repo.or.cz
/
bioperl-live.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
small pointer to wiki page (will update along with wiki closer to release)
2008-10-29
cjf
i
elds
[bu
g
2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfields
[b
u
g 2630]
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
eld
s
Fix
unl
i
n
k
()
w
arning
commit
|
commitdiff
|
tree
2008-10-26
cjfi
e
lds
end = start if only st
a
r
t
is passed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
u
se v
a
lid
_
Locatio
n
to check Location s
t
ate
commit
|
commitdiff
|
tree
2008-10-26
c
j
f
i
e
lds
add docs for LocationI m
e
thod val
i
d_Location
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bu
g
2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[
b
ug
2
62
4
]
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
[bug 2621
]
commit
|
commitdiff
|
tree
2008-10-25
cjfields
bu
l
let-
p
roof prot
o
t
ype
test
commit
|
commitdiff
|
tree
2008-10-22
c
jfields
fix fi
l
e properties
commit
|
commitdiff
|
tree
2008-10-22
c
jfields
new mod
u
le
f
or parsing vecscreen -f 3 ou
t
put, courtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfields
add -source for ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfie
l
ds
[bug
2
563]
commit
|
commitdiff
|
tree
2008-10-10
cj
f
i
e
lds
t
ypo
commit
|
commitdiff
|
tree
2008-10-10
cjfiel
d
s
[bug 2
5
19]
commit
|
commitdiff
|
tree
2008-10-10
cjf
i
elds
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
cj
f
i
elds
add svn
t
ag
commit
|
commitdiff
|
tree
2008-10-07
cjfields
TODO's
w
or
k
commit
|
commitdiff
|
tree
2008-10-07
cjf
i
e
l
ds
[
b
u
g 2
6
12
]
commit
|
commitdiff
|
tree
2008-10-07
cjfie
l
d
s
[bug 26
1
2]
commit
|
commitdiff
|
tree
2008-10-02
cjfields
clean up
XMFA parsing, allow spaces in par
s
ing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfields
[BUG] bu
g
2598
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[
BUG] bugfix f
o
r # 2598
(add 'J')
commit
|
commitdiff
|
tree
2008-09-26
cjfield
s
[BUG]
b
ug 2593
commit
|
commitdiff
|
tree
2008-09-26
cjfiel
d
s
[BUG]
f
ix bug
2
5
95
commit
|
commitdiff
|
tree
2008-09-18
c
jfields
Use '
w
arni
n
g_like' for instances
wh
e
re a regex match
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfie
l
d
s
*
No long
e
r a stub
commit
|
commitdiff
|
tree
2008-09-17
cjfields
1965 + 6
-
1
=
1970, not
1
999
commit
|
commitdiff
|
tree
2008-09-17
cjfields
passing TODO's (?!?)
commit
|
commitdiff
|
tree
2008-09-17
c
j
fields
upd
a
te t
e
sts (
s
eq
length chan
g
e in r
e
c
o
r
d
v
e
r
i
fied)
commit
|
commitdiff
|
tree
2008-09-17
cjfields
set
-end to coorespond to
sequ
e
nce end
commit
|
commitdiff
|
tree
2008-09-16
cjfields
te
s
t
result changed (
s
tart
a
lways < end)
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Fix nexus issues
w
it
h
seq
.
ambiguity
symbol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfields
MEGA now rese
t
s $GAP_SYMBOLS and $
O
THER_S
Y
MBOLS
to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
c
j
fiel
d
s
T
e
st
data matche
s
n
e
w
X
MFA
e
xa
m
ple
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
d
s
* XMF
A
alignment doe
s
n't correspond
to
XMF
A
spec (http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfi
e
lds
f
i
x xmfa
.
pm
p
arsi
n
g oops
commit
|
commitdiff
|
tree
2008-09-16
cjfields
make LocatableSeq::end
(
) consistent
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
elds
* fix start/en
d
/
strand
commit
|
commitdiff
|
tree
2008-09-16
c
j
fields
typo
commit
|
commitdiff
|
tree
2008-09-15
c
j
fields
remove de
b
ug
g
i
n
g sta
t
ement
commit
|
commitdiff
|
tree
2008-09-15
cjfields
p
a
rtial fix fo
r
ar
p
(
-end now w
o
rks
a
n
d
counts ? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfi
e
lds
-end parame
t
er does not tak
e
gaps
into acco
u
nt
commit
|
commitdiff
|
tree
2008-09-15
cjfiel
d
s
* always warn
a
bout passing wr
o
ng end() coo
r
dinate
commit
|
commitdiff
|
tree
2008-09-14
cjfields
Create Data::Stag nod
e
l
azi
l
y; always use
n
ode
(
) to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfiel
d
s
add
a few
new (untested)
U
RLA
P
I parameters
commit
|
commitdiff
|
tree
2008-09-14
cjfiel
d
s
use
d
irect
o
bject syntax
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 2579
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 2580
commit
|
commitdiff
|
tree
2008-08-29
cjfields
Allow other Bio::Seq
F
eature::CollectionI
commit
|
commitdiff
|
tree
2008-08-28
cjfie
l
d
s
[bu
g
2576]
commit
|
commitdiff
|
tree
2008-08-27
cjf
i
elds
grep not neede
d
(check for ontology
i
s in Ontology
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfie
l
ds
[bu
g
2573]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
Upd
a
te documenta
t
i
o
n
commit
|
commitdiff
|
tree
2008-08-27
cjf
i
elds
complete sentence
commit
|
commitdiff
|
tree
2008-08-25
cjfields
Ad
d
so
m
e pr
i
nt_* meth
o
d
s
for einfo,
e
su
m
mary, etc
.
