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move to Test::More
2007-04-12
cjfie
l
ds
move to T
e
st::M
o
re
commit
|
commitdiff
|
tree
2007-04-12
cjfields
Finish M-N (convert to Test:
:
Mo
r
e)
commit
|
commitdiff
|
tree
2007-04-11
cjf
i
elds
Don't forget lu
c
y!
commit
|
commitdiff
|
tree
2007-04-11
cjfie
l
ds
Finish
e
d
L's (move to Test::More)
commit
|
commitdiff
|
tree
2007-04-11
cjfields
convert
to Test::More
commit
|
commitdiff
|
tree
2007-04-11
cjfie
l
ds
c
o
nvert to Test::Mo
r
e
commit
|
commitdiff
|
tree
2007-04-11
cj
f
ields
c
o
n
v
er
t
to Test
:
:M
o
re
commit
|
commitdiff
|
tree
2007-04-11
cjfields
C
o
nvert to Test
:
:
M
o
re
commit
|
commitdiff
|
tree
2007-04-11
cjfields
co
n
vert to Te
s
t
::More
commit
|
commitdiff
|
tree
2007-04-11
cjfields
conv
e
rt t
o
Test::More
commit
|
commitdiff
|
tree
2007-04-11
cjf
i
elds
select
_
n
o
ncont() sorts numerically by default (fixed
.
.
.
commit
|
commitdiff
|
tree
2007-04-11
cjfie
l
ds
bug 226
4
, 2265
commit
|
commitdiff
|
tree
2007-04-05
c
jf
i
elds
b
ug 2263
commit
|
commitdiff
|
tree
2007-04-02
cjfields
wri
t
e
_
s
eq() is no
t
implemented
commit
|
commitdiff
|
tree
2007-04-02
c
j
f
i
e
l
ds
b
u
g 2246
commit
|
commitdiff
|
tree
2007-04-02
cjfields
bug 223
7
commit
|
commitdiff
|
tree
2007-03-30
cjfields
S
m
all bug
which botches s
o
me
repo
r
t p
a
rsing
commit
|
commitdiff
|
tree
2007-03-29
cjfields
F
ix '
.
'
being appended to scientif
i
c_name
commit
|
commitdiff
|
tree
2007-03-28
cj
f
ields
is(), not ok()
commit
|
commitdiff
|
tree
2007-03-27
cj
f
ie
l
ds
reroute data
f
l
ow through data_handler() for centra
l
ized
.
.
.
commit
|
commitdiff
|
tree
2007-03-26
cjfields
pass data in chunk
s
u
s
ing element_h
a
s
h
()
commit
|
commitdiff
|
tree
2007-03-26
cjfie
l
ds
t
ests
c
h
anges and additions
commit
|
commitdiff
|
tree
2007-03-26
c
j
fields
a
d
d warni
n
gs for
unsuppor
t
ed method
s
commit
|
commitdiff
|
tree
2007-03-26
c
jfie
l
d
s
rna
m
otif fi
x
es
commit
|
commitdiff
|
tree
2007-03-26
cjfields
parsing fixe
s
commit
|
commitdiff
|
tree
2007-03-22
cjfields
b
ug 2246 tentati
v
e fix
commit
|
commitdiff
|
tree
2007-03-22
cjfields
bu
g
2245
(
enhanc
e
me
n
t to allo
w
relative
pat
h
s
for in
d
ex
.
.
.
commit
|
commitdiff
|
tree
2007-03-22
cjfie
l
ds
fix som
e
tests
commit
|
commitdiff
|
tree
2007-03-22
cjfields
test
dat
a
for BI
C
tests
commit
|
commitdiff
|
tree
2007-03-21
c
j
fields
R
e
moving red
u
n
da
n
t module;
passes flat
.
t
commit
|
commitdiff
|
tree
2007-03-21
c
j
fi
e
lds
b
ug 224
2
commit
|
commitdiff
|
tree
2007-03-21
cjfield
s
Now passes v3 tests (
a
t least the v3 ou
t
pu
t
we have
.
.
.
)
commit
|
commitdiff
|
tree
2007-03-21
cj
f
ields
Neil &
C
o
.
'
s
modified Signalp parser
(bug 2203) - pa
s
ses
.
.
.
commit
|
commitdiff
|
tree
2007-03-20
c
j
fie
l
d
s
Cha
n
g
ed throw() due to verbose
output from
Infernal
.
.
