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remove Bio::Graphics (separate package now)
2008-12-10
c
j
fields
r
e
move Bio::Gra
p
hics
(
s
epa
r
a
t
e pa
c
ka
g
e no
w
)
commit
|
commitdiff
|
tree
2008-12-10
c
j
fi
e
lds
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-10
cjfields
Remove depen
d
en
c
i
e
s for
Bio::Gr
a
phics and deprecated
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Squ
a
sh warning
commit
|
commitdiff
|
tree
2008-12-09
cjfie
l
ds
diag() only o
n
verbose
commit
|
commitdiff
|
tree
2008-12-09
c
jfields
Fix last loop tests, move
some to can_ok
commit
|
commitdiff
|
tree
2008-12-09
cjf
i
elds
Modif
y
t
o test new temp classes and ensure tha
t
add
e
d
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
up
d
ate Mauricio's
e
mail
commit
|
commitdiff
|
tree
2008-12-08
cjfields
U
p
dat
e
Roy's email
commit
|
commitdiff
|
tree
2008-12-08
cjfields
R
oy
'
s email
(a
n
d b
i
operl
.
org
n
ot bioper
l
.
ed
u
)
commit
|
commitdiff
|
tree
2008-12-08
cjfields
Updated emails
commit
|
commitdiff
|
tree
2008-12-07
cjf
i
elds
[bug
2
699]
commit
|
commitdiff
|
tree
2008-12-05
cj
f
ields
Need to retrieve the tree for
outpu
t
commit
|
commitdiff
|
tree
2008-12-05
cjfie
l
ds
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-04
cjf
i
elds
Make T
a
r
g
et a true DBLink
commit
|
commitdiff
|
tree
2008-12-04
cjfiel
d
s
Directory is no longer n
e
eded (Heik
k
i split th
i
s up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
c
j
field
s
ad
d
f
orce_nse te
s
ts
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
lds
leave ID undefined if it isn't present, b
u
t all
o
w the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
c
jfiel
d
s
Remove
f
ile
s
a
cc
i
den
t
l
y added from last com
m
it
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
lds
R
e
organize
Tools
tests
(
n
eeds some more splitting)
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
lds
Rem
o
v
e
(tests are re
d
u
ndant,
in
Consed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
Merge te
s
ts and remove re
d
undant file
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Updat
e
t
est count
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
Merge tests
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
Remove redu
n
dant fi
l
e
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove old file
s
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
el
d
s
S
t
art Tools mov
e
commit
|
commitdiff
|
tree
2008-12-03
cjfields
sm
a
ll updates:
commit
|
commitdiff
|
tree
2008-12-03
cj
f
i
e
l
ds
forgot
to increment t
e
st count
commit
|
commitdiff
|
tree
2008-12-03
cjfiel
d
s
Add a couple of tests for seq
_
id
(
s
mall but signi
f
icant
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug
2
450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[b
u
g 2450
]
commit
|
commitdiff
|
tree
2008-12-02
c
jf
i
elds
[
bug
2
450
]
commit
|
commitdiff
|
tree
2008-12-02
cjfiel
d
s
some
p
od upda
t
es
commit
|
commitdiff
|
tree
2008-12-02
cj
f
ields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
c
j
fie
l
ds
fix e
r
roneously renamed stockholm tests
commit
|
commitdiff
|
tree
2008-12-02
cjfi
e
lds
s
m
all pod fix
commit
|
commitdiff
|
tree
2008-11-30
c
j
fi
e
l
d
s
silence Gu
e
ssSeqFormat
.
