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Merge commit 'remotes/mkszuba/cleanup'
2009-09-04
Chr
i
stoph
e
r Lee
Merge commit 'remo
t
es/mksz
u
ba/
c
leanup'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
Merge commit 'r
e
m
o
tes/mkszuba/bsddb_bsddb3
'
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher Le
e
corr
e
cted Cl
a
ssicUnpickler reference
to p
o
int
to classutil
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stopher Lee
removed
u
n
u
sed
sh
e
lve import
commit
|
commitdiff
|
tree
2009-09-04
Chris
t
op
h
e
r
Le
e
removed unus
e
d import item
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r Lee
Merge bran
c
h 'tutorial'
commit
|
commitdiff
|
tree
2009-09-04
Chri
s
topher
L
ee
a
d
ded arg
u
ment to make MapVi
e
w inverse able
t
o rec
o
n
s
titut
e
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
C
h
ristopher Lee
added test
of l
e
n() method for
S
QLTable
commit
|
commitdiff
|
tree
2009-09-04
Chri
s
topher Lee
added db
tutori
a
l (mapping) back to guidelist table
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christop
h
er Lee
m
a
p
ping tutorial j
u
st cover
s
mappings
,
so removed reference
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christ
o
pher Lee
added Map
V
iew inverse ex
a
mp
l
e
to tutori
a
l
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
ad
d
ed
M
a
p
View docs
commit
|
commitdiff
|
tree
2009-09-04
C
h
ristopher Lee
a
d
d
e
d
tes
t
for tr
a
pping
non
-
inver
t
ible MapView
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
ad
d
ed
test for
_
_
i
nver
t
__ method to
M
a
pVie
w
commit
|
commitdiff
|
tree
2009-09-04
Christopher Le
e
a
d
ded
_
_invert_
_
method to MapView
commit
|
commitdiff
|
tree
2009-09-04
Christop
h
er
L
ee
a
d
ded material on
SQL MapView
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added
sections on m
a
pping to disk / wor
l
dbase
commit
|
commitdiff
|
tree
2009-09-04
Chri
s
toph
e
r Lee
cha
n
g
e
d title of x
m
lrp
c
tutorial
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
minor
f
i
xe
s
to gene tutoria
l
commit
|
commitdiff
|
tree
2009-09-04
C
h
ri
s
topher
L
ee
moved material ou
t
of
w
orldbase
.
r
s
t to worldbase2
.
rst
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
separa
t
e
tu
t
orial on saving data to worldbase
commit
|
commitdiff
|
tree
2009-09-04
Christ
o
phe
r
Lee
moved
s
chema material to worldb
a
se2
.
rst tu
t
orial
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istopher
Lee
a
d
ded worldba
s
e s
e
c
u
rity warning
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
more revisions about do
w
nlo
a
ding tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christo
p
her
L
ee
revi
s
io
n
s to do
w
n
l
oad=True sectio
n
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stopher Lee
added dependency section in worldbase
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
C
h
ristop
h
er Lee
a
d
d
ed worldba
s
e
.
dir()
tuto
r
ial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added in
t
ro
s
ection
to wor
l
dbase
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stop
h
er Lee
added Pur
p
ose to al
i
gnment
.
rs
t
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
i
s
toph
e
r Lee
more little changes to an
n
o
t
ation2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
adde
d
Purpose and intro
t
o annot
a
t
i
ons2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christoph
e
r Lee
moved ne
w
basi
c
tutorial
s
to top of guide
l
i
s
t
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stopher
Lee
min
o
r fix to db
_
basic
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christ
o
p
her Lee
updates to
refe
r
en
c
e
/sqlgra
p
h
.
rst
d
o
cs
commit
|
commitdiff
|
tree
2009-09-03
C
h
ristop
h
e
r L
e
e
added SQL sa
v
ing secti
o
n to db tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
bas
i
c
database tutoria
l
commit
|
commitdiff
|
tree
2009-09-03
Christopher L
e
e
a
dded back
_
_len__(
)
to SQL
T
a
b
l
e
Bas
e
.
