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correct test file name
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
elds
r
ename (recursive tests think thi
s
is a test file)
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ield
s
recurse int
o
te
s
t subdirectories (means any
n
on-test
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
remo
v
e
re
d
undant copy
commit
|
commitdiff
|
tree
2008-11-28
c
jfield
s
move
in
t
o
direc
t
ory structu
r
e
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
move
i
nto directo
r
y structure
(D
a
v
e
M++)
commit
|
commitdiff
|
tree
2008-11-26
cjfield
s
[bug 2567]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
Redundant; f
i
le was rena
m
ed Searc
h
IO_blast_pull
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
cjfields
[
b
ug 2686]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
fix sub
v
ersion
t
ags
commit
|
commitdiff
|
tree
2008-11-25
cjfields
p
o
, not
p
oa
commit
|
commitdiff
|
tree
2008-11-25
cjfield
s
fix undefined va
l
ue
war
n
ings
commit
|
commitdiff
|
tree
2008-11-25
cjfiel
d
s
[bug
2
6
86]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[
b
u
g 26
4
1,
2
6
4
2
]
commit
|
commitdiff
|
tree
2008-11-25
cjfield
s
split up AlignIO t
e
s
t
s
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 2682]
commit
|
commitdiff
|
tree
2008-11-25
cjfiel
d
s
[bug 2630
]
commit
|
commitdiff
|
tree
2008-11-24
c
jfields
[bug 2633]
commit
|
commitdiff
|
tree
2008-11-24
cj
f
iel
d
s
[bug
2
6
6
3]
commit
|
commitdiff
|
tree
2008-11-24
cj
f
i
elds
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 2630]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 2262]
commit
|
commitdiff
|
tree
2008-11-24
cjfie
l
ds
[
bug 2
6
30]
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* Double-checke
d
d
ata, te
s
ted r
e
sults were wrong
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* seq_inds is not
defined for Model-ba
s
e
d
HSPs
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* fix POD
commit
|
commitdiff
|
tree
2008-11-17
c
jfi
e
lds
*
'highly' (and I get r15
0
00!)
commit
|
commitdiff
|
tree
2008-11-17
cjfields
Remove redundant test f
i
les
commit
|
commitdiff
|
tree
2008-11-17
cjfields
[tests]
commit
|
commitdiff
|
tree
2008-11-17
c
jf
i
el
d
s
move resu
l
ts2hash test utili
t
y su
b
to SearchUtils
commit
|
commitdiff
|
tree
2008-11-16
c
j
fiel
d
s
[
b
ug 2663]
commit
|
commitdiff
|
tree
2008-11-16
cjfields
perl
t
idy
commit
|
commitdiff
|
tree
2008-11-16
c
j
fields
[bug
2635]
commit
|
commitdiff
|
tree
2008-11-14
cjfields
[
b
u
g 2656]
commit
|
commitdiff
|
tree
2008-11-11
cjfi
e
lds
remove
d
ebugging lines
commit
|
commitdiff
|
tree
2008-11-11
c
j
f
ields
r
emove
fixed verbo
s
e flag
commit
|
commitdiff
|
tree
2008-11-11
c
jfields
[
bug 265
0
]
commit
|
commitdiff
|
tree
2008-11-11
cjfie
l
ds
Clarify re
s
ult_count (discus
s
i
o
ns o
n
mail list per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2
6
32]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[bug 264
5
]
commit
|
commitdiff
|
tree
2008-11-04
cj
f
ields
wr
a
p
t
e
x
t
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse
'
Featu
r
e
s
i
n
this
p
art
of s
u
bj
e
ct se
q
u
ence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* par
s
e 'Features
i
n
this pa
r
t of subject sequence
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
c
j
f
i
elds
[bug 2632]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
fix
s
eq_inds(); wasn't calli
n
g
i
dentic
a
l residues for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
c
jfields
[b
u
g 2630]
commit
|
commitdiff
|
tree
2008-10-26
cjfie
l
ds
Fix u
n
link() warni
n
g
commit
|
commitdiff
|
tree
2008-10-26
c
j
fi
e
lds
end = start if only
s
t
art is passed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
u
se valid_Location to check Location state
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
el
d
s
add
docs for Loc
a
tionI method valid
_
Loca
t
ion
commit
|
commitdiff
|
tree
2008-10-26
c
j
fields
[bug 26
2
1
