repo.or.cz
/
bioperl-live.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
sync trunk with branch
2008-11-25
cjfie
l
d
s
[bug
2686]
commit
|
commitdiff
|
tree
2008-11-25
cjfi
e
lds
[bu
g
2641,
2642]
commit
|
commitdiff
|
tree
2008-11-25
cjfiel
d
s
s
p
l
i
t up
AlignIO te
s
t
s
commit
|
commitdiff
|
tree
2008-11-25
cjf
i
eld
s
[bug 2682]
commit
|
commitdiff
|
tree
2008-11-25
cjfi
e
l
ds
[bug 2
6
30]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[
bug
2633]
commit
|
commitdiff
|
tree
2008-11-24
cjf
i
elds
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-24
cjfie
l
ds
[bug 26
6
3]
commit
|
commitdiff
|
tree
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
2
630]
commit
|
commitdiff
|
tree
2008-11-18
cjfie
l
ds
* Dou
b
le-checked
data, tes
t
ed results were w
r
on
g
commit
|
commitdiff
|
tree
2008-11-18
cjfiel
d
s
*
seq_inds i
s
n
o
t def
i
ned for Model-based HSPs
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* fix POD
commit
|
commitdiff
|
tree
2008-11-17
cjfield
s
* 'h
i
ghly' (and I get r15000!)
commit
|
commitdiff
|
tree
2008-11-17
cjfiel
d
s
Re
m
ove redu
n
dant test fi
l
es
commit
|
commitdiff
|
tree
2008-11-17
cjfields
[tests
]
commit
|
commitdiff
|
tree
2008-11-17
cjfiel
d
s
move results2hash
t
e
s
t ut
i
lity
s
ub to SearchUtils
commit
|
commitdiff
|
tree
2008-11-16
cjf
i
eld
s
[
b
u
g
2
663]
commit
|
commitdiff
|
tree
2008-11-16
cjfield
s
per
l
tidy
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[b
u
g 2
6
35]
commit
|
commitdiff
|
tree
2008-11-14
c
j
fields
[bug 2656]
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
elds
remove
debugging li
n
es
commit
|
commitdiff
|
tree
2008-11-11
cjfie
l
d
s
remov
e
fi
x
ed verbose flag
commit
|
commitdiff
|
tree
2008-11-11
c
jf
i
e
lds
[bug 2650]
commit
|
commitdiff
|
tree
2008-11-11
cjfi
e
lds
Clarify resul
t
_count (discussion
s
on mail lis
t
per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2632]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[b
u
g 264
5
]
commit
|
commitdiff
|
tree
2008-11-04
cjfields
wrap text
commit
|
commitdiff
|
tree
2008-11-04
cj
f
ields
* parse
'Feature
s
i
n
this par
t
of sub
j
ec
t
sequence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse
'
Feature
s
in this
p
ar
t
of subject sequence
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[bug 2632]
commit
|
commitdiff
|
tree
2008-10-29
cjfield
s
fix
s
eq_inds();
wasn't ca
l
ling iden
t
ical r
e
sid
u
es for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfi
e
lds
[bug 2630]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
F
ix
u
nlin
k
()
warning
commit
|
commitdiff
|
tree
2008-10-26
c
j
fields
end
= sta
r
t if
only
start
i
s
passed
commit
|
commitdiff
|
tree
2008-10-26
cjfields
use
valid
_
Lo
c
atio
n
to chec
k
Location state
commit
|
commitdiff
|
tree
2008-10-26
cjfield
s
add docs for Location
I
m
e
thod
valid_Loc
a
tio
n
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
[bug
2
621]
commit
|
commitdiff
|
tree
2008-10-26
cj
f
ie
l
ds
[b
u
g
26
2
1]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[
b
ug 2624]
commit
|
commitdiff
|
tree
2008-10-26
cjfi
e
lds
[bug
2
621]
commit
|
commitdiff
|
tree
2008-10-25
cj
f
ields
bullet
-
pro
o
f proto
t
ype test
commit
|
commitdiff
|
tree
2008-10-22
cjfie
l
ds
fix file
p
r
operties
commit
|
commitdiff
|
tree
2008-10-22
cjfiel
d
s
new m
o
dule for parsing vecs
c
reen -f 3 output, co
u
rte
s
y
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
c
j
fie
l
ds
add -source fo
r
ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfie
l
ds
[bug 2563]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
t
y
po
commit
|
commitdiff
|
tree
2008-10-10
c
j
fi
e
lds
[bug 251
9
]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bu
g
2
5
19]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
add svn tag
commit
|
commitdiff
|
tree
2008-10-07
cjfields
TODO's work
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
[bug 2612]
commit
|
commitdiff
|
tree
2008-10-02
cjfields
clean up
XMFA par
s
ing, allo
w
spaces in parsing (ende
.
.
.
commit
|
commitdiff
|
tree
2008-09-27
c
jfields
[BUG] bug
2
5
98
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[B
U
G] bugfix for # 2598 (add
'J')
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BU
G
]
b
u
g
2593
commit
|
commitdiff
|
tree
2008-09-26
cjfields
[BUG] fix bug 2595
commit
|
commitdiff
|
tree
2008-09-18
cj
f
ields
Use
'
warning_li
k
e' for instance
s
where a regex match
.
.
