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bug 2549; fixed small bug in Bio::Taxon which doesn't catch -common_name
2008-07-29
cjfie
l
ds
b
ug 25
4
9
;
fixed small bug in Bio::Taxon whi
c
h
doesn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfie
l
ds
add multiple re
c
ord support (c
o
urtesy of
J
o
rge Duar
t
e
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
c
jfields
bulletproof te
s
t; remote tab
u
lar
B
LAST is failing
f
o
r
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjfields
bug 2534
commit
|
commitdiff
|
tree
2008-07-08
cjfields
C
a
n't inhe
r
it from oneself
commit
|
commitdiff
|
tree
2008-07-08
cjfiel
d
s
bug 253
9
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bug 2423
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bug
2
423
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 2
5
12 (
G
ene
O
ntolo
g
y changes)
commit
|
commitdiff
|
tree
2008-06-14
c
jfield
s
bug
2
5
1
9
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 2518
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 2
5
17
commit
|
commitdiff
|
tree
2008-05-27
cjfie
l
ds
RT#12802 (v
i
a CPA
N
RT)
commit
|
commitdiff
|
tree
2008-04-22
cjfields
b
ug
2485 an
d
related fixes
commit
|
commitdiff
|
tree
2008-04-22
c
jfields
correct # o
f
skipped t
e
s
ts
commit
|
commitdiff
|
tree
2008-04-22
c
j
fields
bug 24
9
0
(small
t
est)
commit
|
commitdiff
|
tree
2008-04-22
cjfie
l
ds
b
u
g
24
9
0
commit
|
commitdiff
|
tree
2008-04-22
c
j
fi
e
l
d
s
n
e
w
N
CBI BLAST UR
L
(works w
i
th Re
m
oteBlast
.
t)
commit
|
commitdiff
|
tree
2008-04-22
cj
f
ield
s
b
u
g
2490
commit
|
commitdiff
|
tree
2008-04-21
cjfields
Fix failing
t
ests
commit
|
commitdiff
|
tree
2008-04-21
cjfields
updat
e
test (seq in remote db has changed
)
commit
|
commitdiff
|
tree
2008-04-21
cjfields
b
u
llet
-
proof; this n
e
eds mo
r
e stringent tests
commit
|
commitdiff
|
tree
2008-04-14
cjfiel
d
s
bug 2484
commit
|
commitdiff
|
tree
2008-04-08
cjfi
e
l
d
s
bug
2479
commit
|
commitdiff
|
tree
2008-04-08
cjfields
bug
2478
commit
|
commitdiff
|
tree
2008-04-07
cjfield
s
u
p
dates; may switch
s
ome d
a
t
a
obj
e
cts over to (
l
igh
t
wei
g
ht
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfields
A
dd some tests to
catch tag naming
commit
|
commitdiff
|
tree
2008-04-02
cjfields
F
i
x bad si
l
ent bu
g
which d
o
e
s
n'
t
set exon tags corr
e
ctly
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfields
m
e
rge back
previous commits from
S
e
ndu
and I
commit
|
commitdiff
|
tree
2008-04-02
cjfields
get rid of variable redef
i
ned warn
i
n
g
s
commit
|
commitdiff
|
tree
2008-04-02
cjfi
e
lds
test
not matching er
r
or message (oop
s
!)
commit
|
commitdiff
|
tree
2008-04-02
c
j
f
ields
RefSeq redirection now requires explicit
s
e
tting (no
t
e
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cj
f
iel
d
s
S
quash unini
t
.
valu
e
warnings
commit
|
commitdiff
|
tree
2008-04-01
cjfields
R
e
move extraneous code; update docs
commit
|
commitdiff
|
tree
2008-04-01
cj
f
ields
bug 24
6
6 :
commit
|
commitdiff
|
tree
2008-04-01
cjfields
M
a
ke
regex matches safe
r
commit
|
commitdiff
|
tree
2008-03-28
cjf
i
elds
add some se
q
_
in
d
s() tests (appears fine)
commit
|
commitdiff
|
tree
2008-03-28
cjfields
*
r
evert sy
m
bo
l
passing (forgot quer
y
and hit
hav
e
.
.
