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mini pod fix
2008-10-26
cjfield
s
[bug
2
6
2
1]
commit
|
commitdiff
|
tree
2008-10-25
cjfields
b
ul
l
et
-
proo
f
p
ro
t
otype
test
commit
|
commitdiff
|
tree
2008-10-22
cjfields
fix file prop
e
rties
commit
|
commitdiff
|
tree
2008-10-22
c
j
field
s
new m
o
d
ule for
parsi
n
g vecscreen -f 3 output, courtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfields
add -sourc
e
f
or ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfields
[bu
g
2563]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
typo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[
b
ug
2519]
commit
|
commitdiff
|
tree
2008-10-10
cjfi
e
lds
[
bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
cjf
i
elds
add svn tag
commit
|
commitdiff
|
tree
2008-10-07
cjfield
s
TOD
O
's work
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[bug
2
6
1
2]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-02
cjfields
clean up XMF
A
parsing, allow
s
paces in parsing
(
ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfields
[BUG]
b
ug
2598
commit
|
commitdiff
|
tree
2008-09-26
cjfie
l
d
s
[
B
UG]
bugfi
x
f
or # 2598 (
a
dd
'
J')
commit
|
commitdiff
|
tree
2008-09-26
cjfield
s
[BUG] bu
g
2
593
commit
|
commitdiff
|
tree
2008-09-26
c
jfields
[BUG] fix bug 2
5
95
commit
|
commitdiff
|
tree
2008-09-18
cjfie
l
ds
U
s
e
'
w
ar
n
ing_like' for instances where a
r
e
g
ex ma
t
ch
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfields
*
No longer a stub
commit
|
commitdiff
|
tree
2008-09-17
cjfields
196
5
+ 6
-1 = 1970, n
o
t 1999
commit
|
commitdiff
|
tree
2008-09-17
c
j
fields
pa
s
sing TODO's (?!?)
commit
|
commitdiff
|
tree
2008-09-17
c
jfields
updat
e
t
e
sts (
s
eq
l
ength change in record verifi
e
d)
commit
|
commitdiff
|
tree
2008-09-17
cjf
i
e
lds
set -end to coores
p
ond to
se
q
u
e
n
c
e
e
nd
commit
|
commitdiff
|
tree
2008-09-16
cjfields
t
e
s
t
res
u
l
t
changed (start alway
s
<
end)
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Fix nexus issues with seq
.
ambigu
i
t
y sy
m
bol
'
.
'
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
MEGA
n
ow
r
esets $GAP_SYMBOLS and $OTHER_SYMBOLS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Te
s
t
d
ata matches n
e
w XMFA example
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
elds
*
X
MFA
al
i
gnm
e
nt doesn't
corresp
o
nd to XMFA spec (ht
t
p
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfiel
d
s
fix xmfa
.
pm parsi
n
g oops
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
eld
s
ma
k
e
L
oca
t
a
bleS
e
q
::end() consi
s
tent
commit
|
commitdiff
|
tree
2008-09-16
cjfields
* f
i
x
start
/
end/st
r
a
n
d
commit
|
commitdiff
|
tree
2008-09-16
c
j
fields
typo
commit
|
commitdiff
|
tree
2008-09-15
c
jfields
remo
v
e debug
g
i
ng s
t
at
e
ment
commit
|
commitdiff
|
tree
2008-09-15
cjfie
l
ds
parti
a
l fix for arp (-e
n
d now works and cou
n
ts ? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfields
-e
n
d parameter does not
t
ake
g
aps
into acc
o
unt
commit
|
commitdiff
|
tree
2008-09-15
cjfields
* alw
a
ys
w
arn about passing wrong end() coordina
t
e
commit
|
commitdiff
|
tree
2008-09-14
cjfields
Create Data::Stag node lazily;
always use node()
t
o
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfiel
d
s
add a fe
w
new
(untested) URLAPI parameters
commit
|
commitdiff
|
tree
2008-09-14
cjfield
s
use direct object s
y
nta
x
commit
|
commitdiff
|
tree
2008-09-09
cjfiel
d
s
bu
g
25
7
9
commit
|
commitdiff
|
tree
2008-09-09
cjfield
s
bug
2580
commit
|
commitdiff
|
tree
2008-08-29
c
jf
i
elds
Allow other Bio::SeqFeature::Collection
I
commit
|
commitdiff
|
tree
2008-08-28
cjfields
[bug 2576]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
grep not
n
eeded
(
check for
o
ntology
is
i
n O
n
tology
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfi
e
lds
[bug
257
3
]
commit
|
commitdiff
|
tree
2008-08-27
c
j
fie
l
ds
U
p
d
ate
d
o
c
ume
n
tation
commit
|
commitdiff
|
tree
2008-08-27
cjfields
comp
l
e
t
e s
e
ntence
commit
|
commitdiff
|
tree
2008-08-25
cjfields
Add some print
_
*
methods for einfo,
e
summary, et
c
.
commit
|
commitdiff
|
tree
2008-08-21
cjfields
* write PROJECT support
commit
|
commitdiff
|
tree
2008-08-21
cjfield
s
a
d
d PROJECT s
u
p
po
r
t (bug 2569)
commit
|
commitdiff
|
tree
2008-08-05
c
jf
i
eld
s
For new NCBI blasttable format
commit
|
commitdiff
|
tree
2008-08-05
c
j
fields
Previous changes ki
l
l
ed RemoteBlast again; make a li
t
tle
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
c
jfields
Ad
d
a
f
ew new GET/PUT par
a
me
t
ers
.
