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Remove Bio::Graphics examples and scripts
2008-11-28
cjf
i
elds
te
s
t fi
l
e name a
n
d test # correction
commit
|
commitdiff
|
tree
2008-11-28
cjfi
e
l
d
s
correct test
file n
a
me
commit
|
commitdiff
|
tree
2008-11-28
c
j
fields
'::', not ':'
commit
|
commitdiff
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tree
2008-11-28
cjfields
r
e
name (recur
s
ive te
s
ts th
i
nk this
i
s
a
tes
t
file)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
re
c
urse in
t
o test subdi
r
ector
i
e
s (m
e
ans any non-t
e
st
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfields
remove redundant
c
op
y
commit
|
commitdiff
|
tree
2008-11-28
cjfields
move into di
r
ectory structure
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ield
s
mo
v
e
into di
r
ec
t
ory struct
u
re (
D
ave
M
++)
commit
|
commitdiff
|
tree
2008-11-26
c
j
fiel
d
s
[bu
g
2567]
commit
|
commitdiff
|
tree
2008-11-26
cjfi
e
lds
R
e
dundant
;
file
w
as renamed
S
earchIO_blast
_
pull
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
cjfields
[bug 2686]
commit
|
commitdiff
|
tree
2008-11-26
cjfie
l
ds
f
i
x s
u
bversion
t
ags
commit
|
commitdiff
|
tree
2008-11-25
cjfields
po, not p
o
a
commit
|
commitdiff
|
tree
2008-11-25
cjfi
e
lds
fix und
e
fined value warnings
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 268
6
]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[b
u
g 2
6
41, 264
2
]
commit
|
commitdiff
|
tree
2008-11-25
c
jfields
sp
l
it up Ali
g
nIO tests
commit
|
commitdiff
|
tree
2008-11-25
cjf
i
e
l
ds
[bug 2682]
commit
|
commitdiff
|
tree
2008-11-25
cjf
i
eld
s
[bug 2630]
commit
|
commitdiff
|
tree
2008-11-24
cjfi
e
l
d
s
[bug
2633]
commit
|
commitdiff
|
tree
2008-11-24
cj
f
ields
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-24
c
j
f
ie
l
ds
[
b
ug
2
663]
commit
|
commitdiff
|
tree
2008-11-24
cj
f
ield
s
[bu
g
2630]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[
b
ug
2
262]
commit
|
commitdiff
|
tree
2008-11-24
c
jfields
[bug 2630]
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* Double-ch
e
cked data, te
s
t
ed
r
esult
s
w
ere wrong
commit
|
commitdiff
|
tree
2008-11-18
c
j
fields
*
s
eq_inds is not
d
efin
e
d for Model-b
a
sed HSPs
commit
|
commitdiff
|
tree
2008-11-18
cjfields
*
fix
P
O
D
commit
|
commitdiff
|
tree
2008-11-17
cjfield
s
* 'highly'
(and
I get r
1
50
0
0!)
commit
|
commitdiff
|
tree
2008-11-17
cjfields
Remove r
e
dundant te
s
t
f
iles
commit
|
commitdiff
|
tree
2008-11-17
c
j
fiel
d
s
[tests]
commit
|
commitdiff
|
tree
2008-11-17
c
jfields
m
o
ve
r
esults2hash tes
t
utilit
y
sub to SearchU
t
ils
commit
|
commitdiff
|
tree
2008-11-16
cjf
i
elds
[bu
g
2
6
63
]
commit
|
commitdiff
|
tree
2008-11-16
cjfie
l
d
s
perltidy
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[
b
ug 2635]
commit
|
commitdiff
|
tree
2008-11-14
cjfields
[
bug 2656
]
commit
|
commitdiff
|
tree
2008-11-11
cj
f
ield
s
remove
deb
u
gg
i
ng lines
commit
|
commitdiff
|
tree
2008-11-11
c
jfields
remove fixed verbose flag
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
e
l
ds
[bug 2650]
commit
|
commitdiff
|
tree
2008-11-11
c
j
fields
Clarify result_count (discussions on mail
list
per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfie
l
ds
[bug 2632]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[b
u
g
2
6
45]
commit
|
commitdiff
|
tree
2008-11-04
cjfields
wra
p
text
commit
|
commitdiff
|
tree
2008-11-04
cjfield
s
* parse 'Features
in this p
a
rt of sub
j
e
ct seq
u
e
n
c
e
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfi
e
lds
*
parse
'
Features in
t
his
p
art of subject sequ
e
n
ce
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[bug 2
6
32]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
f
ix s
e
q_inds(); wa
s
n't calling identica
l
residues for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
c
jfiel
d
s
[
b
ug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfiel
d
s
[b
u
g 2630]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
Fix u
n
lin
k
() warning
commit
|
commitdiff
|
tree
2008-10-26
cjfi
e
ld
s
end = start if only start is