.
commit
|
commitdiff
|
tree
2008-03-28
cjfields
* Allow gap symbol to be set
commit
|
commitdiff
|
tree
2008-03-27
cj
f
i
elds
r
e
mo
v
e extr
a
n
e
ous comment
commit
|
commitdiff
|
tree
2008-03-27
cjfields
us
i
ng seq_inds() wi
t
h 'gap
s
' now repeats sequence indices
.
.
.
commit
|
commitdiff
|
tree
2008-03-27
cjfields
Collapse repeated sequence indices in
t
o one position
commit
|
commitdiff
|
tree
2008-03-27
cjfields
M
a
rc's bug
f
r
o
m mai
l
list; repeat the s
e
q
position
.
.
.
commit
|
commitdiff
|
tree
2008-03-25
cjfields
bug 2473 (wi
t
h tests)
commit
|
commitdiff
|
tree
2008-03-04
cjfi
e
lds
b
ug 1707
commit
|
commitdiff
|
tree
2008-03-03
cjfields
b
ug 2465
commit
|
commitdiff
|
tree
2008-03-03
cjfields
bug 2449
commit
|
commitdiff
|
tree
2008-03-03
cjf
i
elds
s
ome
m
ore for bug 2349
commit
|
commitdiff
|
tree
2008-03-03
cjfields
p
a
rtial fix
f
or
bug
2
439
commit
|
commitdiff
|
tree
2008-03-02
c
jfield
s
Bug 2378
commit
|
commitdiff
|
tree
2008-03-01
cjf
i
elds
fix undef
.
variable
i
ssue when n
o
ancestor ind
i
cated
.
.
.
commit
|
commitdiff
|
tree
2008-03-01
cjf
i
elds
a
dd some flexi
b
ility for name length, defaultin
g
to 10
commit
|
commitdiff
|
tree
2008-03-01
cjfields
bug 2356 (check for correct numb
e
r
with multiple tree
s
)
commit
|
commitdiff
|
tree
2008-03-01
cj
f
ie
l
ds
b
u
g 2356
commit
|
commitdiff
|
tree
2008-03-01
cj
f
i
e
lds
add
driv
e
r/handler support (will clean
t
h
e
se
u
p more
.
.
.
commit
|
commitdiff
|
tree
2008-03-01
cjfields
a
d
d
s
o
m
e d
o
cs
commit
|
commitdiff
|
tree
2008-03-01
cjfi
e
lds
added prototype
-
checking
m
ethod (bug 21
7
9)
commit
|
commitdiff
|
tree
2008-03-01
cjfields
clean
u
p inh
e
ritance t
r
ee; add remo
t
e dat
a
ba
s
e test
commit
|
commitdiff
|
tree
2008-02-29
cjfields
Add in support for grabbing
mos
t
cur
r
e
n
t dat
a
via ftp
.
.
.
commit
|
commitdiff
|
tree
2008-02-29
cjfields
parser for n
e
o/prototype forma
t
from REBAS
E
commit
|
commitdiff
|
tree
2008-02-29
c
j
fi
e
lds
bu
g
2
1
7
9
commit
|
commitdiff
|
tree
2008-02-29
cjfields
bug 2128
commit
|
commitdiff
|
tree
2008-02-29
cjfields
Note
ab
o
ut XML forma
t
(relat
e
d to bug
2018)
commit
|
commitdiff
|
tree
2008-02-28
c
j
fields
fix Handler t
e
sts
commit
|
commitdiff
|
tree
2008-02-28
cjfield
s
* Implement StructureValue-like ge
t
_
a
ll_values() (
f
lattened
.
.
.
commit
|
commitdiff
|
tree
2008-02-28
cjfields
add Da
t
a:
:
S
tag to r
e
q
uire (may ch
a
nge to recommend
.
.
.
commit
|
commitdiff
|
tree
2008-02-28
cjfields
m
i
nor word wrapping fo
r
error message
commit
|
commitdiff
|
tree
2008-02-28
cjf
i
elds
bug 182
5
commit
|
commitdiff
|
tree
2008-02-28
cjfiel
d
s
b
ug 18
2
5:
u
pdating swiss
.
pm/tests to try out
T
agTree
.
.
