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
move results2hash test utility sub to SearchUtils
2008-11-17
cjfields
m
o
ve results2
h
ash test
utility su
b
to Se
a
rchUtils
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[bug
2
66
3
]
commit
|
commitdiff
|
tree
2008-11-16
cjfields
p
e
rltidy
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[bug 2635]
commit
|
commitdiff
|
tree
2008-11-14
cjfields
[bug
2
656]
commit
|
commitdiff
|
tree
2008-11-11
cjfi
e
lds
remo
v
e
d
ebuggi
n
g lines
commit
|
commitdiff
|
tree
2008-11-11
c
j
field
s
remove fixed ve
r
bose flag
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2650
]
commit
|
commitdiff
|
tree
2008-11-11
c
j
fi
e
lds
Cl
a
rify resul
t
_count (discussions on m
a
il list per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
elds
[bug 2632]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[
b
ug
2645
]
commit
|
commitdiff
|
tree
2008-11-04
cjfield
s
wrap
text
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse 'Feature
s
in this part o
f
subject sequenc
e
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfie
l
d
s
* parse 'Features
in this part of
s
ubject sequ
e
nce
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfiel
d
s
[
bug
2
632]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
fix se
q
_
i
n
d
s
()
;
wasn't
c
al
l
ing identical resid
u
es fo
r
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[bug
2
6
33
]
commit
|
commitdiff
|
tree
2008-10-28
cj
f
ields
[
bu
g
2
6
3
0]
commit
|
commitdiff
|
tree
2008-10-26
cj
f
ields
Fix unlink() w
a
rning
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
end = start if
only start is pas
s
e
d
commit
|
commitdiff
|
tree
2008-10-26
cjfi
e
lds
use valid_Location to
c
h
eck Lo
c
ation state
commit
|
commitdiff
|
tree
2008-10-26
cjfields
add docs for LocationI method valid_Location
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
[bug 262
1
]
commit
|
commitdiff
|
tree
2008-10-26
cj
f
ield
s
[bu
g
2
6
2
4]
commit
|
commitdiff
|
tree
2008-10-26
c
j
field
s
[
bug 2621]
commit
|
commitdiff
|
tree
2008-10-25
cjfields
bullet-proof
prot
o
t
y
pe t
e
st
commit
|
commitdiff
|
tree
2008-10-22
c
jfi
e
l
ds
fix file
pro
p
e
r
ties
commit
|
commitdiff
|
tree
2008-10-22
cjfields
n
ew
m
odule for parsi
n
g vecscreen
-
f
3 output, c
o
urtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfiel
d
s
add
-source
for ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfie
l
ds
[bug 2
5
63]
commit
|
commitdiff
|
tree
2008-10-10
c
j
fields
t
ypo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-10
cjf
i
elds
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
c
j
field
s
add svn tag
commit
|
commitdiff
|
tree
2008-10-07
cj
f
ields
T
O
D
O
's wor
k
commit
|
commitdiff
|
tree
2008-10-07
cjfi
e
lds
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-07
cjf
i
elds
[
b
ug 2612
]
commit
|
commitdiff
|
tree
2008-10-02
c
j
fields
clean up XMFA parsing, a
l
low s
p
aces in
parsing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfiel
d
s
[BUG] bug 2598
commit
|
commitdiff
|
tree
2008-09-26
c
j
f
i
eld
s
[BUG] bugfix
f
or # 25
9
8
(add
'J')
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BUG] bug 2593
commit
|
commitdiff
|
tree
2008-09-26
cj
f
ields
[BUG]
f
i
x bug 2595
commit
|
commitdiff
|
tree
2008-09-18
cjfields
Use 'warning_lik
e
'
f
or instanc
e
s where
a regex match
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfields
* No longer a
s
tub
commit
|
commitdiff
|
tree
2008-09-17
cjfields
1965 +
6
-
1
= 19
7
0,
n
o
t 19
9
9
commit
|
commitdiff
|
tree
2008-09-17
c
j
fields
pas
s
ing TODO's (?!?)
commit
|
commitdiff
|
tree
2008-09-17
cjfie
l
ds
update test
s
(seq length
c
hange in record
v
erified)
commit
|
commitdiff
|
tree
2008-09-17
cjfields
set -end to coorespond to seq
u
en
c
e
end
commit
|
commitdiff
|
tree
2008-09-16
cjfiel
d
s
test re
s
u
l
t changed (star
t
always
< end)
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Fix nexu
s
is
s
ues with seq
.
amb
i
gui
t
y symbol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfield
s
M
E
GA now r
e
sets $GAP_SY
M
BOL
S
and $OTHER
_
SYMBOLS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Test
d
ata
m
at
c
hes new XMFA
e
xample
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
elds
* XMFA ali
g
n
ment doesn't corres
p
ond to
XM
F
A spec (http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
fix xmfa
.
