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0c4c37d5
Commit
0c4c37d5
authored
Feb 22, 2016
by
Celine Mercier
1
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The fasta parser should not have unrecognized characters anymore
parent
fa22ffb4
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2 changed files
with
47 additions
and
41 deletions
+47
-41
fasta_header_parser.c
libfasta/fasta_header_parser.c
+45
-39
fasta_header_parser.l
libfasta/fasta_header_parser.l
+2
-2
No files found.
libfasta/fasta_header_parser.c
View file @
0c4c37d5
...
...
@@ -27,7 +27,7 @@
#define FLEX_SCANNER
#define YY_FLEX_MAJOR_VERSION 2
#define YY_FLEX_MINOR_VERSION 5
#define YY_FLEX_SUBMINOR_VERSION 3
7
#define YY_FLEX_SUBMINOR_VERSION 3
5
#if YY_FLEX_SUBMINOR_VERSION > 0
#define FLEX_BETA
#endif
...
...
@@ -65,6 +65,7 @@ typedef int16_t flex_int16_t;
typedef
uint16_t
flex_uint16_t
;
typedef
int32_t
flex_int32_t
;
typedef
uint32_t
flex_uint32_t
;
typedef
uint64_t
flex_uint64_t
;
#else
typedef
signed
char
flex_int8_t
;
typedef
short
int
flex_int16_t
;
...
...
@@ -72,6 +73,7 @@ typedef int flex_int32_t;
typedef
unsigned
char
flex_uint8_t
;
typedef
unsigned
short
int
flex_uint16_t
;
typedef
unsigned
int
flex_uint32_t
;
#endif
/* ! C99 */
/* Limits of integral types. */
#ifndef INT8_MIN
...
...
@@ -102,8 +104,6 @@ typedef unsigned int flex_uint32_t;
#define UINT32_MAX (4294967295U)
#endif
#endif
/* ! C99 */
#endif
/* ! FLEXINT_H */
#ifdef __cplusplus
...
...
@@ -374,7 +374,7 @@ static void yy_fatal_error (yyconst char msg[] );
*/
#define YY_DO_BEFORE_ACTION \
(yytext_ptr) = yy_bp; \
header_yyleng = (size_t) (yy_cp - yy_bp); \
header_yyleng = (
yy_
size_t) (yy_cp - yy_bp); \
(yy_hold_char) = *yy_cp; \
*yy_cp = '\0'; \
(yy_c_buf_p) = yy_cp;
...
...
@@ -390,9 +390,9 @@ struct yy_trans_info
};
static
yyconst
flex_int16_t
yy_accept
[
29
]
=
{
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
13
,
1
2
,
3
,
2
,
1
,
5
,
4
,
7
,
6
,
9
,
8
,
10
,
11
,
3
,
2
,
5
,
4
,
9
,
8
,
0
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
13
,
2
,
3
,
1
,
12
,
4
,
5
,
7
,
6
,
8
,
9
,
10
,
11
,
2
,
3
,
4
,
5
,
8
,
9
,
0
}
;
static
yyconst
flex_int32_t
yy_ec
[
256
]
=
...
...
@@ -400,17 +400,17 @@ static yyconst flex_int32_t yy_ec[256] =
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
2
,
1
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1
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1
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,
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,
1
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3
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3
,
3
,
3
,
1
,
3
,
3
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3
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1
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6
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1
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1
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1
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1
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1
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6
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1
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1
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1
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1
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,
...
...
@@ -429,38 +429,38 @@ static yyconst flex_int32_t yy_ec[256] =
static
yyconst
flex_int32_t
yy_meta
[
7
]
=
{
0
,
1
,
2
,
3
,
4
,
4
,
1
1
,
2
,
3
,
3
,
4
,
4
}
;
static
yyconst
flex_int16_t
yy_base
[
35
]
=
{
0
,
0
,
0
,
2
2
,
21
,
6
,
0
,
12
,
0
,
26
,
29
,
0
,
0
,
29
,
0
,
0
,
29
,
29
,
0
,
0
,
29
,
29
,
0
,
0
,
0
,
0
,
0
,
0
,
29
,
23
,
16
,
2
2
,
20
,
20
,
18
0
,
0
,
2
3
,
22
,
6
,
0
,
12
,
0
,
26
,
0
,
0
,
29
,
29
,
0
,
0
,
29
,
29
,
0
,
0
,
29
,
29
,
0
,
0
,
0
,
0
,
0
,
0
,
29
,
18
,
23
,
2
3
,
21
,
21
,
18
}
;
static
yyconst
flex_int16_t
yy_def
[
35
]
=
{
0
,
28
,
1
,
1
,
1
,
28
,
5
,
28
,
7
,
28
,
2
8
,
29
,
30
,
28
,
31
,
32
,
28
,
28
,
33
,
34
,
28
,
28
,
1
,
1
,
1
,
28
,
5
,
28
,
7
,
28
,
2
9
,
30
,
28
,
28
,
31
,
32
,
28
,
28
,
33
,
34
,
28
,
28
,
29
,
30
,
31
,
32
,
33
,
34
,
0
,
28
,
28
,
28
,
28
,
28
,
28
}
;
static
yyconst
flex_int16_t
yy_nxt
[
36
]
=
{
0
,
10
,
11
,
1
2
,
12
,
12
,
13
,
10
,
14
,
15
,
16
,
1
7
,
10
,
10
,
18
,
19
,
20
,
21
,
10
,
23
,
23
,
2
7
,
26
,
25
,
24
,
22
,
28
,
10
,
10
,
9
,
28
,
10
,
11
,
1
0
,
10
,
12
,
13
,
14
,
15
,
16
,
17
,
1
3
,
13
,
18
,
19
,
20
,
21
,
13
,
13
,
22
,
27
,
2
2
,
26
,
25
,
24
,
23
,
28
,
13
,
13
,
9
,
28
,
28
,
28
,
28
,
28
,
28
}
;
static
yyconst
flex_int16_t
yy_chk
[
36
]
=
{
0
,
1
,
1
,
1
,
1
,
1
,
1
,
5
,
5
,
5
,
5
,
5
,
5
,
7
,
7
,
7
,
7
,
7
,
7
,
30
,
30
,
34
,
33
,
32
,
31
,
29
,
9
,
4
,
3
,
28
,
28
,
5
,
5
,
7
,
7
,
7
,
7
,
7
,
7
,
29
,
34
,
29
,
33
,
32
,
31
,
30
,
9
,
4
,
3
,
28
,
28
,
28
,
28
,
28
,
28
,
28
}
;
...
