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protect mysql tests using mysql_enabled()
2009-09-01
Chr
i
s
t
ophe
r
Lee
Me
r
ge commit 'remotes/c
t
b/doc_annotations' into tutorial
commit
|
commitdiff
|
tree
2009-09-01
Chri
s
topher L
e
e
ex
t
racted material
f
o
r
separate
d
a
t
aba
s
e tutorial
commit
|
commitdiff
|
tree
2009-08-29
Chr
i
stopher
Lee
removed u
n
nece
s
sary stat a
n
d shutil impo
r
t from setu
p
.
py
commit
|
commitdiff
|
tree
2009-08-14
C
h
ristopher Lee
fixed
e
a
s
y
_
install bug by pro
t
ecting coordinator
.
ResourceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
ristopher Lee
fixed
b
last
_
t
est:
rename
d
test_seq_without_db() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
hristoph
e
r
Lee
Mer
g
e
comm
i
t
'
remot
e
s/ctb/m
i
nor_
f
ixes'
i
nto mino
r
_
f
ixe
s
commit
|
commitdiff
|
tree
2009-08-04
Christo
p
her Lee
fix port
p
assing in testutil
.
T
estXMLRPCServer
commit
|
commitdiff
|
tree
2009-08-04
C
hristoph
e
r Lee
use pair_identity_t
u
ple
(
) fo
r
b
l
ast_
t
est formattin
g
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christop
h
er Lee
added BlastBase
.
t
earDo
w
n()
to close seqdbs as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christo
p
h
er
L
ee
Merge
c
ommit 'remot
e
s/mks
z
u
ba/doc_ma
k
e
'
commit
|
commitdiff
|
tree
2009-08-04
Christopher
Lee
Merge commit 'remotes
/
mk
s
zuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
C
h
r
istopher Lee
go
t
rid of BlastMapping
.
warn_ab
o
ut_self_matches()
commit
|
commitdiff
|
tree
2009-07-29
Chri
s
topher
L
ee
changed NLMSA pairwis
e
M
o
d
e
to allow rep
o
rting
of
s
elf
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
M
erge
commit 'remotes/mkszuba/debian
'
commit
|
commitdiff
|
tree
2009-07-29
Christophe
r
Lee
retry
r
eading port_file
in TestXMLRP
C
S
e
r
ver several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
C
h
ris
t
opher
Lee
added co
m
ments to pr
o
cess_
b
last()
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
fix pro
b
lem introduced in process_blast() by com
m
it
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christoph
e
r
L
e
e
handl
e
mi
s
s
ing WI
N
DIR c
a
se on Windows
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
added
SeqTranslato
r
.
__repr__()
commit
|
commitdiff
|
tree
2009-07-28
Chris
t
opher Lee
Merge co
m
mit '
r
em
o
tes/c
t
b/s
i
mpleframe_formatdb_cleanu
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Le
e
Merge branch
'
m
aster' into simpleframe
commit
|
commitdiff
|
tree
2009-07-28
C
h
r
i
s
topher
Lee
a
d
ded
S
eqT
r
anslator
.
iter_
f
rames() m
e
thod, used in BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Le
e
Mer
g
e commit 'r
e
mote
s
/ctb/simpleframe_do
c
_align' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
protect 2 more test
s
using blast_e
n
abled() check
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher Lee
f
i
xed syn
t
ax
error
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
a
d
ded p
y
t
hon 2
.
3
c
ode for FileP
o
pen to detect bad exi
t
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher
L
ee
Me
r
ge branch 'no_edge_db'
commit
|
commitdiff
|
tree
2009-07-27
C
hristopher Lee
Merge
b
ranch
'silen
c
io'
commit
|
commitdiff
|
tree
2009-07-27
Christop
h
e
r Lee
added showF
o
rma
t
dbMes
s
ages option to BlastMapping
commit
|
commitdiff
|
tree
2009-07-25
Christopher Lee
added
support for no-edgeDB case in
m
apping
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christopher Lee
a
d
ded option for latex output of the ref
e
ren
c
e ma
n
u
al
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
Mer
g
e c
o
m
mit 'rem
o
tes/ctb/bl
a
s
t
_
tes
t
_rc' into sim
p
lef
r
ame
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
added mor
e
d
o
cstrings for blast
.
py
commit
|
commitdiff
|
tree
2009-07-16
C
h
ri
s
topher Lee
remov
e
d old Blast
x
Mapp
i
ng code
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
opher Lee
new, gr
e
a
t
l
y simplified Blast
x
Ma
p
p
ing
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
switched t
e
st_blastx
_
s
e
rver to use ne
w
Tra
n
slation
D
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
added
r
ead_blast_alignment() translat
e
Dest
o
ption
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
istophe
r
Lee
add
e
d NLMSA
.