.
commit
|
commitdiff
|
tree
2007-03-19
cjf
i
eld
s
TargetP parser,
da
t
a, and tests
commit
|
commitdiff
|
tree
2007-03-19
cjfields
bu
g
224
0
commit
|
commitdiff
|
tree
2007-03-16
c
j
fields
getter/setter
for comment type
(
not implem
e
nte
d
yet)
commit
|
commitdiff
|
tree
2007-03-16
cjfields
tes
t
s
(
write_seq()
for driver
s
not implemented yet)
commit
|
commitdiff
|
tree
2007-03-16
cjfie
l
ds
seq format drivers an
d
single ha
n
dler
m
od
u
le for
Ge
n
Bank
.
.
.
commit
|
commitdiff
|
tree
2007-03-16
cjfield
s
Handl
e
r
-
bas
e
d parsing
i
nt
e
rface
commit
|
commitdiff
|
tree
2007-03-15
cjfields
Move to
Test:
:
More
commit
|
commitdiff
|
tree
2007-03-15
cjfiel
d
s
moved t
o
Test:
:
M
ore
commit
|
commitdiff
|
tree
2007-03-15
cjfie
l
ds
move to Test::M
o
re
commit
|
commitdiff
|
tree
2007-03-15
cjfields
n
e
w signalp pars
e
r (n
e
ed
t
o merge code and tests
for
.
.
.
commit
|
commitdiff
|
tree
2007-03-15
cjfields
s
i
gnal
p
te
s
t dat
a
commit
|
commitdiff
|
tree
2007-03-15
cjfi
e
lds
new signa
l
p tests; change
to Test::M
o
re
commit
|
commitdiff
|
tree
2007-03-14
c
j
f
i
elds
Move to T
e
st::More
commit
|
commitdiff
|
tree
2007-03-14
cjfields
Fix which checks
f
or
B
LAST
heade
r
for te
x
t/t
a
b
ular
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
cjfie
l
ds
Bu
g
2221
commit
|
commitdiff
|
tree
2007-03-13
c
jfields
TandemRepea
t
sFinder parser (bu
g
22
3
3)
commit
|
commitdiff
|
tree
2007-03-08
cjfields
switch
t
o XML::SAX
(not heavily tested); thi
s
modu
l
e
.
.
.
commit
|
commitdiff
|
tree
2007-03-08
cjfields
params use '-'
commit
|
commitdiff
|
tree
2007-03-08
cjfi
e
lds
add sim
p
le bracket_s
t
ring() tests
commit
|
commitdiff
|
tree
2007-03-08
cjfields
D* tests t
o
Test::More
commit
|
commitdiff
|
tree
2007-03-08
cjfi
e
lds
Finish
converting C* tests to
Test::Mo
r
e
commit
|
commitdiff
|
tree
2007-03-08
cjfields
remo
v
ed tests from
old br
a
cket_string
m
ethod (wi
l
l
.
.
.
commit
|
commitdiff
|
tree
2007-03-08
c
j
f
ields
chang
e
to Te
s
t
:
:More
commit
|
commitdiff
|
tree
2007-03-08
cjfi
e
lds
change t
o
T
e
st::Mo
r
e
commit
|
commitdiff
|
tree
2007-03-08
cjfields
conve
r
t to Test::
M
ore
commit
|
commitdiff
|
tree
2007-03-08
cjfields
mov
e
to Test::More
commit
|
commitdiff
|
tree
2007-03-07
cjfields
bug 2221
;
this sh
o
u
ld catc
h
mo
s
t translate
d
ata ou
t
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
c
jfield
s
A
d
ded data t
o
spaces
.
nex for NEXUS
T
reeIO test
s
, n
o
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
cjfiel
d
s
t
h
is s
h
ould deal wi
t
h all variet
i
es of translate lines
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
cjfields
Bug 2221
commit
|
commitdiff
|
tree
2007-03-07
cjfields
bug 22
0
5
commit
|
commitdiff
|
tree
2007-03-06
cjfiel
d
s
p
erltid
y
and unt
a
b
i
fy
(no bug
fix
f
or
2221 yet)
commit
|
commitdiff
|
tree
2007-03-06
c
jfields
change
t
o Test::
M
ore; added some tests for bug 2221
.
.
