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Bug 2426
2007-03-22
cjfields
bug 2
2
4
5
(enhancement to allow relativ
e
pat
h
s for in
d
ex
.
.
.
commit
|
commitdiff
|
tree
2007-03-22
cjfields
fix some test
s
commit
|
commitdiff
|
tree
2007-03-22
cjfields
test data
f
or BIC tests
commit
|
commitdiff
|
tree
2007-03-21
c
j
fields
Remov
i
ng redundant module; p
a
s
ses flat
.
t
commit
|
commitdiff
|
tree
2007-03-21
cjfields
bug 2242
commit
|
commitdiff
|
tree
2007-03-21
cjfields
No
w
pa
s
ses v3
t
ests (at lea
s
t
t
he
v3 output we have
.
.
.
)
commit
|
commitdiff
|
tree
2007-03-21
cjfields
Nei
l
& Co
.
's
m
odified
Signalp parser (bug 2203) - passes
.
.
.
commit
|
commitdiff
|
tree
2007-03-20
cjfields
Changed throw()
due
t
o verbose output from
Infernal
.
.
.
commit
|
commitdiff
|
tree
2007-03-19
c
j
fields
T
a
r
g
etP pa
r
ser, data,
a
n
d
t
ests
commit
|
commitdiff
|
tree
2007-03-19
cjfi
e
lds
bug 2240
commit
|
commitdiff
|
tree
2007-03-16
cjf
i
elds
ge
t
t
er/sett
e
r for
c
o
m
me
n
t type (not implem
e
nted
y
et
)
commit
|
commitdiff
|
tree
2007-03-16
cjfields
test
s
(
writ
e
_seq() for drivers not i
m
plemented yet)
commit
|
commitdiff
|
tree
2007-03-16
cjfi
e
lds
seq for
m
at
drivers and single handler
m
o
d
u
le fo
r
GenBank
.
.
.
commit
|
commitdiff
|
tree
2007-03-16
cj
f
ields
Handler
-
b
ased parsing i
n
terface
commit
|
commitdiff
|
tree
2007-03-15
cjfiel
d
s
Move to
Test::More
commit
|
commitdiff
|
tree
2007-03-15
c
j
f
ields
mo
v
ed
to
T
e
st::More
commit
|
commitdiff
|
tree
2007-03-15
c
j
fields
move to Test::M
o
re
commit
|
commitdiff
|
tree
2007-03-15
c
jfields
new signalp parser (need to merge code and
t
ests f
o
r
.
.
.
commit
|
commitdiff
|
tree
2007-03-15
cjfields
signalp
t
e
s
t
data
commit
|
commitdiff
|
tree
2007-03-15
cjfiel
d
s
new signa
l
p
tests; change to Test::More
commit
|
commitdiff
|
tree
2007-03-14
c
jf
i
elds
Move to Test:
:
More
commit
|
commitdiff
|
tree
2007-03-14
cjf
i
e
lds
Fix whic
h
chec
k
s
fo
r
BLAST head
e
r
f
o
r
t
ext/t
a
bul
a
r
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
cjf
i
elds
Bug 2221
commit
|
commitdiff
|
tree
2007-03-13
cjfields
TandemRepeatsFinder
p
arser (b
u
g 22
3
3)
commit
|
commitdiff
|
tree
2007-03-08
cjfields
s
witch to XML::SAX (not heavily
tested); t
h
is module
.
.
.
commit
|
commitdiff
|
tree
2007-03-08
cjfield
s
params use '-'
commit
|
commitdiff
|
tree
2007-03-08
cjfi
e
ld
s
add
simp
l
e bracket_string()
t
ests
commit
|
commitdiff
|
tree
2007-03-08
cj
f
i
elds
D* tests to T
e
st::More
commit
|
commitdiff
|
tree
2007-03-08
cjfi
e
lds
Finish con
v
erting C* t
e
sts to Test::More
commit
|
commitdiff
|
tree
2007-03-08
cjfields
re
m
oved
t
e
sts from old
b
racket_str
i
ng method
(
wi
l
l
.
.
