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perltidy
2008-11-16
cjfields
perltidy
commit
|
commitdiff
|
tree
2008-11-16
cj
f
ields
[
bug 263
5
]
commit
|
commitdiff
|
tree
2008-11-14
cjfields
[bu
g
2656]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
remove
d
ebugging lines
commit
|
commitdiff
|
tree
2008-11-11
cjfield
s
remove fixed verbos
e
fla
g
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug
26
5
0]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
Clarify result_count
(
discussions on ma
i
l list
p
e
r
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2632]
commit
|
commitdiff
|
tree
2008-11-10
cjfi
e
lds
[bug
2645
]
commit
|
commitdiff
|
tree
2008-11-04
cjfields
wrap text
commit
|
commitdiff
|
tree
2008-11-04
cjfield
s
* par
s
e
'Features in
t
his part o
f
s
u
bject sequence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse 'Features in this pa
r
t of subject s
e
quence
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfie
l
ds
[bu
g
2632]
commit
|
commitdiff
|
tree
2008-10-29
cjfiel
d
s
fix se
q
_inds(); wasn't
c
a
lling identical re
s
id
u
es for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cj
f
i
eld
s
[bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfields
[b
u
g
2630]
commit
|
commitdiff
|
tree
2008-10-26
c
j
fields
Fix unlink() warning
commit
|
commitdiff
|
tree
2008-10-26
cjfields
end
= start if only
s
tart is pa
s
sed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
u
s
e
v
alid_Location to check Location stat
e
commit
|
commitdiff
|
tree
2008-10-26
cjfields
add
d
o
c
s for LocationI m
e
thod vali
d
_Locat
i
on
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[
b
u
g
2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2624]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-25
c
jfields
bul
l
et-pro
o
f
prototype
test
commit
|
commitdiff
|
tree
2008-10-22
cjfields
fix file
p
r
o
pert
i
es
commit
|
commitdiff
|
tree
2008-10-22
cjfields
new
mo
d
ule for parsing ve
c
screen -
f
3 out
p
ut,
c
ourte
s
y
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
c
j
f
i
elds
add -source for ARP
commit
|
commitdiff
|
tree
2008-10-15
cj
f
ie
l
d
s
[bu
g
2
563]
commit
|
commitdiff
|
tree
2008-10-10
c
jfields
t
ypo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bu
g
2519]
commit
|
commitdiff
|
tree
2008-10-10
cj
f
ie
l
ds
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
cj
f
ields
add
svn tag
commit
|
commitdiff
|
tree
2008-10-07
c
j
fi
e
lds
TODO's work
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[b
u
g 261
2
]
commit
|
commitdiff
|
tree
2008-10-07
cjfi
e
lds
[bug 2612
]
commit
|
commitdiff
|
tree
2008-10-02
cjfields
c
l
ean
u
p XMFA parsing, allow s
p
aces in parsing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
c
j
fields
[BU
G
] bug 2598
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BUG]
bugfix for # 2598 (add '
J
')
commit
|
commitdiff
|
tree
2008-09-26
cjfie
l
ds
[BUG] bug 2593
commit
|
commitdiff
|
tree
2008-09-26
cjf
i
e
lds
[BUG] fix bu
g
2595
commit
|
commitdiff
|
tree
2008-09-18
cjfi
e
lds
Use 'w
a
rning
_
like' for instances where
a
regex mat
c
h
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfields
* No l
o
nger a s
t
u
b
commit
|
commitdiff
|
tree
2008-09-17
c
jfiel
d
s
1965 +
6 -1 = 1970, not 1999
commit
|
commitdiff
|
tree
2008-09-17
cjfields
p
assing TODO's (?!?)
commit
|
commitdiff
|
tree
2008-09-17
cjfields
update tes
t
s (seq
l
ength
chan
g
e in re
c
ord verified)
commit
|
commitdiff
|
tree
2008-09-17
cjfield
s
set -end to coorespond to sequence e
n
d
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
elds
tes
t
result changed
(
st
a
rt alw
a
ys < en
d
)
commit
|
commitdiff
|
tree
2008-09-16
cjfiel
d
s
Fix nexus i
s
sues with seq
.
amb
i
g
uity symbol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
ds
M
E
GA now resets $GAP_SYMBO
L
S
and $OTHER_SYMBOLS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
ds
T
e
st d
a
ta
m
a
t
ches new XMFA
e
xampl
e
commit
|
commitdiff
|
tree
2008-09-16
cjfield
s
* XMFA alignment doesn
'
t correspond to
X
MFA spec (http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
fix x
m
f
a
.
pm pa
r
sing o
o
ps
commit
|
commitdiff
|
tree
2008-09-16
cjfields
make LocatableSe
q
::end()
c
onsisten
t
commit
|
commitdiff
|
tree
2008-09-16
cjfields
* fix start/end/strand
commit
|
commitdiff
|
tree
2008-09-16
c
j
f
i
elds
t
ypo
commit
|
commitdiff
|
tree
2008-09-15
cjfields
r
e
m
o
ve d
e
buggin
g
s
t
at
e
me
n
t
commit
|
commitdiff
|
tree
2008-09-15
cjfields
par
t
ial fi
x
fo
r
arp (-end now
w
o
rk
s
and
coun
t
s ?