edges() method
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
istopher Lee
switched test_tbla
s
tn_pa
r
ser to use new
T
r
anslationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher Lee
switch tblastn to use new
Tr
a
nslationD
B
appr
o
ach
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
p
h
e
r
Lee
a
d
ded translationDB
.
p
y
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
o
p
her L
e
e
mov
e
d
dbname d
e
fault into ge
t
_
b
ound_subclass()
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
i
stopher Lee
m
a
k
e
CoordsToInte
r
vals / get_
i
nterval() use
seq
.
a
b
s
o
lute_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
cleaned up S
e
qPath
.
classy
S
lice()
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
opher Lee
Merge commi
t
'
remotes/mkszuba/nlmsa_no_ve
r
b
ose' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
oph
e
r Lee
Merge
c
o
m
mit '
r
emotes
/
mkszuba/cnestedl
i
st_n
o
tice' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher Lee
incomplete new cod
e
for Tra
n
slationD
B
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
o
pher Lee
c
l
eaned up r
e
versePath constructi
o
n
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
i
s
to
p
her Le
e
add absol
u
te
_
slice() metho
d
t
o SeqP
a
th
commit
|
commitdiff
|
tree
2009-07-14
Chris
t
opher Lee
Merge com
m
it
'
remotes/mkszub
a
/
c
n
e
stedlist
_
logger' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christopher L
e
e
Merge branc
h
'master'
i
nto megatests
commit
|
commitdiff
|
tree
2009-07-03
Christ
o
phe
r
Lee
Me
r
g
e
branch
'format
d
b_fail'
commit
|
commitdiff
|
tree
2009-07-03
Christopher Le
e
improved
wh
i
tespace
path warning
commit
|
commitdiff
|
tree
2009-07-03
Christ
o
pher Lee
add
e
d warning for whitespace in path
commit
|
commitdiff
|
tree
2009-07-01
C
hrist
o
phe
r
Lee
Merge co
m
mit 'remotes/
m
kszu
b
a/megate
s
ts'
commit
|
commitdiff
|
tree
2009-07-01
C
h
ristopher Lee
use glo
b
.
g
l
ob
(
) instead of os
.
listdi
r
()
;
cle
a
ned up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Chr
i
s
topher
Lee
Merge commit 're
m
otes/mks
z
uba/mimete
x
t'
commit
|
commitdiff
|
tree
2009-07-01
C
h
ristophe
r
Lee
Merge
commit 'remotes/mkszuba/docfixes'
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
Me
r
ge comm
i
t
'
remotes/mksz
u
ba/has
h
l
i
b'
commit
|
commitdiff
|
tree
2009-06-26
C
h
ristopher Lee
fixed caching bug introdu
c
ed
i
n co
m
mit 8d9966 i
n
PrefixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
C
hristopher Lee
deprec
a
ted cursor argument to SQLTa
b
l
e
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
fixed issu
e
99
commit
|
commitdiff
|
tree
2009-06-20
Christopher
L
ee
added test f
o
r issue 99
commit
|
commitdiff
|
tree
2009-06-20
Christophe
r
Lee
cleaned up SQ
L
iteServerInfo
commit
|
commitdiff
|
tree
2009-06-20
Christoph
e
r Lee
adde
d
DB
S
e
rverI
n
fo
.
n
e
w_cursor() met
h
od
commit
|
commitdiff
|
tree
2009-06-13
Chris
t
o
p
her Le
e
Merge commit '
r
emot
e
s/mkszub
a
/issue97_
t
e
st' in
t
o
i
ssue97_t
e
st
commit
|
commitdiff
|
tree
2009-06-13
Chr
i
stopher Lee
removed red
u
ndant and bugg
y
rstrip
(
"
.
p
y
") call f
r
om
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Chris
t
opher L
e
e
fix pyrex c
d
ef
commit
|
commitdiff
|
tree
2009-06-12
C
h
rist
o
pher Lee
fix i
s
sue97
commit
|
commitdiff
|
tree
2009-06-12
Christophe
r
Lee
raised minimum i
d
entity for relaxed blast tests to 60%
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
istopher
L
ee
r
ep
l
aced a fe
w
remaining refs in
t
h
e
d
o
cs to pygr
.
