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mini pod fix
2008-12-10
cjfields
mini pod fix
commit
|
commitdiff
|
tree
2008-12-10
c
jfi
e
lds
u
p
date d
e
precation list
commit
|
commitdiff
|
tree
2008-12-10
cj
f
ields
remove B
i
o:
:
Graphics (separate pack
a
ge now
)
commit
|
commitdiff
|
tree
2008-12-10
c
jfields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-10
cjfi
e
lds
Remove depen
d
encies fo
r
Bio::Gra
p
hi
c
s and
deprec
a
ted
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfield
s
Squa
s
h w
a
rning
commit
|
commitdiff
|
tree
2008-12-09
cjfields
d
iag() only on verbos
e
commit
|
commitdiff
|
tree
2008-12-09
cj
f
i
elds
Fix last loop tests,
m
o
ve some to can_ok
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Modify
t
o
test n
e
w
t
em
p
cla
s
ses
a
n
d
e
nsu
r
e that added
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
upda
t
e Mauricio's email
commit
|
commitdiff
|
tree
2008-12-08
cjfiel
d
s
Update R
o
y's email
commit
|
commitdiff
|
tree
2008-12-08
cjfield
s
Roy's email
(
and b
i
o
perl
.
o
r
g not bioper
l
.
edu)
commit
|
commitdiff
|
tree
2008-12-08
cjfields
Updated e
m
a
ils
commit
|
commitdiff
|
tree
2008-12-07
c
jfield
s
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-05
cjfields
N
e
ed to retrieve the
t
r
ee
for output
commit
|
commitdiff
|
tree
2008-12-05
cjfields
[bug 2
4
50]
commit
|
commitdiff
|
tree
2008-12-04
cjfields
Ma
k
e Target a true DB
L
ink
commit
|
commitdiff
|
tree
2008-12-04
cjfi
e
lds
Directory is no
l
onger neede
d
(Heikki spl
i
t th
i
s up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
add force_nse
tests
commit
|
commitdiff
|
tree
2008-12-03
cjfields
leave ID unde
f
ined i
f
i
t is
n
't
p
res
e
nt
,
bu
t
allow the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfiel
d
s
Re
m
ove fi
l
es accidently
a
dded fr
o
m last
c
ommit
commit
|
commitdiff
|
tree
2008-12-03
cjfields
R
eorganiz
e
Tools tests (needs some
m
ore s
p
l
i
t
ting)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove (tests
a
r
e
re
d
undant, in Co
n
sed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
M
erge tests and rem
o
v
e
redundant
f
ile
commit
|
commitdiff
|
tree
2008-12-03
cjfields
U
p
da
t
e
t
e
st count
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Merge tests
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remo
v
e re
d
un
d
ant file
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Re
m
o
v
e old files
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
elds
Start Tools move
commit
|
commitdiff
|
tree
2008-12-03
cjfields
small
updates:
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
forgot to
i
n
crement test count
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Add a couple of tests
for
s
e
q
_id (s
m
all
but si
g
nificant
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
c
j
fie
l
d
s
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
c
jfi
e
lds
[b
u
g 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cj
f
i
elds
[b
u
g
2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfi
e
l
ds
s
o
me pod update
s
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug
2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
fix er
r
o
n
eousl
y
renamed stock
h
o
l
m tests
commit
|
commitdiff
|
tree
2008-12-02
cjfields
s
m
a
ll pod f
i
x
commit
|
commitdiff
|
tree
2008-11-30
cjfields
s
i
l
ence Guess
S
eqFormat
.
