repo.or.cz
/
pygr.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
protect mysql tests using mysql_enabled()
2009-09-01
Christoph
e
r
L
ee
Merge comm
i
t 'remotes/ctb/doc_anno
t
ations' into
t
utori
a
l
commit
|
commitdiff
|
tree
2009-09-01
Christop
h
er
L
ee
ex
t
rac
t
ed material for separa
t
e database
t
ut
o
rial
commit
|
commitdiff
|
tree
2009-08-29
Christopher Lee
removed
u
nn
e
ce
s
sary
s
t
a
t
and shutil import from setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
C
hristop
h
er Lee
f
ixed easy_install bug by protect
i
ng
c
oordinator
.
ResourceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
ristoph
e
r L
e
e
fixed blast_
t
e
st: ren
a
med test_seq_without_db() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Merge commit 'r
e
motes/ct
b
/mi
n
o
r
_fixes' int
o
minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
ist
o
p
her Lee
fix port passing in
tes
t
util
.
TestXMLR
P
C
S
erver
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
use pair_i
d
entity_tuple()
for
blast_test
f
ormat
t
ing
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christop
h
er Lee
added
B
lastBa
s
e
.
tearD
o
wn(
)
to close seqdbs as th
e
y
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
ri
s
topher Lee
Merge commit
'
r
emotes/mkszuba/doc_
m
a
k
e'
commit
|
commitdiff
|
tree
2009-08-04
Christoph
e
r Lee
Merge commit 'remotes/m
k
szuba/rp
m
'
commit
|
commitdiff
|
tree
2009-07-29
Christop
h
er Lee
got rid of BlastMappin
g
.
warn_about_self_m
a
tches()
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
change
d
N
LMSA
p
airwiseMode to allow r
e
por
t
ing of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher Le
e
Merge comm
i
t 'remot
e
s/
m
kszuba/debian'
commit
|
commitdiff
|
tree
2009-07-29
C
h
ris
t
op
h
er Lee
retry readin
g
port
_
fil
e
in
T
e
s
tXMLRPCServer
several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Chri
s
topher
L
e
e
ad
d
ed comment
s
to process
_
blast()
commit
|
commitdiff
|
tree
2009-07-29
Christopher L
e
e
fix pr
o
blem introduced in process_blast() by commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristopher
L
ee
h
a
nd
l
e m
i
ssing
W
INDIR case on Windows
commit
|
commitdiff
|
tree
2009-07-28
Christop
h
er Lee
added SeqTranslator
.
__rep
r
__()
commit
|
commitdiff
|
tree
2009-07-28
Christopher L
e
e
Merge commit 'remotes/ctb/simpleframe_formatdb_c
l
eanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
M
erge
b
r
anch '
m
aster' i
n
to simpleframe
commit
|
commitdiff
|
tree
2009-07-28
Christo
p
her
L
ee
added SeqTrans
l
ator
.
ite
r
_
frames()
m
ethod, us
e
d in B
l
astxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
M
e
rge commit '
r
emotes/ctb/simpleframe_doc_align'
i
nto
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
istophe
r
Lee
protect 2 more tests using blast_enabled
(
)
c
heck
commit
|
commitdiff
|
tree
2009-07-27
C
hristopher Lee
fixed syntax error
commit
|
commitdiff
|
tree
2009-07-27
Chris
t
opher Lee
added python 2
.
3 code f
o
r
FilePopen to detect ba
d
exi
t
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Chris
t
ophe
r
Lee
Merge b
r
anch
'no_edge
_
db'
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
i
s
t
oph
e
r Lee
Merge
b
r
a
n
ch 'silencio'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
added
s
howFormatdbMess
a
ges o
p
tion
t
o BlastMapping
commit
|
commitdiff
|
tree
2009-07-25
Christo
p
h
e
r
Lee
added support for no-edgeDB case in mappin
g
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christopher
L
ee
added option for latex ou
t
put
of the
r
e
f
e
r
enc
e
m
a
n
ual
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r Lee
Merge commit
're
m
otes/ctb/blast_te
s
t_rc' into
simple
f
rame
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
added more docstrings for bl
a
st
.
py
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher Lee
r
emoved old BlastxMapping code
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r Lee
ne
w
,
great
l
y simplified Blast
x
Mapping
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher Lee
switched
t
e
s
t_blastx_se
r
ver
to use new Trans
l
at
i
o
n
D
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
istopher Lee
added
r
ead_blast_
a
lignmen
t
(
) translateDest optio
n
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
added NLMSA
.