pm parsing oo
p
s
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
e
lds
make Locatab
l
e
Se
q
::end() consist
e
nt
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
d
s
* fix st
a
rt/end/
s
trand
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ield
s
t
y
po
commit
|
commitdiff
|
tree
2008-09-15
cjfields
remov
e
debugging statement
commit
|
commitdiff
|
tree
2008-09-15
cjfields
partial fix for arp (-end now works
and counts
?
as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjf
i
e
lds
-en
d
pa
r
ameter does
not ta
k
e gap
s
into acc
o
unt
commit
|
commitdiff
|
tree
2008-09-15
cjfields
*
a
lways war
n
about
passing w
r
ong end(
)
c
oor
d
in
a
t
e
commit
|
commitdiff
|
tree
2008-09-14
c
jfields
Create Data::Stag n
o
d
e la
z
ily; alway
s
use no
d
e
(
)
to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfields
add a few new
(
unteste
d
) URLAPI
para
m
eters
commit
|
commitdiff
|
tree
2008-09-14
cjfields
use
d
i
rect objec
t
synt
a
x
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 2579
commit
|
commitdiff
|
tree
2008-09-09
cjf
i
e
l
ds
bug 2580
commit
|
commitdiff
|
tree
2008-08-29
cjfields
All
o
w other Bio::SeqF
e
ature::
C
o
llecti
o
nI
commit
|
commitdiff
|
tree
2008-08-28
cjfields
[bug 25
7
6]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
g
r
ep not need
e
d
(
c
heck for ontology is in
O
nt
o
l
o
gy
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfields
[bug 2573]
commit
|
commitdiff
|
tree
2008-08-27
cj
f
i
elds
Upda
t
e
d
ocumen
t
ation
commit
|
commitdiff
|
tree
2008-08-27
cjfields
complete sen
t
ence
commit
|
commitdiff
|
tree
2008-08-25
cjfi
e
lds
A
dd some print_* methods
for ein
f
o
, esummary
,
etc
.
commit
|
commitdiff
|
tree
2008-08-21
cjfie
l
d
s
* write PRO
J
ECT support
commit
|
commitdiff
|
tree
2008-08-21
cjf
i
elds
add PROJECT support (bug 2569)
commit
|
commitdiff
|
tree
2008-08-05
cjfields
F
o
r
n
ew NCBI blasttable format
commit
|
commitdiff
|
tree
2008-08-05
cjf
i
elds
Previous changes
killed Remote
B
last
a
g
a
in; make a
l
ittle
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
c
jfields
Ad
d
a few
n
e
w GE
T
/PUT parameters
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Se
q
uences were
n
't being par
s
ed correctly; unfortu
n
ately
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfi
e
l
d
s
tests should use is/is
n
t when possible, not ok()
commit
|
commitdiff
|
tree
2008-07-30
cj
f
ie
l
ds
revert Ro
y
'
s patch
(my
ba
d
)
commit
|
commitdiff
|
tree
2008-07-30
cjfield
s
b
ug 2556:
commit
|
commitdiff
|
tree
2008-07-30
cjf
i
elds
Bug 2546
commit
|
commitdiff
|
tree
2008-07-29
cjfi
e
l
d
s
b
ug 2555
commit
|
commitdiff
|
tree
2008-07-29
cjfie
l
ds
bug 254
9
; fixed small bu
g
in B
i
o::Taxon whi
c
h
doesn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
c
j
fi
e
lds
add mult
i
pl
e
re
c
ord support (courtesy of Jorge Duarte
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
cjfie
l
ds
bulletproof test
;
remo
t
e tabular BLAST is
f
aili
n
g for
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjfields
b
u
g 2534
commit
|
commitdiff
|
tree
2008-07-08
cjfi
e
lds
Can't inherit
from one
s
elf
commit
|
commitdiff
|
tree
2008-07-08
cjfields
bug 2539
commit
|
commitdiff
|
tree
2008-06-17
cjfiel
d
s
bug
2
423
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bu
g
2
4
23
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 251
2
(G
e
ne Ontology changes)
commit
|
commitdiff
|
tree
2008-06-14
c
jfields
b
u
g 2519
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 251
8
commit
|
commitdiff
|
tree
2008-06-14
cjfield
s
bug 2517
commit
|
commitdiff
|
tree
2008-05-27
c
jfields
RT#12802 (
v
ia CPAN RT)
commit
|
commitdiff
|
tree
2008-04-22
c
j
f
ields
bu
g
2485 and related fixes
commit
|
commitdiff
|
tree
2008-04-22
cjfields
corre
c
t
#
o
f skipped tests
commit
|
commitdiff
|
tree
next