.
commit
|
commitdiff
|
tree
2008-02-28
cj
f
ields
c
heck tagtree
i
n collectio
n
commit
|
commitdiff
|
tree
2008-02-28
cjfield
s
More tests
commit
|
commitdiff
|
tree
2008-02-27
cjfiel
d
s
bug 2462
commit
|
commitdiff
|
tree
2008-02-27
c
j
f
ields
Ch
a
nge
name
t
o TagTr
e
e
commit
|
commitdiff
|
tree
2008-02-27
cj
f
ields
change
s
and a
d
ditions (can't
f
airly
i
m
plement StructureValue
.
.
.
commit
|
commitdiff
|
tree
2008-02-27
cj
f
ields
Add some tests, more
to foll
o
w
upon imp
l
ementation
.
.
.
commit
|
commitdiff
|
tree
2008-02-27
cjfields
Re
m
o
ve Data::St
a
g cruft
(use a reimplement
a
tion ins
t
ea
d
)
commit
|
commitdiff
|
tree
2008-02-27
cjf
i
elds
S
t
r
u
cturedTag
- Annotatio
n
I whi
c
h
uses Data
:
:Stag for
.
.
.
commit
|
commitdiff
|
tree
2008-02-27
cjfiel
d
s
add error message
for callbacks if no code
reference
commit
|
commitdiff
|
tree
2008-02-26
cjfiel
d
s
bug 2458
commit
|
commitdiff
|
tree
2008-02-26
c
jfi
e
lds
Russell'
s
fixes
commit
|
commitdiff
|
tree
2008-02-24
cjfields
GN changes
commit
|
commitdiff
|
tree
2008-02-22
cjfields
revert last commit (go
o
d catch
S
e
n
du)
commit
|
commitdiff
|
tree
2008-02-21
cjfi
e
lds
run
t
ests
d
irectly in Build
.
PL
(
d
o
n't
p
ass code refs
.
.
.
commit
|
commitdiff
|
tree
2008-02-21
cjfields
TODO no
w
works
commit
|
commitdiff
|
tree
2008-02-21
c
j
fi
e
lds
f
a
l
l ba
c
k t
o
empty set
commit
|
commitdiff
|
tree
2008-02-21
cjfields
now deprecated
commit
|
commitdiff
|
tree
2008-02-21
cjfields
Se
q
ue
n
ce gained a nucle
o
tide
commit
|
commitdiff
|
tree
2008-02-21
cjfields
bug 2438
.
'X' can't be comp
l
e
t
ely
d
isambiguated from
.
.
.
commit
|
commitdiff
|
tree
2008-02-21
cjfields
add
f
ile
t
e
s
t
, unl
i
nk
i
f already presen
t
commit
|
commitdiff
|
tree
2008-02-21
cjfields
add Graph::Directed
t
o requiremen
t
s f
o
r te
s
ts
commit
|
commitdiff
|
tree
2008-02-21
cjfields
fix
C
UTG te
s
t
s
commit
|
commitdiff
|
tree
2008-02-21
cjfields
Now p
a
s
s
es
tests; added w
a
rn
i
ngs for
no returned exons
.
.
.
commit
|
commitdiff
|
tree
2008-02-20
cj
f
ields
tests for bug 24
5
3
commit
|
commitdiff
|
tree
2008-02-20
cjfiel
d
s
B
ug 2453; n
e
eds tests
commit
|
commitdiff
|
tree
2008-02-20
cjfie
l
ds
Oops
!
Bug
2
4
53
a
gain
.
commit
|
commitdiff
|
tree
2008-02-20
cjfields
small fix for bug 2453, but
se
e
bugzilla for reasons
.
.
.
commit
|
commitdiff
|
tree
2008-02-20
cjf
i
e
l
d
s
bug 24
5
2
commit
|
commitdiff
|
tree
2008-02-19
cjfields
TODO no
w
works
commit
|
commitdiff
|
tree
2008-02-13
cjfiel
d
s
update interface documentat
i
on
commit
|
commitdiff
|
tree
2008-02-13
c
j
fields
not 1
.
5
.
3 (modu
l
es don
'
t work
a
n
y
m
o
r
e)
commit
|
commitdiff
|
tree
next