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Sync branch with trunk
2008-12-24
cj
f
ields
Syn
c
branch with tr
u
nk
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Remove Bio::Microarray
from branch (s
t
ill in deve
l
opment
.
.
.
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Re
m
ove (me
r
ge didn't
r
emove this fo
r
some reason)
commit
|
commitdiff
|
tree
2008-12-24
cjf
i
elds
Remove
(
merge didn't remove this fo
r
some reason)
commit
|
commitdiff
|
tree
2008-12-22
c
jfi
e
l
ds
sync trunk with branch
commit
|
commitdiff
|
tree
2008-12-20
c
jfields
5
.
6
.
1 is min perl version required for all core m
o
dules now
commit
|
commitdiff
|
tree
2008-12-19
c
jfields
update N
A
MES
commit
|
commitdiff
|
tree
2008-12-19
c
jfields
small
t
ypo
commit
|
commitdiff
|
tree
2008-12-18
cjfields
typ
o
commit
|
commitdiff
|
tree
2008-12-18
cjfield
s
[bug 2714]
commit
|
commitdiff
|
tree
2008-12-17
cjfields
fix test number
commit
|
commitdiff
|
tree
2008-12-17
cjfields
update Test::W
a
rn (fixes Qual
.
t t
e
st probl
e
m
s
w
ith
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
c
jf
i
elds
missed one
commit
|
commitdiff
|
tree
2008-12-16
cjfields
E
U
tilities remot
e
t
ests bac
k
online (simp
l
e tests only)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EUti
l
ities remot
e
tests b
a
ck on
l
in
e
(simple test
s
o
n
ly)
commit
|
commitdiff
|
tree
2008-12-16
cjfie
l
ds
Yo
u
must actually te
s
t
data i
f
you want this module
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
e
lds
Don't us
e
p
rint!
Cha
n
g
i
ng
to $self->de
b
ug or commenting out
commit
|
commitdiff
|
tree
2008-12-16
cj
f
ields
Bio::Graph depr
e
cated in 1
.
6
commit
|
commitdiff
|
tree
2008-12-16
cjfi
e
lds
stifle wa
r
n
i
ngs whe
n
pas
s
ing
s
tring instead of integer
commit
|
commitdiff
|
tree
2008-12-16
cjfields
hash ref, not array re
f
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
c
j
field
s
[bu
g
2637]
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
elds
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[bug 26
3
7]
commit
|
commitdiff
|
tree
2008-12-15
c
j
fields
[bug
2
63
7
]
commit
|
commitdiff
|
tree
2008-12-15
cjf
i
eld
s
[bug
2
712]
commit
|
commitdiff
|
tree
2008-12-15
c
jfields
scores
commit
|
commitdiff
|
tree
2008-12-15
cjfields
remaining tes
t
s
for Bio
:
:Tool::EUtilities
commit
|
commitdiff
|
tree
2008-12-15
c
j
f
ields
mor
e
test d
a
ta
commit
|
commitdiff
|
tree
2008-12-15
cjfields
U
pdat
e
s:
commit
|
commitdiff
|
tree
2008-12-13
cjfields
initial ba
t
c
h
of EUt
i
lP
a
rameters tests
commit
|
commitdiff
|
tree
2008-12-13
cjfields
einfo te
s
ts
commit
|
commitdiff
|
tree
2008-12-12
cj
f
iel
d
s
s
ome EUtilities tests (parsing from files)
commit
|
commitdiff
|
tree
2008-12-12
c
j
fields
som
e
t
est data for Bio::Tools::EUtilit
i
e
s
commit
|
commitdiff
|
tree
2008-12-12
cjfields
u
pdate
s
to EUtilities
(
g
etting read
y
for docs, t
e
sts
.
.
.
commit
|
commitdiff
|
tree
2008-12-12
cjf
i
elds
Move EUtilPa
r
ame
t
er
s
to T
o
ols (s
e
ems mo
r
e ap
p
r
o
priate
)
commit
|
commitdiff
|
tree
2008-12-11
cjfields
f
ix
f
o
r
bug
w
h
e
n
g
e
tting cached response with filename
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
c
j
fiel
d
s
sm
a
ll
point
e
r to wiki pag
e
(will
u
pda
t
e along wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfields
small
u
pdate
commit
|
commitdiff
|
tree
2008-12-11
cjfiel
d
s
updates
commit
|
commitdiff
|
tree
2008-12-11
cjfie
l
ds
return, not '
r
eturn undef'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
r
e
tu
r
n
, not 'return
u
ndef'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug 269
9
]
commit
|
commitdiff
|
tree
2008-12-11
cjfiel
d
s
[b
u
g 269
9
]
commit
|
commitdiff
|
tree
2008-12-11
c
j
fiel
d
s
[bug 2
7
07]
commit
|
commitdiff
|
tree
2008-12-10
cjfields
Removing from
H
EA
D
(
deprecated for
1
.
