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perltidy
2008-11-16
cjfi
e
lds
pe
r
lt
i
d
y
commit
|
commitdiff
|
tree
2008-11-16
cjf
i
e
lds
[b
u
g
26
3
5]
commit
|
commitdiff
|
tree
2008-11-14
cjfields
[bu
g
265
6
]
commit
|
commitdiff
|
tree
2008-11-11
c
jfields
r
e
move debugg
i
ng lines
commit
|
commitdiff
|
tree
2008-11-11
cjfields
remove fixed
verbose flag
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 26
5
0]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
Clarify result_c
o
unt (discu
s
sions on mail lis
t
per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[
bug 26
3
2]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[b
u
g
2645]
commit
|
commitdiff
|
tree
2008-11-04
cjfields
wrap t
e
xt
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse 'Fe
a
tures in this
part o
f
s
u
bject
s
equence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* pa
r
se
'
Features in this part of subject sequ
e
nc
e
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
c
jfields
[
bug 2632]
commit
|
commitdiff
|
tree
2008-10-29
c
j
field
s
fix seq_
i
nds(); wasn't calling
i
dentical re
s
i
dues for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[
bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfields
[bu
g
2630]
commit
|
commitdiff
|
tree
2008-10-26
cjfie
l
ds
F
i
x unlink() warning
commit
|
commitdiff
|
tree
2008-10-26
c
jfi
e
lds
end
=
sta
r
t if only star
t
i
s
passed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
use valid_
L
ocation to
c
heck
L
o
c
atio
n
sta
t
e
commit
|
commitdiff
|
tree
2008-10-26
cjfields
add d
o
c
s
for
LocationI
metho
d
valid_Location
commit
|
commitdiff
|
tree
2008-10-26
cjfield
s
[bug
2
621]
commit
|
commitdiff
|
tree
2008-10-26
cjfiel
d
s
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfield
s
[bug
2624]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[b
u
g 2621]
commit
|
commitdiff
|
tree
2008-10-25
cjfields
bullet-proof prototy
p
e t
e
st
commit
|
commitdiff
|
tree
2008-10-22
cjfields
fix file
p
roperties
commit
|
commitdiff
|
tree
2008-10-22
cjfields
n
e
w modul
e
for
parsing v
e
cscreen -f 3 o
u
t
put, courtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfie
l
ds
add
-
source for ARP
commit
|
commitdiff
|
tree
2008-10-15
c
jfi
e
lds
[bug
2
563
]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
typo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bug
2519]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[
bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
add svn tag
commit
|
commitdiff
|
tree
2008-10-07
c
jfields
TODO
'
s
work
commit
|
commitdiff
|
tree
2008-10-07
cjfi
e
lds
[b
u
g 2612]
commit
|
commitdiff
|
tree
2008-10-07
cjf
i
elds
[b
u
g 2612]
commit
|
commitdiff
|
tree
2008-10-02
cjfields
cl
e
an up X
M
FA pa
r
s
i
ng, a
l
l
o
w
s
paces
i
n
p
a
r
sing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfields
[BUG]
b
ug 2598
commit
|
commitdiff
|
tree
2008-09-26
c
j
field
s
[BUG] bugf
i
x for # 2598 (
a
dd 'J')
commit
|
commitdiff
|
tree
2008-09-26
cjfie
l
ds
[BUG] bug 2593
commit
|
commitdiff
|
tree
2008-09-26
cjfie
l
ds
[BUG] fix bug 2
5
95
commit
|
commitdiff
|
tree
2008-09-18
c
j
fields
Use 'warning_like' for
i
n
stan
c
es where a regex match
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
c
jfields
* No longer a
stub
commit
|
commitdiff
|
tree
2008-09-17
cjf
i
elds
1965 + 6
-
1 = 1970, not
1
999
commit
|
commitdiff
|
tree
2008-09-17
cjfields
passing TODO's (?!?)
commit
|
commitdiff
|
tree
2008-09-17
c
jfie
l
ds
update tests (seq lengt
h
change in re
c
ord v
e
rif
i
ed)
commit
|
commitdiff
|
tree
2008-09-17
cjf
i
el
d
s
set -
e
n
d
to coorespond t
o
sequenc
e
end
commit
|
commitdiff
|
tree
2008-09-16
cjfield
s
test
r
e
s
ult cha
n
ged
(
s
t
a
rt alw
a
y
s
< end)
commit
|
commitdiff
|
tree
2008-09-16
cjfields
F
ix nexus iss
u
es
with seq
.
ambigui
t
y
s
y
m
bo
l
'
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
ds
MEG
A
n
ow
rese
t
s $GAP_SYMBOLS and $O
T
H
E
R_SYMBOLS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
Test data
match
e
s new XMFA ex
a
mp
l
e
commit
|
commitdiff
|
tree
2008-09-16
cjfields
*
XMFA
a
l
ignme
n
t doesn't
correspond to XMFA s
p
ec (
h
ttp
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
fix x
m
fa
.
