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bug 2549; fixed small bug in Bio::Taxon which doesn't catch -common_name
2008-07-29
cjfields
bug 25
4
9;
fi
x
e
d
small
bug in Bio::Taxon whic
h
doesn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfiel
d
s
add multiple re
c
ord
s
upport
(courte
s
y of Jorge Duarte
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
c
jfields
b
u
lletproof test;
rem
o
te
tabular BLA
S
T is failing
for
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjfiel
d
s
bu
g
2534
commit
|
commitdiff
|
tree
2008-07-08
cjfields
Can't inherit from oneself
commit
|
commitdiff
|
tree
2008-07-08
cj
f
i
e
l
d
s
bug 253
9
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bug
2423
commit
|
commitdiff
|
tree
2008-06-17
cjfie
l
d
s
b
u
g 2423
commit
|
commitdiff
|
tree
2008-06-14
c
j
field
s
bug
2
512 (Ge
n
e Ontology changes)
commit
|
commitdiff
|
tree
2008-06-14
c
jf
i
e
ld
s
bug
2
519
commit
|
commitdiff
|
tree
2008-06-14
cjfiel
d
s
bug
2
518
commit
|
commitdiff
|
tree
2008-06-14
cj
f
ields
bu
g
2517
commit
|
commitdiff
|
tree
2008-05-27
cjfields
RT#12802 (via CPAN RT)
commit
|
commitdiff
|
tree
2008-04-22
c
jfi
e
lds
bug 2485
a
n
d rel
a
ted
f
ixes
commit
|
commitdiff
|
tree
2008-04-22
c
j
fields
co
r
r
e
ct # of ski
p
ped t
e
sts
commit
|
commitdiff
|
tree
2008-04-22
cjf
i
e
ld
s
bug 2490
(
s
mall test)
commit
|
commitdiff
|
tree
2008-04-22
cjfields
b
u
g
2
490
commit
|
commitdiff
|
tree
2008-04-22
c
j
fields
ne
w
NCBI BL
A
ST UR
L
(
w
or
k
s with Remo
t
eBlast
.
t
)
commit
|
commitdiff
|
tree
2008-04-22
cjfi
e
lds
bug 2490
commit
|
commitdiff
|
tree
2008-04-21
c
j
field
s
F
ix failing tests
commit
|
commitdiff
|
tree
2008-04-21
cjf
i
elds
update test (seq in r
e
m
ote db has changed)
commit
|
commitdiff
|
tree
2008-04-21
cjfield
s
bullet-proof; this needs
more st
r
i
n
gen
t
tests
commit
|
commitdiff
|
tree
2008-04-14
cjfi
e
ld
s
bu
g
2484
commit
|
commitdiff
|
tree
2008-04-08
cjfiel
d
s
bug 2479
commit
|
commitdiff
|
tree
2008-04-08
cjfie
l
ds
b
u
g 2
4
7
8
commit
|
commitdiff
|
tree
2008-04-07
cjfields
updates; may switch some data objects over to (
l
ightweight
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfields
Add some te
s
ts to catch tag nami
n
g
commit
|
commitdiff
|
tree
2008-04-02
c
jfields
Fix bad silent bu
g
which doesn't
s
e
t exon tag
s
correct
l
y
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfi
e
lds
merge
b
ack
p
reviou
s
commits
f
r
o
m Send
u
and I
commit
|
commitdiff
|
tree
2008-04-02
c
jfields
g
e
t rid
o
f variabl
e
redefined
w
ar
n
ings
commit
|
commitdiff
|
tree
2008-04-02
c
j
f
i
e
l
ds
test not
m
atch
i
ng error
m
e
s
s
a
g
e (oops!)
commit
|
commitdiff
|
tree
2008-04-02
cjfields
RefSeq re
d
irecti
o
n no
w
re
q
uires
e
xplicit se
t
ti
n
g (note
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjf
i
elds
Squash uni
n
i
t
.
va
l
ue warn
i
ngs
commit
|
commitdiff
|
tree
2008-04-01
c
j
field
s
Remove extra
n
eous c
o
de; update docs
commit
|
commitdiff
|
tree
2008-04-01
cjfields
bug 2466 :
commit
|
commitdiff
|
tree
2008-04-01
c
jfields
Make regex ma
t
c
h
es safer
commit
|
commitdiff
|
tree
2008-03-28
cjfields
add some se
q
_inds() tes
t
s (appears fine)
commit
|
commitdiff
|
tree
2008-03-28
cjfield
s
* rev
e
rt s
y
mbol p
a
ssi
n
g (for
g
ot qu
e
ry and
hi
t
have
.
