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
typo
2008-09-16
cjfields
typo
commit
|
commitdiff
|
tree
2008-09-15
cjfie
l
ds
remove debugging stateme
n
t
commit
|
commitdiff
|
tree
2008-09-15
cjfields
pa
r
tial fix fo
r
ar
p
(-end now works and counts ? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
c
jfields
-end parame
t
e
r
does not take gaps into account
commit
|
commitdiff
|
tree
2008-09-15
cjfie
l
ds
*
a
lways war
n
about passing wrong end() coordinate
commit
|
commitdiff
|
tree
2008-09-14
cjfields
C
r
eate
D
ata::Stag n
o
de lazily;
a
l
ways use
node() to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfields
add a few
n
ew (u
n
tested) URL
A
PI param
e
ters
commit
|
commitdiff
|
tree
2008-09-14
cjfields
use direct
o
bject syntax
commit
|
commitdiff
|
tree
2008-09-09
c
j
f
ields
bug 2579
commit
|
commitdiff
|
tree
2008-09-09
c
jf
i
elds
bug 2580
commit
|
commitdiff
|
tree
2008-08-29
cjfields
A
l
low other Bio:
:
S
e
qFe
a
ture::CollectionI
commit
|
commitdiff
|
tree
2008-08-28
cjfields
[bug
2
576]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
gre
p
n
ot
n
e
e
ded
(
chec
k
for ont
o
logy is i
n
Onto
l
ogy
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfields
[bug
2
573]
commit
|
commitdiff
|
tree
2008-08-27
c
jfields
Update documentat
i
on
commit
|
commitdiff
|
tree
2008-08-27
cjfields
complete sentence
commit
|
commitdiff
|
tree
2008-08-25
cjfiel
d
s
Add so
m
e prin
t
_* m
e
thods for
einfo
,
esummary,
e
t
c
.
commit
|
commitdiff
|
tree
2008-08-21
cjfields
* write PROJECT s
u
pport
commit
|
commitdiff
|
tree
2008-08-21
c
j
f
iel
d
s
a
dd PROJECT
s
upport (
b
ug 2569)
commit
|
commitdiff
|
tree
2008-08-05
cjfields
For new NC
B
I blastt
a
ble forma
t
commit
|
commitdiff
|
tree
2008-08-05
cj
f
ields
Previous changes
k
illed RemoteB
l
ast again; ma
k
e a little
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Add a
f
ew new GET/PUT
p
arameters
.
commit
|
commitdiff
|
tree
2008-08-04
cjfiel
d
s
Sequences
w
e
ren
'
t being
p
arsed correctl
y
;
u
nfortunat
e
ly
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfiel
d
s
tests sho
u
ld
u
se
i
s
/isnt when
p
o
ssible,
n
ot ok()
commit
|
commitdiff
|
tree
2008-07-30
cj
f
ields
r
e
v
ert
Ro
y
's
patch (my ba
d
)
commit
|
commitdiff
|
tree
2008-07-30
cjfields
bug
2556:
commit
|
commitdiff
|
tree
2008-07-30
cjfields
Bu
g
254
6
commit
|
commitdiff
|
tree
2008-07-29
cjfie
l
ds
bug 2
5
55
commit
|
commitdiff
|
tree
2008-07-29
cjfields
bu
g
2549; fix
e
d
smal
l
b
u
g in Bio::Ta
x
on which doesn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfields
add m
u
ltiple
r
e
c
ord support (court
e
s
y of Jor
g
e Du
a
r
t
e
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
cjfields
b
u
l
l
e
tpro
o
f tes
t
; remot
e
tabular
BLAST is faili
n
g f
o
r
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjfields
bug 2534
commit
|
commitdiff
|
tree
2008-07-08
cj
f
ields
Ca
n
't in
h
er
i
t from
onese
l
f
commit
|
commitdiff
|
tree
2008-07-08
cjfiel
d
s
bug 2539
commit
|
commitdiff
|
tree
2008-06-17
cjfields
b
ug 2423
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bug
2
4
23
commit
|
commitdiff
|
tree
2008-06-14
c
jf
i
elds
bug 2512 (Gene Ontology cha
n
g
e
s)
commit
|
commitdiff
|
tree
2008-06-14
c
jfields
bug 2519
commit
|
commitdiff
|
tree
2008-06-14
c
j
f
ields
bug 2518
commit
|
commitdiff
|
tree
2008-06-14
c
j
f
ields
bug 2517
commit
|
commitdiff
|
tree
2008-05-27
cjfiel
d
s
RT
#
12802 (via C
P
AN RT)
commit
|
commitdiff
|
tree
2008-04-22
cj
f
ields
bug 2485 and rel
a
ted fixes
commit
|
commitdiff
|
tree
2008-04-22
cj
f
ields
correct #
o
f skipped te
s
t
s
commit
|
commitdiff
|
tree
2008-04-22
cjf
i
el
d
s
bug
2490 (small
test)
commit
|
commitdiff
|
tree
2008-04-22
cj
f
ields
b
ug 24
9
0
commit
|
commitdiff
|
tree
2008-04-22
cjfields
new NCBI
B
L
A
ST URL (works
wi
t
h
Rem
o
teBlast
.