H
o
w in heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
a
dded section on PrefixU
n
ionDict
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
added s
e
c
t
ion on plugging in your own seque
n
ce
p
a
r
ser
commit
|
commitdiff
|
tree
2009-09-02
Christopher
L
ee
moved old
m
aterial
o
ut to
compgenomic
s
.
rst
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
some minor sequence t
u
torial revisions
commit
|
commitdiff
|
tree
2009-09-02
Chri
s
topher Lee
added tutorial section on acc
e
s
s
ing
sequence
databa
s
e
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
s
p
l
i
t
u
p bullet poi
n
ts to i
n
teg
r
ate in
t
o
the code ex
a
mple
commit
|
commitdiff
|
tree
2009-09-02
Christo
p
her Lee
re
v
i
s
ed sequence tutorial in
t
ro (first part)
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
Merge commi
t
'remotes/ctb/xmlrpc_tutorial' into
t
utorial
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er
Lee
Merge commit 'r
e
motes/ctb/d
o
c_alignment' i
n
to tu
t
orial
commit
|
commitdiff
|
tree
2009-09-02
C
hristopher Lee
re
v
ised gff3 c
o
de
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher L
e
e
a
d
ded GFF3 exampl
e
of gene
b
uilding
commit
|
commitdiff
|
tree
2009-09-01
Christopher
L
e
e
Merge commit 'remotes
/
mksz
u
ba/x
m
lrpc_tutorial' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Christopher Lee
Mer
g
e commit 'remotes/ct
b
/d
o
c
_
annotations' into t
u
torial
commit
|
commitdiff
|
tree
2009-09-01
C
h
ri
s
topher Lee
extracted
m
ate
r
ial for separate
d
atabase tutorial
commit
|
commitdiff
|
tree
2009-08-29
Christopher L
e
e
removed unnecess
a
ry stat a
n
d shutil imp
o
r
t
from
setup
.
p
y
commit
|
commitdiff
|
tree
2009-08-14
Chri
s
topher L
e
e
fixed easy_instal
l
bug by pr
o
tecting
c
o
o
r
d
inator
.
Resource
F
il
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stophe
r
Lee
fixed blast_t
e
st: r
e
name
d
test_seq_without_db() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chri
s
topher
L
ee
Merge
c
om
m
it 'remotes/ctb/mino
r
_fix
e
s'
into
minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
Christop
h
er Lee
fix port passing i
n
t
e
st
u
til
.
T
e
stXMLRPCServer
commit
|
commitdiff
|
tree
2009-08-04
Christopher Le
e
use
pair_identity_tuple() for blast_test formatting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chris
t
oph
e
r Lee
a
dd
e
d BlastBase
.
t
earDown() to c
l
o
s
e seqdbs
a
s
they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
is
t
opher Lee
Merge commit 'rem
o
tes/m
k
s
zuba/doc
_
make
'
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
istopher
Lee
Merge commit '
r
emotes/mkszuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
C
hristop
h
er
L
ee
got
r
id of BlastMapping
.
warn_about
_
s
e
lf_matches()
commit
|
commitdiff
|
tree
2009-07-29
C
h
r
i
st
o
p
her Lee
c
h
anged NL
M
SA pairwiseMode t
o
allow
r
epo
r
ting of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher L
e
e
Merge commi
t
'
remotes/mkszuba/debian'
commit
|
commitdiff
|
tree
2009-07-29
Christ
o
phe
r
Lee
retry r
e
ading po
r
t_f
i
le
i
n
TestXMLR
P
CS
e
rver
se
v
eral
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Chr
i
stopher Lee
added
comment
s
to process_blast()
commit
|
commitdiff
|
tree
2009-07-29
C
hris
t
o
phe
r
Lee
fix prob
l
em introduced in
p
roc
e
ss_blas
t
(
)
by co
m
mit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher L
e
e
handle
m
issing WINDIR
c
ase on Wi
n
dows
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristopher L
e
e
add
e
d SeqTra
n
slator
.
