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Sync that last bit with trunk. I'll have to merge that over to the tag for the next RC.
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cj
f
i
elds
some
pod updates
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 245
0
]
commit
|
commitdiff
|
tree
2008-12-02
c
jf
i
e
lds
fix erroneousl
y
rena
m
ed st
o
ckholm tests
commit
|
commitdiff
|
tree
2008-12-02
cjfields
small p
o
d fix
commit
|
commitdiff
|
tree
2008-11-30
c
jfields
s
ilence
GuessSeqFormat
.
t warning
s
(not sure if old
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfie
l
d
s
r
e
arra
n
ge to avoid u
n
nece
s
sary
war
n
ings
commit
|
commitdiff
|
tree
2008-11-28
cjfields
Add warning for miss
i
ng data (r
e
al bug
)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
has
h
ref, n
o
t a
h
a
s
h
commit
|
commitdiff
|
tree
2008-11-28
cjfields
test file name and t
e
st # c
o
rrection
commit
|
commitdiff
|
tree
2008-11-28
cjfields
correct test file name
commit
|
commitdiff
|
tree
2008-11-28
cjfiel
d
s
'::
'
,
not ':'
commit
|
commitdiff
|
tree
2008-11-28
cjf
i
e
l
d
s
rename (recu
r
sive tes
t
s th
i
nk
t
h
i
s is a test file)
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ie
l
ds
r
e
curse
int
o
t
e
st
subdir
e
ctories (me
a
ns any non-test
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cj
f
i
elds
remove redundant
co
p
y
commit
|
commitdiff
|
tree
2008-11-28
cjfields
move into directory stru
c
t
u
re
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
mov
e
into directory structure
(Da
v
eM+
+
)
commit
|
commitdiff
|
tree
2008-11-26
cjfields
[bug
2
567]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
Re
d
und
a
nt; fil
e
was renamed SearchIO_blast_pul
l
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
cjf
i
e
lds
[
b
u
g 268
6
]
commit
|
commitdiff
|
tree
2008-11-26
c
j
fields
fix
sub
v
ersion tags
commit
|
commitdiff
|
tree
2008-11-25
cjfields
po, not po
a
commit
|
commitdiff
|
tree
2008-11-25
cjfields
fix undefined value warnings
commit
|
commitdiff
|
tree
2008-11-25
cjfie
l
ds
[bug 2686]
commit
|
commitdiff
|
tree
2008-11-25
cjf
i
elds
[bug 2641
,
26
4
2]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
split up AlignIO te
s
ts
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[
b
u
g
2682]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[b
u
g 2630]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[
b
ug
2633]
commit
|
commitdiff
|
tree
2008-11-24
c
j
fields
[b
u
g 2663]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug
2
663]
commit
|
commitdiff
|
tree
2008-11-24
c
j
fields
[b
u
g
2630]
commit
|
commitdiff
|
tree
2008-11-24
cjfiel
d
s
[bug 2262]
commit
|
commitdiff
|
tree
2008-11-24
cj
f
ields
[
b
u
g
2630
]
commit
|
commitdiff
|
tree
2008-11-18
cjfields
*
Double-checked data, teste
d
result
s
were wrong
commit
|
commitdiff
|
tree
2008-11-18
cjfie
l
ds
* se
q
_inds is no
t
defined
f
or M
o
d
e
l-based
H
SPs
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* fix POD
commit
|
commitdiff
|
tree
2008-11-17
c
j
fie
l
d
s
* 'h
i
g
hl
y
' (and
I get
r15000!)
