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mini pod fix
2008-12-10
cjfields
mini pod fi
x
commit
|
commitdiff
|
tree
2008-12-10
c
jfields
update deprecation lis
t
commit
|
commitdiff
|
tree
2008-12-10
cjfields
remove Bio:
:
G
r
aphics (separa
t
e
pa
c
kage now)
commit
|
commitdiff
|
tree
2008-12-10
c
jfields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-10
cjf
i
elds
Remov
e
dependenci
e
s
for Bio::Graphics and deprecate
d
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
c
j
fi
e
lds
Squash warning
commit
|
commitdiff
|
tree
2008-12-09
cjfields
d
i
a
g(
)
only on ver
b
ose
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Fix last loop tests
,
m
ove some
to can_ok
commit
|
commitdiff
|
tree
2008-12-09
c
jfield
s
Modify to t
e
s
t
n
e
w temp cla
s
ses a
n
d
ensur
e
that
a
dd
e
d
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cj
f
ields
u
p
date Mauric
i
o's e
m
a
i
l
commit
|
commitdiff
|
tree
2008-12-08
cjfield
s
U
pdate Roy's email
commit
|
commitdiff
|
tree
2008-12-08
c
jfields
Roy'
s
email (and biop
e
rl
.
org no
t
bioperl
.
edu)
commit
|
commitdiff
|
tree
2008-12-08
c
jfields
Up
d
a
t
ed
e
mails
commit
|
commitdiff
|
tree
2008-12-07
c
j
fields
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-05
cj
f
ields
N
eed to
retrieve the tre
e
for
o
utput
commit
|
commitdiff
|
tree
2008-12-05
c
jfie
l
d
s
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-04
cjfi
e
lds
Make Target a true
DBLink
commit
|
commitdiff
|
tree
2008-12-04
cj
f
ield
s
Di
r
e
c
tory is no longer n
e
eded (Heikki split thi
s
up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
add f
o
rce_nse
t
ests
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ields
leave I
D
undefined
if
it isn't p
r
es
e
nt, but
a
llow th
e
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
ds
R
e
move
files acc
i
dent
l
y
adde
d
f
r
om last commi
t
commit
|
commitdiff
|
tree
2008-12-03
c
jfiel
d
s
Reorgan
i
z
e
Tools tests (n
e
eds some
more spl
i
tting)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove
(tes
t
s are
r
edundant
,
in
Consed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Merge tests
a
n
d
remove r
e
dundant
f
i
le
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
ds
U
p
d
a
te test cou
n
t
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
elds
Merg
e
tests
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
ds
Remove
redundant fi
l
e
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
ds
R
emove old
f
i
les
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Start
Tools move
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
e
lds
small upda
t
es:
commit
|
commitdiff
|
tree
2008-12-03
cjfields
f
orgot to in
c
r
e
me
n
t
test cou
n
t
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
Add a couple of tests f
o
r seq_id (s
m
all but si
g
nificant
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cj
f
i
e
lds
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjf
i
elds
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
c
j
f
i
elds
[bu
g
2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfiel
d
s
som
e
p
od updates
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bu
g
2450]
commit
|
commitdiff
|
tree
2008-12-02
cjf
i
e
lds
f
ix erroneously
r
enamed
s
tockholm tests
commit
|
commitdiff
|
tree
2008-12-02
cjfields
s
mal
l
p
o
d fix
commit
|
commitdiff
|
tree
2008-11-30
cjfields
si
l
ence
GuessSe
q
For
m
at
.