...
@@ -590,7 +590,7 @@ static int input (void );
/* This used to be an fputs(), but since the string might contain NUL's,
* we now use fwrite().
*/
#define ECHO
do { if (fwrite( header_yytext, header_yyleng, 1, header_yyout )) {} } while (0
)
#define ECHO
fwrite( header_yytext, header_yyleng, 1, header_yyout
)
#endif
/* Gets input and stuffs it into "buf". number of characters read, or YY_NULL,
...
...
@@ -601,7 +601,7 @@ static int input (void );
if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \
{ \
int c = '*'; \
size_t n; \
yy_
size_t n; \
for ( n = 0; n < max_size && \
(c = getc( header_yyin )) != EOF && c != '\n'; ++n ) \
buf[n] = (char) c; \
...
...
@@ -784,6 +784,7 @@ YY_RULE_SETUP
}
YY_BREAK
case
2
:
/* rule 2 can match eol */
YY_RULE_SETUP
#line 45 "fasta_header_parser.l"
{
...
...
@@ -808,6 +809,7 @@ YY_RULE_SETUP
}
YY_BREAK
case
4
:
/* rule 4 can match eol */
YY_RULE_SETUP
#line 64 "fasta_header_parser.l"
{
...
...
@@ -846,6 +848,7 @@ YY_RULE_SETUP
}
YY_BREAK
case
8
:
/* rule 8 can match eol */
YY_RULE_SETUP
#line 90 "fasta_header_parser.l"
{
...
...
@@ -911,7 +914,7 @@ YY_RULE_SETUP
#line 136 "fasta_header_parser.l"
ECHO
;
YY_BREAK
#line 91
5
"<stdout>"
#line 91
8
"<stdout>"
case
YY_STATE_EOF
(
INITIAL
):
case
YY_STATE_EOF
(
REGID
):
yyterminate
();
...
...
@@ -1105,7 +1108,7 @@ static int yy_get_next_buffer (void)
{
/* Not enough room in the buffer - grow it. */
/* just a shorter name for the current buffer */
YY_BUFFER_STATE
b
=
YY_CURRENT_BUFFER
_LVALUE
;
YY_BUFFER_STATE
b
=
YY_CURRENT_BUFFER
;
int
yy_c_buf_p_offset
=
(
int
)
((
yy_c_buf_p
)
-
b
->
yy_ch_buf
);
...
...
@@ -1326,7 +1329,7 @@ static int yy_get_next_buffer (void)
case
EOB_ACT_END_OF_FILE
:
{
if
(
header_yywrap
(
)
)
return
EOF
;
return
0
;
if
(
!
(
yy_did_buffer_switch_on_eof
)
)
YY_NEW_FILE
;
...
...
@@ -1462,6 +1465,10 @@ static void header_yy_load_buffer_state (void)
header_yyfree
((
void
*
)
b
);
}
#ifndef __cplusplus
extern
int
isatty
(
int
);
#endif
/* __cplusplus */
/* Initializes or reinitializes a buffer.
* This function is sometimes called more than once on the same buffer,
* such as during a header_yyrestart() or at EOF.
...
...
@@ -1666,8 +1673,8 @@ YY_BUFFER_STATE header_yy_scan_string (yyconst char * yystr )
/** Setup the input buffer state to scan the given bytes. The next call to header_yylex() will
* scan from a @e copy of @a bytes.
* @param
yy
bytes the byte buffer to scan
* @param
_yybytes_
len the number of bytes in the buffer pointed to by @a bytes.
* @param bytes the byte buffer to scan
* @param len the number of bytes in the buffer pointed to by @a bytes.
*
* @return the newly allocated buffer state object.
*/
...
...
@@ -1675,8 +1682,7 @@ YY_BUFFER_STATE header_yy_scan_bytes (yyconst char * yybytes, yy_size_t _yybyt
{
YY_BUFFER_STATE
b
;
char
*
buf
;
yy_size_t
n
;
int
i
;
yy_size_t
n
,
i
;
/* Get memory for full buffer, including space for trailing EOB's. */
n
=
_yybytes_len
+
2
;
...
...
libfasta/fasta_header_parser.l
View file @
0c4c37d5
...
...
@@ -21,8 +21,8 @@
%}
WORD
[[:alnum:]:\-.{},'_()\#\[\]\|\&\"\'\/\%\+
]+
WORDID
[[:alnum:]:\-.{},'_()\#\[\]\|\&\"\'\/\%\+=;
]+
WORD
[^>\\n[:blank:]=;
]+
WORDID
[^>\\n[:blank:]
]+
SUP >
EOL \n
SEP ;
...
...
Celine Mercier
@mercier
mentioned in issue
sumaclust#1 (closed)
Feb 22, 2016
mentioned in issue
sumaclust#1 (closed)
mentioned in issue obitools/sumaclust#1
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