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perltidy
2008-11-16
cj
f
ield
s
per
l
tidy
commit
|
commitdiff
|
tree
2008-11-16
c
j
f
ields
[bug 2635]
commit
|
commitdiff
|
tree
2008-11-14
c
jfi
e
lds
[
bug 2656]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
remov
e
debugging li
n
es
commit
|
commitdiff
|
tree
2008-11-11
c
jfields
remove
f
ixed
v
erbo
s
e flag
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
elds
[bu
g
2
65
0
]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
Clarify result_
c
ount (disc
u
ssions on mail li
s
t
per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2632
]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[bug
2
645]
commit
|
commitdiff
|
tree
2008-11-04
cjfie
l
d
s
wrap text
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse 'Features in this p
a
r
t of subject sequence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjf
i
elds
*
p
arse 'Feat
u
res in this part of su
b
ject sequ
e
nce
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[bug
263
2
]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
fix seq_inds
(
); w
a
sn't calling
iden
t
ical res
i
dues
f
or
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
c
j
fields
[bu
g
26
3
0]
commit
|
commitdiff
|
tree
2008-10-26
c
j
fields
Fix unlin
k
()
w
a
rning
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
e
n
d =
start if only start is passed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
use valid_Location
t
o
c
h
ec
k
Location s
t
at
e
commit
|
commitdiff
|
tree
2008-10-26
c
j
fie
l
ds
ad
d
d
ocs for
Loc
a
tionI m
e
th
o
d
v
alid_Location
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
e
ld
s
[
bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[
bug 2624]
commit
|
commitdiff
|
tree
2008-10-26
cj
f
i
elds
[bug 2
6
21
]
commit
|
commitdiff
|
tree
2008-10-25
cjf
i
elds
bullet-proof prototype test
commit
|
commitdiff
|
tree
2008-10-22
cjfie
l
ds
fi
x
fil
e
properties
commit
|
commitdiff
|
tree
2008-10-22
cjfields
new module f
o
r pa
r
s
ing vecsc
r
een -f 3 output, courtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfields
a
dd
-source for ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfields
[
bug 2563]
commit
|
commitdiff
|
tree
2008-10-10
cjfield
s
typo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bu
g
25
1
9]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bug
2519]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
add sv
n
tag
commit
|
commitdiff
|
tree
2008-10-07
c
jfields
TODO's work
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-02
cjfields
cl
e
a
n up XMF
A
parsin
g
,
a
llow s
p
aces in parsing
(
e
nde
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cj
f
ields
[BUG] bu
g
2598
commit
|
commitdiff
|
tree
2008-09-26
c
j
fields
[
B
UG] bugfix
f
or #
2
598 (add
'
J')
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BUG] bug 25
9
3
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BUG] fi
x
b
ug 2595
commit
|
commitdiff
|
tree
2008-09-18
cjfields
Use '
w
a
r
ning_like'
for instances where a regex
match
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfields
* No lon
g
er a stub
commit
|
commitdiff
|
tree
2008-09-17
cjfields
1965 + 6
-
1 = 1970, not
1
999
commit
|
commitdiff
|
tree
2008-09-17
cjfields
pas
s
ing TOD
O
'
s (?!?)
commit
|
commitdiff
|
tree
2008-09-17
c
j
field
s
u
pdate tes
t
s (seq length change
i
n
record verified)
commit
|
commitdiff
|
tree
2008-09-17
cjf
i
elds
set -end to
c
o
orespond t
o
sequ
e
nce end
commit
|
commitdiff
|
tree
2008-09-16
c
j
fields
test resu
l
t
changed (
s
tart always < end)
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
elds
Fix
n
exus issues wi
t
h
seq
.
a
mbiguit
y
sym
b
ol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfields
MEGA now resets
$GAP_SYMBOLS
a
nd $OTHER_SYMB
O
LS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
T
e
st data matches new XM
F
A example
commit
|
commitdiff
|
tree
2008-09-16
cj
f
iel
d
s
*
X
MFA alignment doesn't
correspond to
X
MFA spec (http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
f
i
x
xmfa
.
