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[bug 2630]
2008-11-24
cjfields
[
bug
2630]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 22
6
2]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 2630]
commit
|
commitdiff
|
tree
2008-11-18
cjfi
e
lds
* Doubl
e
-checke
d
data,
te
s
t
ed results
we
r
e wrong
commit
|
commitdiff
|
tree
2008-11-18
cjfie
l
ds
* seq_inds is n
o
t defin
e
d for
M
odel-base
d
HSPs
commit
|
commitdiff
|
tree
2008-11-18
cjfi
e
lds
* fi
x
P
O
D
commit
|
commitdiff
|
tree
2008-11-17
cjfields
*
'
high
l
y'
(
and I
g
et r
1
5000!)
commit
|
commitdiff
|
tree
2008-11-17
cjfi
e
lds
R
emove redundant
test
f
i
les
commit
|
commitdiff
|
tree
2008-11-17
cjfields
[tests]
commit
|
commitdiff
|
tree
2008-11-17
cjfi
e
lds
move r
e
sults2hash test
utility sub to SearchU
t
il
s
commit
|
commitdiff
|
tree
2008-11-16
c
j
fields
[bug 2663
]
commit
|
commitdiff
|
tree
2008-11-16
cjfields
perltidy
commit
|
commitdiff
|
tree
2008-11-16
cjf
i
elds
[bug
2
635]
commit
|
commitdiff
|
tree
2008-11-14
cjfiel
d
s
[
b
u
g 2656]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
rem
o
ve
debugging line
s
commit
|
commitdiff
|
tree
2008-11-11
cjfields
remove f
i
xed verbo
s
e flag
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
el
d
s
[
bug
2
6
50]
commit
|
commitdiff
|
tree
2008-11-11
c
j
field
s
C
larify result_
c
o
unt (
d
iscus
s
io
n
s on ma
i
l
list
p
er
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug
2
632]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[bug
2645
]
commit
|
commitdiff
|
tree
2008-11-04
cjfields
wrap tex
t
commit
|
commitdiff
|
tree
2008-11-04
c
j
f
ield
s
* parse 'Fe
a
tures in th
i
s par
t
of subject se
q
ue
n
ce
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
c
j
f
ields
* parse 'F
e
atures
i
n this pa
r
t of
s
ubject
s
eque
n
c
e
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
c
j
fields
[bug 2632]
commit
|
commitdiff
|
tree
2008-10-29
cjf
i
elds
fix seq_inds(); wasn't
calli
n
g iden
t
ical res
i
dues for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjf
i
e
l
ds
[
bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfi
e
lds
[bug 26
3
0]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
Fix unli
n
k() warning
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
end = start if only start is pa
s
sed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
use valid_Location to check Locatio
n
sta
t
e
commit
|
commitdiff
|
tree
2008-10-26
cjfi
e
lds
add docs for LocationI method valid_Location
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bug
2
621]
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
[bug
2621]
commit
|
commitdiff
|
tree
2008-10-26
c
j
fields
[b
u
g
2
624]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[bu
g
2621
]
commit
|
commitdiff
|
tree
2008-10-25
cjfields
bulle
t
-
p
roof
prototype test
commit
|
commitdiff
|
tree
2008-10-22
cjfields
fix file
p
rop
e
rties
commit
|
commitdiff
|
tree
2008-10-22
cjfields
new module for parsing ve
c
screen -
f
3
o
utput,
c
ourtesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfield
s
add -s
o
urc
e
for ARP
commit
|
commitdiff
|
tree
2008-10-15
c
jfields
[bug
2
563]
commit
|
commitdiff
|
tree
2008-10-10
c
jfi
e
lds
typo
commit
|
commitdiff
|
tree
2008-10-10
cjfie
l
ds
[bug 251
9
]
commit
|
commitdiff
|
tree
2008-10-10
cj
f
i
elds
[bu
g
2519
]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
a
d
d sv
n
tag
commit
|
commitdiff
|
tree
2008-10-07
cjfield
s
TODO's work
commit
|
commitdiff
|
tree
2008-10-07
cjfield
s
[bug 261
2
]
commit
|
commitdiff
|
tree
2008-10-07
c
jfields
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-02
cjfie
l
d
s
cl
e
an up
XMFA parsing,
allow
s
p
ac
e
s in parsing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
c
j
fields
[BUG]
bug 2598
commit
|
commitdiff
|
tree
2008-09-26
c
jfiel
d
s
[BUG] bugfix for # 2
5
98
(add 'J')
commit
|
commitdiff
|
tree
2008-09-26
c
jfield
s
[B
U
G] bu
g
2593
commit
|
commitdiff
|
tree
2008-09-26
cjfield
s
[BUG] fix bug
2595
commit
|
commitdiff
|
tree
2008-09-18
cjfields
U
s
e 'w
a
rning_like' fo
r
instances wh
e
re a
r
e
g
ex match
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
c
j
fiel
d
s
* No longer a stu
b
commit
|
commitdiff
|
tree
2008-09-17
cjfields
1965 + 6 -1 = 1970
,
n
ot 1
9
99
commit
|
commitdiff
|
tree
2008-09-17
cjfields
passing
T
ODO's (?!?)
