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sync last bits with main trunk
2008-12-08
c
jfields
Update
d
emails
commit
|
commitdiff
|
tree
2008-12-07
cjfields
[bug
2
699]
commit
|
commitdiff
|
tree
2008-12-05
c
jfields
N
e
ed to r
e
trieve the tree for ou
t
put
commit
|
commitdiff
|
tree
2008-12-05
cjfields
[bug 2450
]
commit
|
commitdiff
|
tree
2008-12-04
cjfi
e
lds
Mak
e
Target a true DBLink
commit
|
commitdiff
|
tree
2008-12-04
c
j
fields
Di
r
e
ct
o
r
y
is no
l
onger nee
d
ed (Heikki spl
i
t this
up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
add for
c
e
_
nse
te
s
ts
commit
|
commitdiff
|
tree
2008-12-03
cjfields
leav
e
ID
u
ndefin
e
d if it isn't presen
t
, but allow the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove
f
i
les
a
ccidently add
e
d f
r
om
last
c
o
m
mit
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Reorga
n
iz
e
Tools tes
t
s
(needs some more splitting)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
R
emove (t
e
sts are red
u
nda
n
t
,
in Consed
.
t
)
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
elds
Merg
e
tests
and remove redu
n
d
ant fi
l
e
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Upd
a
te test count
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ields
M
erge tests
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ields
Remove redundan
t
file
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remo
v
e
o
l
d
f
i
l
e
s
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
Star
t
Tools move
commit
|
commitdiff
|
tree
2008-12-03
cjfields
small
u
p
d
ates:
commit
|
commitdiff
|
tree
2008-12-03
cjfields
f
orgot to increme
n
t test
co
u
n
t
commit
|
commitdiff
|
tree
2008-12-03
c
jfi
e
lds
A
d
d a couple of tests for seq_id (sm
a
ll but si
g
nificant
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cjfie
l
ds
[
b
u
g
2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[
b
ug
2
450
]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[b
u
g 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug
2
450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
s
ome
po
d
updates
commit
|
commitdiff
|
tree
2008-12-02
c
j
fields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
c
j
fields
fix erro
n
eously
renamed stockh
o
lm tests
commit
|
commitdiff
|
tree
2008-12-02
c
j
f
i
elds
smal
l
p
o
d fix
commit
|
commitdiff
|
tree
2008-11-30
cjfield
s
s
i
lenc
e
Gu
e
ssSe
q
Form
a
t
.
t warnings (not sure if ol
d
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjf
i
elds
rearrange to avoid unnecessary wa
r
n
ings
commit
|
commitdiff
|
tree
2008-11-28
c
j
f
i
elds
Ad
d
w
arnin
g
for
m
issing data (real bug)
commit
|
commitdiff
|
tree
2008-11-28
cj
f
iel
d
s
hash ref, n
o
t a
hash
commit
|
commitdiff
|
tree
2008-11-28
cjfields
te
s
t file name and
t
est #
correction
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
corre
c
t test file
name
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
'::', not ':'
commit
|
commitdiff
|
tree
2008-11-28
cjfields
rename (recursiv
e
tes
t
s think thi
s
i
s a tes
t
file)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
rec
u
rse into tes
t
subdire
c
tori
e
s (means any
n
on-test
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfie
l
d
s
remo
v
e redundant copy
commit
|
commitdiff
|
tree
2008-11-28
cjfields
move
into directo
r
y
structure
commit
|
commitdiff
|
tree
2008-11-28
c
j
fields
mov
e
in
t
o directory structur
e
(D
a
v
e
M++)
commit
|
commitdiff
|
tree
2008-11-26
cj
f
ield
s
[b
u
g
2
5
67]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
Redundant;
file was renamed Searc
h
IO
_
blast_pull
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
cjf
i
el
d
s
[bug
26
8
6]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
fi
x
subversion ta
g
s
commit
|
commitdiff
|
tree
2008-11-25
cj
f
ield
s
po, not poa
commit
|
commitdiff
|
tree
2008-11-25
c
j
f
i
e
lds
fix
u
n
defined
v
alue warn
i
ng
s
commit
|
commitdiff
|
tree
2008-11-25
cjfie
l
ds
[bug
2
686]
commit
|
commitdiff
|
tree
2008-11-25
cjf
i
elds
[bug 2641, 26
4
2]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
split
u
p Al
i
gnIO
tests
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug
2
682]
commit
|
commitdiff
|
tree
2008-11-25
c
j
fiel
d
s
[bug
2
630]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 2
6
33]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 266
3
]
commit
|
commitdiff
|
tree
2008-11-24
cjfield
s
[bug 263
0
]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 2262]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 26
3
0]
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* Double-checked data, tested results were wrong
commit
|
commitdiff
|
tree
2008-11-18
cj
f
ields
* seq_inds is not defi
n
e
d
for Model
-
bas
e
d HSP
s
commit
|
commitdiff
|
tree
2008-11-18
cjf
i
elds
* f
i
x POD
commit
|
commitdiff
|
tree
2008-11-17
cjfields
* 'highl
y
' (and I get r15000!)
