dash)
{
const Nlm_Char FAR PNTR s;
const Nlm_Char FAR PNTR sb; /* the nearest breakable position */
size_t n_lead = 0;
size_t n_tail = 0;
size_t len = Nlm_StringLen( str );
len = max_col < len ? max_col : len;
*dash = 0;
if (len == 0 || can_break(str[len-1], str[len]))
return len;
/* go to the beginning of the last completely fit word */
for (sb = &str[len-1];
sb != str && !IS_WHITESP(*sb) && !can_break(*sb, *(sb+1));
sb--) continue;
while (sb != str && IS_WHITESP(*sb))
sb--;
if (sb == str)
{ /* the first word is longer than "max_col" */
if (len > MAX_NO_DASH && IS_ALPHA(str[len-1]) && IS_ALPHA(str[len]))
*dash = 1; /* recommend use dash in the place of last symbol */
return len;
}
/* decide of whether and how to break the last alphabet word */
/* count the lead and the tail of the last non-fit word */
for (s = &str[len]; *s != '\0' && IS_ALPHA(*s); s++, n_tail++) continue;
for (s = &str[len-1]; IS_ALPHA(*s); s--, n_lead++) continue;
ASSERT ( s > str );
/* try to "move" symbols from lead in the sake of tail */
while (n_lead > MIN_LEAD && n_tail < MIN_TAIL) {
n_lead--;
n_tail++;
}
if (n_lead < MIN_LEAD || n_tail < MIN_TAIL)
{ /* no luck this time -- move the whole non-fit word to the next line */
return (sb - str + 1);
}
else
{
*dash = 1;
return (s - str + n_lead + 1);
}
}
NLM_EXTERN Nlm_CharPtr LIBCALL Nlm_text2stream(const Nlm_Char FAR PNTR str)
{
int on_space = 0;
Nlm_CharPtr line, s;
if ( !str )
return NULL;
while (*str && IS_WHITESP( *str ))
str++;
if ( !*str )
return NULL;
s = line = (Nlm_CharPtr) Nlm_MemNew(Nlm_StringLen(str) + 1);
for ( ; *str; str++)
{
if ( IS_WHITESP(*str) )
{
if (*str == '\n')
*s = '\n';
on_space = 1;
}
else
{
if ( on_space ) {
if (*s == '\n' &&
s - line > 1 && *(s-1) == '-' && IS_ALPHA(*(s-2)))
{
*s = '\0';
s--; /* eat dash before end-of-line, merge the broken word */
}
else
*s++ = SPACE;
*s++ = *str;
on_space = 0;
}
else
*s++ = *str;
}
}
*s = '\0';
return (Nlm_CharPtr) realloc(line, Nlm_StringLen(line) + 1);
}
/* Set of conditions when the decision on the line breaking can be
* made having only 2 symbols("ch0" and "ch1" -- to the left and to the
* right of the break, respectively)
*/
static int can_break(Nlm_Char ch0, Nlm_Char ch1)
{
if (ch1 == '\0' ||
IS_WHITESP(ch1) || IS_WHITESP(ch0))
return 1;
switch ( ch1 )
{
case '(':
case '[':
case '{':
return 1;
}
switch ( ch0 )
{
case '-':
case '+':
case '=':
case '&':
case '|':
case ')':
case '}':
case ']':
if (ch1 != ch0)
return 1;
break;
case '\\':
case '/':
case '*':
case ';':
case ':':
case ',':
return 1;
case '?':
case '!':
case '.':
if (ch1 != '.' && ch1 != '?' && ch1 != '!')
return 1;
break;
}
return 0;
}
static Nlm_Uint8 s_StringToUint8(const char *str, const char **endptr, int *sgn)
{
int sign = 0; /* actual sign */
Nlm_Uint8 limdiv, limoff, result;
const char *s, *save;
char c;
/* assume error */
*endptr = 0;
if (!str)
return 0;
s = str;
while (IS_WHITESP(*s))
s++;
/* empty string - error */
if (*s == '\0')
return 0;
if (*sgn == 1) {
if (*s == '-') {
sign = 1;
s++;
} else if (*s == '+') {
s++;
}
}
save = s;
limdiv = UINT8_MAX / 10;
limoff = UINT8_MAX % 10;
result = 0;
for (c = *s; c; c = *++s) {
if (!IS_DIGIT(c)) {
break;
}
c -= '0';
if (result > limdiv || (result == limdiv && c > limoff)) {
/* overflow */
return 0;
}
result *= 10;
result += c;
}
/* there was no conversion - error */
if (save == s)
return 0;
*sgn = sign;
*endptr = s;
return result;
}
/* Act like a regular memcpy but replace all space symbols to #SPACE
*/
static void x_memcpy(Nlm_Char FAR PNTR targ, const Nlm_Char FAR PNTR src,
size_t n)
{
for ( ; n--; src++)
{
ASSERT ( *src );
if ( IS_WHITESP(*src) )
*targ++ = SPACE;
else
*targ++ = *src;
}
}
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;
}
}
/*****************************************************************************
*
* Int4 AsnTypeStringToHex(from, len, to, left)
* converts an octet string to binary
* returns number of hex digits created if all ok
* *left is chars left at the end of the buffer including first letter of
* a remaining digit (from does not have an even number of letters)
* since this could include white space, could be more than 1