t warnings (not sure if old
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
rea
r
range to avoid unnecessary wa
r
nings
commit
|
commitdiff
|
tree
2008-11-28
cjfie
l
ds
A
dd warning for missing data (r
e
al bug)
commit
|
commitdiff
|
tree
2008-11-28
cjf
i
elds
hash
r
ef, not a
h
ash
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
test file name and te
s
t # corr
e
cti
o
n
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ields
correct test fi
l
e
nam
e
commit
|
commitdiff
|
tree
2008-11-28
cjfields
':
:
', not ':'
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ields
r
e
name (
r
ec
u
rsiv
e
tests think
t
his is
a
test
f
ile)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
re
c
urse into test subdirectories (means
any non-test
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfields
remove re
d
und
a
n
t
co
p
y
commit
|
commitdiff
|
tree
2008-11-28
cjf
i
elds
move int
o
d
irec
t
ory struc
t
ure
commit
|
commitdiff
|
tree
2008-11-28
cjfields
m
ove into dir
e
ctor
y
structure (
D
aveM++)
commit
|
commitdiff
|
tree
2008-11-26
cjfields
[bug
256
7
]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
Redun
d
a
nt; file was re
n
amed SearchIO
_
b
l
ast_pull
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
cjfi
e
lds
[bug 2686]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
f
i
x subversion tags
commit
|
commitdiff
|
tree
2008-11-25
cjfields
po,
n
o
t
po
a
commit
|
commitdiff
|
tree
2008-11-25
c
jfi
e
l
d
s
fix undefined val
u
e warnings
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 26
8
6
]
commit
|
commitdiff
|
tree
2008-11-25
cjfiel
d
s
[bug 2641, 264
2
]
commit
|
commitdiff
|
tree
2008-11-25
cjfield
s
split up AlignI
O
tests
commit
|
commitdiff
|
tree
2008-11-25
cjfi
e
lds
[bug 2682]
commit
|
commitdiff
|
tree
2008-11-25
cjfi
e
lds
[
b
u
g
2630
]
commit
|
commitdiff
|
tree
2008-11-24
cjf
i
elds
[bug
2633]
commit
|
commitdiff
|
tree
2008-11-24
cjf
i
elds
[bu
g
2663]
commit
|
commitdiff
|
tree
2008-11-24
cjfie
l
ds
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-24
c
jfields
[bug
2
630]
commit
|
commitdiff
|
tree
2008-11-24
cjfi
e
lds
[bug 22
6
2]
commit
|
commitdiff
|
tree
2008-11-24
cj
f
ields
[
bug
2630]
commit
|
commitdiff
|
tree
2008-11-18
cjfields
*
Do
u
ble-ch
e
cke
d
data,
t
este
d
res
u
lts were wrong
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* seq_inds is not d
e
fined for
M
o
del-bas
e
d HSPs
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* fix POD
commit
|
commitdiff
|
tree
2008-11-17
cjfields
* 'highl
y
' (a
n
d
I
get r15000!)
commit
|
commitdiff
|
tree
2008-11-17
cjfie
l
ds
R
emove redundant test files
commit
|
commitdiff
|
tree
2008-11-17
cjf
i
elds
[tests]
commit
|
commitdiff
|
tree
2008-11-17
cjfield
s
move res
u
lts2
h
ash test utility sub to SearchUtils
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-16
cjfields
perltidy
commit
|
commitdiff
|
tree
2008-11-16
c
jfields
[bug 263
5
]
commit
|
commitdiff
|
tree
2008-11-14
cjf
i
elds
[bug 2656]
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
elds
remo
v
e debugging lines
commit
|
commitdiff
|
tree
2008-11-11
cjfie
l
ds
re
m
ove fixed verbose
fl
a
g
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2
6
50]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
Clarif
y
result_count (disc
u
ssions on mail list per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
c
j
f
ields
[bug 263
2
]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[bug 2645]
commit
|
commitdiff
|
tree
2008-11-04
cjfie
l
ds
wra
p
text
commit
|
commitdiff
|
tree
2008-11-04
cjfield
s
*
parse 'Features in this
p
art o
f
subject
s
equence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse
'
Features
in this
p
ar
t
of subject seq
u
ence
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[
b
ug
2632
]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
fix
s
e
q_inds(); w
a
sn'
t
ca
l
ling identical res
i
dues for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfie
l
ds
[bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfields
[bug 2630]
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
Fix unlink() war
n
ing
commit
|
commitdiff
|
tree
2008-10-26
c
j
field
s
end = sta
r
t
if only
sta
r
t
i
s
passed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
use
va
l
id_Loca
t
ion to check
Loc
a
t
i
on state
commit
|
commitdiff
|
tree
2008-10-26
cjfields
ad
d
docs fo
r
LocationI method v
a
lid_Loca
t
ion
commit
|
commitdiff
|
tree
2008-10-26
cjfie
l
ds
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 26
2
1
]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2624]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug
2
6
2
1]
commit
|
commitdiff
|
tree
2008-10-25
cjfields
bullet-
p
ro
o
f prototype tes
t
commit
|
commitdiff
|
tree
next