commit
|
commitdiff
|
tree
2008-11-17
cjf
i
el
d
s
Remove redunda
n
t test fi
l
es
commit
|
commitdiff
|
tree
2008-11-17
cjfields
[test
s
]
commit
|
commitdiff
|
tree
2008-11-17
cjfields
move res
u
lts2hash test uti
l
i
t
y
s
u
b
to
Sea
r
chUtils
commit
|
commitdiff
|
tree
2008-11-16
c
jfi
e
lds
[
bug 2663]
commit
|
commitdiff
|
tree
2008-11-16
cjfields
perltidy
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[bug 2635]
commit
|
commitdiff
|
tree
2008-11-14
cjfi
e
l
ds
[bug 2656
]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
remove
debug
g
ing li
n
e
s
commit
|
commitdiff
|
tree
2008-11-11
cjfields
re
m
ove fixed verbose fl
a
g
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2650]
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
elds
Clarify result_co
u
nt
(discus
s
ions o
n
m
a
il list per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
c
jfields
[bug
2632
]
commit
|
commitdiff
|
tree
2008-11-10
cjfield
s
[bug 2645
]
commit
|
commitdiff
|
tree
2008-11-04
cjfield
s
wrap
t
ext
commit
|
commitdiff
|
tree
2008-11-04
cjfie
l
ds
* parse 'Features in this p
a
rt of subject sequence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfie
l
ds
* par
s
e 'Features in this part of
subject sequence
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[bug 2632]
commit
|
commitdiff
|
tree
2008-10-29
cj
f
i
elds
fix
s
e
q_inds()
;
w
as
n
't
c
a
ll
i
ng identical resi
d
u
es for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cj
f
ields
[bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfields
[bug 2630]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
Fix unlink() warnin
g
commit
|
commitdiff
|
tree
2008-10-26
cjfields
end = start i
f
only start is pa
s
sed
commit
|
commitdiff
|
tree
2008-10-26
cj
f
iel
d
s
u
s
e valid_Location to check Lo
c
ation
state
commit
|
commitdiff
|
tree
2008-10-26
cjfiel
d
s
add doc
s
fo
r
LocationI method vali
d
_Lo
c
at
i
o
n
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
[
b
ug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 262
1
]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2624]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug
2
621]
commit
|
commitdiff
|
tree
2008-10-25
cjfields
bulle
t
-proo
f
prototyp
e
tes
t
commit
|
commitdiff
|
tree
2008-10-22
cjfields
fix file pro
p
e
r
tie
s
commit
|
commitdiff
|
tree
2008-10-22
c
j
f
ie
l
ds
new module for parsin
g
vecs
c
r
e
en -f 3 output, courtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfi
e
lds
add -source for ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfields
[
bug 2563]
commit
|
commitdiff
|
tree
2008-10-10
cjfie
l
ds
typo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bug 25
1
9]
commit
|
commitdiff
|
tree
2008-10-10
cjf
i
elds
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
add
s
v
n tag
commit
|
commitdiff
|
tree
2008-10-07
c
j
f
ie
l
ds
T
O
DO's
w
ork
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[
bug 2612]
commit
|
commitdiff
|
tree
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