* returns a negative number on an error
* skips over internal or trailing white space
* left can be NULL in which case it is ignored
*
*****************************************************************************/
NLM_EXTERN Int4 LIBCALL AsnTypeStringToHex (Pointer from, Int4 len, Pointer to, Int4Ptr left)
{
BytePtr f, t;
Byte octet = 0, value;
int i;
Int4 added = 0;
f = (BytePtr) from;
t = (BytePtr) to;
if (left != NULL)
*left = 0;
i = 16;
while (len)
{
if (! IS_WHITESP(*f)) /* skip spaces */
{
if (i == 16) /* first letter of pair */
{
octet = 0;
if (left != NULL)
*left = len; /* point at it in case one letter left */
}
value = TO_UPPER(*f);
if ((value >= 'A') && (value <= 'F'))
octet += (((value - 'A') + 10) * i);
else if ((value >= '0') && (value <= '9'))
octet += ((value - '0') * i);
else
return (Int4)(-1);
if (i == 16) /* first letter of pair */
i = 1; /* goto second letter */
else /* letter pair was read */
{
i = 16; /* reset for first letter */
if (left != NULL)
*left = 0; /* nothing left so far */
*t = octet; /* record the hex digit */
t++; added++;
}
}
len--;
f++;
}
return added;
}
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 Int2 AsnLexWordEx (AsnIoPtr aip, Uint1 fix_non_print)
{
register CharPtr pos;
Int1 state;
Int2 token;
register int linepos, len;
int done;
if (aip->tagsaved) /* had to read ahead */
{
aip->tagsaved = FALSE;
return aip->token;
}
if (! aip->bytes) /* no data loaded */
AsnIoGets(aip);
linepos = aip->linepos;
pos = aip->linebuf + linepos;
state = aip->state;
len = 0;
while (*pos == '\n' || *pos == '\r') /* skip empty lines */
{
pos = AsnIoGets(aip); /* get a line */
if (pos == NULL)
return EOF_TOKEN;
}
if (state == IN_STRING_STATE)
{
aip->word = pos;
if ((* pos == '\"') && (*(pos + 1) != '\"')) /* end of string */
{
token = END_STRING;
pos++;
state = 0; /* reset state */
}
else
{
token = IN_STRING;
while ((* pos != '\"') && (* pos != '\n') && (* pos != '\r'))
{
if ((fix_non_print != 2) && ((*pos < ' ') || (*pos > '~')))
{
done = (int)(*pos);
*pos = '\0';
if ((fix_non_print == 0) || (fix_non_print == 3))
{
AsnIoErrorMsg(aip, 106, done, aip->word);
}
done = 0;
*pos = '#'; /* replace with # */
}
pos++; len++;
}
if ((*pos != '\n') && (*pos != '\r') && (* (pos + 1) == '\"')) /* internal quote */
{
len++; /* include in previous string */
pos += 2; /* point to rest of string */
}
}
}
else if (state == IN_BITHEX_STATE)
{
aip->word = pos;
if (*pos == '\'') /* end of binhex */
{
state = 0; /* set to normal */
pos++; /* move past quote */
while (IS_WHITESP(*pos))
{
if (*pos == '\n' || *pos == '\r') /* skip empty lines */
{
pos = AsnIoGets(aip); /* get a line */
if (pos == NULL)
return EOF_TOKEN;
}
else
pos++;
}
if (* pos == 'H')
token = OCTETS;
else if (* pos == 'B')
token = ASNBITS;
else
{
AsnIoErrorMsg(aip, 58, aip->linenumber);
token = ERROR_TOKEN;
}
pos++; /* move past H or B */
}
else
{
token = IN_BITHEX;
while ((* pos != '\'') && (* pos != '\n') && (* pos != '\r'))
{
pos++; len++;
}
}
}
else /* normal scanning */
{
while ((* pos <= ' ') || ((*pos == '-') && (*(pos+1) == '-'))) /* skip leading white space */
{
if (*pos == '\n' || *pos == '\r')
{
pos = AsnIoGets(aip);
if (pos == NULL)
return EOF_TOKEN;
}
else if ((*pos == '-') && (*(pos+1) == '-')) /* skip comments */
{
pos += 2;
done = 0;
while (! done)
{
if ((*pos == '-') && (*(pos +1) == '-'))
{
pos += 2;
done = 1;
}
else if (*pos == '\n' || *pos == '\r')
done = 1;
else
pos++;
}
}
else
pos++;
}
aip->word = pos;
if (* pos == '\"')
{
token = START_STRING;
state = IN_STRING_STATE;
}
else if (* pos == '\'')
{
token = START_BITHEX;
state = IN_BITHEX_STATE;
}
else if (* pos == ',')
token = COMMA;
else if (* pos == '{')
token = START_STRUCT;
else if (* pos == '}')
token = END_STRUCT;
else if (* pos == '[')
token = START_TAG;
else if (* pos == ']')
token = END_TAG;
else if (* pos == '(')
token = OPEN_PAREN;
else if (* pos == ')')
token = CLOSE_PAREN;
else if (* pos == ';')
token = SEMI_COLON;
else if (* pos == ':')
{
if ((*(pos + 1) == ':') && (*(pos + 2) == '='))
{
token = ISDEF;
pos += 2;
len = 3;
}
else
{
AsnIoErrorMsg(aip, 59, *pos, aip->linenumber);
token = ERROR_TOKEN;
}
}
else if (IS_UPPER(*pos)) /* a reference or keyword */