.
commit
|
commitdiff
|
tree
2007-03-08
cj
f
ields
cha
n
g
e
to
Test::
M
ore
commit
|
commitdiff
|
tree
2007-03-08
c
jfields
cha
n
g
e
to Test
:
:More
commit
|
commitdiff
|
tree
2007-03-08
cjfields
convert t
o
Te
s
t::
M
ore
commit
|
commitdiff
|
tree
2007-03-08
c
j
fields
move to
T
est::More
commit
|
commitdiff
|
tree
2007-03-07
c
j
fields
bug 22
2
1; this should catch most translate data out
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
cjfields
Added
d
a
t
a to space
s
.
nex for N
E
XUS T
r
e
e
IO tests,
n
o
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
c
jf
i
eld
s
this should deal with all varieties of tra
n
slate lines
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
cjf
i
elds
Bug 2221
commit
|
commitdiff
|
tree
2007-03-07
cjfields
bug 220
5
commit
|
commitdiff
|
tree
2007-03-06
cjfields
per
l
tidy and untabify (no bug fix for 22
2
1 yet)
commit
|
commitdiff
|
tree
2007-03-06
cjfields
change to Test::More;
added some t
e
st
s
f
o
r bug 2221
.
.
.
commit
|
commitdiff
|
tree
2007-03-02
cjfields
a
d
ditional spl
i
c
e
d_seq
t
ests (per Jay Hann
a
h)
commit
|
commitdiff
|
tree
2007-02-27
cjfiel
d
s
Add doi() get/
s
etter
commit
|
commitdiff
|
tree
2007-02-27
cjfi
e
lds
move to T
e
st::More
commit
|
commitdiff
|
tree
2007-02-26
cjfields
Some POD fixe
s
fo
r
bracket_string and s
o
rt_by_start
commit
|
commitdiff
|
tree
2007-02-26
c
j
f
ields
Made bra
c
ket_string a class method
commit
|
commitdiff
|
tree
2007-02-26
cjfields
re
m
ove
b
r
acket_
s
tr
i
ngs (moving
t
o SimpleAli
g
n)
commit
|
commitdiff
|
tree
2007-02-22
cjfields
Bug 2
2
15
commit
|
commitdiff
|
tree
2007-02-20
cjfields
R
e
m
o
v
ed per Chris Mungall's
reques
t
commit
|
commitdiff
|
tree
2007-02-19
cjfields
Typo; add CVS
ta
g
commit
|
commitdiff
|
tree
2007-02-17
cjf
i
elds
infernal p
a
r
s
in
g
fixes
commit
|
commitdiff
|
tree
2007-02-16
cjfields
Remove XEMBL
t
e
s
ts (no
l
onger
a
c
t
ive)
commit
|
commitdiff
|
tree
2007-02-16
c
jfields
Add
d
eprecation warning
commit
|
commitdiff
|
tree
2007-02-16
c
j
fie
l
ds
Removed
extran
e
ous line
.
commit
|
commitdiff
|
tree
2007-02-15
cjfields
Ad
d
back pe
r
sac's
request
.
.
.
commit
|
commitdiff
|
tree
2007-02-15
cjf
i
elds
XE
M
BL no
longer is available
commit
|
commitdiff
|
tree
2007-02-15
cjfie
l
ds
No
l
o
n
ger nee
d
ed; te
s
ts should use
G
limmer*
.
o
u
t and
.
.
.
commit
|
commitdiff
|
tree
2007-02-15
cjf
i
elds
Bug 2206 - updates to
a
llow all Glimm
e
r formats to
.
.
.
commit
|
commitdiff
|
tree
2007-02-15
cjfields
F
i
x
for remote DB
s
ort order
change
commit
|
commitdiff
|
tree
2007-02-10
cjfields
XM
L
::SAX
0
.
1
5 is
re
q
'd; may not need Bundle f
o
r
XML
.
.
.
commit
|
commitdiff
|
tree
2007-02-08
c
jfields
fixe
d
saxparser
(
), made tests stricte
r
(!)
commit
|
commitdiff
|
tree
2007-02-08
cjfields
blastxml
s
h
o
uld now
r
etu
r
n
all descrip
t
ion data for
.
.
.
commit
|
commitdiff
|
tree
2007-02-04
cjfields
our->my;
fi
x
GI erro
r
commit
|
commitdiff
|
tree
2007-02-04
cjfields
erpin,
rnamot
i
f
S
earchIO
-
based parsers
w
ith some tes
t
s
.
.
.
commit
|
commitdiff
|
tree
2007-02-04
cjfields
use qu
o
temeta JIC for
r
e
ge
x
es
commit
|
commitdiff
|
tree
2007-02-04
cjfields
small
changes
commit
|
commitdiff
|
tree
2007-02-04
cjfi
e
lds
RNA-base
d
SearchIO stu
f
f (keep separ
a
te
f
rom Searc
h
IO
.
