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sync last bits with main trunk
2008-10-07
cjfields
[bug 2612
]
commit
|
commitdiff
|
tree
2008-10-02
cjfields
clean up
X
M
FA p
a
rs
i
ng, allow spaces
in
p
arsing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfields
[BUG
]
bug 25
9
8
commit
|
commitdiff
|
tree
2008-09-26
cjfie
l
ds
[BU
G
] bugfix for #
2
598 (add 'J
'
)
commit
|
commitdiff
|
tree
2008-09-26
c
j
field
s
[BUG]
b
ug 2593
commit
|
commitdiff
|
tree
2008-09-26
cjfield
s
[BUG] fix bug 2
5
95
commit
|
commitdiff
|
tree
2008-09-18
cjfi
e
lds
Use 'warnin
g
_like' for instances where a r
e
gex match
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfields
*
No l
o
nger a stub
commit
|
commitdiff
|
tree
2008-09-17
cjfiel
d
s
1965
+
6
-
1 = 197
0
,
n
o
t
1999
commit
|
commitdiff
|
tree
2008-09-17
cjfields
pas
s
ing TODO's (?!?)
commit
|
commitdiff
|
tree
2008-09-17
cjfields
update t
e
sts
(
se
q
len
g
th change
in record verifie
d
)
commit
|
commitdiff
|
tree
2008-09-17
cjfields
s
e
t
-end to cooresp
o
nd to s
e
quence end
commit
|
commitdiff
|
tree
2008-09-16
cjfield
s
test result changed (start
a
lw
a
ys < end)
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Fi
x
nexus iss
u
es wi
t
h seq
.
ambi
g
ui
t
y symbol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfields
MEGA
n
ow resets $GAP_SYMBOLS and $OTH
E
R_SYMBOL
S
to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Test data m
a
tches new XMFA ex
a
m
ple
commit
|
commitdiff
|
tree
2008-09-16
c
j
fields
* XMFA align
m
ent
d
o
esn't
c
orre
s
po
n
d to XMFA spec
(http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
f
i
x xmfa
.
pm
p
arsing oops
commit
|
commitdiff
|
tree
2008-09-16
c
jfields
m
a
k
e
Locatab
l
e
S
eq::end
(
) consistent
commit
|
commitdiff
|
tree
2008-09-16
cjfields
*
fix s
t
art/end/strand
commit
|
commitdiff
|
tree
2008-09-16
cjfields
t
y
p
o
commit
|
commitdiff
|
tree
2008-09-15
cjfields
remove debu
g
g
i
n
g
statement
commit
|
commitdiff
|
tree
2008-09-15
cjfield
s
parti
a
l fix for arp
(
-end now wo
r
ks and counts ? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfields
-end parameter d
o
es no
t
t
a
ke gaps into a
c
c
ount
commit
|
commitdiff
|
tree
2008-09-15
cjfields
* a
l
ways warn
ab
o
ut
p
assing wrong
e
nd() coordinate
commit
|
commitdiff
|
tree
2008-09-14
cjfi
e
ld
s
Cre
a
te D
a
ta::Stag node
l
azily; alwa
y
s
u
se node() to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfields
ad
d
a fe
w
new (untested) URLAPI parameters
commit
|
commitdiff
|
tree
2008-09-14
cjfields
us
e
direct
o
bject synta
x
commit
|
commitdiff
|
tree
2008-09-09
cj
f
ields
bug 25
7
9
commit
|
commitdiff
|
tree
2008-09-09
cjfields
b
u
g 2580
commit
|
commitdiff
|
tree
2008-08-29
cjfi
e
l
d
s
Allow other Bio::SeqFeature::Collectio
n
I
commit
|
commitdiff
|
tree
2008-08-28
cjfie
l
ds
[bug 2576]
commit
|
commitdiff
|
tree
2008-08-27
c
j
fiel
d
s
grep
n
ot nee
d
e
d
(check
f
or ontolo
g
y is in Ontology
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfi
e
lds
[bug 2573]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
Updat
e
documentation
commit
|
commitdiff
|
tree
2008-08-27
cjf
i
e
l
d
s
comp
l
et
e
sent
e
nce
commit
|
commitdiff
|
tree
2008-08-25
cj
f
ields
Ad
d
some pri
n
t_* methods for
einfo, esumma
r
y, etc
.