.
commit
|
commitdiff
|
tree
2008-09-17
cjfie
l
ds
* No
l
onger a s
t
u
b
commit
|
commitdiff
|
tree
2008-09-17
cjfields
1965 + 6 -
1
=
1
970
,
not 1999
commit
|
commitdiff
|
tree
2008-09-17
cj
f
i
e
lds
passing TODO's (?
!
?)
commit
|
commitdiff
|
tree
2008-09-17
c
jfields
update tests (seq l
e
ngth
ch
a
nge in rec
o
rd v
e
ri
f
ie
d
)
commit
|
commitdiff
|
tree
2008-09-17
cjfields
set -end to coorespond to seq
u
ence end
commit
|
commitdiff
|
tree
2008-09-16
c
j
fields
t
e
st
result chang
e
d (
s
tar
t
always < end)
commit
|
commitdiff
|
tree
2008-09-16
cjfields
Fix
n
exus issues
w
i
t
h
s
e
q
.
am
b
i
gui
t
y symbol '
.
'
commit
|
commitdiff
|
tree
2008-09-16
cjfields
M
EGA now res
e
ts $GAP_SYMB
O
L
S
a
nd $OTHER_SYMBO
L
S t
o
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
c
j
fields
Test data matc
h
es new X
M
FA exampl
e
commit
|
commitdiff
|
tree
2008-09-16
c
jfields
* XMFA alignment doesn't c
o
rresp
o
nd to XM
F
A spec (http
.
.
.
commit
|
commitdiff
|
tree
2008-09-16
cjfi
e
lds
fix xmfa
.
p
m parsi
n
g oops
commit
|
commitdiff
|
tree
2008-09-16
c
j
f
i
elds
make
LocatableSeq:
:
end
(
) consis
t
ent
commit
|
commitdiff
|
tree
2008-09-16
cjfi
e
l
ds
* fix start/end/strand
commit
|
commitdiff
|
tree
2008-09-16
cj
f
ields
t
ypo
commit
|
commitdiff
|
tree
2008-09-15
cjfi
e
ld
s
remove debu
g
ging s
t
a
t
em
e
nt
commit
|
commitdiff
|
tree
2008-09-15
cjfi
e
lds
pa
r
tial fi
x
for
arp (-end n
o
w
works and cou
n
t
s
? as
.
.
.
commit
|
commitdiff
|
tree
2008-09-15
c
jfields
-end
p
arame
t
er doe
s
no
t
t
a
ke g
a
ps into account
commit
|
commitdiff
|
tree
2008-09-15
cjfi
e
l
d
s
*
always warn about passing wrong en
d
() coordin
a
te
commit
|
commitdiff
|
tree
2008-09-14
cjfields
Cr
e
at
e
Data::Stag node lazil
y
;
a
lway
s
us
e
no
d
e() to
.
.
.
commit
|
commitdiff
|
tree
2008-09-14
cjfields
add a few new (untested) URLAPI p
a
rameters
commit
|
commitdiff
|
tree
2008-09-14
cj
f
i
elds
use direc
t
object syntax
commit
|
commitdiff
|
tree
2008-09-09
cjfie
l
ds
bug 2579
commit
|
commitdiff
|
tree
2008-09-09
c
j
fiel
d
s
bug 2580
commit
|
commitdiff
|
tree
2008-08-29
cjfields
Allow other Bio:
:
SeqFe
a
tur
e
::Coll
e
ctio
n
I
commit
|
commitdiff
|
tree
2008-08-28
cjfi
e
lds
[bug 2576]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
grep not
n
e
ed
e
d (check for on
t
ology is in Ontology
.
.
.
commit
|
commitdiff
|
tree
2008-08-27
cjfields
[bug 2573]
commit
|
commitdiff
|
tree
2008-08-27
cjfields
Update documen
t
a
t
ion
commit
|
commitdiff
|
tree
2008-08-27
c
jfields
complete sente
n
ce
commit
|
commitdiff
|
tree
2008-08-25
cj
f
iel
d
s
Add som
e
pri
n
t
_
*
m
ethods for einfo,
e
summa
r
y, etc
.
commit
|
commitdiff
|
tree
2008-08-21
cjfields
* write PROJ
E
CT support
commit
|
commitdiff
|
tree
2008-08-21
c
jfields
add PROJECT support (bug 2569)
commit
|
commitdiff
|
tree
2008-08-05
cjfields
F
or new N
C
BI bl
a
sttable format
commit
|
commitdiff
|
tree
2008-08-05
cjfie
l
ds
Previous
changes killed Rem
o
t
e
Bl
a
st again; ma
k
e a li
t
t
le
.
.
.
commit
|
commitdiff
|
tree
2008-08-04
cjfields
Ad
d
a few n
e
w GET/PUT
p
arameters
.
commit
|
commitdiff
|
tree
2008-08-04
cjfi
e
lds
Sequences weren't being parsed correctly; unfortunately
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
c
jfields
tests should
u
se
i
s/isnt when poss
i
bl
e
, not ok()
commit
|
commitdiff
|
tree
2008-07-30
c
j
f
ields
rever
t
Roy's patch (my bad)
commit
|
commitdiff
|
tree
2008-07-30
cjfields
bug
25
5
6
:
commit
|
commitdiff
|
tree
next