t warnings (n
o
t sure if
old
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
c
jfiel
d
s
rearrange t
o
avoid unn
e
cessary
warnings
commit
|
commitdiff
|
tree
2008-11-28
cjfie
l
ds
Add warning
fo
r
m
i
ssin
g
d
ata (real bug)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
hash ref, n
o
t a hash
commit
|
commitdiff
|
tree
2008-11-28
cjfields
test
f
ile name a
n
d test #
c
orrectio
n
commit
|
commitdiff
|
tree
2008-11-28
cjfi
e
lds
cor
r
ect test file name
commit
|
commitdiff
|
tree
2008-11-28
c
j
field
s
'::', not ':
'
commit
|
commitdiff
|
tree
2008-11-28
cjfields
r
e
name (
r
e
c
u
rs
i
ve tests t
h
ink th
i
s
is a
test fi
l
e)
commit
|
commitdiff
|
tree
2008-11-28
c
jfields
recurse into test subdirectories
(means an
y
non-test
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjf
i
elds
remove re
d
un
d
ant co
p
y
commit
|
commitdiff
|
tree
2008-11-28
cj
f
iel
d
s
m
o
ve into d
i
recto
r
y structure
commit
|
commitdiff
|
tree
2008-11-28
cjfields
mov
e
in
t
o d
i
rectory
s
tructur
e
(
D
aveM+
+
)
commit
|
commitdiff
|
tree
2008-11-26
cjfields
[bu
g
25
6
7]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
R
edundant;
file was renamed Sea
r
c
hIO_blast_pull
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
cjfields
[b
u
g 2686]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
fix subversion
tags
commit
|
commitdiff
|
tree
2008-11-25
cjfields
po
,
not
p
o
a
commit
|
commitdiff
|
tree
2008-11-25
c
j
fields
fix undefined
v
alu
e
warnings
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[
b
u
g
2686]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[
b
u
g 2641, 2642]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
split up
A
lignI
O
t
e
sts
commit
|
commitdiff
|
tree
2008-11-25
c
jfi
e
lds
[bug 2682]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug
2
630]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 2633]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 2
6
63]
commit
|
commitdiff
|
tree
2008-11-24
c
j
fields
[
b
ug 2663]
commit
|
commitdiff
|
tree
2008-11-24
cjfie
l
d
s
[bug 26
3
0]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[b
u
g 2262]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bu
g
2630
]
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* Doubl
e
-checked data, tested
results w
e
re wr
o
ng
commit
|
commitdiff
|
tree
2008-11-18
cjfields
*
s
eq_inds is
n
ot de
f
i
n
ed for Model-based
HSPs
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* fix
PO
D
commit
|
commitdiff
|
tree
2008-11-17
cjfields
* 'h
i
ghly' (and I get
r
15000!
)
commit
|
commitdiff
|
tree
2008-11-17
cjfields
Remove redunda
n
t test file
s
commit
|
commitdiff
|
tree
2008-11-17
cjfie
l
ds
[tests]
commit
|
commitdiff
|
tree
2008-11-17
cjfields
move r
e
sults2hash tes
t
utility
s
u
b
to Searc
h
Utils
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[b
u
g 266
3
]
commit
|
commitdiff
|
tree
2008-11-16
cjfields
perltidy
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[bu
g
2635]
commit
|
commitdiff
|
tree
2008-11-14
c
j
fields
[
b
ug 2656]
commit
|
commitdiff
|
tree
2008-11-11
cjfie
l
ds
remove debugging line
s
commit
|
commitdiff
|
tree
2008-11-11
cjfie
l
ds
remove fixed verbose
fla
g
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2650]
commit
|
commitdiff
|
tree
2008-11-11
cj
f
ields
Clarify result_cou
n
t
(discussions
o
n ma
i
l lis
t
p
e
r
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug
2
6
32
]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[b
u
g 2645]
commit
|
commitdiff
|
tree
2008-11-04
cjfields
wrap tex
t
commit
|
commitdiff
|
tree
2008-11-04
c
j
f
ields
* pars
e
'Featu
r
es
i
n this p
a
rt of subj
e
ct sequ
e
nc
e
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfield
s
* pars
e
'
F
eatures in this part of subject sequen
c
e
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjf
i
elds
[bug 2632]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
fix seq_inds(); w
a
sn't
calling
iden
t
ical residues for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[
bug
2
6
3
3]
commit
|
commitdiff
|
tree
2008-10-28
c
jfields
[b
u
g
2630]
commit
|
commitdiff
|
tree
2008-10-26
cjfi
e
lds
F
i
x
unl
i
nk() wa
r
ning
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
end = start if only s
t
art is passed
commit
|
commitdiff
|
tree
2008-10-26
c
j
f
i
elds
use vali
d
_Location to check Lo
c
ation
state
commit
|
commitdiff
|
tree
2008-10-26
cjfields
add
d
o
cs for
Locat
i
onI me
t
hod valid
_
Locat
i
on
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2621
]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[
b
ug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
[bug 2624]
commit
|
commitdiff
|
tree
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