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generalized iter_keys(), added orderBy support
2009-07-27
Christopher Lee
a
dd
e
d
show
F
ormatdbMessa
g
es option to
BlastM
a
p
p
ing
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
d
ed
option fo
r
latex output of t
h
e ref
e
rence manual
commit
|
commitdiff
|
tree
2009-07-16
C
hr
i
stopher Lee
Merge
co
m
m
i
t 're
m
otes/
c
tb/blast
_
t
est_r
c
' into s
i
m
plefram
e
commit
|
commitdiff
|
tree
2009-07-16
Christop
h
e
r
Lee
add
e
d more doc
s
tring
s
for b
l
a
st
.
py
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
removed o
l
d Bla
s
txMapping code
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristop
h
e
r
Lee
n
e
w
, great
l
y simplified Blast
x
Map
p
ing
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
istopher Lee
switched test_blastx_server to use
new
T
ranslationD
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
C
h
r
istopher Lee
a
d
ded r
e
ad_
b
last_alignment() translateDe
s
t option
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
opher Lee
added NLMSA
.
edges() method
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher
L
ee
switched t
e
st_tblast
n
_parser to use new
T
ra
n
slat
i
onDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
swi
t
c
h
tblastn to us
e
n
e
w T
r
anslationDB approach
commit
|
commitdiff
|
tree
2009-07-15
C
h
r
i
stoph
e
r L
e
e
a
d
ded trans
l
ationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
C
hristo
p
her
L
ee
moved dbnam
e
default
into
g
e
t_bound_subc
l
ass()
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
make Co
o
rds
T
oIntervals / ge
t
_inte
r
v
a
l()
u
se seq
.
absolute_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
c
l
ea
n
ed up
S
eq
P
a
t
h
.
c
l
assySlice()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
Merg
e
comm
i
t
'
remotes/mks
z
uba/n
l
m
sa_no_verbose' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher Lee
Merge
commit
'remote
s
/mk
s
zuba/cnestedlist_notice' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
o
pher Lee
i
ncomplete new code for TranslationD
B
commit
|
commitdiff
|
tree
2009-07-15
Christoph
e
r Le
e
cleaned
u
p
revers
e
Path construction
commit
|
commitdiff
|
tree
2009-07-15
C
h
ristoph
e
r Lee
add abso
l
ute_
s
lice() m
e
thod to Seq
P
at
h
commit
|
commitdiff
|
tree
2009-07-14
Chri
s
t
opher Lee
Merge commi
t
'remotes/mkszuba/cnested
l
ist_logger' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Marek Szuba
G
i
v
e
n
existing isola
t
ion problems
b
etween test
s
run
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christopher Lee
Merge branch 'master' into megatests
commit
|
commitdiff
|
tree
2009-07-03
Christopher Lee
Merge bran
c
h 'formatdb_f
a
il
'
commit
|
commitdiff
|
tree
2009-07-03
Christopher Lee
i
mproved wh
i
t
espace pat
h
warn
i
ng
commit
|
commitdiff
|
tree
2009-07-03
Ch
r
istopher Lee
add
e
d warn
i
ng for whi
t
e
s
pace in path
commit
|
commitdiff
|
tree
2009-07-01
C
h
ri
s
to
p
her Lee
Merge commit 'remotes/mkszuba/megatests'
commit
|
commitdiff
|
tree
2009-07-01
Chr
i
stopher Lee
use glob
.
glob() i
n
stead of os
.
listdir(
)
; cleaned up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christ
o
pher Lee
Merge comm
i
t 'r
e
motes/m
k
szuba/mimetext'
commit
|
commitdiff
|
tree
2009-07-01
C
hristopher Lee
Merge
com
m
i
t
're
m
otes/mkszuba/d
o
cfixe
s
'
commit
|
commitdiff
|
tree
2009-07-01
C
h
ris
t
opher Lee
Merge co
m
mit 'remotes/mks
z
uba/hashlib'
commit
|
commitdiff
|
tree
2009-06-26
Christopher Le
e
fix
e
d caching bu
g
introduc
e
d
in commit 8d9966 i
n
Pr
e
fixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christ
o
pher Lee
d
e
preca
t
e
d curso
r
argument
to SQLTable
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
fix
e
d iss
u
e 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
adde
d
t
e
s
t
f
or iss
u
e
9
9
commit
|
commitdiff
|
tree
2009-06-20
C
h
r
i
stopher Lee
cl
e
aned up SQLiteServerInfo
commit
|
commitdiff
|
tree
2009-06-20
C
h
ristopher
Lee
added D
B
ServerInfo
.
n
e
w
_
cursor() method
commit
|
commitdiff
|
tree
2009-06-13
C
hristoph
e
r Lee
Merge
commi
t
'
r
emotes/mksz
u
ba/iss
u
e97
_
test' i
n
t
o issue97_test
commit
|
commitdiff
|
tree
2009-06-13
C
hristop
h
er Lee
re
m
oved redund
a
nt and
b
uggy rstrip("
.