commit
|
commitdiff
|
tree
2008-11-17
cjf
i
elds
Rem
o
v
e red
u
n
dant test files
commit
|
commitdiff
|
tree
2008-11-17
cjfields
[tests]
commit
|
commitdiff
|
tree
2008-11-17
cjf
i
elds
mov
e
r
esul
t
s2hash test utility su
b
to Se
a
rchUtils
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[
b
u
g
2
663]
commit
|
commitdiff
|
tree
2008-11-16
cjfields
perlti
d
y
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[bug
2635]
commit
|
commitdiff
|
tree
2008-11-14
cjfields
[b
u
g
2656]
commit
|
commitdiff
|
tree
2008-11-11
cjfi
e
l
ds
re
m
ove debugging lines
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
elds
remove fixe
d
ver
b
o
se flag
commit
|
commitdiff
|
tree
2008-11-11
cj
f
ields
[bug
2650]
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
e
l
ds
Clarify
r
es
u
lt_count (discuss
i
ons on mail
l
i
s
t
p
e
r
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfi
e
lds
[
bug 2632]
commit
|
commitdiff
|
tree
2008-11-10
cjfiel
d
s
[bug 2645]
commit
|
commitdiff
|
tree
2008-11-04
cj
f
i
e
lds
wrap te
x
t
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* pa
r
se 'Features in th
i
s
p
art o
f
subje
c
t sequence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse 'Features in this part of subject sequence
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[bug 263
2
]
commit
|
commitdiff
|
tree
2008-10-29
cjfiel
d
s
fix seq_
i
nds(); was
n
't calli
n
g i
d
entical residues for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[
bu
g
2633]
commit
|
commitdiff
|
tree
2008-10-28
c
j
fields
[bu
g
26
3
0
]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
F
i
x unlink(
)
warning
commit
|
commitdiff
|
tree
2008-10-26
cjfields
e
n
d = s
t
art if only star
t
is passed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
use valid_Lo
c
ation to check Locatio
n
stat
e
commit
|
commitdiff
|
tree
2008-10-26
cjfields
add docs for Locati
o
nI meth
o
d valid_Location
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[
bug
2621
]
commit
|
commitdiff
|
tree
2008-10-26
c
j
fields
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug 2624]
commit
|
commitdiff
|
tree
2008-10-26
cjfie
l
d
s
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-25
c
j
field
s
bu
l
let-
p
r
oof prototy
p
e test
commit
|
commitdiff
|
tree
2008-10-22
cjfields
fix file p
r
o
perti
e
s
commit
|
commitdiff
|
tree
2008-10-22
cjfields
ne
w
module for parsing vecscreen
-f 3 ou
t
put, cou
r
tesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfields
add
-
s
o
urce for A
R
P
commit
|
commitdiff
|
tree
2008-10-15
cjfi
e
lds
[
bug 2563]
commit
|
commitdiff
|
tree
2008-10-10
cjfiel
d
s
typo
commit
|
commitdiff
|
tree
2008-10-10
c
j
fields
[
bug 25
1
9]
commit
|
commitdiff
|
tree
2008-10-10
cjf
i
elds
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
cjfi
e
lds
add svn tag
commit
|
commitdiff
|
tree
2008-10-07
cjfie
l
ds
T
O
DO's work
commit
|
commitdiff
|
tree
2008-10-07
c
j
f
ields
[bug 26
1
2
]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-02
cjfields
clea
n
up XMFA
pars
i
ng
,
allo
w
sp
a
ce
s
i
n
parsing (end
e
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfield
s
[BUG] bu
g
2598
commit
|
commitdiff
|
tree
2008-09-26
c
j
fields
[BUG] bugfi
x
for # 2598 (a
d
d 'J')
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BU
G
]
bug
2593
commit
|
commitdiff
|
tree
2008-09-26
c
jf
i
e
lds
[BUG] fix bug 2595
commit
|
commitdiff
|
tree
2008-09-18
c
j
fields
Use
'
warning_like' for instances wh
e
re a
regex matc
h
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfields
*
No long
e
r
a
stub
commit
|
commitdiff
|
tree
2008-09-17
cjfields
1965
+
6 -1 = 1970
,
not 19
9
9
commit
|
commitdiff
|
tree
2008-09-17
cjfields
pa
s
sing
T
ODO'
s
(?!?)
commit
|
commitdiff
|
tree
2008-09-17
c
j
f
ields
upda
t
e
tests
(
seq l
e
n
gth change in record verif
i
e
d)
commit
|
commitdiff
|
tree
2008-09-17
c
j
f
ields
se
t
-
e
n
d
to coorespond to sequ
e
nce
e
nd
commit
|
commitdiff
|
tree
2008-09-16
cjfields
test result changed (star
t
al
w
ays < end)
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Fix nexus issues w
i
th
s
e
q
.
ambiguity symbol
'
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfields
ME
G
A now resets $
G
AP_SYMBOLS and $OTHER_SYMB
O
LS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Tes
t
data
m
a
tche
s
new
XMFA
e
x
ample
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
ds
*
X
M
FA alignme
n
t
d
o
e
s
n't correspond to XMFA spec
(
h
t
t
p
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
fix
x
mfa
.
pm parsing oops
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
mak
e
LocatableSeq::end() co
n
s
i
ste
n
t
commit
|
commitdiff
|
tree
2008-09-16
cjfields
*
f
i
x
s
t
a
r
t
/end/stran
d
commit
|
commitdiff
|
tree
2008-09-16
c
jfields
typo
commit
|
commitdiff
|
tree
2008-09-15
cjfields
r
emove debugging state
m
ent
commit
|
commitdiff
|
tree
2008-09-15
cj
f
i
elds
partia
l
f
i
x for arp (-
e
nd
n
ow works and co
u
nts
?
as
.
.
.
commit
|
commitdiff
|
tree
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