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update Test::Warn (fixes Qual.t test problems with warnings_like)
2008-11-24
cjfields
[b
u
g 2663
]
commit
|
commitdiff
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tree
2008-11-24
c
j
f
ie
l
ds
[bug 2630
]
commit
|
commitdiff
|
tree
2008-11-24
cjfie
l
ds
[
bug 2262]
commit
|
commitdiff
|
tree
2008-11-24
cjf
i
e
l
ds
[
b
ug 2630]
commit
|
commitdiff
|
tree
2008-11-18
cj
f
ields
* Double-chec
k
ed data, tested results w
e
re wro
n
g
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|
commitdiff
|
tree
2008-11-18
cjfields
* seq_inds is not defined
f
o
r
Model-base
d
H
S
Ps
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|
commitdiff
|
tree
2008-11-18
c
j
fields
* fix
POD
commit
|
commitdiff
|
tree
2008-11-17
c
j
f
ie
l
ds
*
'highly' (and I get r15000!)
commit
|
commitdiff
|
tree
2008-11-17
c
j
fi
e
lds
Remove redundant test files
commit
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commitdiff
|
tree
2008-11-17
cjfields
[te
s
t
s]
commit
|
commitdiff
|
tree
2008-11-17
cjf
i
e
lds
move results2h
a
sh test utility
s
ub to
Search
U
ti
l
s
commit
|
commitdiff
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tree
2008-11-16
cjf
i
elds
[bug 2663]
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|
commitdiff
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tree
2008-11-16
cjfield
s
p
e
r
ltidy
commit
|
commitdiff
|
tree
2008-11-16
c
jfields
[bug 263
5
]
commit
|
commitdiff
|
tree
2008-11-14
cjfields
[bug 2656
]
commit
|
commitdiff
|
tree
2008-11-11
cjfiel
d
s
remove d
e
bugging lines
commit
|
commitdiff
|
tree
2008-11-11
cj
f
i
e
lds
remove f
i
xed verbose
flag
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2650]
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|
commitdiff
|
tree
2008-11-11
cjfields
Clarify re
s
ult_co
u
nt (discussions on mail list per
.
.
.
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|
commitdiff
|
tree
2008-11-11
cjfie
l
ds
[bug 2632]
commit
|
commitdiff
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tree
2008-11-10
cjfields
[bug 2645]
commit
|
commitdiff
|
tree
2008-11-04
cjfields
wrap text
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|
commitdiff
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tree
2008-11-04
cjfi
e
lds
* parse 'Fea
t
u
res in this part o
f
s
u
bject se
q
uenc
e
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfi
e
lds
* pars
e
'Fe
a
tures in t
h
is part of subject
sequ
e
nce
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfiel
d
s
[bu
g
2
632]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
fix seq_inds();
w
asn't calling id
e
ntical r
e
sidue
s
for
.
.
.
commit
|
commitdiff
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tree
2008-10-29
c
jfiel
d
s
[bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfields
[bug 2630]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
F
ix
unlink() war
n
i
ng
commit
|
commitdiff
|
tree
2008-10-26
cjfields
end = start i
f
o
n
ly start i
s
passed
commit
|
commitdiff
|
tree
2008-10-26
cjfiel
d
s
use valid_Loca
t
i
on to check Location state
commit
|
commitdiff
|
tree
2008-10-26
cj
f
ie
l
ds
add docs for LocationI me
t
hod valid_Loca
t
i
on
commit
|
commitdiff
|
tree
2008-10-26
cjfield
s
[
bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfield
s
[bu
g
2
6
2
1]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2624]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bu
g
2621]
commit
|
commitdiff
|
tree
2008-10-25
cjfiel
d
s
bull
e
t-p
r
o
of prototy
p
e
test
commit
|
commitdiff
|
tree
2008-10-22
cjfields
fix file p
r
operties
commit
|
commitdiff
|
tree
2008-10-22
cjfield
s
new module for parsing
v
e
c
scre
e
n -f 3
o
utput, cou
r
tes
y
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfiel
d
s
a
d
d
-source for ARP
commit
|
commitdiff
|
tree
2008-10-15
c
j
fields
[
bug
2563]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
ty
p
o
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|
commitdiff
|
tree
2008-10-10
c
j
f
ields
[bug 25
1
9]
commit
|
commitdiff
|
tree
2008-10-10
c
j
f
ields
[b
u
g 2519]
commit
|
commitdiff
|
tree
2008-10-07
cjf
i
elds
add s
v
n t
a
g
commit
|
commitdiff
|
tree
2008-10-07
cjfields
T
O
DO's work
commit
|
commitdiff
|
tree
2008-10-07
c
jfiel
d
s
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-07
c
j
fie
l
d
s
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-02
cj
f
ields
clean
up XMFA
parsing
,
allow spaces
in parsing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfields
[BUG] bug
2
5
9
8
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|
commitdiff
|
tree
2008-09-26
cjfields
[B
U
G] bugfix
f
or
# 2598 (add
'
J'
)
commit
|
commitdiff
|
tree
2008-09-26
cjfie
l
d
s
[BUG] bug 2593
commit
|
commitdiff
|
tree
2008-09-26
cjfi
e
lds
[BU
G
] fix b
u
g 2595
commit
|
commitdiff
|
tree
2008-09-18
cjfields
Us
e
'warning_like'
f
o
r in
s
t
ances whe
r
e
a
re
g
ex match
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfields
* No longer a stub
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|
commitdiff
|
tree
2008-09-17
cjf
i
e
l
ds
196
5
+ 6 -1 = 1
9
70, n
o
t
1999
commit
|
commitdiff
|
tree
2008-09-17
c
j
fi
e
lds
p
a
ssing TO
D
O
's (?!?)