p
m parsing oop
s
commit
|
commitdiff
|
tree
2008-09-16
cj
f
i
e
ld
s
ma
k
e LocatableSeq::end() consi
s
tent
commit
|
commitdiff
|
tree
2008-09-16
cjfields
* fix start
/
end/strand
commit
|
commitdiff
|
tree
2008-09-16
cjfields
typ
o
commit
|
commitdiff
|
tree
2008-09-15
cjfields
r
emo
v
e d
e
b
u
gging statemen
t
commit
|
commitdiff
|
tree
2008-09-15
c
jfield
s
partia
l
f
ix for ar
p
(-en
d
n
ow wo
r
k
s
and counts ? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfields
-en
d
parameter doe
s
no
t
take gap
s
into account
commit
|
commitdiff
|
tree
2008-09-15
cjfie
l
ds
*
a
l
w
ays w
a
rn abo
u
t passing wron
g
end() coordin
a
te
commit
|
commitdiff
|
tree
2008-09-14
cjfiel
d
s
Create Data:
:
Sta
g
n
od
e
lazily
;
always
use nod
e
() to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfi
e
ld
s
ad
d
a
f
e
w
new (unteste
d
) URLA
P
I parameters
commit
|
commitdiff
|
tree
2008-09-14
cjfiel
d
s
use dir
e
ct
ob
j
ect syn
t
ax
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug
25
7
9
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 258
0
commit
|
commitdiff
|
tree
2008-08-29
cjfields
Allow other Bio::S
e
qFeatu
r
e
::Collecti
o
nI
commit
|
commitdiff
|
tree
2008-08-28
cjf
i
elds
[bug 2576]
commit
|
commitdiff
|
tree
2008-08-27
c
jfields
grep not
needed (check for onto
l
o
g
y
is
i
n Ontology
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfield
s
[bug 2573]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
Update documentation
commit
|
commitdiff
|
tree
2008-08-27
cjfield
s
c
o
mpl
e
te sentence
commit
|
commitdiff
|
tree
2008-08-25
cj
f
i
e
lds
Ad
d
s
ome print_* meth
o
ds for
e
i
n
f
o, esummary, etc
.
commit
|
commitdiff
|
tree
2008-08-21
cjfie
l
ds
* write PROJECT s
u
pport
commit
|
commitdiff
|
tree
2008-08-21
cjfields
add
PROJECT su
p
port
(
bug
2569)
commit
|
commitdiff
|
tree
2008-08-05
c
j
f
i
elds
For ne
w
NCBI blasttable format
commit
|
commitdiff
|
tree
2008-08-05
cj
f
i
e
lds
Previou
s
chan
g
es killed Remot
e
Blast a
g
ain; make a little
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cjfield
s
Add a few new GET/PUT
p
arameters
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Sequences were
n
't being
p
arsed correct
l
y
; unfortunately
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfields
tests
should use
i
s/isn
t
whe
n
p
ossible, not ok
(
)
commit
|
commitdiff
|
tree
2008-07-30
cjfiel
d
s
revert
Roy's patch (my bad)
commit
|
commitdiff
|
tree
2008-07-30
cjfiel
d
s
bug 2
5
5
6
:
commit
|
commitdiff
|
tree
2008-07-30
cj
f
ields
Bug
2
546
commit
|
commitdiff
|
tree
2008-07-29
cjfields
bug 2555
commit
|
commitdiff
|
tree
2008-07-29
cjfields
bug 2
5
49; fixed small bug in Bio::Taxon which d
o
esn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfields
a
dd multiple
r
ecord
s
upport (court
e
sy of J
o
r
g
e Duart
e
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
cjfields
bulletproof t
e
st
;
remote tabular B
L
AS
T
is faili
n
g for
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cj
f
i
elds
bu
g
2
5
34
commit
|
commitdiff
|
tree
2008-07-08
cjfields
Can't inheri
t
f
rom onese
l
f
commit
|
commitdiff
|
tree
2008-07-08
cjfi
e
lds
bu
g
25
3
9
commit
|
commitdiff
|
tree
2008-06-17
cjfield
s
bug 2423
commit
|
commitdiff
|
tree
2008-06-17
cjf
i
elds
bug 2
4
23
commit
|
commitdiff
|
tree
2008-06-14
cjfie
l
d
s
bug 2512
(
Gene Ontology changes)
commit
|
commitdiff
|
tree
2008-06-14
c
j
fields
bug
25
1
9
commit
|
commitdiff
|
tree
2008-06-14
cj
f
ields
bug 2518
commit
|
commitdiff
|
tree
2008-06-14
cjf
i
el
d
s
bug 251
7
commit
|
commitdiff
|
tree
2008-05-27
c
jfields
RT#1
2
8
02 (via CPA
N
RT)
commit
|
commitdiff
|
tree
2008-04-22
c
jfie
l
d
s
bug 2485
and related
f
ix
e
s
commit
|
commitdiff
|
tree
2008-04-22
cjfields
correct # of skipped t
e
sts
commit
|
commitdiff
|
tree
2008-04-22
c
jfields
bug 2490 (s
m
all test)
commit
|
commitdiff
|
tree
2008-04-22
cjfields
bug 2490
commit
|
commitdiff
|
tree
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