commit
|
commitdiff
|
tree
2008-08-21
cjfields
*
write PROJECT su
p
port
commit
|
commitdiff
|
tree
2008-08-21
cjf
i
elds
ad
d
PROJECT supp
o
rt (bug 2569)
commit
|
commitdiff
|
tree
2008-08-05
cjfi
e
lds
For new NC
B
I bl
a
sttable
form
a
t
commit
|
commitdiff
|
tree
2008-08-05
cjfields
Previous changes
killed Remote
B
last a
g
ain; make a little
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cj
f
ields
Add a few new GET/PUT parameters
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Sequ
e
nces
weren't
b
e
i
ng parsed correctly; un
f
ortunately
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfields
tests sh
o
u
ld use is/
i
snt when poss
i
bl
e
,
n
ot ok()
commit
|
commitdiff
|
tree
2008-07-30
cjfiel
d
s
reve
r
t Roy'
s
patch (my bad)
commit
|
commitdiff
|
tree
2008-07-30
cjfields
bug 2556:
commit
|
commitdiff
|
tree
2008-07-30
cjfields
Bug 2546
commit
|
commitdiff
|
tree
2008-07-29
cjfi
e
lds
bug 2555
commit
|
commitdiff
|
tree
2008-07-29
cjfield
s
b
ug 25
4
9; fixed small bug in
Bio::T
a
xon which doesn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfields
add multiple
record support (courtes
y
o
f
Jorge Duarte
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
cjfie
l
ds
bull
e
t
proo
f
test; remot
e
tabula
r
BLAST
is failing
f
or
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjfiel
d
s
bug 2534
commit
|
commitdiff
|
tree
2008-07-08
cjfields
C
a
n't inherit
f
ro
m
ones
e
lf
commit
|
commitdiff
|
tree
2008-07-08
cjfi
e
lds
bug 2539
commit
|
commitdiff
|
tree
2008-06-17
c
jfields
bug 2423
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bug
2
423
commit
|
commitdiff
|
tree
2008-06-14
cjfie
l
ds
b
u
g 251
2
(
G
e
n
e
O
n
t
ol
o
g
y
changes
)
commit
|
commitdiff
|
tree
2008-06-14
cj
f
i
e
lds
bug
2519
commit
|
commitdiff
|
tree
2008-06-14
cjfields
bug 25
1
8
commit
|
commitdiff
|
tree
2008-06-14
c
j
field
s
bug 2517
commit
|
commitdiff
|
tree
2008-05-27
cjfield
s
RT#12802
(
v
i
a CPAN
RT)
commit
|
commitdiff
|
tree
2008-04-22
cj
f
ields
bug
2
485
a
nd r
e
lated
f
i
xes
commit
|
commitdiff
|
tree
2008-04-22
cjfiel
d
s
cor
r
ect # of sk
i
pped te
s
ts
commit
|
commitdiff
|
tree
2008-04-22
c
j
f
i
elds
bug 2490
(
sm
a
ll test)
commit
|
commitdiff
|
tree
2008-04-22
c
j
fields
bug 2490
commit
|
commitdiff
|
tree
2008-04-22
cjfields
new
N
C
B
I BLAST UR
L
(works with R
e
moteBlast
.