__repr__()
commit
|
commitdiff
|
tree
2009-07-28
Chri
s
topher Le
e
M
e
rge commit
'
rem
o
tes/ctb/simp
l
e
f
r
a
me_format
d
b_c
l
ean
u
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Chr
i
stopher
Lee
Merge
branch 'master' i
n
to simple
f
rame
commit
|
commitdiff
|
tree
2009-07-28
Chr
i
s
topher Lee
a
dded SeqTran
s
lator
.
iter_frames() method,
u
se
d
in
B
lastxMap
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
istopher Lee
M
erge commit '
r
emotes/ctb/s
i
m
p
leframe
_
doc_align' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
C
hristopher Lee
p
rotect 2 more tests usi
n
g bla
s
t_enabled() check
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
fixed syntax error
commit
|
commitdiff
|
tree
2009-07-27
Christophe
r
Lee
a
dded python 2
.
3
c
o
de for FilePopen to detect bad exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
istopher Lee
Me
r
g
e branch
'
no_e
d
ge_
d
b'
commit
|
commitdiff
|
tree
2009-07-27
C
hristo
p
h
e
r
L
ee
Merg
e
bra
n
ch 's
i
lencio'
commit
|
commitdiff
|
tree
2009-07-27
Christopher L
e
e
added
showFormatdbMessag
e
s option to B
l
astMapp
i
n
g
commit
|
commitdiff
|
tree
2009-07-25
Christopher Lee
added
s
upport for no-edgeDB case in mapping
.
G
raph
:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christop
h
er Le
e
added opti
o
n
for la
t
e
x
output of th
e
reference manual
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher Lee
Me
r
ge commit
'
r
e
mot
e
s/ctb
/
blast_test_rc
'
into simpleframe
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher Lee
added more docstrings for bla
s
t
.
py
commit
|
commitdiff
|
tree
2009-07-16
C
hrist
o
phe
r
Lee
r
e
moved o
l
d
Blast
x
Mapping code
commit
|
commitdiff
|
tree
2009-07-16
Christop
h
er Lee
new, greatly si
m
plified Blastx
M
app
i
ng
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r Lee
switched te
s
t
_
blastx_serv
e
r to use
new Trans
l
a
tionDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christop
h
er
L
ee
adde
d
read_blast_
a
l
ignment() tran
s
lateDest opt
i
o
n
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
added NLMSA
.
edges
(
) metho
d
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
istopher
L
ee
switched test_tblast
n
_parser to us
e
new Transla
t
ionDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
switc
h
tb
l
astn
to u
s
e
n
e
w Tr
a
nslation
D
B
a
p
p
roach
commit
|
commitdiff
|
tree
2009-07-15
Christopher
L
ee
add
e
d t
r
a
n
slationD
B
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christopher
L
ee
moved dbname de
f
aul
t
i
n
to get
_
bound
_
subc
l
as
s
()
commit
|
commitdiff
|
tree
2009-07-15
Christopher L
e
e
make Coor
d
sT
o
Inter
v
a
l
s
/
g
et_inter
v
al() use seq
.
abs
o
l
u
te_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
hristopher Lee
c
l
ean
e
d up SeqPath
.
classy
S
lice
(
)
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
i
s
topher Lee
M
erge commit
'remotes/mkszuba
/
nl
m
sa_no_verbose' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
opher Lee
Merge commit 'remotes/mkszuba/cne
s
tedlist
_
n
o
t
i
c
e' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
in
c
omp
l
ete new code for Transla
t
ionDB
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher Lee
cleaned
up r
e
versePath construction
commit
|
commitdiff
|
tree
2009-07-15
C
hri
s
topher Lee
add
ab
s
olute_slice() metho
d
to SeqPath
commit
|
commitdiff
|
tree
2009-07-14
Christopher Lee
Merge commit
'remotes/mkszuba
/
cnestedlist_logge
r
'
i
nto
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
M
arek Szuba
Give
n
ex
i
sting isolation
problems between tests
run
.
.
.
commit
|
commitdiff
|
tree
next