.
.
commit
|
commitdiff
|
tree
2008-03-28
cj
f
ields
* Allow
g
ap
s
ymbol
t
o
be set
commit
|
commitdiff
|
tree
2008-03-27
cj
f
ields
remove e
x
traneous commen
t
commit
|
commitdiff
|
tree
2008-03-27
cjfie
l
ds
us
i
n
g
seq_inds() w
i
th 'gaps' now repeats seque
n
ce indice
s
.
.
.
commit
|
commitdiff
|
tree
2008-03-27
c
jfi
e
lds
Co
l
laps
e
repe
a
ted
sequence indices
i
n
t
o one po
s
i
t
ion
commit
|
commitdiff
|
tree
2008-03-27
cjfields
M
a
rc's bug fro
m
mail l
i
st; rep
e
at the seq position
.
.
.
commit
|
commitdiff
|
tree
2008-03-25
cjfields
bug 2473 (with tests)
commit
|
commitdiff
|
tree
2008-03-04
cjfi
e
lds
bu
g
1707
commit
|
commitdiff
|
tree
2008-03-03
c
j
fi
e
lds
b
ug 246
5
commit
|
commitdiff
|
tree
2008-03-03
cjfields
bug 2449
commit
|
commitdiff
|
tree
2008-03-03
cjfie
l
ds
so
m
e mo
r
e for
bug 234
9
commit
|
commitdiff
|
tree
2008-03-03
c
jfields
partial fix for bug 2439
commit
|
commitdiff
|
tree
2008-03-02
cjfields
Bug 2378
commit
|
commitdiff
|
tree
2008-03-01
cjfields
fix undef
.
variable issue when no ancestor in
d
icate
d
.
.
.
commit
|
commitdiff
|
tree
2008-03-01
cjfields
add some f
l
exibility for na
m
e lengt
h
,
defa
u
lting
t
o 10
commit
|
commitdiff
|
tree
2008-03-01
cjfie
l
ds
bug 2356 (check for cor
r
ect number wit
h
m
ultiple
trees)
commit
|
commitdiff
|
tree
2008-03-01
cjfield
s
bug 2356
commit
|
commitdiff
|
tree
2008-03-01
c
j
fields
a
d
d
d
r
iver/handler supp
o
r
t (wil
l
cle
a
n
t
hese up
more
.
.
.
commit
|
commitdiff
|
tree
2008-03-01
cjfi
e
lds
a
d
d
s
o
me docs
commit
|
commitdiff
|
tree
2008-03-01
cjfields
adde
d
prototype-
c
h
ecking
method (bug
2179)
commit
|
commitdiff
|
tree
2008-03-01
cjfi
e
lds
clean u
p
inheritance tree; a
d
d remot
e
dat
a
b
a
se test
commit
|
commitdiff
|
tree
2008-02-29
c
j
fields
A
d
d
i
n suppor
t
for gr
a
bbing most
current data via
f
tp
.
.
.
commit
|
commitdiff
|
tree
2008-02-29
cjf
i
el
d
s
pars
e
r fo
r
ne
o
/prototype format from REBASE
commit
|
commitdiff
|
tree
2008-02-29
cj
f
iel
d
s
bug 2179
commit
|
commitdiff
|
tree
2008-02-29
cjfiel
d
s
bug 2128
commit
|
commitdiff
|
tree
2008-02-29
cjfield
s
Note about
X
M
L format (re
l
ated to bug
2
018)
commit
|
commitdiff
|
tree
2008-02-28
c
j
fields
fix Handler tests
commit
|
commitdiff
|
tree
2008-02-28
cjfields
* Im
p
l
e
ment
S
tructureValue-like get_all_values() (flattened
.
.
.
commit
|
commitdiff
|
tree
2008-02-28
c
j
fi
e
lds
add
Data::Stag to re
q
ui
r
e (
m
a
y chang
e
to r
e
co
m
mend
.
.
.
commit
|
commitdiff
|
tree
2008-02-28
cjfields
minor
word
w
r
a
pping fo
r
error messag
e
commit
|
commitdiff
|
tree
2008-02-28
c
jfields
bug 1825
commit
|
commitdiff
|
tree
2008-02-28
cjfields
bug 1825: updating swiss
.
p
m
/
tests to try out TagTree
.