commit
|
commitdiff
|
tree
2008-08-21
cjfield
s
* write
P
ROJECT s
u
pport
commit
|
commitdiff
|
tree
2008-08-21
cjfie
l
ds
ad
d
PROJECT support (bug 2569)
commit
|
commitdiff
|
tree
2008-08-05
cjfi
e
lds
For new NCBI blasttable forma
t
commit
|
commitdiff
|
tree
2008-08-05
c
j
fie
l
ds
Previous changes killed
Re
m
o
t
eBl
a
st again;
mak
e
a
litt
l
e
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Ad
d
a few new GET/PUT parameters
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Sequences weren't being
p
ars
e
d correctly; unfortunate
l
y
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjf
i
elds
tests should u
s
e
i
s/isnt w
h
en poss
i
ble, no
t
o
k
()
commit
|
commitdiff
|
tree
2008-07-30
c
j
fiel
d
s
re
v
e
rt Ro
y
's patch (m
y
bad)
commit
|
commitdiff
|
tree
2008-07-30
c
jfie
l
d
s
b
u
g 255
6
:
commit
|
commitdiff
|
tree
2008-07-30
cjfields
Bug 2546
commit
|
commitdiff
|
tree
2008-07-29
cjfields
bug 2
5
55
commit
|
commitdiff
|
tree
2008-07-29
cjfields
bug 2549; f
i
xed small bug
in B
i
o::Taxo
n
w
hich doesn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfiel
d
s
add multiple record suppor
t
(courtesy of
J
orge
D
ua
r
te
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
c
jfiel
d
s
bulletproof test; remote tabular
B
LAST is fa
i
ling for
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cj
f
i
elds
b
ug 2534
commit
|
commitdiff
|
tree
2008-07-08
cjfields
Can't in
h
erit from
on
e
s
e
lf
commit
|
commitdiff
|
tree
2008-07-08
cjf
i
elds
bug 2539
commit
|
commitdiff
|
tree
2008-06-17
c
jfields
bug 2423
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bug 2423
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bu
g
2512 (Gen
e
Ontol
o
gy c
h
a
nges)
commit
|
commitdiff
|
tree
2008-06-14
cjfiel
d
s
bu
g
2519
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 2518
commit
|
commitdiff
|
tree
2008-06-14
c
j
field
s
bug 2517
commit
|
commitdiff
|
tree
2008-05-27
cjfields
RT#128
0
2 (via CPAN RT)
commit
|
commitdiff
|
tree
2008-04-22
c
jfields
b
u
g
2485 and related fix
e
s
commit
|
commitdiff
|
tree
2008-04-22
cjfields
correct # of skipped tests
commit
|
commitdiff
|
tree
2008-04-22
cjfields
bug 2490 (small t
e
s
t
)
commit
|
commitdiff
|
tree
2008-04-22
cj
f
ields
bug 2490
commit
|
commitdiff
|
tree
2008-04-22
cjfields
new NCBI
B
L
A
S
T
URL (works with R
e
moteBlast
.
t)
commit
|
commitdiff
|
tree
2008-04-22
cjfi
e
lds
bug 2
4
90
commit
|
commitdiff
|
tree
2008-04-21
c
jf
i
elds
Fi
x
fail
i
n
g
tests
commit
|
commitdiff
|
tree
2008-04-21
cjfields
u
p
date test (seq in re
m
o
t
e db has changed)
commit
|
commitdiff
|
tree
2008-04-21
c
jfie
l
ds
bullet-
p
roof; this need
s
more stringent tes
t
s
commit
|
commitdiff
|
tree
2008-04-14
cjfi
e
lds
bug
2
484
commit
|
commitdiff
|
tree
2008-04-08
cjfie
l
ds
b
ug 2479
commit
|
commitdiff
|
tree
2008-04-08
cj
f
ields
bug 24
7
8
commit
|
commitdiff
|
tree
2008-04-07
cjfields
upda
t
es; may switch some data objects over to
(
lightweight
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfields
A
d
d s
o
me t
e
sts to catc
h
t
a
g
nami
n
g
commit
|
commitdiff
|
tree
2008-04-02
cjfields
F
ix bad s
i
len
t
bug
which
doesn't
set exon
tag
s
correctly
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
c
jfields
mer
g
e
b
ack pre
v
i
o
us commits from Sendu and I
commit
|
commitdiff
|
tree
2008-04-02
cjfields
get r
i
d
o
f
v
a
ria
b
le red
e
fined warnings
commit
|
commitdiff
|
tree
2008-04-02
cj
f
ields
test not matching erro
r
message (oops
!
)
commit
|
commitdiff
|
tree
next