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[bug 2630]
2008-11-24
cjfi
e
lds
[bug 2630]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 22
6
2]
commit
|
commitdiff
|
tree
2008-11-24
cjf
i
el
d
s
[bug 2630]
commit
|
commitdiff
|
tree
2008-11-18
cjfie
l
d
s
* Doubl
e
-
c
h
ecked data, te
s
t
ed results were wrong
commit
|
commitdiff
|
tree
2008-11-18
cjfi
e
lds
*
seq
_
inds is not defined fo
r
Model-based H
S
Ps
commit
|
commitdiff
|
tree
2008-11-18
cj
f
ields
*
f
ix PO
D
commit
|
commitdiff
|
tree
2008-11-17
cjfi
e
lds
* 'hi
g
hly' (and I
get r15
0
00
!
)
commit
|
commitdiff
|
tree
2008-11-17
cjfiel
d
s
Remove redu
n
dant t
e
st files
commit
|
commitdiff
|
tree
2008-11-17
cjf
i
elds
[
t
e
sts]
commit
|
commitdiff
|
tree
2008-11-17
cjfields
move results2hash
test utility sub to SearchU
t
ils
commit
|
commitdiff
|
tree
2008-11-16
cj
f
ield
s
[bug 26
6
3]
commit
|
commitdiff
|
tree
2008-11-16
cjfi
e
l
d
s
perl
t
idy
commit
|
commitdiff
|
tree
2008-11-16
c
j
fi
e
lds
[bug 2635
]
commit
|
commitdiff
|
tree
2008-11-14
cj
f
ield
s
[bug 2656]
commit
|
commitdiff
|
tree
2008-11-11
c
j
fie
l
ds
remove debugging
l
in
e
s
commit
|
commitdiff
|
tree
2008-11-11
cjfiel
d
s
remove fixed verb
o
se flag
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 26
5
0]
commit
|
commitdiff
|
tree
2008-11-11
cjfiel
d
s
Clarify
r
esult_coun
t
(discussions on
m
ail list per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[
b
ug 2632]
commit
|
commitdiff
|
tree
2008-11-10
cj
f
ields
[bug 2
6
45]
commit
|
commitdiff
|
tree
2008-11-04
cjfiel
d
s
wr
a
p
t
ext
commit
|
commitdiff
|
tree
2008-11-04
cjf
i
elds
* parse 'Features in this part
o
f subjec
t
sequence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfields
*
p
arse 'F
e
atures in
t
h
i
s part of subject sequence
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[bu
g
2632]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
fix seq_
i
nds()
;
wasn'
t
calling i
d
entical resi
d
ues
fo
r
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[bug 2633
]
commit
|
commitdiff
|
tree
2008-10-28
cjfield
s
[
b
ug 2630]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
Fix unlink()
warning
commit
|
commitdiff
|
tree
2008-10-26
cjfi
e
lds
end = start
if
o
n
l
y
start is
p
assed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
use valid_Location
to che
c
k Location s
t
ate
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
add do
c
s f
o
r LocationI method valid_
L
ocatio
n
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[
bug 2621
]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug
2
621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[
bug 2624]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2
6
21]
commit
|
commitdiff
|
tree
2008-10-25
cjfi
e
l
d
s
b
u
llet-proo
f
prototype
t
est
commit
|
commitdiff
|
tree
2008-10-22
cjfields
f
i
x
fi
l
e pr
o
perties
commit
|
commitdiff
|
tree
2008-10-22
cjfields
new module for
par
s
i
ng vecscreen -f 3 o
u
tput,
courtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cj
f
iel
d
s
add -source
for ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfields
[bug 256
3
]
commit
|
commitdiff
|
tree
2008-10-10
cjf
i
eld
s
typo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[
b
ug 2519]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bug 2519
]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
a
d
d svn tag
commit
|
commitdiff
|
tree
2008-10-07
cj
f
ields
TODO
'
s wo
r
k
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[b
u
g
261
2
]
commit
|
commitdiff
|
tree
2008-10-07
c
jfields
[bu
g
2612]
commit
|
commitdiff
|
tree
2008-10-02
cjfi
e
l
d
s
clean up XMFA parsin
g
, allow sp
a
ce
s
in parsing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfields
[BUG] b
u
g 2598
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BUG] bugfix
f
or # 2598 (add
'
J')
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BUG] bug 2
5
93
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[
BUG] fi
x
bug 259
5
commit
|
commitdiff
|
tree
2008-09-18
cjfiel
d
s
U
s
e
'
warning_
l
ike'
f
or instan
c
es where a reg
e
x ma
t
ch
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfields
*
N
o
lo
n
ge
r
a stub
commit
|
commitdiff
|
tree
2008-09-17
c
j
fields
1965 + 6
-
1 = 1970, no
t
1
9
99
commit
|
commitdiff
|
tree
2008-09-17
c
j
fiel
d
s
p
a
ssin
g
TODO's
(
?!?)