edges()
m
ethod
commit
|
commitdiff
|
tree
2009-07-16
Christopher
L
ee
switched test_
t
blas
t
n_
p
ars
e
r to
use new Translati
o
nDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christop
h
er Le
e
s
w
itch tblastn to
use new Tran
s
lationDB approach
commit
|
commitdiff
|
tree
2009-07-15
C
hristopher Lee
a
dded translationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
m
o
ved d
b
name default into get_boun
d
_subclass()
commit
|
commitdiff
|
tree
2009-07-15
C
hrist
o
pher L
e
e
make CoordsToIntervals / get_int
e
rval() use seq
.
absolute_
s
li
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
cleaned
up SeqPath
.
classySl
i
ce
(
)
commit
|
commitdiff
|
tree
2009-07-15
C
hristo
p
her Lee
Merge commit 're
m
otes/mkszuba/nlmsa_no_verbose' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
hristopher Lee
Merge commit 'r
e
motes/mkszuba/cnestedlist_notice' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
i
ncomp
l
ete n
e
w code fo
r
T
ransla
t
i
o
nDB
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher
L
e
e
cleaned up reversePath
c
onst
r
u
ction
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher
L
ee
add ab
s
olute_slice() met
h
od to SeqPath
commit
|
commitdiff
|
tree
2009-07-14
Chr
i
stophe
r
L
e
e
Merge
comm
i
t 're
m
otes/mkszuba/cnestedlist_l
o
gg
e
r' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christopher
Lee
M
erge branch 'master' into megatests
commit
|
commitdiff
|
tree
2009-07-03
Christopher
Le
e
M
e
r
ge branch
'
f
o
r
matdb_fail'
commit
|
commitdiff
|
tree
2009-07-03
Ch
r
istop
h
er Lee
i
m
p
r
oved whitespace pat
h
warnin
g
commit
|
commitdiff
|
tree
2009-07-03
Christophe
r
Lee
a
d
ded
warning f
o
r whitespace in
p
a
th
commit
|
commitdiff
|
tree
2009-07-01
Chr
i
s
top
h
er Lee
Merge co
m
mit 'remotes/mkszuba/megatests'
commit
|
commitdiff
|
tree
2009-07-01
Christopher
Lee
use glob
.
gl
o
b(
)
i
n
s
tead of os
.
listdir(); cl
e
ane
d
up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christo
p
he
r
Lee
Merge commit 're
m
otes/mkszuba/mimetext'
commit
|
commitdiff
|
tree
2009-07-01
C
hristo
p
her Lee
Merge commit 're
m
otes/mk
s
zu
b
a/docfixes'
commit
|
commitdiff
|
tree
2009-07-01
Ch
r
isto
p
her Lee
Merge commit 'r
e
m
o
tes/mks
z
uba/hashlib'
commit
|
commitdiff
|
tree
2009-06-26
Chri
s
to
p
her Lee
f
ixed caching bug
intr
o
duced
in
commit 8d9966 in PrefixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
deprecated
curso
r
argument to
SQL
T
able
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
fixe
d
issue 9
9
commit
|
commitdiff
|
tree
2009-06-20
C
hristopher Lee
a
d
d
e
d
t
est f
o
r issue 99
commit
|
commitdiff
|
tree
2009-06-20
Ch
r
istop
h
er Le
e
cleaned up SQLite
S
erverInfo
commit
|
commitdiff
|
tree
2009-06-20
C
h
ristopher Lee
added DB
S
e
rverI
n
fo
.
new_
c
urs
o
r
() method
commit
|
commitdiff
|
tree
2009-06-13
Ch
r
is
t
opher Lee
Me
r
ge commit 're
m
ote
s
/mksz
u
ba/issue97_test' into i
s
sue97_t
e
s
t
commit
|
commitdiff
|
tree
2009-06-13
Christopher Lee
removed
r
edun
d
ant and buggy rs
t
r
ip("
.
py") c
a
ll from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
C
h
ristopher L
e
e
fix
pyrex cdef
commit
|
commitdiff
|
tree
2009-06-12
Christop
h
e
r
Lee
fix issue97
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
raised minimum
i
d
entity for r
e
l
axed
blast tests
t
o 60%
commit
|
commitdiff
|
tree
2009-06-09
Chri
s
topher Lee
r
e
placed a few remaining refs in the docs t
o
p
ygr
.