t warnings (not sure if old
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfi
e
lds
rearrange
t
o avoid unnecessary wa
r
nings
commit
|
commitdiff
|
tree
2008-11-28
c
j
fields
Add warning fo
r
missing data (real
bu
g
)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
hash r
e
f, not a hash
commit
|
commitdiff
|
tree
2008-11-28
cjfields
test file name a
n
d test #
corre
c
tion
commit
|
commitdiff
|
tree
2008-11-28
cjfields
correct test f
i
le name
commit
|
commitdiff
|
tree
2008-11-28
cjfields
'::', n
o
t
':'
commit
|
commitdiff
|
tree
2008-11-28
cjfi
e
lds
rename (recursive
tests th
i
nk thi
s
i
s a test f
i
le)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
recurse into
test
s
ubdirectories (means any non-test
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfiel
d
s
remove redundant cop
y
commit
|
commitdiff
|
tree
2008-11-28
cjfields
m
o
ve into dir
e
c
tory st
r
ucture
commit
|
commitdiff
|
tree
2008-11-28
cjfields
move into direct
o
ry struc
t
ure (DaveM++)
commit
|
commitdiff
|
tree
2008-11-26
c
j
fields
[bug 2
5
6
7]
commit
|
commitdiff
|
tree
2008-11-26
cjfield
s
Redundant;
fil
e
was renamed SearchIO_blast_pull
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
cjf
i
el
d
s
[bu
g
2686]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
fix
s
ubversi
o
n tags
commit
|
commitdiff
|
tree
2008-11-25
cjf
i
elds
po, not
p
oa
commit
|
commitdiff
|
tree
2008-11-25
cjfiel
d
s
fix
unde
f
ined val
u
e warnings
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 2686]
commit
|
commitdiff
|
tree
2008-11-25
c
jfields
[bug
2
6
4
1
, 2642]
commit
|
commitdiff
|
tree
2008-11-25
cjfie
l
ds
split
up AlignIO tests
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 2682]
commit
|
commitdiff
|
tree
2008-11-25
c
jfields
[bug
2
6
30]
commit
|
commitdiff
|
tree
2008-11-24
c
j
f
i
e
lds
[bug 2633]
commit
|
commitdiff
|
tree
2008-11-24
c
j
f
i
elds
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-24
cjfie
l
d
s
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-24
c
jfiel
d
s
[bug 2630]
commit
|
commitdiff
|
tree
2008-11-24
c
jf
i
el
d
s
[bug 2262]
commit
|
commitdiff
|
tree
2008-11-24
cjfield
s
[bug
263
0
]
commit
|
commitdiff
|
tree
2008-11-18
cj
f
ields
* D
o
uble-
c
hec
k
e
d
data, t
e
st
e
d
results were wrong
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* seq_inds is not defined f
o
r Model-
b
ase
d
H
SPs
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* fix
P
OD
commit
|
commitdiff
|
tree
2008-11-17
cjfie
l
ds
*
'hi
g
hly'
(
and I
g
et
r
1
5000!)
commit
|
commitdiff
|
tree
2008-11-17
cjf
i
elds
Remove redundant t
e
st files
commit
|
commitdiff
|
tree
2008-11-17
cjfields
[
tests]
commit
|
commitdiff
|
tree
2008-11-17
cjfie
l
d
s
move results2hash
t
es
t
utility sub to Searc
h
Utils
commit
|
commitdiff
|
tree
2008-11-16
cjfield
s
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-16
cjfields
perltidy
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[
b
ug 2635]
commit
|
commitdiff
|
tree
2008-11-14
cjf
i
elds
[
b
ug 2656]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
remove
d
ebu
g
ging lin
e
s
commit
|
commitdiff
|
tree
2008-11-11
cjfields
remove
f
i
x
ed
ver
b
ose flag
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[
bug 2
6
50]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
Cl
a
rify result_
c
ount (d
i
s
cussions on
m
ail list per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cj
f
ields
[bug 2
6
32]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[bug 2645]
commit
|
commitdiff
|
tree
2008-11-04
c
j
f
i
el
d
s
w
rap text
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse 'Features in this part of subject sequence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfie
l
ds
* parse 'Feature
s
in this p
a
rt of subject seque
n
ce
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[bug 2632]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
f
i
x seq_in
d
s(); wasn't calling id
e
ntic
a
l residues
f
o
r
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfields
[bug 2630]
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
Fix un
l
ink() warning
commit
|
commitdiff
|
tree
2008-10-26
cjfields
en
d
= start
i
f onl
y
s
t
a
r
t
i
s passed
commit
|
commitdiff
|
tree
2008-10-26
cj
f
i
e
lds
use valid_Location to check Location sta
t
e
commit
|
commitdiff
|
tree
2008-10-26
cjfie
l
ds
a
dd docs for LocationI
method
v
a
l
id_L
o
ca
t
ion
commit
|
commitdiff
|
tree
2008-10-26
cjfie
l
ds
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
c
j
f
i
e
l
ds
[b
u
g 26
2
1]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2624]
commit
|
commitdiff
|
tree
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