6)
commit
|
commitdiff
|
tree
2008-12-10
c
jfields
min
i
po
d
fix
commit
|
commitdiff
|
tree
2008-12-10
cj
f
ield
s
update depre
c
ati
o
n list
commit
|
commitdiff
|
tree
2008-12-10
cj
f
ields
remove Bio::
G
ra
p
hics (separ
a
te package n
o
w)
commit
|
commitdiff
|
tree
2008-12-10
c
j
fiel
d
s
[bug
2637]
commit
|
commitdiff
|
tree
2008-12-10
c
j
fields
Remove d
e
pendencies fo
r
Bio::Graphics
a
nd deprec
a
ted
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Squash warning
commit
|
commitdiff
|
tree
2008-12-09
cjfi
e
lds
diag()
o
nly
o
n verbose
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Fix last loop tests, mov
e
some to can_ok
commit
|
commitdiff
|
tree
2008-12-09
cjfield
s
Modify to
t
est new tem
p
cl
a
ss
e
s and ensure
that added
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjf
i
eld
s
u
pdate Maur
i
cio's email
commit
|
commitdiff
|
tree
2008-12-08
cjfields
U
pda
t
e Roy'
s
ema
i
l
commit
|
commitdiff
|
tree
2008-12-08
cjfields
Roy's email (and bioperl
.
org
n
ot bi
o
perl
.
edu
)
commit
|
commitdiff
|
tree
2008-12-08
c
jfields
Update
d
emails
commit
|
commitdiff
|
tree
2008-12-07
cjfields
[b
u
g 2699]
commit
|
commitdiff
|
tree
2008-12-05
cjfields
Need to retrieve the tree for output
commit
|
commitdiff
|
tree
2008-12-05
cjfield
s
[bug
2
450]
commit
|
commitdiff
|
tree
2008-12-04
cj
f
i
elds
Make Ta
r
get a t
r
ue DB
L
i
nk
commit
|
commitdiff
|
tree
2008-12-04
cjfields
Dire
c
t
ory i
s
no lon
g
er
n
eeded (Heikki spli
t
th
i
s
u
p
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
c
j
f
ields
a
dd
force
_
nse tests
commit
|
commitdiff
|
tree
2008-12-03
c
j
fields
leave ID
u
nd
e
fined if i
t
isn't pre
s
e
n
t, but al
l
ow
t
he
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
ds
Remove fil
e
s acciden
t
ly added
f
rom last com
m
it
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ields
R
eorganize
T
ools t
e
sts (need
s
s
o
me more splittin
g
)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove
(tests a
r
e
redun
d
ant, in C
o
nsed
.
t
)
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
ds
Merge te
s
ts a
n
d
remove redun
d
ant file
commit
|
commitdiff
|
tree
2008-12-03
cjfiel
d
s
Update test count
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
Merge
t
es
t
s
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove redun
d
an
t
file
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove
o
ld files
commit
|
commitdiff
|
tree
2008-12-03
c
jfiel
d
s
Start Tools
move
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ie
l
ds
s
mall up
d
ate
s
:
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
l
d
s
forgot to increment test co
u
nt
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Add a couple
o
f tests f
o
r seq_id (
s
mall but si
g
nificant
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfi
e
lds
[bug
2
450]
commit
|
commitdiff
|
tree
2008-12-02
cjfi
e
lds
[bug
2450]
commit
|
commitdiff
|
tree
2008-12-02
c
j
f
ields
[bug 2
4
50]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
some p
o
d updates
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[b
u
g 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjf
i
elds
fix erroneously renamed st
o
ckholm
te
s
ts
commit
|
commitdiff
|
tree
2008-12-02
cjfiel
d
s
small
p
od f
i
x
commit
|
commitdiff
|
tree
2008-11-30
c
jfiel
d
s
silence
Gu
e
ssSeqFo
r
mat
.
t warn
i
ng
s
(not sure if old
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfields
rearrange
t
o avoid unn
e
ces
s
ary warnings
commit
|
commitdiff
|
tree
2008-11-28
c
j
fi
e
lds
Add war
n
ing for missi
n
g
d
ata (real bug)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
h
a
sh ref, not
a hash
commit
|
commitdiff
|
tree
2008-11-28
cjfields
test file
n
ame
a
n
d test # correctio
n
commit
|
commitdiff
|
tree
2008-11-28
cjfields
correct test fi
l
e name
commit
|
commitdiff
|
tree
2008-11-28
cjfields
'::', not ':'
commit
|
commitdiff
|
tree
2008-11-28
c
jfield
s
rena
m
e (recursive tests think thi
s
is a
te
s
t fi
l
e)
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ield
s
r
ecur
s
e into
t
est subdirectories (mean
s
any non-test
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
remove r
e
dundan
t
copy
commit
|
commitdiff
|
tree
2008-11-28
cjfi
e
lds
move into
d
irectory
structure
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
m
ove
i
nto direct
o
r
y
s
truc
t
u
r
e (DaveM++)
commit
|
commitdiff
|
tree
2008-11-26
c
j
fields
[bug 2567]
commit
|
commitdiff
|
tree
2008-11-26
cjf
i
elds
Redund
a
nt;
f
il
e
w
as
rename
d
Sear
c
hIO
_
blas
t
_
p
u
l
l
.
t
.
commit
|
commitdiff
|
tree
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