.
.
commit
|
commitdiff
|
tree
2007-02-04
c
jfield
s
cm
s
earch
(
Infernal) SearchIO-based p
a
rser; HSP
m
o
d
el
.
.
.
commit
|
commitdiff
|
tree
2007-02-04
c
j
f
ields
Add priva
t
e sub
for getting GI/accession
/
versio
n
if
.
.
.
commit
|
commitdiff
|
tree
2007-02-02
cjfields
Move to
T
est::More
commit
|
commitdiff
|
tree
2007-02-01
cj
f
ields
bug 21
8
9
commit
|
commitdiff
|
tree
2007-01-30
c
j
fields
XML::SAX::Expat (v
.
0
.
38)
works for XML parsing now
.
.
.
commit
|
commitdiff
|
tree
2007-01-30
cjfi
e
lds
A
dded tests
f
or sort_by_start
commit
|
commitdiff
|
tree
2007-01-30
cjfields
G
r
r
.
.
.
remove Data::Dumper (from d
e
bug
g
ing)
commit
|
commitdiff
|
tree
2007-01-30
cjfield
s
tests for bug 2195
commit
|
commitdiff
|
tree
2007-01-30
c
j
fields
B
u
g 2195
commit
|
commitdiff
|
tree
2007-01-30
cjfields
B
u
gs
2197,
2
092
commit
|
commitdiff
|
tree
2007-01-29
cjfields
B
u
g 2
1
98
commit
|
commitdiff
|
tree
2007-01-29
cjfiel
d
s
Bug 2197
commit
|
commitdiff
|
tree
2007-01-27
cjfields
s
m
all
t
weak to
g
et
r
i
d
o
f
warning
commit
|
commitdiff
|
tree
2007-01-25
cjfi
e
lds
Mov
e
to Test::More; clean up; make WG
S
te
s
ts mor
e
expl
i
cit
commit
|
commitdiff
|
tree
2007-01-24
cjfie
l
ds
Bulletpr
o
o
f
some more
.
.
.
commit
|
commitdiff
|
tree
2007-01-19
cjfields
BI
C
format st
u
f
f
commit
|
commitdiff
|
tree
2007-01-19
c
jfields
bracketed
c
on
s
en
s
us
(
BIC?)
commit
|
commitdiff
|
tree
2007-01-19
cjfields
change Fil
e
:
:Pat
h
verbosity to only
b
e
TRU
E
when debugging
commit
|
commitdiff
|
tree
2007-01-18
cjfields
small
c
hange (ba
d
exam
p
le
data)
commit
|
commitdiff
|
tree
2007-01-18
cjfields
f
o
r fut
u
r
e
Sear
c
hIO-b
a
sed t
e
sts
commit
|
commitdiff
|
tree
2007-01-18
cjfield
s
remov
e
c
o
m
ments;
c
leanup() should now
w
ork
(fing
e
rs
.
.
.
commit
|
commitdiff
|
tree
2007-01-18
cjfields
r
evert back to normal fro
m
de
b
ugging
commit
|
commitdiff
|
tree
2007-01-18
cjfields
B
ug 2
1
83
commit
|
commitdiff
|
tree
2007-01-18
cjfi
e
lds
s
mall POD change
commit
|
commitdiff
|
tree
2007-01-18
cjfi
e
lds
POD changes
commit
|
commitdiff
|
tree
2007-01-18
c
j
fields
A
dded
B
io::Tools::Infernal tests
commit
|
commitdiff
|
tree
2007-01-18
cjfields
Bug 2189; did some pre-spri
n
g c
l
ean
i
ng
commit
|
commitdiff
|
tree
2007-01-17
cjfield
s
Sm
a
l
l
cha
n
ge
commit
|
commitdiff
|
tree
2007-01-16
cjfields
fix
f
i
leha
n
dl
e
issue for
NEXUS pars
i
ng
commit
|
commitdiff
|
tree
2007-01-16
cjfields
file
h
andle t
e
sts (NEXUS
still doesn't work)
commit
|
commitdiff
|
tree
2007-01-16
cjf
i
elds
f
ix for
f
ilehandle IO
commit
|
commitdiff
|
tree
2007-01-16
cjfi
e
lds
Bug 2
1
85
commit
|
commitdiff
|
tree
2007-01-11
cjfields
Bug 2
1
82
commit
|
commitdiff
|
tree
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