]
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
[
bug
2
62
1
]
commit
|
commitdiff
|
tree
2008-10-26
c
j
fields
[bug 262
4
]
commit
|
commitdiff
|
tree
2008-10-26
cjfi
e
lds
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-25
cjfields
bull
e
t-pr
o
of proto
t
ype test
commit
|
commitdiff
|
tree
2008-10-22
cjfields
fix file pro
p
erties
commit
|
commitdiff
|
tree
2008-10-22
cjfields
n
ew module for parsi
n
g vecscreen
-
f
3 output, courtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cj
f
ield
s
add -source for ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfields
[bu
g
2
5
63]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
typo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[
b
ug 2519]
commit
|
commitdiff
|
tree
2008-10-10
cjfie
l
ds
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
cjfiel
d
s
add svn t
a
g
commit
|
commitdiff
|
tree
2008-10-07
cjfiel
d
s
TODO
'
s
work
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[bu
g
2612]
commit
|
commitdiff
|
tree
2008-10-07
c
jfields
[bug
2
61
2
]
commit
|
commitdiff
|
tree
2008-10-02
cj
f
ields
c
l
e
an up XMFA p
a
rsi
n
g, allow spa
c
e
s
in pa
r
sing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
cjfiel
d
s
[B
U
G]
b
ug
2
598
commit
|
commitdiff
|
tree
2008-09-26
cjfiel
d
s
[BUG] bugfi
x
for # 2
5
98 (add 'J')
commit
|
commitdiff
|
tree
2008-09-26
cjf
i
eld
s
[BUG]
b
ug 2593
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BUG
]
fix bug 259
5
commit
|
commitdiff
|
tree
2008-09-18
cjfields
Use 'wa
r
ning_like' for instances where a regex match
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
c
j
fi
e
lds
*
No long
e
r a s
t
ub
commit
|
commitdiff
|
tree
2008-09-17
cjfields
1965 +
6
-1 = 1970, not 1999
commit
|
commitdiff
|
tree
2008-09-17
cjfields
pa
s
sing TODO's (?!?)
commit
|
commitdiff
|
tree
2008-09-17
cjfields
upd
a
t
e tests (seq length change in
rec
o
rd verified)
commit
|
commitdiff
|
tree
2008-09-17
cjfield
s
set -end to coorespond to sequence end
commit
|
commitdiff
|
tree
2008-09-16
c
j
fields
test resul
t
c
h
anged
(
sta
r
t
a
lways < end)
commit
|
commitdiff
|
tree
2008-09-16
c
jfields
F
ix
n
e
xu
s
issues w
i
th seq
.
am
b
iguity
symbol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
MEGA n
o
w
resets $GAP_S
Y
MBOLS and $O
T
HER
_
SYMBO
L
S to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
T
e
st data
matches ne
w
XMFA exa
m
ple
commit
|
commitdiff
|
tree
2008-09-16
cjfi
e
lds
* X
M
FA
alig
n
men
t
doesn't correspond
t
o XMFA spec (http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfield
s
fix xmfa
.
pm
parsing oops
commit
|
commitdiff
|
tree
2008-09-16
cj
f
iel
d
s
m
ake LocatableSeq::end() consistent
commit
|
commitdiff
|
tree
2008-09-16
cjfields
*
f
i
x
s
t
art/end
/
strand
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
t
ypo
commit
|
commitdiff
|
tree
2008-09-15
cjfiel
d
s
r
e
m
ove de
b
ug
g
i
ng s
t
atement
commit
|
commitdiff
|
tree
2008-09-15
cjfields
p
a
r
tial fix for arp (-end n
o
w works and count
s
? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfields
-
end parameter does n
o
t take ga
p
s into a
c
count
commit
|
commitdiff
|
tree
2008-09-15
c
jfield
s
* alwa
y
s wa
r
n
about passing wrong
e
n
d() coordinate
commit
|
commitdiff
|
tree
2008-09-14
cjfields
Create
Data::Stag node l
a
zi
l
y; alwa
y
s
use
n
od
e
() to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfields
add a few new (unte
s
t
e
d) URLAPI parame
t
ers
commit
|
commitdiff
|
tree
2008-09-14
cjfields
use di
r
ect o
b
je
c
t syn
t
ax
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 2579
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 2580
commit
|
commitdiff
|
tree
2008-08-29
cjfields
A
l
low other Bio
:
:SeqFe
a
ture:
:
Colle
c
tionI
commit
|
commitdiff
|
tree
2008-08-28
cjfields
[bug
2
5
76
]
commit
|
commitdiff
|
tree
2008-08-27
c
jfields
g
rep not n
e
ede
d
(check for o
n
tol
o
gy
is in On
t
ology
.
.
.
commit
|
commitdiff
|
tree
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