Data
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Christopher
L
e
e
Merge
commi
t
'
rem
o
tes/mkszub
a
/deb'
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
i
s
topher
L
e
e
Merge comm
i
t 'remotes/mkszuba/renames'
commit
|
commitdiff
|
tree
2009-06-09
Christo
p
her Lee
Merge branch
'
i
n
terval_filters' into bl
a
st_
t
es
t
s
commit
|
commitdiff
|
tree
2009-06-09
Chris
t
oph
e
r Lee
relaxe
d
-
tests had a bug t
h
at made
t
h
em pass the compari
s
o
n
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
h
ristopher Lee
must close FilePopen objec
t
befo
r
e
e
xitin
g
Bla
s
txMapping
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christoph
e
r Lee
me
r
ged in ctb
/
bla
s
tx_datab
a
se
commit
|
commitdiff
|
tree
2009-06-04
Chris
t
o
pher Lee
Merg
e
commi
t
'rem
o
tes/ctb
/
blastx_generator' into ct
b
_tmp
commit
|
commitdiff
|
tree
2009-06-04
Christo
p
h
e
r Lee
P
E
P
8
a
nd whitespace fix
e
s to nlms
a
_
uti
l
s
.
py; no functionalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chris
t
opher L
e
e
c
o
nv
e
r
t
ed add_aligned_intervals functionality into
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chr
i
stopher Lee
cl
e
an up Att
r
ibuteInterface acc
o
rding to Tit
u
s su
g
ges
t
ions
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
Merg
e
commit
'
rem
o
tes/ctb/ctb_inte
r
vals' into interval_filte
r
s
commit
|
commitdiff
|
tree
2009-06-03
Christop
h
er Le
e
Merge
commit 'remotes/c
t
b
/
ctb_blast2
'
into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Christophe
r
Le
e
Mer
g
e comm
i
t
'
remotes/c
t
b
/
minor_doc_fixes' into
c
t
b_
t
mp
commit
|
commitdiff
|
tree
2009-06-03
Christoph
e
r Lee
m
erg
e
d in ct
b
/anno
t
ati
o
n
commit
|
commitdiff
|
tree
2009-06-03
Chri
s
top
h
er Lee
merg
e
d in ct
b
/
b
last_skip conflict with ct
b
/
blas
t
_cache
commit
|
commitdiff
|
tree
2009-06-03
Chris
t
opher Lee
M
e
rge co
m
mit
'remotes/ctb/blast_cache' into
ctb_tmp
commit
|
commitdiff
|
tree
2009-05-29
C
hristopher Lee
Merg
e
c
o
mmit '
r
emotes/ctb/nl
m
sa_iter_repr'
commit
|
commitdiff
|
tree
2009-05-29
Chri
s
toph
e
r
L
ee
rem
o
ved unnece
s
s
a
r
y import
commit
|
commitdiff
|
tree
2009-05-29
Chr
i
stopher Le
e
con
v
erte
d
test_
m
ultiblast_
s
in
g
l
e
() back to test against
.
.
.
commit
|
commitdiff
|
tree
2009-05-29
C
h
ristopher L
e
e
r
ename
t
o
a
v
o
id
false implicatio
n
t
his
test i
n
volves
.
.
.
commit
|
commitdiff
|
tree
2009-05-27
C
hristo
p
h
e
r Lee
M
erge commit 'remotes/mkszuba/trove'
into m
a
rek_tmp
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
ad
d
ed co
m
pariso
n
with single
seq b
l
a
st in
t
est_multiblas
t
commit
|
commitdiff
|
tree
2009-05-27
Christo
p
her Lee
added text file for che
c
k
i
ng long pa
r
ser
res
u
lts
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
put close() wi
t
hin t
r
y-fi
n
a
lly
as
a
l
ways
commit
|
commitdiff
|
tree
2009-05-27
Chris
t
opher Lee
Merge commit 'remotes/mkszuba/b
l
as
t
_test' into marek_tmp
commit
|
commitdiff
|
tree
2009-05-27
Christ
o
pher Lee
Merge commit 'r
e
m
otes/mkszuba
/
ebu
i
lds' into marek
_
tm
p
commit
|
commitdiff
|
tree
2009-05-23
Christ
o
p
h
e
r
L
e
e
adde
d
Resourc
e
Server register()
/
serve
_
forever() doc
s
commit
|
commitdiff
|
tree
2009-05-23
Ch
r
i
s
topher Lee
use os
.
pat
h
.
j
o
i
n() in det
a
c
h_as
_
demon_process
(
)
commit
|
commitdiff
|
tree
2009-05-23
Chri
s
to
p
h
er Lee
Merge commit
'remotes/mkszuba/blastx_co
m
ment' into
.
.
.
commit
|
commitdiff
|
tree
next