commit
|
commitdiff
|
tree
2008-09-17
c
j
fields
update tests (seq l
e
ngth chang
e
in record ver
i
fied)
commit
|
commitdiff
|
tree
2008-09-17
cjfields
set
-
end to cooresp
o
nd to s
e
quence end
commit
|
commitdiff
|
tree
2008-09-16
cjfiel
d
s
test res
u
lt changed (start always < end)
commit
|
commitdiff
|
tree
2008-09-16
cjfields
F
i
x nexus issues wi
t
h seq
.
a
m
b
i
guit
y
symbol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
c
jfields
MEGA
n
ow rese
t
s $GAP
_
SYMBOLS and $OTHE
R
_SYMBOLS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
elds
Test data
matches new X
M
FA e
x
a
m
ple
commit
|
commitdiff
|
tree
2008-09-16
c
j
fiel
d
s
*
XMFA
a
lignmen
t
doe
s
n't
c
o
rr
e
spond to
X
M
FA
s
pec (http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
fix xmfa
.
p
m parsing oops
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
ds
make LocatableS
e
q::end() cons
i
stent
commit
|
commitdiff
|
tree
2008-09-16
cjfields
*
f
ix
s
tart/end/strand
commit
|
commitdiff
|
tree
2008-09-16
cjfields
typo
commit
|
commitdiff
|
tree
2008-09-15
cjfields
remove debugging statement
commit
|
commitdiff
|
tree
2008-09-15
cj
f
ields
par
t
ial fix
f
or
a
r
p (-end now
works an
d
counts ? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfi
e
lds
-e
n
d
parameter does no
t
take gaps into accou
n
t
commit
|
commitdiff
|
tree
2008-09-15
cjfields
*
always warn ab
o
ut passing wrong end() coordinate
commit
|
commitdiff
|
tree
2008-09-14
cjfields
Create D
a
ta::Stag node lazily; always use node()
t
o
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfie
l
ds
add a fe
w
new
(
u
ntested) URLAPI
p
arameters
commit
|
commitdiff
|
tree
2008-09-14
cjfields
use dir
e
ct o
b
ject syn
t
ax
commit
|
commitdiff
|
tree
2008-09-09
cjfi
e
lds
bug 2579
commit
|
commitdiff
|
tree
2008-09-09
cj
f
ields
bug
2
5
80
commit
|
commitdiff
|
tree
2008-08-29
c
jfields
Allo
w
othe
r
Bio
:
:SeqFe
a
t
u
re::Col
l
ec
t
i
onI
commit
|
commitdiff
|
tree
2008-08-28
c
jfie
l
ds
[bu
g
2576]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
g
r
e
p
not
n
eeded (check for ontology
is in Ontology
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjf
i
elds
[
b
u
g
2573]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
Upd
a
te documentation
commit
|
commitdiff
|
tree
2008-08-27
cjf
i
eld
s
complete sen
t
ence
commit
|
commitdiff
|
tree
2008-08-25
c
j
fie
l
ds
Add som
e
prin
t
_* m
e
tho
d
s for
einfo, esummary, etc
.
commit
|
commitdiff
|
tree
2008-08-21
cjfields
* writ
e
PROJ
E
CT su
p
port
commit
|
commitdiff
|
tree
2008-08-21
cjf
i
eld
s
add
P
ROJECT support (bug 2569
)
commit
|
commitdiff
|
tree
2008-08-05
c
jfields
For new NCBI b
l
as
t
tab
l
e f
o
rmat
commit
|
commitdiff
|
tree
2008-08-05
cjfields
Previous
c
hang
e
s kille
d
Remot
e
Blast again
;
make a little
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cjf
i
elds
Add a few new GET/PUT paramet
e
rs
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Seq
u
e
n
c
e
s
w
e
ren
'
t being parsed correctly;
u
nfort
u
nate
l
y
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfields
tests shoul
d
use
i
s/isnt when possible,
n
ot ok()
commit
|
commitdiff
|
tree
2008-07-30
c
jfields
re
v
ert Roy's pa
t
ch (my bad)
commit
|
commitdiff
|
tree
2008-07-30
c
j
field
s
bug 2556:
commit
|
commitdiff
|
tree
2008-07-30
cjfields
Bug 2546
commit
|
commitdiff
|
tree
2008-07-29
c
jfie
l
ds
bug 2555
commit
|
commitdiff
|
tree
2008-07-29
cjfields
bug 2549; fixed small bug in Bio::T
a
xon wh
i
c
h
does
n
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cj
f
ie
l
ds
add multiple re
c
o
r
d support (court
e
sy of Jorge
D
uarte
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
cjfields
bulle
t
proof
test; remote tabul
a
r
BLAST is
f
ailing for
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjfi
e
lds
bug 2534
commit
|
commitdiff
|
tree
2008-07-08
cjfiel
d
s
C
a
n't
i
nherit f
r
om one
s
elf
commit
|
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