{
token = REF;
while ((IS_ALPHANUM(*pos)) || (*pos == '-'))
{
pos++; len++;
}
pos--; /* move back for increment at end */
len--;
}
else if (IS_LOWER(*pos)) /* an identifier or valuereference */
{
token = IDENT;
while ((IS_ALPHANUM(*pos)) || (*pos == '-'))
{
pos++; len++;
}
pos--; /* move back for increment at end */
len--;
}
else if ((IS_DIGIT(*pos)) || ((*pos == '-') && (IS_DIGIT(*(pos+1)))))
{
token = NUMBER;
if (*pos == '-')
{
pos++; len++;
}
while (IS_DIGIT(*pos))
{
pos++; len++;
}
pos--; /* move back for increment at end */
len--;
}
else
{
AsnIoErrorMsg(aip, 59, *pos, aip->linenumber);
token = ERROR_TOKEN;
}
len++; pos++; /* move over last symbol */
}
aip->linepos = pos - aip->linebuf;
/******************** check on MSWIN
linepos = 0;
while (pos != linebuf)
{
linepos++;
pos++;
}
aip->linepos = linepos;
**********************/
aip->state = state;
aip->wordlen = len;
aip->token = token;
return token;
}
static OtherLineInfoPtr s_ParseOtherLine (CharPtr lineStr)
{
Char ch;
CharPtr otherStr;
Int4 otherPosition;
Int4 position;
Int2 state;
Int4 wordCount;
OtherLineInfoPtr otherLinePtr;
/* Parse the line character by character */
otherStr = (CharPtr) MemNew (StringLen(lineStr)+1);
otherPosition = 0;
state = OTHER_PRE_DATA;
wordCount = 0;
for (position = 0; lineStr[position] != '\0'; position++)
{
ch = lineStr[position];
switch (state)
{
case OTHER_PRE_DATA :
if (IS_WHITESP(ch))
continue;
else
{
wordCount = 1;
state = OTHER_DATA;
otherStr[otherPosition] = ch;
otherPosition++;
}
break;
case OTHER_DATA :
if (IS_WHITESP(ch))
wordCount++;
otherStr[otherPosition] = ch;
otherPosition++;
break;
default:
break;
}
}
/* Check for blank line */
if (state == OTHER_PRE_DATA)
{
MemFree(otherStr);
return NULL;
}
/* If we made it to here, then */
/* it's a valid definition line. */
otherStr[otherPosition] = '\0';
otherLinePtr = (OtherLineInfoPtr) MemNew (sizeof (OtherLineInfo));
if ((wordCount == 1) && IsValidId(otherStr))
{
otherLinePtr->id = otherStr;
otherLinePtr->other = NULL;
}
else
{
otherLinePtr->id = NULL;
otherLinePtr->other = otherStr;
}
/* Return successfully */
return otherLinePtr;
}
NLM_EXTERN Nlm_CharPtr LIBCALL Nlm_rule_line(const Nlm_Char FAR PNTR str,
size_t len,
enumRuleLine method)
{
size_t str_len;
size_t n_space;
/* allocate and initialize the resulting string */
Nlm_CharPtr s = (Nlm_CharPtr) Nlm_MemNew(len + 1);
Nlm_MemSet(s, SPACE, len);
s[len] = '\0';
/* skip leading and trailing spaces */
while ( IS_WHITESP(*str) )
str++;
if ( !*str )
return s;
for (str_len = Nlm_StringLen( str ); IS_WHITESP(str[str_len-1]); str_len--) continue;
/* truncate the original string if doesn't fit */
if (len <= str_len) {
x_memcpy(s, str, len);
return s;
}
n_space = len - str_len;
switch ( method )
{
case RL_Left:
{
x_memcpy(s, str, str_len);
break;
}
case RL_Right:
{
x_memcpy(s + n_space, str, str_len);
break;
}
case RL_Spread:
{
size_t n_gap = 0;
int prev_space = 0;
const Nlm_Char FAR PNTR _str = str;
size_t i = str_len;
for ( ; i--; _str++)
{
ASSERT ( *_str );
if ( IS_WHITESP(*_str) )
{
if ( !prev_space ) {
n_gap++;
prev_space = 1;
}
n_space++;
}
else
prev_space = 0;
}
ASSERT ( !prev_space );
if ( n_gap )
{
size_t n_div = n_space / n_gap;
size_t n_mod = n_space % n_gap;
Nlm_CharPtr _s = s;
for (_str = str; *_str; )
{
if ( !IS_WHITESP( *_str ) )
*_s++ = *_str++;
else if ( n_space )
{
size_t n_add = n_div;
if (n_mod > 0) {
n_add++;
n_mod--;
}
n_space -= n_add;
while ( n_add-- )
*_s++ = SPACE;
for (_str++; IS_WHITESP(*_str); _str++) continue;
}
else
break;
}
ASSERT ( _s == s + len );
break;
} /* else -- use RL_Center */
}
case RL_Center:
{
x_memcpy(s + n_space/2, str, str_len);
break;
}
default:
ASSERT ( 0 );
Nlm_MemFree( s );
return 0;
}
return s;
}
static SeqLineInfoPtr s_ParseSequenceLine (CharPtr lineStr,
AliConfigInfoPtr configPtr)
{
CharPtr seqStr;
Int4 seqPosition = 0;
CharPtr idStr;
Int4 idPosition = 0;
Int4 firstWordLen = 0;
Char ch;
Int2 state = PRE_DATA;
Int4 position;
Boolean firstWordNotSequence = FALSE;
Boolean sequenceFound = FALSE;
CharPtr tempStr;
Boolean corruptSequence = FALSE;
SeqLineInfoPtr seqLinePtr;
if (StringLen(lineStr) == 0)
return NULL;
