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schwede
openstructure
Commits
e1aacf96
Commit
e1aacf96
authored
13 years ago
by
Bienchen
Browse files
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Fixes infinite loop problem in the StarParser (BZDNG-298).
parent
a642faca
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Changes
3
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3 changed files
modules/io/src/mol/star_parser.cc
+3
-3
3 additions, 3 deletions
modules/io/src/mol/star_parser.cc
modules/io/tests/test_star_parser.cc
+7
-1
7 additions, 1 deletion
modules/io/tests/test_star_parser.cc
modules/io/tests/testfiles/loop.cif
+3
-2
3 additions, 2 deletions
modules/io/tests/testfiles/loop.cif
with
13 additions
and
6 deletions
modules/io/src/mol/star_parser.cc
+
3
−
3
View file @
e1aacf96
...
@@ -247,7 +247,9 @@ void StarParser::ParseLoop()
...
@@ -247,7 +247,9 @@ void StarParser::ParseLoop()
this
->
ParseMultilineValue
(
s
,
true
);
this
->
ParseMultilineValue
(
s
,
true
);
}
}
break
;
break
;
case
'd'
:
case
'_'
:
return
;
case
'd'
:
if
(
tline
.
length
()
>=
5
&&
StringRef
(
"data_"
,
5
)
==
tline
.
substr
(
0
,
5
))
{
if
(
tline
.
length
()
>=
5
&&
StringRef
(
"data_"
,
5
)
==
tline
.
substr
(
0
,
5
))
{
return
;
return
;
}
}
...
@@ -255,8 +257,6 @@ void StarParser::ParseLoop()
...
@@ -255,8 +257,6 @@ void StarParser::ParseLoop()
if
(
StringRef
(
"loop_"
,
5
)
==
tline
)
{
if
(
StringRef
(
"loop_"
,
5
)
==
tline
)
{
return
;
return
;
}
}
case
'_'
:
return
;
default
:
default
:
if
(
process_rows
)
{
if
(
process_rows
)
{
int
before
=
columns
.
size
();
int
before
=
columns
.
size
();
...
...
This diff is collapsed.
Click to expand it.
modules/io/tests/test_star_parser.cc
+
7
−
1
View file @
e1aacf96
...
@@ -284,10 +284,11 @@ BOOST_AUTO_TEST_CASE(star_multi)
...
@@ -284,10 +284,11 @@ BOOST_AUTO_TEST_CASE(star_multi)
BOOST_AUTO_TEST_CASE
(
star_loop
)
BOOST_AUTO_TEST_CASE
(
star_loop
)
{
{
BOOST_MESSAGE
(
" Running star_loop tests..."
);
std
::
ifstream
s
(
"testfiles/loop.cif"
);
std
::
ifstream
s
(
"testfiles/loop.cif"
);
LoopTestParser
star_p
(
s
);
LoopTestParser
star_p
(
s
);
star_p
.
Parse
();
star_p
.
Parse
();
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
0
][
0
],
"
1
"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
0
][
0
],
"
d
"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
0
][
1
],
"2"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
0
][
1
],
"2"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
0
][
2
],
"3"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
0
][
2
],
"3"
);
...
@@ -306,12 +307,15 @@ BOOST_AUTO_TEST_CASE(star_loop)
...
@@ -306,12 +307,15 @@ BOOST_AUTO_TEST_CASE(star_loop)
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
4
][
0
],
"13"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
4
][
0
],
"13"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
4
][
1
],
"14"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
4
][
1
],
"14"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
4
][
2
],
"15"
);
BOOST_CHECK_EQUAL
(
star_p
.
lines
[
4
][
2
],
"15"
);
BOOST_MESSAGE
(
" done."
);
}
}
BOOST_AUTO_TEST_CASE
(
star_items_as_row
)
BOOST_AUTO_TEST_CASE
(
star_items_as_row
)
{
{
BOOST_MESSAGE
(
" Running star_items_as_row tests..."
);
std
::
ifstream
s
(
"testfiles/items-as-row.cif"
);
std
::
ifstream
s
(
"testfiles/items-as-row.cif"
);
ItemsAsRowTestParser
star_p
(
s
);
ItemsAsRowTestParser
star_p
(
s
);
BOOST_MESSAGE
(
" checking parsing abilities..."
);
star_p
.
Parse
();
star_p
.
Parse
();
BOOST_CHECK_EQUAL
(
star_p
.
s1
,
"a"
);
BOOST_CHECK_EQUAL
(
star_p
.
s1
,
"a"
);
BOOST_CHECK_EQUAL
(
star_p
.
s2
,
"a b c"
);
BOOST_CHECK_EQUAL
(
star_p
.
s2
,
"a b c"
);
...
@@ -330,6 +334,8 @@ BOOST_AUTO_TEST_CASE(star_items_as_row)
...
@@ -330,6 +334,8 @@ BOOST_AUTO_TEST_CASE(star_items_as_row)
BOOST_CHECK_EQUAL
(
star_p
.
s6
,
"1.22"
);
BOOST_CHECK_EQUAL
(
star_p
.
s6
,
"1.22"
);
BOOST_CHECK_EQUAL
(
star_p
.
s7
,
"1.33"
);
BOOST_CHECK_EQUAL
(
star_p
.
s7
,
"1.33"
);
BOOST_CHECK_EQUAL
(
star_p
.
s8
,
"1.44"
);
BOOST_CHECK_EQUAL
(
star_p
.
s8
,
"1.44"
);
BOOST_MESSAGE
(
" done."
);
BOOST_MESSAGE
(
" done."
);
}
}
BOOST_AUTO_TEST_CASE
(
star_missing_data
)
BOOST_AUTO_TEST_CASE
(
star_missing_data
)
...
...
This diff is collapsed.
Click to expand it.
modules/io/tests/testfiles/loop.cif
+
3
−
2
View file @
e1aacf96
...
@@ -4,7 +4,8 @@ loop_
...
@@ -4,7 +4,8 @@ loop_
_loop.s1
_loop.s1
_loop.s2
_loop.s2
_loop.s3
_loop.s3
1 2 3
# the 'd' is needed to test for BZDNG-298
d 2 3
'4 x' 5 6
'4 x' 5 6
7 8
7 8
;
;
...
@@ -17,4 +18,4 @@ _loop.s3
...
@@ -17,4 +18,4 @@ _loop.s3
13
13
;14
;14
;
;
15
15
\ No newline at end of file
This diff is collapsed.
Click to expand it.
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