p
assed
commit
|
commitdiff
|
tree
2008-10-26
cj
f
ie
l
ds
use
v
alid_
L
ocation
to check Locat
i
o
n
state
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
a
dd doc
s
for L
o
c
ationI metho
d
va
l
id_Locat
i
on
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[b
u
g 2621
]
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
[bug 262
1
]
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
[bug 2624]
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
e
l
ds
[
bug
262
1
]
commit
|
commitdiff
|
tree
2008-10-25
cjf
i
elds
bulle
t
-proo
f
p
rototype te
s
t
commit
|
commitdiff
|
tree
2008-10-22
c
jfie
l
ds
fi
x
fi
l
e propert
i
es
commit
|
commitdiff
|
tree
2008-10-22
cjfields
new module
f
or p
a
rsing
v
ec
s
creen -f 3 o
u
t
p
ut, courtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
c
jfiel
d
s
add
-
source for A
R
P
commit
|
commitdiff
|
tree
2008-10-15
cj
f
ields
[b
u
g 25
6
3]
commit
|
commitdiff
|
tree
2008-10-10
c
j
f
i
elds
typo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[b
u
g
2519]
commit
|
commitdiff
|
tree
2008-10-07
cjf
i
e
l
ds
a
d
d svn ta
g
commit
|
commitdiff
|
tree
2008-10-07
cjfiel
d
s
TODO's work
commit
|
commitdiff
|
tree
2008-10-07
c
jfields
[bug 2
6
1
2
]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-02
cjfields
c
l
e
an
u
p
X
M
FA p
a
rsing, allow spaces in parsing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfields
[BUG]
b
ug 2598
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[
BUG
]
bugf
i
x for # 2598 (add 'J')
commit
|
commitdiff
|
tree
2008-09-26
c
j
f
i
e
lds
[BUG] bug 25
9
3
commit
|
commitdiff
|
tree
2008-09-26
cjfield
s
[
BU
G
] f
i
x bug 2
5
95
commit
|
commitdiff
|
tree
2008-09-18
c
j
fields
U
s
e 'warning_like'
f
or
inst
a
nces
wh
e
re
a rege
x
m
a
tch
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfields
* No longe
r
a
s
tub
commit
|
commitdiff
|
tree
2008-09-17
c
jfi
e
lds
1965 + 6 -1 = 1970, not 1999
commit
|
commitdiff
|
tree
2008-09-17
cjfields
p
a
s
sing TODO's
(
?!?)
commit
|
commitdiff
|
tree
2008-09-17
cj
f
ields
update tests (seq leng
t
h change in record
verified)
commit
|
commitdiff
|
tree
2008-09-17
cjfi
e
ld
s
s
et
-
e
nd to coorespon
d
to s
e
quence en
d
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
e
l
ds
t
e
st result changed (start alwa
y
s <
end)
commit
|
commitdiff
|
tree
2008-09-16
c
jfield
s
Fix
n
e
x
u
s
issu
e
s with
seq
.
ambiguity symbol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
c
jfiel
d
s
MEGA
n
ow rese
t
s $GAP_SYMB
O
L
S
and $OTHE
R
_SYM
B
OLS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
c
j
fields
T
e
s
t data matche
s
new
X
MFA exampl
e
commit
|
commitdiff
|
tree
2008-09-16
cjfields
* X
M
FA
alignment d
o
e
sn't
correspond to XMFA spec (http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
fix x
m
fa
.
pm parsing oop
s
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
d
s
m
ake
L
o
c
a
tableSeq::end()
c
ons
i
st
e
nt
commit
|
commitdiff
|
tree
2008-09-16
cjf
i
elds
* fix start/end/strand
commit
|
commitdiff
|
tree
2008-09-16
cjfield
s
typ
o
commit
|
commitdiff
|
tree
2008-09-15
cjfi
e
lds
remove de
b
ug
g
i
ng statement
commit
|
commitdiff
|
tree
2008-09-15
cjfie
l
d
s
p
artial fix for
arp (-end now w
o
rks and counts ?
a
s
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfields
-end parameter
d
oes not take
g
aps into account
commit
|
commitdiff
|
tree
2008-09-15
cj
f
ields
*
always
war
n
ab
o
ut p
a
s
sing wrong en
d
() coordin
a
te
commit
|
commitdiff
|
tree
2008-09-14
cjfields
Crea
t
e
Data::Stag n
o
de lazily; al
w
ay
s
use no
d
e() to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfields
add a few new
(
untes
t
ed)
U
RLA
P
I param
e
ters
commit
|
commitdiff
|
tree
2008-09-14
cjfields
use direct object
syntax
commit
|
commitdiff
|
tree
2008-09-09
cj
f
ields
bug 2579
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 2580
commit
|
commitdiff
|
tree
2008-08-29
c
jfields
Allow ot
h
er
Bio::SeqFeatur
e
::CollectionI
commit
|
commitdiff
|
tree
2008-08-28
cjfi
e
lds
[
bug 2576]
commit
|
commitdiff
|
tree
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