t
)
commit
|
commitdiff
|
tree
2008-04-22
cjfields
b
ug 2490
commit
|
commitdiff
|
tree
2008-04-21
cjfields
Fix faili
n
g
t
e
sts
commit
|
commitdiff
|
tree
2008-04-21
cjfields
update test (
s
eq in remot
e
db has c
h
an
g
ed)
commit
|
commitdiff
|
tree
2008-04-21
cjf
i
e
l
ds
bullet-proof; thi
s
n
eeds m
o
re stringent tests
commit
|
commitdiff
|
tree
2008-04-14
cjfields
b
u
g 24
8
4
commit
|
commitdiff
|
tree
2008-04-08
cj
f
i
e
l
d
s
bug 2479
commit
|
commitdiff
|
tree
2008-04-08
cjfields
bug 24
7
8
commit
|
commitdiff
|
tree
2008-04-07
c
j
fields
up
d
ates;
m
ay sw
i
tch some data objects over to
(
ligh
t
weight
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfields
Add some te
s
ts to catch tag naming
commit
|
commitdiff
|
tree
2008-04-02
cjfields
Fix bad silent
b
ug which do
e
sn't set exon t
a
gs co
r
re
c
tly
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfields
merg
e
back previous commit
s
from
S
endu and I
commit
|
commitdiff
|
tree
2008-04-02
cj
f
ields
g
e
t ri
d
of
v
ariable redefine
d
warnings
commit
|
commitdiff
|
tree
2008-04-02
cjfields
test
n
ot matc
h
ing err
o
r mess
a
ge (oo
p
s!)
commit
|
commitdiff
|
tree
2008-04-02
cjfields
R
e
f
S
eq
r
edirection now requir
e
s ex
p
licit
s
etting (note
.
.
.
commit
|
commitdiff
|
tree
2008-04-02
cjfields
S
quash uninit
.
va
l
ue war
n
ings
commit
|
commitdiff
|
tree
2008-04-01
c
j
fields
Remove extraneous code; u
p
date docs
commit
|
commitdiff
|
tree
2008-04-01
cjfi
e
l
d
s
bug 2466 :
commit
|
commitdiff
|
tree
2008-04-01
cjfields
Make reg
e
x ma
t
ches s
a
fer
commit
|
commitdiff
|
tree
2008-03-28
cjfields
a
dd some seq_inds(
)
tests (a
p
pears
f
ine)
commit
|
commitdiff
|
tree
2008-03-28
cjfields
* r
e
vert symbol passing (forgot query and hit have
.
.
.
commit
|
commitdiff
|
tree
2008-03-28
cjfields
* Allow gap
symbol to b
e
set
commit
|
commitdiff
|
tree
2008-03-27
cjfields
remove extra
n
eous comment
commit
|
commitdiff
|
tree
2008-03-27
cjfields
using seq_inds() with 'gaps'
n
ow repea
t
s sequence in
d
ices
.
.
.
commit
|
commitdiff
|
tree
2008-03-27
cjfields
C
o
llapse repeat
e
d sequenc
e
indices into one pos
i
tion
commit
|
commitdiff
|
tree
2008-03-27
c
jfields
Ma
r
c'
s
b
u
g fro
m
mail list
;
repeat the
seq position
.
.
.
commit
|
commitdiff
|
tree
2008-03-25
cjfields
bug 2473 (w
i
th tests)
commit
|
commitdiff
|
tree
2008-03-04
cjfields
bug 1707
commit
|
commitdiff
|
tree
2008-03-03
cj
f
ield
s
bug 2465
commit
|
commitdiff
|
tree
2008-03-03
c
j
fiel
d
s
bu
g
2449
commit
|
commitdiff
|
tree
2008-03-03
cjf
i
eld
s
some more for bug 2349
commit
|
commitdiff
|
tree
2008-03-03
cjfiel
d
s
p
arti
a
l
fix for bug 2439
commit
|
commitdiff
|
tree
2008-03-02
c
j
f
i
elds
Bug 23
7
8
commit
|
commitdiff
|
tree
2008-03-01
c
j
fields
fix un
d
ef
.
v
a
riable issue
w
hen no a
n
c
e
s
to
r
i
ndicated
.
.
.
commit
|
commitdiff
|
tree
2008-03-01
cjfie
l
ds
add some
f
l
e
xibility fo
r
name len
g
th,
d
efaulting to 10
commit
|
commitdiff
|
tree
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