pm par
s
ing oops
commit
|
commitdiff
|
tree
2008-09-16
cjfield
s
m
ake Loca
t
abl
e
Seq:
:
end() cons
i
stent
commit
|
commitdiff
|
tree
2008-09-16
cjfields
*
fix start/en
d
/s
t
rand
commit
|
commitdiff
|
tree
2008-09-16
cjfields
typo
commit
|
commitdiff
|
tree
2008-09-15
cjfie
l
ds
remove debugging statement
commit
|
commitdiff
|
tree
2008-09-15
cjfields
parti
a
l fix for
a
rp (
-
end now
w
orks an
d
co
u
n
t
s
? a
s
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfie
l
ds
-end parameter does
not take gaps into account
commit
|
commitdiff
|
tree
2008-09-15
cjfields
*
always warn
a
b
o
ut p
a
ssing wrong end() coordinate
commit
|
commitdiff
|
tree
2008-09-14
cjfields
Crea
t
e Data::Stag nod
e
l
a
zily; alw
a
ys
use node() t
o
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
c
j
fields
add a fe
w
new (untested) URLAPI p
a
ra
m
eters
commit
|
commitdiff
|
tree
2008-09-14
cjfields
u
s
e
d
ir
e
ct ob
j
ect s
y
n
tax
commit
|
commitdiff
|
tree
2008-09-09
cjf
i
el
d
s
bug 2579
commit
|
commitdiff
|
tree
2008-09-09
cjfiel
d
s
bug 2580
commit
|
commitdiff
|
tree
2008-08-29
c
jfields
Allow other Bio::SeqFe
a
ture::Collect
i
onI
commit
|
commitdiff
|
tree
2008-08-28
cjfield
s
[
b
ug 2576]
commit
|
commitdiff
|
tree
2008-08-27
cj
f
ie
l
ds
gr
e
p not needed (check for
ontology is in Ontology
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfields
[bug 2573]
commit
|
commitdiff
|
tree
2008-08-27
cjfie
l
d
s
Update d
o
cumen
t
ation
commit
|
commitdiff
|
tree
2008-08-27
c
jfields
complete se
n
tence
commit
|
commitdiff
|
tree
2008-08-25
cjfields
Add
s
ome print_* methods
f
or einfo, esummary, etc
.
commit
|
commitdiff
|
tree
2008-08-21
cjfields
* write
PRO
J
ECT support
commit
|
commitdiff
|
tree
2008-08-21
cjf
i
elds
add P
R
OJECT sup
p
o
r
t
(
b
ug
2569)
commit
|
commitdiff
|
tree
2008-08-05
cjfields
For new NCBI
b
l
asttable f
o
rmat
commit
|
commitdiff
|
tree
2008-08-05
c
jfields
Pr
e
v
i
ous chan
g
es killed RemoteBlast
a
gai
n
; ma
k
e a little
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cjf
i
e
l
ds
Add a few n
e
w
GET/
P
UT parameters
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Seque
n
ces
weren't being parsed c
o
rrec
t
ly; unfortun
a
t
ely
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfields
tests should use is/isnt when po
s
sib
l
e, not o
k
()
commit
|
commitdiff
|
tree
2008-07-30
cj
f
i
el
d
s
revert Roy's patch
(
my bad)
commit
|
commitdiff
|
tree
2008-07-30
cjfields
bug 2556:
commit
|
commitdiff
|
tree
2008-07-30
cjfields
B
ug
2546
commit
|
commitdiff
|
tree
2008-07-29
cjfields
bug 2555
commit
|
commitdiff
|
tree
2008-07-29
c
jfields
bug 2549
;
fixed sma
l
l bug
i
n Bio:
:
Taxon which d
o
esn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfields
add
m
ultipl
e
recor
d
sup
p
ort (courtesy of Jo
r
g
e
Duarte
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
c
j
f
ield
s
bulletproo
f
test; remote tabul
a
r
B
L
AST is failing fo
r
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjfields
bug 2534
commit
|
commitdiff
|
tree
2008-07-08
cjfi
e
lds
Can't inherit from on
e
self
commit
|
commitdiff
|
tree
2008-07-08
cjfields
b
ug 2539
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bug 2423
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bu
g
2423
commit
|
commitdiff
|
tree
2008-06-14
cj
f
ie
l
d
s
bug 2512 (Ge
n
e Ontolo
g
y cha
n
ges)
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 2519
commit
|
commitdiff
|
tree
2008-06-14
cjfie
l
ds
bug 2518
commit
|
commitdiff
|
tree
2008-06-14
cjfields
b
u
g 2517
commit
|
commitdiff
|
tree
2008-05-27
cjfiel
d
s
RT#1280
2
(via CPAN RT)
commit
|
commitdiff
|
tree
2008-04-22
cjfie
l
ds
bug 2485 and related fi
x
es
commit
|
commitdiff
|
tree
2008-04-22
cjfields
c
orrect # of skipp
e
d t
e
st
s
commit
|
commitdiff
|
tree
2008-04-22
cjfi
e
l
ds
bug 2490
(small test)
commit
|
commitdiff
|
tree
2008-04-22
c
jfields
bug 2490
commit
|
commitdiff
|
tree
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