commit
|
commitdiff
|
tree
2008-09-17
cjfields
update tests
(seq length cha
n
ge
in rec
o
rd verified)
commit
|
commitdiff
|
tree
2008-09-17
c
j
field
s
set -end to coorespond to sequence
end
commit
|
commitdiff
|
tree
2008-09-16
cjfields
t
e
st resu
l
t change
d
(start always < en
d
)
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
Fix nexus issues with seq
.
am
b
i
guity sy
m
bol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfields
MEGA now
r
eset
s
$G
A
P_SYMBOLS an
d
$OTH
E
R_SYMBOLS to
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfiel
d
s
Test
d
a
ta matc
h
e
s
new XMFA
e
xample
commit
|
commitdiff
|
tree
2008-09-16
c
jfields
* XMFA alignment doesn
'
t
correspond to XMFA spec (http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfields
fix xmf
a
.
pm parsi
n
g oops
commit
|
commitdiff
|
tree
2008-09-16
cj
f
i
elds
ma
k
e LocatableSeq::end() consisten
t
commit
|
commitdiff
|
tree
2008-09-16
cjfie
l
ds
* fix start/end/str
a
nd
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
t
ypo
commit
|
commitdiff
|
tree
2008-09-15
cjfields
remove de
b
ug
g
ing statement
commit
|
commitdiff
|
tree
2008-09-15
cjfields
partial
fix for arp
(-end now works and counts ? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
cjfields
-
en
d
p
a
rameter d
o
es no
t
take gaps i
n
to accoun
t
commit
|
commitdiff
|
tree
2008-09-15
cj
f
ields
*
a
lways war
n
ab
o
ut p
a
ssing
w
rong end() coordinate
commit
|
commitdiff
|
tree
2008-09-14
cjfields
Creat
e
Data
:
:Stag
n
ode lazily; always use
n
ode()
to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfields
add
a few new (u
n
tes
t
ed)
U
R
LAPI
parameters
commit
|
commitdiff
|
tree
2008-09-14
cjfiel
d
s
u
s
e dir
e
ct object
syntax
commit
|
commitdiff
|
tree
2008-09-09
cjfields
bug 2579
commit
|
commitdiff
|
tree
2008-09-09
cjfie
l
d
s
bug 25
8
0
commit
|
commitdiff
|
tree
2008-08-29
cjf
i
elds
Allo
w
other Bio:
:
SeqF
e
ature::CollectionI
commit
|
commitdiff
|
tree
2008-08-28
cjfields
[bug 2576]
commit
|
commitdiff
|
tree
2008-08-27
cj
f
iel
d
s
grep
not needed
(
c
heck for ontology is in Ontolog
y
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfie
l
ds
[bug
2
573]
commit
|
commitdiff
|
tree
2008-08-27
cjf
i
el
d
s
Upd
a
t
e
documentation
commit
|
commitdiff
|
tree
2008-08-27
c
jfields
complete s
e
ntence
commit
|
commitdiff
|
tree
2008-08-25
cjfields
Add so
m
e print_* meth
o
ds for e
i
n
f
o, esumma
r
y, etc
.
commit
|
commitdiff
|
tree
2008-08-21
cjfie
l
ds
* wri
t
e PRO
J
ECT
s
u
p
p
ort
commit
|
commitdiff
|
tree
2008-08-21
cjfields
add P
R
OJECT
support (bug
2
569)
commit
|
commitdiff
|
tree
2008-08-05
cjfields
For new NCBI b
l
as
t
table format
commit
|
commitdiff
|
tree
2008-08-05
cjfields
Previous
c
han
g
es killed
R
e
m
o
teBlast
a
gain; make a litt
l
e
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cjfield
s
A
d
d
a few new G
E
T
/PUT parameters
.
commit
|
commitdiff
|
tree
2008-08-04
cjf
i
elds
Sequences w
e
re
n
'
t
being
parsed c
o
rrectly
;
u
n
fortunatel
y
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cj
f
ields
tests sh
o
u
ld
u
se is/i
s
nt wh
e
n possib
l
e,
not ok()
commit
|
commitdiff
|
tree
2008-07-30
cjfiel
d
s
revert
R
oy's patch (my
b
ad)
commit
|
commitdiff
|
tree
2008-07-30
cjfields
b
u
g 2556:
commit
|
commitdiff
|
tree
2008-07-30
cjfields
Bug
2
546
commit
|
commitdiff
|
tree
2008-07-29
cjfields
bu
g
2555
commit
|
commitdiff
|
tree
2008-07-29
c
jfields
b
ug 2549; f
i
xed sm
a
ll
bug in
Bio::Taxon which doe
s
n
.
.
.
commit
|
commitdiff
|
tree
2008-07-28
cjfields
add multiple record support
(
c
o
urtesy of Jo
r
ge Dua
r
t
e
.
.
.
commit
|
commitdiff
|
tree
2008-07-18
cjfiel
d
s
bull
e
tpro
o
f test; remote tabular BLAST is f
a
i
l
ing for
.
.
.
commit
|
commitdiff
|
tree
2008-07-09
cjfie
l
ds
bu
g
2534
commit
|
commitdiff
|
tree
2008-07-08
cjf
i
elds
Can't inherit fro
m
ones
e
lf
commit
|
commitdiff
|
tree
2008-07-08
cjfields
bug 2539
commit
|
commitdiff
|
tree
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