py") call
f
rom
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Ch
r
istoph
e
r
Lee
fix
p
yrex cdef
commit
|
commitdiff
|
tree
2009-06-12
C
hristoph
e
r Lee
f
ix issue
9
7
commit
|
commitdiff
|
tree
2009-06-12
Chri
s
topher Lee
raised minimu
m
i
dentit
y
f
o
r relaxed blas
t
te
s
ts
t
o 60%
commit
|
commitdiff
|
tree
2009-06-09
C
h
ris
t
oph
e
r Lee
replac
e
d a few rema
i
ning refs in the docs to pygr
.
Data
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Christopher L
e
e
Merg
e
c
o
mmit 'remotes/mkszuba/deb'
commit
|
commitdiff
|
tree
2009-06-09
Christopher
L
ee
Merge com
m
it 'remotes
/
m
kszuba/rena
m
e
s
'
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
istopher Lee
Merge branch 'int
e
r
val_filters' into blast_t
e
sts
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
rela
x
ed-tests had
a b
u
g that made them pas
s
the
comp
a
rison
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chris
t
ophe
r
Lee
must
c
lose
F
ilePopen ob
j
ect before e
x
it
i
ng BlastxMapping
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christoph
e
r Lee
merged in ctb/b
l
astx_da
t
ab
a
s
e
commit
|
commitdiff
|
tree
2009-06-04
Christophe
r
L
e
e
Merge commit 'remotes/ctb/
b
lastx_genera
t
or' into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-04
Chr
i
stophe
r
Lee
PEP8 and whit
e
spac
e
fixe
s
to
nlmsa_
u
tils
.
p
y; no functionalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christoph
e
r
Lee
converted add_alig
n
ed_intervals funct
i
onalit
y
i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chr
i
stopher
Le
e
cle
a
n u
p
AttributeI
n
terface ac
c
ordi
n
g to T
i
tus suggestion
s
commit
|
commitdiff
|
tree
2009-06-04
Christop
h
er
Lee
Merge
c
ommit
'remote
s
/
c
t
b/c
t
b_inte
r
vals' into interva
l
_filters
commit
|
commitdiff
|
tree
2009-06-03
Christopher Le
e
M
e
rg
e
c
o
mmit 're
m
otes
/
ctb/ctb_bl
a
st2'
i
nto ct
b
_tmp
commit
|
commitdiff
|
tree
2009-06-03
Ch
r
istopher L
e
e
Merge commit 'remotes/ctb/minor_doc_
f
i
x
es
'
into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Ch
r
is
t
opher
Lee
m
erge
d
in
c
tb/a
n
n
ota
t
ion
commit
|
commitdiff
|
tree
2009-06-03
Christopher Lee
m
e
rged in ctb/blast_
s
kip conflict with c
t
b/blas
t
_cach
e
commit
|
commitdiff
|
tree
2009-06-03
Chris
t
opher L
e
e
Merg
e
c
o
mm
i
t 'remotes/c
t
b/blast_cache' into ctb_tmp
commit
|
commitdiff
|
tree
2009-05-29
C
hristoph
e
r Lee
Merge commit
'
re
m
otes
/
c
t
b
/
nlmsa_iter_repr
'
commit
|
commitdiff
|
tree
2009-05-29
Christop
h
er Lee
removed unne
c
essary imp
o
rt
commit
|
commitdiff
|
tree
2009-05-29
Chr
i
stopher
L
e
e
converted test_multi
b
last_single() b
a
ck to test against
.
.
.
commit
|
commitdiff
|
tree
2009-05-29
C
h
ristopher Lee
rename t
o
a
void
f
a
ls
e
implication t
h
is test in
v
o
l
ves
.
.
.
commit
|
commitdiff
|
tree
2009-05-28
Titus
B
r
o
wn
fixed typo in c
n
estedlist: MaskEnd =>
m
askEnd
commit
|
commitdiff
|
tree
2009-05-27
Chris
t
opher
L
ee
Merge
commit 're
m
otes/mksz
u
ba/
t
r
ove' into marek_tmp
commit
|
commitdiff
|
tree
2009-05-27
Christopher
L
ee
a
d
ded comp
a
ri
s
on with single
seq blast i
n
test_multiblast
commit
|
commitdiff
|
tree
2009-05-27
Christoph
e
r
Lee
added tex
t
file for checking lon
g
parser results
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
put clo
s
e() within try
-
f
i
nally as always
commit
|
commitdiff
|
tree
2009-05-27
Chri
s
t
o
p
her Le
e
Merge
c
ommit 'rem
o
tes/mkszuba/blast_test' into marek_tmp
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
M
erge
c
o
mmit
'
remotes/mkszuba/ebui
l
ds' into marek_tmp
commit
|
commitdiff
|
tree
2009-05-23
Christopher Lee
added ResourceServer
register() / serve
_
forever() docs
commit
|
commitdiff
|
tree
2009-05-23
Christoph
e
r Lee
use os
.
path
.
jo
i
n() in detach_as_demon_proc
e
ss()
commit
|
commitdiff
|
tree
2009-05-23
Chr
i
stopher Lee
M
e
r
g
e
commit
'
remotes/mkszub
a
/blastx_
c
omment' into
.