t)
commit
|
commitdiff
|
tree
2008-04-22
cjfields
b
u
g 2490
commit
|
commitdiff
|
tree
2008-04-21
c
jfield
s
F
ix failin
g
tests
commit
|
commitdiff
|
tree
2008-04-21
cjfields
up
d
ate test (seq
i
n
r
emote db has cha
n
ged
)
commit
|
commitdiff
|
tree
2008-04-21
cjfield
s
bullet
-
pr
o
of; this n
e
ed
s
mo
r
e st
r
in
g
ent
tests
commit
|
commitdiff
|
tree
2008-04-14
c
j
fi
e
l
ds
bug 2484
commit
|
commitdiff
|
tree
2008-04-08
cjfie
l
ds
bug 2
4
79
commit
|
commitdiff
|
tree
2008-04-08
cjfi
e
lds
bug 2
4
78
commit
|
commitdiff
|
tree
2008-04-07
cj
f
ields
updates; m
a
y sw
i
tch s
o
me data obj
e
cts
o
ver
t
o (ligh
t
weight
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cj
f
ields
Add
some tests t
o
catch tag nami
n
g
commit
|
commitdiff
|
tree
2008-04-02
cj
f
i
e
lds
Fix
b
ad s
i
lent bug whi
c
h doesn't set exon
t
ags correctly
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
c
j
fields
merge ba
c
k previous commits from Sendu and I
commit
|
commitdiff
|
tree
2008-04-02
cjfi
e
lds
ge
t
rid of variable red
e
f
i
ned warn
i
ngs
commit
|
commitdiff
|
tree
2008-04-02
cjfields
test not matching erro
r
message (oops!)
commit
|
commitdiff
|
tree
2008-04-02
cjfields
Re
f
Seq redirection now requ
i
res
e
xplicit setting (note
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfie
l
ds
Squash unini
t
.
value warnings
commit
|
commitdiff
|
tree
2008-04-01
cjfields
Remo
v
e ex
t
ran
e
ous code; up
d
ate docs
commit
|
commitdiff
|
tree
2008-04-01
cjfiel
d
s
bug 2466 :
commit
|
commitdiff
|
tree
2008-04-01
cjfiel
d
s
M
a
ke regex
matches
s
afer
commit
|
commitdiff
|
tree
2008-03-28
cjfields
ad
d
s
o
me
seq_inds()
t
ests (appears
f
i
n
e)
commit
|
commitdiff
|
tree
2008-03-28
cjfields
* revert
s
ymbol passing (forgot query and hit have
.
.
.
commit
|
commitdiff
|
tree
2008-03-28
cjfield
s
* Allow gap
s
ymbol to be se
t
commit
|
commitdiff
|
tree
2008-03-27
cjfields
remove extran
e
ous
c
omment
commit
|
commitdiff
|
tree
2008-03-27
cjfiel
d
s
us
i
ng
s
eq_inds() with
'gaps' now repeats
s
equence indic
e
s
.
.
.
commit
|
commitdiff
|
tree
2008-03-27
cjfi
e
lds
Collapse repeated
s
equence indices into one position
commit
|
commitdiff
|
tree
2008-03-27
cjfields
Marc's bug from
m
ail
l
ist; repeat the seq pos
i
tio
n
.