a
s
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfi
e
lds
-en
d
par
a
m
eter does
not
take gaps
i
nto account
commit
|
commitdiff
|
tree
2008-09-15
cjfields
* always
warn about p
a
ssing wrong end() coord
i
nate
commit
|
commitdiff
|
tree
2008-09-14
cjfield
s
Create
D
a
ta::Stag node l
a
zily; al
w
ays use node(
)
to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfields
add a few new (u
n
tested)
U
RLA
P
I parameters
commit
|
commitdiff
|
tree
2008-09-14
c
j
fields
use
d
irect
o
b
ject syn
t
ax
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 25
7
9
commit
|
commitdiff
|
tree
2008-09-09
cjfiel
d
s
bug 2580
commit
|
commitdiff
|
tree
2008-08-29
cjfields
A
l
lo
w
other Bio::SeqFeatur
e
::CollectionI
commit
|
commitdiff
|
tree
2008-08-28
cjfields
[bug 2576]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
grep not n
e
eded
(check
f
or ontol
o
gy is
i
n
Ontology
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfie
l
ds
[bug
25
7
3
]
commit
|
commitdiff
|
tree
2008-08-27
cjf
i
eld
s
Update
d
o
cumentation
commit
|
commitdiff
|
tree
2008-08-27
cjfields
compl
e
te sentence
commit
|
commitdiff
|
tree
2008-08-25
cjfi
e
l
ds
A
d
d some print_* methods for einfo, esummary
,
etc
.
commit
|
commitdiff
|
tree
2008-08-21
cjfields
* write PRO
J
ECT suppor
t
commit
|
commitdiff
|
tree
2008-08-21
c
j
fields
a
dd PROJECT support (bug 2
5
69)
commit
|
commitdiff
|
tree
2008-08-05
cjfields
F
or new N
C
BI blast
t
able format
commit
|
commitdiff
|
tree
2008-08-05
cjfields
Previous changes killed R
e
moteBlast ag
a
in; make a little
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
A
d
d
a f
e
w new G
E
T/PUT paramete
r
s
.
commit
|
commitdiff
|
tree
2008-08-04
cj
f
ields
S
equ
e
nces weren'
t
being pa
r
se
d
correct
l
y; unfortunately
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfields
tests should use is/isnt when possi
b
le, n
o
t ok()
commit
|
commitdiff
|
tree
2008-07-30
cjfi
e
lds
revert Roy
'
s patch (my bad)
commit
|
commitdiff
|
tree
2008-07-30
c
j
fi
e
lds
bug 2556
:
commit
|
commitdiff
|
tree
2008-07-30
c
jfields
Bug 2546
commit
|
commitdiff
|
tree
2008-07-29
cjfields
b
u
g
2
5
55
commit
|
commitdiff
|
tree
2008-07-29
c
jfie
l
ds
bug 2549;
f
ixed s
m
all bug in B
i
o::Tax
o
n whi
c
h doesn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfields
add multiple
rec
o
rd
suppo
r
t (courtes
y
of Jo
r
ge Duarte
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
cjfields
bulletpr
o
of test; r
e
mote tabular BLAST is faili
n
g for
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjfields
bu
g
2534
commit
|
commitdiff
|
tree
2008-07-08
cjfields
Can't
i
nherit from one
s
elf
commit
|
commitdiff
|
tree
2008-07-08
cjfields
bug 2539
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bug 2423
commit
|
commitdiff
|
tree
2008-06-17
cjfields
bu
g
24
2
3
commit
|
commitdiff
|
tree
2008-06-14
cj
f
ields
bug 25
1
2
(
Gene
O
n
tology chang
e
s)
commit
|
commitdiff
|
tree
2008-06-14
cj
f
ields
bug 2519
commit
|
commitdiff
|
tree
2008-06-14
cjfi
e
lds
b
ug 2518
commit
|
commitdiff
|
tree
2008-06-14
cj
f
i
e
lds
bug 2517
commit
|
commitdiff
|
tree
2008-05-27
c
j
fields
RT
#
128
0
2 (
v
i
a
CPAN RT)
commit
|
commitdiff
|
tree
2008-04-22
cjfiel
d
s
bu
g
2485 and
related fi
x
es
commit
|
commitdiff
|
tree
2008-04-22
c
j
fi
e
l
d
s
correct # of ski
p
ped tes
t
s
commit
|
commitdiff
|
tree
2008-04-22
cjf
i
elds
bug 2490 (smal
l
tes
t
)
commit
|
commitdiff
|
tree
2008-04-22
c
jfields
bu
g
2490
commit
|
commitdiff
|
tree
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