seqStr = (CharPtr) MemNew (StringLen(lineStr)+1);
idStr = (CharPtr) MemNew (StringLen(lineStr)+1);
for (position = 0; lineStr[position] != '\0'; position++)
{
ch = lineStr[position];
switch (state)
{
case PRE_DATA :
/* If it's the first non-whitespace char */
/* then we've found our first word. */
if (!IS_WHITESP(ch))
{
state = FIRST_WORD;
if (!IsSequenceChar(ch,
configPtr->gapChar,
configPtr->missingChar,
configPtr->unalignedChar))
firstWordNotSequence = TRUE;
idStr[idPosition] = ch;
idPosition++;
firstWordLen++;
}
break;
case FIRST_WORD :
if (IS_WHITESP(ch))
{
state = SEQUENCE_DATA;
if ((idPosition > 0) &&
(firstWordNotSequence == FALSE))
{
tempStr = seqStr;
seqStr = idStr;
idStr = tempStr;
seqPosition = idPosition;
idPosition = 0;
sequenceFound = TRUE;
}
}
else
{
/* If we find a non-sequence char in the */
/* first word then it might be an ID, */
/* with the sequence following. */
if (!IsSequenceChar(ch,
configPtr->gapChar,
configPtr->missingChar,
configPtr->unalignedChar))
firstWordNotSequence = TRUE;
idStr[idPosition] = ch;
idPosition++;
firstWordLen++;
}
break;
case SEQUENCE_DATA :
if (IS_WHITESP(ch))
continue;
/* If we're in a sequence, then a non-sequence */
/* char invalidates it, although we do allow */
/* 'junk' at the end. */
if (!IsSequenceChar(ch,
configPtr->gapChar,
configPtr->missingChar,
configPtr->unalignedChar))
{
if ((lineStr[position - 1] == ' ') && sequenceFound)
state = EOL_JUNK;
else if ((corruptSequence == TRUE) ||
(s_MightBeCorruptSequence (seqPosition,
&(lineStr[position]),
configPtr)))
{
seqStr[seqPosition] = ch;
seqPosition++;
sequenceFound = TRUE;
corruptSequence = TRUE;
}
else
{
MemFree(seqStr);
MemFree(idStr);
return NULL;
}
}
else
{
seqStr[seqPosition] = ch;
seqPosition++;
sequenceFound = TRUE;
}
break;
case EOL_JUNK :
if (IS_WHITESP(ch))
state = POST_JUNK;
break;
case POST_JUNK :
/* Only one 'word' of junk allowed */
if (!IS_WHITESP(ch))
{
MemFree(seqStr);
MemFree(idStr);
return NULL;
}
break;
}
}
/* Check for blank line */
if (state == PRE_DATA)
{
MemFree(seqStr);
MemFree(idStr);
return NULL;
}
if (state == FIRST_WORD)
{
/* If there was just one word, and it isn't */
/* a sequence string, then this isn't a */
/* sequence line. */
if (firstWordNotSequence == TRUE)
{
MemFree(seqStr);
MemFree(idStr);
return NULL;
}
/* If there was just one word, and it IS a sequence */
/* then the idStr is actually the seqStr. */
else
{
tempStr = seqStr;
seqStr = idStr;
idStr = tempStr;
seqPosition = idPosition;
idPosition = 0;
}
}
/* If still no sequence string, */
/* then not a sequence line. */
if (StringLen(seqStr) == 0)
{
MemFree(seqStr);
MemFree(idStr);
return NULL;
}
/* Check to see if the ID is a valid one */
idStr[idPosition] = '\0';
seqStr[seqPosition] = '\0';
if ((idPosition > 0) &&
(IsValidId (idStr) == FALSE) &&
(IsNumString (idStr) == FALSE))
{
MemFree(idStr);
MemFree(seqStr);
return NULL;
}
/* If we made it to here, then */
/* it's a valid sequence line. */
seqLinePtr = (SeqLineInfoPtr) MemNew (sizeof (SeqLineInfo));
seqLinePtr->firstWordLen = firstWordLen;
if (StringLen (seqStr) != 0)
seqLinePtr->sequence = seqStr;
else
{
seqLinePtr->sequence = NULL;
MemFree (seqStr);
}
if (StringLen (idStr) != 0)
seqLinePtr->id = idStr;
else
{
seqLinePtr->id = NULL;
MemFree (idStr);
}
if (corruptSequence)
seqLinePtr->maybe = TRUE;
else
seqLinePtr->maybe = FALSE;
return seqLinePtr;
}
static DefLineInfoPtr s_ParseDefLine (CharPtr lineStr,
Int4 rowNum,
ErrInfoPtr PNTR errorListPtr)
{
Char ch;
CharPtr defStr;
CharPtr idStr;
Int4 defPosition;
Int4 idPosition;
Int4 position;
Int2 state;
DefLineInfoPtr defLinePtr = NULL;
ErrInfoPtr errPtr;
defPosition = 0;
idPosition = 0;
defStr = (CharPtr) MemNew (StringLen(lineStr)+1);
idStr = (CharPtr) MemNew (StringLen(lineStr)+1);
/* Parse the line character by character */
state = DEFLINE_PRE_DATA;
for (position = 0; lineStr[position] != '\0'; position++)
{
ch = lineStr[position];
switch (state)
{
case DEFLINE_PRE_DATA :
if (IS_WHITESP(ch))
continue;
else if (ch == '>')
state = DEFLINE_SEQID;
else
{
MemFree(defStr);
MemFree(idStr);
return NULL; /* Not a defline */
}
break;
case DEFLINE_SEQID :
if (IsValidIdChar(ch))
{