.
.
commit
|
commitdiff
|
tree
2008-03-25
c
j
fiel
d
s
bug 2473
(
wi
t
h
tes
t
s)
commit
|
commitdiff
|
tree
2008-03-04
cjfields
bug
1707
commit
|
commitdiff
|
tree
2008-03-03
cjfield
s
b
u
g 2465
commit
|
commitdiff
|
tree
2008-03-03
c
j
fields
bu
g
2449
commit
|
commitdiff
|
tree
2008-03-03
cjfields
s
o
m
e
more fo
r
bug 2349
commit
|
commitdiff
|
tree
2008-03-03
cjfields
parti
a
l fix f
o
r bug 2
4
39
commit
|
commitdiff
|
tree
2008-03-02
cj
f
ield
s
Bug 237
8
commit
|
commitdiff
|
tree
2008-03-01
cjfields
f
ix u
n
def
.
var
i
abl
e
issue w
h
e
n no ancestor
indic
a
t
e
d
.
.
.
commit
|
commitdiff
|
tree
2008-03-01
cjfie
l
ds
add s
o
me fle
x
ibi
l
ity f
o
r name leng
t
h, de
f
aulting
t
o 1
0
commit
|
commitdiff
|
tree
2008-03-01
cjfields
bug 2356 (ch
e
ck for
c
orre
c
t n
u
mbe
r
with
m
ultiple
tree
s
)
commit
|
commitdiff
|
tree
2008-03-01
c
j
f
i
e
lds
b
ug
2356
commit
|
commitdiff
|
tree
2008-03-01
cjf
i
elds
ad
d
driver/han
d
ler support (will clean t
h
ese up mo
r
e
.
.
.
commit
|
commitdiff
|
tree
2008-03-01
cj
f
ields
add
some docs
commit
|
commitdiff
|
tree
2008-03-01
cj
f
iel
d
s
adde
d
p
rototype-
c
hecking method (bug
2
179)
commit
|
commitdiff
|
tree
2008-03-01
c
jfields
cl
e
an up inheritance tree;
a
dd remote
d
a
t
abase test
commit
|
commitdiff
|
tree
2008-02-29
cjfi
e
lds
Add i
n
support for
grabbing most current data v
i
a ft
p
.
.
.
commit
|
commitdiff
|
tree
2008-02-29
cjfields
parse
r
for neo
/
p
r
oto
t
ype format
fr
o
m R
E
BAS
E
commit
|
commitdiff
|
tree
2008-02-29
cjfields
bug 2179
commit
|
commitdiff
|
tree
2008-02-29
cjfiel
d
s
bug 2
1
28
commit
|
commitdiff
|
tree
2008-02-29
cjfie
l
ds
Note about XML format
(
related to bug
2018)
commit
|
commitdiff
|
tree
2008-02-28
cjfields
fix Han
d
ler t
e
sts
commit
|
commitdiff
|
tree
2008-02-28
cjfie
l
ds
*
I
mplement StructureValue-like
g
et_all
_
v
a
lues() (flatten
e
d
.
.
.
commit
|
commitdiff
|
tree
2008-02-28
cjfields
add Dat
a
::Stag to require (may cha
n
g
e to re
c
ommend
.
.
.
commit
|
commitdiff
|
tree
2008-02-28
cjf
i
elds
m
i
nor word wrapping for error
m
e
ssa
g
e
commit
|
commitdiff
|
tree
2008-02-28
cjfie
l
ds
bug 1825
commit
|
commitdiff
|
tree
2008-02-28
c
jfiel
d
s
bug 1825: updating swiss
.
pm/tests t
o
try
o
ut Ta
g
Tree
.
.
.
commit
|
commitdiff
|
tree
2008-02-28
cjfields
c
h
e
ck tagtree
in
c
oll
e
c
t
io
n
commit
|
commitdiff
|
tree
2008-02-28
cjfields
More tests
commit
|
commitdiff
|
tree
2008-02-27
c
jfiel
d
s
b
u
g 2462
commit
|
commitdiff
|
tree
next