.
.
commit
|
commitdiff
|
tree
2009-05-22
C
hristopher
L
ee
fix
e
d par
s
ing error in m
u
l
t
iseq blast
commit
|
commitdiff
|
tree
2009-05-22
Christopher Lee
updated
s
eqdb
r
e
ference docs for 0
.
8
commit
|
commitdiff
|
tree
2009-05-21
Christopher Lee
revised metabase / wor
l
d
b
a
se re
f
erence docs f
o
r 0
.
8
.
.
.
commit
|
commitdiff
|
tree
2009-05-21
Christopher Lee
f
ixed Metabas
e
Lis
t
.
registe
r
Server(
)
commit
|
commitdiff
|
tree
2009-05-21
Chri
s
topher
L
e
e
adde
d
lis
t
_pending()
to
worldbase
interface
commit
|
commitdiff
|
tree
2009-05-20
Christopher Lee
mor
e
r
e
vision
s
of
worldbase and meta
b
as
e
r
e
ference
.
.
.
commit
|
commitdiff
|
tree
2009-05-20
Christoph
e
r Lee
spl
i
t
of
f
wo
r
l
dbase reference do
c
s for
0
.
8
commit
|
commitdiff
|
tree
2009-05-20
Christop
h
er L
e
e
updated guid
e
li
s
t
to
use wo
r
ldbase tu
t
oria
l
commit
|
commitdiff
|
tree
2009-05-20
Ch
r
istop
h
er L
e
e
renam
e
d pygrdata t
u
t
o
ria
l
a
s
w
o
rldbase
commit
|
commitdiff
|
tree
2009-05-20
Christopher Lee
revised mapping
ref docs for
0
.
8
commit
|
commitdiff
|
tree
2009-05-20
C
h
r
is
t
opher Lee
r
e
v
i
sed coordinator ref docs for 0
.
8
commit
|
commitdiff
|
tree
2009-05-20
C
h
ristopher Lee
r
e
vis
e
d
c
n
este
d
list
ref docs for 0
.
8
commit
|
commitdiff
|
tree
2009-05-20
Christ
o
pher Lee
r
e
v
i
sed
classu
t
il ref docs for 0
.
8
commit
|
commitdiff
|
tree
2009-05-19
Christop
h
e
r
L
e
e
store blastx results in a regu
l
ar P
y
t
h
on list
commit
|
commitdiff
|
tree
2009-05-19
Christopher Lee
r
evised blast refe
r
ence
d
ocs fo
r
0
.
8
commit
|
commitdiff
|
tree
2009-05-19
Christopher Le
e
r
evised annotation reference docs for
0
.
8
commit
|
commitdiff
|
tree
2009-05-19
Christop
h
er Lee
made Ann
o
tationDB
.
add_homo
l
ogy() search argument non
.
.
.
commit
|
commitdiff
|
tree
2009-05-19
Christo
p
her L
e
e
added whatsnew
to
t
able of contents
commit
|
commitdiff
|
tree
2009-05-19
C
h
ris
t
opher Lee
added whatsnew
.
rst to D
o
cs
commit
|
commitdiff
|
tree
2009-05-19
Ch
r
istopher L
e
e
removed obsolete
F
a
s
t
a
DB
commit
|
commitdiff
|
tree
2009-05-19
Christopher Lee
extend metabas
e
ad
d
_reso
u
r
ce() method to accept a dictionary
.
.
.
commit
|
commitdiff
|
tree
2009-05-19
Christopher Lee
updated t
u
t
o
rials
f
or
0
.
8
commit
|
commitdiff
|
tree
2009-05-14
Christ
o
pher Lee
added b
e
tter
e
rror message in case of wacky sequ
e
nce
.
.
.
commit
|
commitdiff
|
tree
2009-05-13
C
h
ristopher Lee
removed old pygr
.
Data r
e
fs from cnestedl
i
st; made
Resou
r
cePa
.
.
.
commit
|
commitdiff
|
tree
2009-05-09
C
hristophe
r
Lee
add warning
:
py
g
r
.
Data
i
s deprecated
commit
|
commitdiff
|
tree
2009-05-09
C
h
ri
s
topher Lee
added
_
_dir__
s
uppor
t
to SQL
R
ow an
d
Tupl
e
O
(
i
.
e
.
SQ
L
Ta
b
le
.
.
.
commit
|
commitdiff
|
tree
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