idStr[idPosition] = ch;
idPosition++;
}
else if (IS_WHITESP(ch))
{
if (idPosition > 0)
{
state = DEFLINE_DEFINITION;
defStr[defPosition] = ch;
defPosition++;
}
else
continue;
}
else if (ch == '[')
{
state = DEFLINE_DEFINITION;
defStr[defPosition] = ch;
defPosition++;
}
else
{
errPtr = Ali_AddError (errorListPtr, ERR_INVALID_DEFLINE,
lineStr, (Int4) ch);
errPtr->rowNum = rowNum;
MemFree(defStr);
MemFree(idStr);
return NULL;
}
break;
case DEFLINE_DEFINITION :
defStr[defPosition] = ch;
defPosition++;
break;
default:
break;
}
}
/* Check for blank line */
if (state == DEFLINE_PRE_DATA)
{
MemFree(defStr);
MemFree(idStr);
return NULL;
}
idStr[idPosition] = '\0';
defStr[defPosition] = '\0';
/* Make sure that it has at least one */
/* set of square brackets. */
if ((StringChr(defStr,'[') == NULL) || (StringChr(defStr,']') == NULL))
{
errPtr = Ali_AddError (errorListPtr, ERR_DEFLINE_NODEFS, lineStr);
errPtr->rowNum = rowNum;
}
/* If we made it to here, then */
/* it's a valid definition line. */
defLinePtr = (DefLineInfoPtr) MemNew (sizeof (DefLineInfo));
if (StringLen (defStr) != 0)
defLinePtr->definitions = defStr;
else
defLinePtr->definitions = NULL;
if (StringLen (idStr) != 0)
defLinePtr->id = idStr;
else
defLinePtr->id = NULL;
return defLinePtr;
}
Nlm_Int2 Nlm_Main( void )
{
#define MAX_COL 24
Nlm_Int4 argc = Nlm_GetArgc();
Nlm_CharPtr *argv = Nlm_GetArgv();
Nlm_Char x_str[MAX_COL * 1024];
FILE *fp = NULL;
int n_read;
FILE *logfile = Nlm_FileOpen("stdout", "w");
ASSERT ( logfile );
if (argc < 2) {
fprintf(logfile, "Usage: %s <file_name>\n", argv[0]);
return 1;
}
fp = Nlm_FileOpen(argv[1], "rb");
if ( !fp ) {
fprintf(logfile, "Cannot open file: \"%s\"\n", argv[1]);
return 2;
}
n_read = FileRead(x_str, 1, sizeof(x_str) - 1, fp);
if (n_read < 2 * MAX_COL) {
fprintf(logfile, "Too few bytes read from \"%s\": %d\n", argv[1], n_read);
return 3;
}
ASSERT ( n_read < sizeof(x_str) );
x_str[n_read] = '\0';
{{
size_t max_col = MAX_COL - 1;
int inc = 1;
enumRuleLine rule_method = RL_Center;
Nlm_CharPtr str = text2stream( x_str );
Nlm_CharPtr text_str = str;
if ( !str ) {
fprintf(logfile, "No non-space symbols in \"%s\"\n", argv[1]);
return 4;
}
while (*str != '\0')
{
Nlm_Char s[MAX_COL + 1];
int dash = -12345;
size_t n_print;
while (*str && IS_WHITESP(*str))
str++;
n_print = stream2text(str, max_col, &dash);
ASSERT ( (max_col > 0 && str && *str) == (n_print > 0) );
ASSERT ( n_print <= max_col );
ASSERT ( dash != -12345 );
Nlm_MemCpy(s, str, n_print);
s[n_print] = '\0';
ASSERT ( dash == 0 || n_print > 1 );
if ( dash )
s[--n_print] = '-';
{{
Nlm_CharPtr ruled_str = rule_line(s,
(rule_method == RL_Right ||
rule_method == RL_Center ) ?
MAX_COL : max_col,
rule_method);
fprintf(logfile, "|%s|\n", ruled_str);
Nlm_MemFree( ruled_str );
}}
str += n_print;
if (max_col == 0 || max_col == MAX_COL)
inc = -inc;
max_col += inc;
if (max_col == 0)
if (rule_method == RL_Spread)
rule_method = RL_Left;
else
rule_method++;
}
Nlm_MemFree( text_str );
}}
Nlm_FileClose( logfile );
Nlm_FileClose( fp );
return 0;
}
/*****************************************************************************
*
* Int2 AsnLexTWord(aip)
* reads words, punctuation, and asn keywords with 2 parts
* returns tokens defined at top
*
*****************************************************************************/
NLM_EXTERN Int2 AsnLexTWord (AsnIoPtr aip)
{
register CharPtr pos;
register int len;
Int1 state;
Int2 token, asntype, linepos;
int done;
Boolean first = FALSE, hitnewline = FALSE;
CharPtr commentptr;
if (! aip->bytes) /* no data loaded */
{
hitnewline = TRUE;
first = TRUE;
AsnIoGets(aip);
}
linepos = aip->linepos;
pos = aip->linebuf + linepos;
state = aip->state;
len = 0;
token = -1;
while (*pos == '\n' || *pos == '\r') /* skip empty lines */
{
hitnewline = TRUE;
pos = AsnIoGets(aip);
if (pos == NULL)
return EOF_TOKEN;
}
if (state == IN_STRING_STATE)
{
aip->word = pos;
if (* pos == '\"') /* end of string */
{
token = END_STRING;
pos++;
state = 0; /* reset state */
}
else
{
token = IN_STRING;
while ((* pos != '\"') && (* pos != '\n') && (* pos != '\r'))
{
pos++; len++;
}
if ((*pos != '\n') && (*pos != '\r') && (* (pos + 1) == '\"')) /* internal quote */