commit
|
commitdiff
|
tree
2008-08-04
cjfield
s
Sequences wer
e
n't
b
ei
n
g p
a
rsed c
o
rrectly;
un
f
ortunately
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjf
i
elds
te
s
ts
should
u
se
is/i
s
nt when poss
i
ble, no
t
o
k
()
commit
|
commitdiff
|
tree
2008-07-30
cjfields
revert Roy's patch (my bad)
commit
|
commitdiff
|
tree
2008-07-30
cjfields
bug
2
556:
commit
|
commitdiff
|
tree
2008-07-30
cjfields
Bug 2546
commit
|
commitdiff
|
tree
2008-07-29
cjfields
b
ug
25
5
5
commit
|
commitdiff
|
tree
2008-07-29
cjfields
bug 25
4
9; fixed sm
a
l
l bug in Bio::Taxon
which doesn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfi
e
lds
add multiple recor
d
su
p
p
or
t
(courtesy of Jorge Duarte
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
cjfields
bulle
t
p
r
o
o
f
test; remote tabular BLAST is
failing
f
o
r
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjf
i
elds
bug 2534
commit
|
commitdiff
|
tree
2008-07-08
cjfields
Can't inherit from
one
s
el
f
commit
|
commitdiff
|
tree
2008-07-08
cj
f
iel
d
s
bug 253
9
commit
|
commitdiff
|
tree
2008-06-17
cj
f
ie
l
ds
bug 2423
commit
|
commitdiff
|
tree
2008-06-17
c
j
fields
bug 2423
commit
|
commitdiff
|
tree
2008-06-14
cjfields
b
ug 2
5
12 (Gene Onto
l
o
gy changes)
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 2519
commit
|
commitdiff
|
tree
2008-06-14
cjfiel
d
s
bu
g
2518
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 2517
commit
|
commitdiff
|
tree
2008-05-27
cjfield
s
RT#12802
(via CP
A
N RT)
commit
|
commitdiff
|
tree
2008-04-22
cj
f
i
elds
b
u
g 2485
a
nd re
l
ated fixes
commit
|
commitdiff
|
tree
2008-04-22
cjf
i
e
lds
correc
t
# of sk
i
pped tests
commit
|
commitdiff
|
tree
2008-04-22
cj
f
i
elds
b
u
g 2490 (small test)
commit
|
commitdiff
|
tree
2008-04-22
c
j
fields
b
ug 2490
commit
|
commitdiff
|
tree
2008-04-22
cjfields
new NCB
I
BLAST UR
L
(works wi
t
h RemoteBlast
.
t
)
commit
|
commitdiff
|
tree
2008-04-22
c
jfields
bug 2490
commit
|
commitdiff
|
tree
2008-04-21
c
j
fields
F
ix failing
t
es
t
s
commit
|
commitdiff
|
tree
2008-04-21
c
j
fields
update
t
es
t
(seq in
rem
o
te db ha
s
cha
n
ged)
commit
|
commitdiff
|
tree
2008-04-21
cjf
i
e
l
ds
bullet-pr
o
of; t
h
is
needs
more strin
g
e
nt
test
s
commit
|
commitdiff
|
tree
2008-04-14
c
jfields
bug
2
484
commit
|
commitdiff
|
tree
2008-04-08
cjfie
l
d
s
bug 2479
commit
|
commitdiff
|
tree
2008-04-08
cjfields
bug 2478
commit
|
commitdiff
|
tree
2008-04-07
cjfiel
d
s
up
d
ates;
m
ay switch some data objec
t
s
over to
(
lig
h
tweight
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjf
i
elds
Ad
d
some test
s
to catch tag naming
commit
|
commitdiff
|
tree
2008-04-02
cjfiel
d
s
Fix bad silent bug w
h
ich d
o
e
s
n'
t
set
e
xon tags c
o
rrectly
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfields
m
e
rge back previous
c
o
mmits from Sendu and I
commit
|
commitdiff
|
tree
2008-04-02
cjf
i
el
d
s
get rid of variable redefined warnings
commit
|
commitdiff
|
tree
2008-04-02
c
j
f
ields
tes
t
n
o
t matchi
n
g
error message (oops!)
commit
|
commitdiff
|
tree
2008-04-02
cjfields
RefSe
q
redi
r
ection now
requires expl
i
c
i
t setting
(
n
ote
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
c
j
f
ields
Squash
uninit
.
val
u
e warnings
commit
|
commitdiff
|
tree
2008-04-01
cjfields
Remo
v
e extraneous code; upda
t
e docs
commit
|
commitdiff
|
tree
2008-04-01
cj
f
iel
d
s
bug 2466 :
commit
|
commitdiff
|
tree
2008-04-01
cjfields
Make regex m
a
tches safe
r
commit
|
commitdiff
|
tree
2008-03-28
cjfields
add some seq_inds() tests (appear
s
f
i
n
e)
commit
|
commitdiff
|
tree
2008-03-28
cjfields
* rev
e
rt symbol passing (forgot qu
e
ry and hit have
.
.
.
commit
|
commitdiff
|
tree
2008-03-28
cjf
i
elds
* Allow ga
p
s
ymb
o
l
to be set
commit
|
commitdiff
|
tree
2008-03-27
cjf
i
e
l
ds
r
emov
e
extraneous comm
e
nt
commit
|
commitdiff
|
tree
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