.
commit
|
commitdiff
|
tree
2007-03-02
cjfields
a
d
ditiona
l
spliced_seq test
s
(per Jay Ha
n
nah)
commit
|
commitdiff
|
tree
2007-02-27
cjfie
l
ds
Add doi() get/sette
r
commit
|
commitdiff
|
tree
2007-02-27
cjfields
move
to
T
e
s
t::More
commit
|
commitdiff
|
tree
2007-02-26
c
jfield
s
Some POD fixes for bracket_s
t
ri
n
g and sor
t
_
by_
s
ta
r
t
commit
|
commitdiff
|
tree
2007-02-26
c
jfields
Made bracket_string
a
class meth
o
d
commit
|
commitdiff
|
tree
2007-02-26
cj
f
ield
s
remo
v
e
b
racket_strings (moving to
S
impleAlign)
commit
|
commitdiff
|
tree
2007-02-22
cjfield
s
Bug 221
5
commit
|
commitdiff
|
tree
2007-02-20
cjfields
Removed p
e
r
Ch
r
is Mungall's r
e
quest
commit
|
commitdiff
|
tree
2007-02-19
c
j
field
s
Typo; add CVS tag
commit
|
commitdiff
|
tree
2007-02-17
cjfi
e
lds
in
f
ernal parsing fixes
commit
|
commitdiff
|
tree
2007-02-16
cjfields
Remov
e
XEMBL tes
t
s (no
l
onger a
c
tive)
commit
|
commitdiff
|
tree
2007-02-16
c
j
f
ields
Add
deprecation warning
commit
|
commitdiff
|
tree
2007-02-16
cjfie
l
d
s
R
e
moved extraneous line
.
commit
|
commitdiff
|
tree
2007-02-15
cjfi
e
lds
Ad
d
back p
e
r s
a
c's request
.
.
.
commit
|
commitdiff
|
tree
2007-02-15
cjfiel
d
s
XE
M
BL no longer is ava
i
lable
commit
|
commitdiff
|
tree
2007-02-15
cjfields
No longe
r
needed; tests
should
u
se Glimme
r
*
.
out a
n
d
.
.
.
commit
|
commitdiff
|
tree
2007-02-15
cjfields
Bug 2206 -
u
pd
a
tes
to allow all Gl
i
mmer f
o
rmats to
.
.
.
commit
|
commitdiff
|
tree
2007-02-15
c
jf
i
e
l
d
s
F
ix for remote DB sort order c
h
ange
commit
|
commitdiff
|
tree
2007-02-10
c
j
f
i
e
ld
s
XML::SAX 0
.
15 is req'd; may not need Bu
n
dle for X
M
L
.
.
.
commit
|
commitdiff
|
tree
2007-02-08
c
jfie
l
ds
fixed saxparser
(
)
,
made
tests stricter(!)
commit
|
commitdiff
|
tree
2007-02-08
cj
f
ie
l
ds
bla
s
txml sho
u
ld now
r
eturn al
l
descrip
t
i
on
d
a
ta for
.
.
.
commit
|
commitdiff
|
tree
2007-02-04
cjfield
s
our->my; fix GI erro
r
commit
|
commitdiff
|
tree
2007-02-04
cjfields
er
p
in, r
n
amotif Searc
h
IO-based
parsers wi
t
h s
o
me test
s
.
.
.
commit
|
commitdiff
|
tree
2007-02-04
cjfields
use quotemeta JIC f
o
r
r
egexe
s
commit
|
commitdiff
|
tree
2007-02-04
cjf
i
elds
small changes
commit
|
commitdiff
|
tree
2007-02-04
cjfields
RNA-based SearchI
O
stuff (keep s
e
par
a
te from
SearchIO
.
.
.
commit
|
commitdiff
|
tree
2007-02-04
cjfields
cmsearch (In
f
ernal) Sea
r
chIO-ba
s
ed parser;
HSP mo
d
el
.
.
.
commit
|
commitdiff
|
tree
2007-02-04
cj
f
i
elds
Ad
d
privat
e
sub fo
r
get
t
ing G
I
/
accessio
n
/v
e
r
sion
i
f
.
.
.
commit
|
commitdiff
|
tree
2007-02-02
cjfields
Move to
Te
s
t::More
commit
|
commitdiff
|
tree
2007-02-01
cjfields
b
ug 2
1
89
commit
|
commitdiff
|
tree
2007-01-30
cjfields
X
M
L::S
A
X:
:
Expat (v
.
0
.
38) wo
r
k
s
f
or XML parsing now
.
.
.
commit
|
commitdiff
|
tree
2007-01-30
cjfi
e
l
ds
Added tests for sort_by
_
star
t
commit
|
commitdiff
|
tree
2007-01-30
cjfields
Grr
.
.
.
remove Da
t
a::Dumper (f
r
o
m
debugging)
commit
|
commitdiff
|
tree
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