commit
|
commitdiff
|
tree
2008-09-17
c
jfields
u
p
d
ate t
e
sts (
s
eq length change in
re
c
ord
v
erified)
commit
|
commitdiff
|
tree
2008-09-17
c
jfields
se
t
-end to cooresp
o
nd
t
o s
e
que
n
ce e
n
d
commit
|
commitdiff
|
tree
2008-09-16
cjfields
t
est r
e
su
l
t
c
hange
d
(start al
w
ays < end)
commit
|
commitdiff
|
tree
2008-09-16
c
j
fields
Fix ne
x
us issue
s
wi
t
h seq
.
a
m
b
iguity symbol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfields
MEGA now
resets $GAP_SYMBOL
S
and $O
T
H
ER_SYMBOLS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
ds
Test data
m
atc
h
es new XMF
A
e
x
ample
commit
|
commitdiff
|
tree
2008-09-16
c
jfi
e
lds
* XMFA alignme
n
t doesn
'
t correspond to XMFA spec
(
http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
fix xmfa
.
p
m parsing o
o
ps
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
make LocatableSeq:
:
e
n
d() consistent
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
elds
* fix start/en
d
/strand
commit
|
commitdiff
|
tree
2008-09-16
cjfields
typo
commit
|
commitdiff
|
tree
2008-09-15
cjfield
s
r
e
m
ove debugging
s
tat
e
ment
commit
|
commitdiff
|
tree
2008-09-15
c
j
f
ields
p
a
r
tial fix for arp (
-
end no
w
wor
k
s and counts ? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfields
-end paramete
r
does no
t
take gap
s
into account
commit
|
commitdiff
|
tree
2008-09-15
c
j
f
i
e
l
ds
* alwa
y
s
wa
r
n about p
a
ssing
w
r
ong
e
nd() coo
r
dinate
commit
|
commitdiff
|
tree
2008-09-14
cjfiel
d
s
Create Data::Stag node l
a
zil
y
; always use
n
ode()
t
o
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfields
add a
fe
w
new (u
n
t
ested) URLA
P
I
para
m
e
t
e
r
s
commit
|
commitdiff
|
tree
2008-09-14
cjfiel
d
s
use
direct object sy
n
tax
commit
|
commitdiff
|
tree
2008-09-09
c
jfi
e
lds
b
ug 2579
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 2580
commit
|
commitdiff
|
tree
2008-08-29
cjfields
Allow other Bio:
:
SeqFeature::Col
l
ection
I
commit
|
commitdiff
|
tree
2008-08-28
cj
f
ields
[bug 2576]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
grep not
n
eeded (ch
e
ck
for o
n
t
olog
y
is in Ontology
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
c
j
fiel
d
s
[bug 2573]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
Upda
t
e
d
o
c
umentation
commit
|
commitdiff
|
tree
2008-08-27
cjf
i
elds
complete sen
t
enc
e
commit
|
commitdiff
|
tree
2008-08-25
cjfi
e
lds
A
d
d some print_* methods for ei
n
fo, esummary, e
t
c
.
commit
|
commitdiff
|
tree
2008-08-21
cjfields
* writ
e
PROJECT suppo
r
t
commit
|
commitdiff
|
tree
2008-08-21
cjfield
s
add
P
ROJECT
s
u
pport (bug 2
5
69)
commit
|
commitdiff
|
tree
2008-08-05
cjfiel
d
s
For
new NCBI blastt
a
ble format
commit
|
commitdiff
|
tree
2008-08-05
c
j
fi
e
lds
Pr
e
v
i
ous changes killed
R
emot
e
B
l
ast again; make a l
i
ttle
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cj
f
i
elds
Add a few
new GET/PUT parameters
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Sequences we
r
en't being parsed correctly; unfortun
a
tely
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfields
tes
t
s should use is
/
isnt when poss
i
b
l
e, not ok()
commit
|
commitdiff
|
tree
2008-07-30
cjfields
revert Roy's patc
h
(my bad)
commit
|
commitdiff
|
tree
2008-07-30
c
j
fields
bug 2556:
commit
|
commitdiff
|
tree
2008-07-30
cjfields
Bu
g
254
6
commit
|
commitdiff
|
tree
2008-07-29
cjfiel
d
s
bu
g
2
55
5
commit
|
commitdiff
|
tree
2008-07-29
c
j
fie
l
ds
bug
2
549; fixed small
b
ug in
B
io::Taxon wh
i
ch doesn
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfie
l
ds
a
dd
mul
t
ip
l
e record support (court
e
sy of Jorge
D
ua
r
t
e
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
cjf
i
elds
bulletpro
o
f test; remote ta
b
ular BLAST is faili
n
g
f
or
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
c
j
fields
b
u
g 2534
commit
|
commitdiff
|
tree
2008-07-08
c
j
fields
Can't inh
e
rit
f
rom oneself
commit
|
commitdiff
|
tree
2008-07-08
cjfields
bug 2539
commit
|
commitdiff
|
tree
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