{
len++; /* include in previous string */
pos += 2; /* point to rest of string */
}
}
}
else if (state == IN_BITHEX_STATE)
{
aip->word = pos;
if (*pos == '\'') /* end of binhex */
{
state = 0; /* set to normal */
pos++; /* move past quote */
while (IS_WHITESP(*pos))
pos++;
if (* pos == 'H')
token = OCTETS;
else if (* pos == 'B')
token = ASNBITS;
else
{
AsnIoErrorMsg(aip, 58, aip->linenumber);
token = ERROR_TOKEN;
}
}
else
{
token = IN_BITHEX;
while ((* pos != '\'') && (* pos != '\n') && (* pos != '\r'))
{
pos++; len++;
}
}
}
else /* normal scanning */
{
done = 0;
while (! done)
{
while (* pos <= ' ') /* skip leading white space */
{
if (*pos == '\n' || *pos == '\r')
{
hitnewline = TRUE;
pos = AsnIoGets(aip);
if (pos == NULL)
return EOF_TOKEN;
}
else
pos++;
}
done = 1;
while (done && (*pos == '-') && (*(pos+1) == '-')) /* skip comments */
{
pos += 2;
if (first) /* could be revision */
{
first = FALSE;
if (StrMatch(asnwords[57], pos, 10)) /* $Revision: */
{
token = REVISION_TOKEN;
pos += 10;
while (IS_WHITESP(*pos))
pos++;
aip->word = pos;
while (IS_DIGIT(*pos)) /* eg. 1.2 */
{
len++;
pos++;
}
if (*pos == '.') /* take after . if present */
{
pos++;
len++;
while (IS_DIGIT(*pos))
{
len++;
pos++;
}
}
}
}
commentptr = pos;
done = 0;
while (! done) /* skip to end of comment */
{
if ((*pos == '-') && (*(pos +1) == '-'))
{
if (token != REVISION_TOKEN)
{
AsnLexTAddComment(commentptr, pos, aip);
if ((! hitnewline) && (aip->token != COMMENT_TOKEN))
token = COMMENT_TOKEN;
}
pos += 2;
done = 1;
}
else if (*pos == '\n' || *pos == '\r')
{
if (token != REVISION_TOKEN)
{
AsnLexTAddComment(commentptr, pos, aip);
if ((! hitnewline) && (aip->token != COMMENT_TOKEN))
token = COMMENT_TOKEN;
}
done = 1;
}
else
pos++;
}
if ((token == REVISION_TOKEN) || (token == COMMENT_TOKEN))
{
aip->linepos = pos - aip->linebuf;
aip->state = state;
aip->wordlen = len;
aip->token = token;
return token;
}
if (*pos <= ' ')
done = 0;
else
done = 1;
}
}
aip->word = pos;
if (* pos == '\"')
{
token = START_STRING;
state = IN_STRING_STATE;
}
else if (* pos == '\'')
{
token = START_BITHEX;
state = IN_BITHEX_STATE;
}
else if (* pos == ',')
token = COMMA;
else if (* pos == '{')
token = START_STRUCT;
else if (* pos == '}')
token = END_STRUCT;
else if (* pos == '[')
token = START_TAG;
else if (* pos == ']')
token = END_TAG;
else if (* pos == '(')
token = OPEN_PAREN;
else if (* pos == ')')
token = CLOSE_PAREN;
else if (* pos == ';')
token = SEMI_COLON;
else if (* pos == ':')
{
if ((*(pos + 1) == ':') && (*(pos + 2) == '='))
{
token = ISDEF;
pos += 2;
len = 3;
}
else
{
AsnIoErrorMsg(aip, 59, *pos, aip->linenumber);
token = ERROR_TOKEN;
}
}
else if (IS_UPPER(*pos)) /* a reference or keyword */
{
token = REF;
while ((IS_ALPHANUM(*pos)) || (*pos == '-'))
{
pos++; len++;
}
aip->wordlen = len;
asntype = AsnLexTMatchToken(aip); /* check types */
if (asntype) /* did it match ? */
{
if ((asntype > 27) && (asntype < 57)) /* not a primitive type */
{
token = asntype + 400; /* make a keyword type */
if (asntype == COMPS_TOKEN) /* COMPONENTS OF */
{
if ((*(pos + 1) == 'O') &&
(*(pos + 2) == 'F') &&
(IS_WHITESP(*(pos+3))))
{
pos += 3; /* move past OF */
len += 3;
}
else
AsnIoErrorMsg(aip, 89, aip->linenumber);
}
}
else if (asntype == 57) /* StringStore */
token = STRSTORE_TYPE;
else if (asntype == 59) /* BitInt */
token = BIGINT_TYPE;
else
{
switch (asntype)
{
case 3: /* BIT */
case 4: /* OCTET */
if (! StrMatch(asnwords[11], (pos+1), 6))
AsnIoErrorMsg(aip, 90, aip->linenumber);
pos += 7; /* move past STRING */
len += 7;
break;
case 11: /* SEQUENCE */
case 13: /* SET */
if ((*(pos + 1) == 'O') &&
(*(pos + 2) == 'F'))
{
asntype++; /* SET or SEQ OF */
pos += 3;
len += 3;
if (! IS_WHITESP(*pos))
AsnIoErrorMsg(aip, 91, aip->linenumber);
}
break;
case 6: /* OBJECT */
if ((! StrMatch(asnwords[55], (pos+1), 10))) /* IDENTIFIER */
AsnIoErrorMsg(aip, 92, aip->linenumber);
pos += 11;
len += 11;
break;
default:
break;
}
token = asntype + 300; /* change to point at type */
}
}
pos--; /* move back for increment at end */
len--;
}
else if (IS_LOWER(*pos)) /* an identifier or valuereference */
{
token = IDENT;