Data
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
C
hristopher Lee
Merge commit
'remo
t
es/mksz
u
ba/
d
eb'
commit
|
commitdiff
|
tree
2009-06-09
C
h
ristopher Lee
Merge commit 'remo
t
es
/
mk
s
zuba/renames'
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
istopher Lee
Mer
g
e bran
c
h 'interval_fi
l
te
r
s
'
i
n
t
o b
l
ast_tests
commit
|
commitdiff
|
tree
2009-06-09
Chris
t
op
h
er Lee
re
l
axed
-
tests h
a
d a bu
g
t
hat made
them pas
s
the comparis
o
n
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher
Lee
mus
t
c
lose FilePopen
o
b
j
ect bef
o
re exitin
g
B
lastxMa
p
pi
n
g
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
hristop
h
e
r
L
e
e
merged i
n
ctb/blastx
_
d
a
t
ab
a
s
e
commit
|
commitdiff
|
tree
2009-06-04
C
hristopher
L
ee
Merge commit 'remotes/ctb/
b
l
ast
x
_gen
e
ra
t
or
'
into ctb
_
tmp
commit
|
commitdiff
|
tree
2009-06-04
C
h
ri
s
t
opher Lee
PEP8 and whi
t
espace fixes
t
o nlmsa_utils
.
py; no functi
o
nalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
h
ristopher L
e
e
con
v
erte
d
add_aligne
d
_
i
nt
e
rvals functio
n
al
i
t
y
i
nto
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher Le
e
clean up
A
t
tr
i
buteInterface ac
c
or
d
ing to
Titus sug
g
estions
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
Merge c
o
m
m
it
'remotes/
c
t
b
/ctb_
i
nterva
l
s' int
o
interval
_
fil
t
ers
commit
|
commitdiff
|
tree
2009-06-03
Christopher Lee
Merge
commit
're
m
o
t
e
s
/ctb/ctb_blast
2
' into ctb
_
tmp
commit
|
commitdiff
|
tree
2009-06-03
Christopher Lee
Merge commit
'remotes/ctb/
m
inor_doc_
f
ixe
s
' i
n
to ctb_
t
m
p
commit
|
commitdiff
|
tree
2009-06-03
Christopher
L
ee
merged in ctb/annotation
commit
|
commitdiff
|
tree
2009-06-03
Christopher
L
ee
mer
g
ed
in ct
b
/blast_skip conf
l
ict with
c
tb/blast_cac
h
e
commit
|
commitdiff
|
tree
2009-06-03
C
hristopher Lee
M
erge commit 'remo
t
es/ctb/blas
t
_
c
ache
'
in
t
o ctb_tmp
commit
|
commitdiff
|
tree
2009-05-29
Christoph
e
r
L
ee
Merge commi
t
'
remotes
/
ct
b
/nlmsa_iter
_
re
p
r'
commit
|
commitdiff
|
tree
2009-05-29
Christoph
e
r Lee
removed unnece
s
sary impo
r
t
commit
|
commitdiff
|
tree
2009-05-29
Chris
t
op
h
e
r
Lee
converted test_multiblast_s
i
ngl
e
() back to test against
.
.
.
commit
|
commitdiff
|
tree
2009-05-29
Christopher Le
e
renam
e
t
o avoid false
im
p
licati
o
n this
t
est invo
l
v
e
s
.
.
.
commit
|
commitdiff
|
tree
2009-05-27
Chri
s
to
p
her L
e
e
Merge commit 're
m
otes/mkszuba/tro
v
e
'
into mare
k
_
tmp
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
ad
d
e
d
compa
r
is
o
n w
i
th si
n
g
l
e seq
blast in
t
est_
m
ultiblast
commit
|
commitdiff
|
tree
2009-05-27
Christophe
r
Lee
added text file for che
c
k
ing long p
a
rser
results
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
put close() within try-finally as always
commit
|
commitdiff
|
tree
2009-05-27
C
h
rist
o
pher Lee
Mer
g
e commit 'r
e
motes/mkszuba/blast_test' into marek_t
m
p
commit
|
commitdiff
|
tree
2009-05-27
Christop
h
er Lee
Merg
e
c
o
mmit '
r
emotes/mk
s
zuba/ebu
i
l
d
s' i
n
to
ma
r
ek_tmp
commit
|
commitdiff
|
tree
2009-05-23
Christophe
r
Lee
adde
d
R
esourceServer registe
r
() / serve_fo
r
ever()
docs
commit
|
commitdiff
|
tree
2009-05-23
C
h
r
is
t
opher Lee
u
se o
s
.
pa
t
h
.
j
o
in(
)
in deta
c
h_as_
d
emon_process
(
)
commit
|
commitdiff
|
tree
2009-05-23
Christopher Lee
Merge commit 'rem
o
te
s
/mkszuba/blastx_comment'
into
.
.
.
commit
|
commitdiff
|
tree
next