.
.
commit
|
commitdiff
|
tree
2008-02-28
cjfields
check
tag
t
ree in collect
i
o
n
commit
|
commitdiff
|
tree
2008-02-28
cjfields
Mo
r
e test
s
commit
|
commitdiff
|
tree
2008-02-27
c
jfi
e
lds
bug 2462
commit
|
commitdiff
|
tree
2008-02-27
cjfields
C
h
a
nge
n
ame to
T
agTree
commit
|
commitdiff
|
tree
2008-02-27
cjfie
l
ds
changes and addition
s
(
can't
f
airly impleme
n
t S
t
r
u
ct
u
reVa
l
ue
.
.
.
commit
|
commitdiff
|
tree
2008-02-27
cjfiel
d
s
Add some tests
,
mo
r
e to
follow upo
n
implementa
t
ion
.
.
.
commit
|
commitdiff
|
tree
2008-02-27
cjfields
Remove Data::St
a
g cr
u
ft (use a reimplementation inste
a
d)
commit
|
commitdiff
|
tree
2008-02-27
cjfiel
d
s
S
t
ructuredTag
-
AnnotationI which us
e
s Data::Stag for
.
.
.
commit
|
commitdiff
|
tree
2008-02-27
cjf
i
elds
ad
d
error mes
s
ag
e
for callbacks if no c
o
de reference
commit
|
commitdiff
|
tree
2008-02-26
cjfields
bug 245
8
commit
|
commitdiff
|
tree
2008-02-26
c
j
fields
Russell's fi
x
es
commit
|
commitdiff
|
tree
2008-02-24
cjf
i
elds
GN changes
commit
|
commitdiff
|
tree
2008-02-22
cjfields
rever
t
last commit (
g
ood
catch Sendu)
commit
|
commitdiff
|
tree
2008-02-21
cjf
i
elds
r
u
n tes
t
s directly in Build
.
PL (don't pass code
r
efs
.
.
.
commit
|
commitdiff
|
tree
2008-02-21
c
jfie
l
ds
TOD
O
n
ow works
commit
|
commitdiff
|
tree
2008-02-21
cjfields
fall ba
c
k
to empty s
e
t
commit
|
commitdiff
|
tree
2008-02-21
c
jfields
now depre
c
ated
commit
|
commitdiff
|
tree
2008-02-21
cjfie
l
d
s
Sequence gained a nuc
l
eotide
commit
|
commitdiff
|
tree
2008-02-21
cjfie
l
ds
bug
2
438
.
'X' can
'
t be complete
l
y disamb
i
guate
d
from
.
.
.
commit
|
commitdiff
|
tree
2008-02-21
cjfields
add file test,
u
nlink if
already presen
t
commit
|
commitdiff
|
tree
2008-02-21
cjfields
add Graph::Dire
c
t
ed to
r
e
q
uirements for tests
commit
|
commitdiff
|
tree
2008-02-21
c
j
fields
fix CU
T
G tests
commit
|
commitdiff
|
tree
2008-02-21
cjfi
e
ld
s
Now passes tests; ad
d
ed war
n
ings for no ret
u
rn
e
d exons
.
.
.
commit
|
commitdiff
|
tree
2008-02-20
cjfield
s
tests
f
or bug 24
5
3
commit
|
commitdiff
|
tree
2008-02-20
cjfields
Bug 2453; needs tests
commit
|
commitdiff
|
tree
2008-02-20
cjfields
Oops
!
Bug
2
453 again
.
commit
|
commitdiff
|
tree
2008-02-20
cjfie
l
ds
sm
a
ll
f
ix for bug 245
3
, but see bugzilla fo
r
rea
s
ons
.
.
.
commit
|
commitdiff
|
tree
2008-02-20
cjfiel
d
s
bug 2
4
52
commit
|
commitdiff
|
tree
2008-02-19
cjfields
TODO now w
o
rks
commit
|
commitdiff
|
tree
2008-02-13
cjfields
u
pdate i
n
terf
a
ce documentatio
n
commit
|
commitdiff
|
tree
2008-02-13
cjfields
not
1
.
5
.
3 (
m
odules
d
on't work any
m
o
r
e
)
commit
|
commitdiff
|
tree
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