while ((IS_ALPHANUM(*pos)) || (*pos == '-'))
{
pos++; len++;
}
pos--; /* move back for increment at end */
len--;
}
else if ((IS_DIGIT(*pos)) || ((*pos == '-') && (IS_DIGIT(*(pos+1)))))
{
token = NUMBER;
if (*pos == '-')
{
pos++; len++;
}
while (IS_DIGIT(*pos))
{
pos++; len++;
}
pos--; /* move back for increment at end */
len--;
}
else
{
AsnIoErrorMsg(aip, 59, *pos, aip->linenumber);
token = ERROR_TOKEN;
}
len++; pos++; /* move over last symbol */
}
aip->linepos = pos - aip->linebuf;
aip->state = state;
aip->wordlen = len;
aip->token = token;
return token;
}
/*****************************************************************************
*
* PubLabelUnique(pubptr, buf, buflen, content, unique)
* makes a short label for any Pub in buf, up to buflen size
* content follows objmgr OM_LABEL_
* if (unique is TRUE, appends a string based on title words to make
* unique key base on ANSI std Z39.56-1991
*
*****************************************************************************/
NLM_EXTERN Int2 LIBCALL PubLabelUnique (ValNodePtr pub, CharPtr buf, Int2 buflen, Uint1 content, Boolean unique)
{
CharPtr typelabel = NULL;
static CharPtr pubtypes [14] = {
"Unknown",
"Generic",
"Submit",
"Medline",
"MUID",
"Article",
"Journal",
"Book",
"Proceedings",
"Patent",
"PatID",
"Manuscript",
"Equiv" ,
"PMID" };
ValNodePtr vnp2=NULL, title=NULL;
Int2 len, diff;
Char tbuf[41];
Boolean first = TRUE;
Int4 muid = 0, pmid = 0;
AuthListPtr alp=NULL;
AuthorPtr ap;
ImprintPtr imp = NULL;
CharPtr year = NULL,
volume = NULL,
issue = NULL,
pages = NULL,
title1=NULL,
title2=NULL,
titleunique = NULL,
part_sup = NULL,
part_supi = NULL;
CitArtPtr cap;
CitJourPtr cjp;
CitBookPtr cbp=NULL;
CitSubPtr csp;
CitPatPtr cpp;
IdPatPtr ipp;
CitGenPtr cgp;
MedlineEntryPtr mep;
DatePtr dp = NULL;
Boolean unpublished = FALSE, done;
ValNodePtr eq[5];
Int2 i;
CharPtr s, cit;
if ((buf == NULL) || (buflen < 1)) return 0;
buf[0] = '?';
buf[1] = '\0';
if (pub == NULL) return 0;
if (pub->choice > 13)
typelabel = pubtypes[0];
else
typelabel = pubtypes[pub->choice];
len = buflen;
if (content == OM_LABEL_TYPE)
return LabelCopy(buf, typelabel, buflen);
if (content == OM_LABEL_BOTH)
{
diff = LabelCopyExtra(buf, typelabel, buflen, NULL, ": ");
buflen -= diff; buf += diff;
}
switch (pub->choice)
{
case PUB_Muid:
sprintf(tbuf, "NLM%ld", (long)(pub->data.intvalue));
diff = LabelCopy(buf, tbuf, buflen);
buflen -= diff;
return (len - buflen); /* already unique */
break;
case PUB_PMid:
sprintf(tbuf, "PM%ld", (long)(pub->data.intvalue));
diff = LabelCopy(buf, tbuf, buflen);
buflen -= diff;
return (len - buflen); /* already unique */
break;
case PUB_Equiv:
for (i = 0; i < 5; i++)
eq[i] = NULL;
i = 0;
for (vnp2 = (ValNodePtr)(pub->data.ptrvalue);
((vnp2 != NULL) && (buflen)); vnp2 = vnp2->next)
{
switch (vnp2->choice)
{
case PUB_Muid:
eq[3] = vnp2;
break;
case PUB_Gen:
cgp = (CitGenPtr)(vnp2->data.ptrvalue);
if (cgp->serial_number > 0)
{
eq[4] = vnp2;
break;
}
default:
if (i < 5)
eq[i] = vnp2;
i++;
break;
}
}
for (i = 0; i < 5; i++)
{
if (eq[i] != NULL)
{
if (! first)
{
diff = LabelCopy(buf, " ", buflen);
buflen -= diff; buf += diff;
}
else
first = FALSE;
diff = PubLabelUnique (eq[i], buf, buflen, OM_LABEL_CONTENT, unique);
buflen -= diff; buf += diff;
}
}
break;
case PUB_Medline:
mep = (MedlineEntryPtr)(pub->data.ptrvalue);
if (mep->pmid > 0)
sprintf(tbuf, "PM%ld", (long)(mep->pmid));
else
sprintf(tbuf, "NLM%ld", (long)(mep->uid));
diff = LabelCopyExtra(buf, tbuf, buflen, NULL, " ");
buflen -= diff; buf += diff;
cap = mep->cit;
goto cit_art;
case PUB_Article:
cap = (CitArtPtr)(pub->data.ptrvalue);
cit_art: alp = cap->authors;
if (cap->title != NULL)
titleunique = (CharPtr)(cap->title->data.ptrvalue);
switch (cap->from)
{
case 1:
cjp = (CitJourPtr)(cap->fromptr);
goto cit_jour;
case 2:
case 3:
cbp = (CitBookPtr)(cap->fromptr);
goto cit_book;
}
break;
case PUB_Journal:
cjp = (CitJourPtr)(pub->data.ptrvalue);
cit_jour: imp = cjp->imp;
title = cjp->title;
break;
case PUB_Book:
case PUB_Proc:
case PUB_Man:
cbp = (CitBookPtr)(pub->data.ptrvalue);
title = cbp->title;
cit_book: imp = cbp->imp;
if (alp == NULL)
alp = cbp->authors;
break;
case PUB_Sub:
csp = (CitSubPtr)(pub->data.ptrvalue);
alp = csp->authors;
imp = csp->imp;
dp = csp->date;
break;
case PUB_Patent:
cpp = (CitPatPtr)(pub->data.ptrvalue);
alp = cpp->authors;
dp = cpp->date_issue;
if (dp == NULL)
dp = cpp->app_date;
title1 = cpp->country;
title2 = cpp->number;
if (title2 == NULL)
title2 = cpp->app_number;
break;
case PUB_Pat_id:
ipp = (IdPatPtr)(pub->data.ptrvalue);
title1 = ipp->country;
title2 = ipp->number;
if (title2 == NULL)
title2 = ipp->app_number;
break;
case PUB_Gen:
cgp = (CitGenPtr)(pub->data.ptrvalue);
if (cgp->serial_number > 0)
{
sprintf(tbuf, "[%d]", (int)(cgp->serial_number));
diff = LabelCopy(buf, tbuf, buflen);
buflen -= diff; buf += diff;
}
if (cgp->muid > 0)
{
sprintf(tbuf, "NLM%ld", (long)(cgp->muid));
diff = LabelCopy(buf, tbuf, buflen);
buflen -= diff; buf += diff;
}
dp = cgp->date;
title = cgp->journal;
alp = cgp->authors;
if (cgp->cit != NULL)
{
if (! StringICmp("Unpublished", cgp->cit))
unpublished = TRUE;
else if (title == NULL)
title2 = cgp->cit;
}
volume = cgp->volume;
issue=cgp->issue;
pages=cgp->pages;
if (cgp->title != NULL)
titleunique = cgp->title;
else if (title2 != NULL)
titleunique = title2;
else if (title == NULL)
titleunique = cgp->cit;
if (title == NULL && alp == NULL && cgp->title == NULL &&
volume == NULL && pages == NULL && issue == NULL) {
titleunique = NULL;
if ((cit = StringSave(cgp->cit)) != NULL) {
if (!unique) {
for (s = cit + StringLen(cit) -1;
s > cit && *s !='|'; s--) continue;
if (*s == '|' ) {
*s = '\0';
}
}
diff = LabelCopy(buf, cit, buflen);
MemFree(cit);
}
return 0;
}
break;
default:
sprintf(tbuf,"Unknown pub[%d]", (int)(pub->choice));
title2 = tbuf;
break;
}
if (imp != NULL)
{
if (dp == NULL)
dp = imp->date;
if (volume == NULL)
volume = imp->volume;
if (issue == NULL)
issue = imp->issue;
if (pages == NULL)
pages = imp->pages;
part_sup = imp->part_sup;
part_supi = imp->part_supi;
}
if (alp != NULL)
{
vnp2 = alp->names;
if (vnp2 != NULL)
{
if (alp->choice == 1) /* std name */
{
ap = (AuthorPtr)(vnp2->data.ptrvalue);
diff = PersonIdLabel(ap->name, buf, buflen, PIDLABEL_GENBANK);
}
else
diff = LabelCopy(buf, (CharPtr)(vnp2->data.ptrvalue), buflen);
buflen -= diff;
buf += diff;
}
}
if (dp != NULL)
{
if (dp->data[0])
{
if (pub->choice == PUB_Sub && dp->data[2] != 0 && dp->data[3] != 0){
sprintf(tbuf, "%d-%d-%d", (int)(dp->data[2]),
(int)(dp->data[3]), (int)(dp->data[1])+1900);
year = tbuf;
} else {
sprintf(tbuf, "%d", (int)(dp->data[1])+1900);
year = tbuf;
}
}
else
year = dp->str;
diff = LabelCopyExtra(buf, year, buflen, " (", ") ");
buflen -= diff; buf += diff;
}
if ((title != NULL) && (titleunique == NULL))
titleunique = (CharPtr)(title->data.ptrvalue);
if (title2 == NULL)
{
if (title != NULL)
title2 = (CharPtr)(title->data.ptrvalue);
}
if (title2 != NULL)
{
if (cbp != NULL)
title1 = "(in) ";
diff = LabelCopyExtra(buf, title2, buflen, title1, " ");
buflen -= diff; buf += diff;
}
if (volume != NULL)
{
if (part_sup != NULL)
title1 = part_sup;
else
title1 = ":";
diff = LabelCopyExtra(buf, volume, buflen, NULL, title1);
buflen -= diff; buf += diff;
if (part_sup != NULL)
{
diff = LabelCopyExtra(buf, ":", buflen, NULL, NULL);
buflen -= diff; buf += diff;
}
}
if (issue != NULL)
{
if (part_supi != NULL)
title1 = part_supi;
else
title1 = ")";
diff = LabelCopyExtra(buf, issue, buflen, "(" , title1);
buflen -= diff; buf += diff;
if (part_supi != NULL)
{
diff = LabelCopyExtra(buf, ")", buflen, NULL, NULL);
buflen -= diff; buf += diff;
}
}
if (pages != NULL)
{
diff = LabelCopy(buf, pages, buflen);
buflen -= diff; buf += diff;
}
if (unpublished)
{
diff = LabelCopy(buf, "Unpublished", buflen);
buflen -= diff; buf += diff;
}
if (unique) /* put on unique tag made from title */
{
done = FALSE;
i=0;
if (titleunique != NULL && *titleunique != '\0')
{
while ((! done) && (i < 40))
{
tbuf[i] = *titleunique;
i++;
while (! IS_WHITESP(*titleunique))
{
titleunique++;
if (*titleunique == '\0')
{
done = TRUE;
break;
}
}
while (IS_WHITESP(*titleunique))
{
titleunique++;
if (*titleunique == '\0')
{
done = TRUE;
break;
}
}
}
}
tbuf[i] = '\0';
diff = LabelCopyExtra(buf, tbuf, buflen, "|" , NULL);
buflen -= diff; buf += diff;
}
return (len - buflen);
}