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added lots of tests for graphs with nodes instead of plain values
2009-09-05
C
hrist
o
pher
L
ee
added lot
s
of tests
f
o
r
graphs with nodes instead of
.
.
.
commit
|
commitdiff
|
tree
2009-09-05
Christopher Le
e
corrected the SQLGraph iterator meth
o
ds a
n
d im
p
r
oved
.
.
.
commit
|
commitdiff
|
tree
2009-09-05
Christopher L
e
e
tes
t
util needed new name of
g
e
t_name_cursor()
commit
|
commitdiff
|
tree
2009-09-05
Christop
h
er Lee
made ge
t
_nam
e
_cursor()
use
D
B
S
erverInfo
commit
|
commitdiff
|
tree
2009-09-05
Christopher Lee
a
d
d
ed it
e
rat
i
on test to graph
_
test
.
py
commit
|
commitdiff
|
tree
2009-09-05
Christop
h
er Lee
us
e
new
iter_ke
y
s() method
commit
|
commitdiff
|
tree
2009-09-05
C
h
ristopher Lee
a
dded
be
t
ter
i
ter method
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
Mer
g
e commit 'remotes/
c
tb/xmlrp
c
_patches'
commit
|
commitdiff
|
tree
2009-09-04
Christo
p
h
er Lee
M
e
rge commit 'remotes/mkszuba/
f
ink'
commit
|
commitdiff
|
tree
2009-09-04
Chri
s
topher
L
ee
removed tests/old
t
e
st
s
/
n
lmsa_dm2
_
megatest
.
py
commit
|
commitdiff
|
tree
2009-09-04
Chri
s
topher L
e
e
Merge commit 'remotes
/
m
k
szuba/
d
ocf
i
x
es'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
Merge c
o
mmit 'r
e
motes/mkszuba/cleanup'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Le
e
Merge commit 'remotes/mksz
u
ba/bsddb_bsddb
3
'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
c
orrecte
d
Class
i
c
Unpic
k
ler refer
e
nce t
o
point
t
o c
l
assutil
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
C
hris
t
op
h
e
r
L
e
e
remove
d
unused shelve i
m
port
commit
|
commitdiff
|
tree
2009-09-04
Christ
o
pher Lee
removed un
u
sed i
m
p
ort
item
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
Merge
b
ranch 'tutoria
l
'
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r
L
ee
added argument
t
o
make MapView inverse ab
l
e to reconstit
u
t
e
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christophe
r
L
e
e
a
dd
e
d
test of
len
(
)
m
ethod for SQLTable
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added db tut
o
rial (mapp
i
ng
)
back to
g
ui
d
elist table
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istop
h
er Lee
mapping tu
t
orial
ju
s
t
c
overs
m
appings
,
so rem
o
ve
d
refere
n
ce
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added Ma
p
View
i
nverse example to tutoria
l
commit
|
commitdiff
|
tree
2009-09-04
Christopher
Lee
added Map
V
iew do
c
s
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
s
t
opher L
e
e
added tes
t
for tr
a
pping non
-
invertib
l
e Map
V
iew
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istop
h
er Lee
a
dded tes
t
for __inv
e
rt__ met
h
od to MapView
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
ist
o
pher
L
e
e
added __i
n
vert__ method to
M
apView
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
adde
d
material on SQL MapView
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
sto
p
h
e
r Lee
added sections
on m
a
p
p
ing
t
o di
s
k
/ worl
d
base
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stopher
L
e
e
changed ti
t
le of xml
r
pc tutori
a
l
commit
|
commitdiff
|
tree
2009-09-04
Christo
p
he
r
Lee
minor fixes to
gene tutorial
commit
|
commitdiff
|
tree
2009-09-04
C
hristopher
Lee
m
o
ved mat
e
rial
o
ut of wo
r
ldbase
.
rst to worldbase
2
.
r
s
t
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
separate tutorial
o
n saving
data to wor
l
dbase
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
moved schema mater
i
al to w
o
rldbase2
.
rs
t
tu
t
orial
commit
|
commitdiff
|
tree
2009-09-03
Chri
s
t
opher Le
e
added worl
d
ba
s
e security
w
arning
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istopher Lee
more rev
i
sions ab
o
ut downl
o
ading tutoria
l
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
ist
o
pher Lee
revisions to download=True s
e
ction
commit
|
commitdiff
|
tree
2009-09-03
Christo
p
her L
e
e
added de
p
e
n
dency secti
o
n in worldba
s
e
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
a
d
ded worldbase
.
di
r
() tutor
i
al
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added intro section to worl
d
base
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
Chri
s
t
o
pher Lee
added Purpose
to alignment
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christoph
e
r L
e
e
more little ch
a
n
ge
s
to an
n
otation2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
C
h
ristopher L
e
e
a
d
ded Purp
o
se and i
n
tro to annotations2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
C
hristoph
e
r
L
e
e
moved new basic tutor
i
als to top of g
u
ide list
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
mino
r
fix to db_b
a
sic
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christ
o
p
her Le
e
updates to reference/sqlgraph
.
r
st d
o
cs
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stopher Lee
added SQL
s
a
vi
n
g
s
ection
to
db tut
o
rial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
basi
c
database tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher
L
e
e
a
d
ded
b
ack __le
n
__() to SQLTableBase
.
How in he
c
k
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
op
h
er Lee
adde
d
section on P
r
efixUnionDict
commit
|
commitdiff
|
tree
2009-09-02
C
hris
t
opher Le
e
add
e
d section on plugging in your o
w
n sequence parser
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristopher Lee
moved old material out to compgenomics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
Christ
o
phe
r
Lee
so
m
e minor sequ
e
nce
tutorial revisions
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
added tutorial sec
t
ion
o
n a
c
cessing
s
equence databa
s
e
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
stophe
r
L
ee
split
up
bullet
p
oints to integrate
in
t
o the
c
ode
e
xa
m
ple
commit
|
commitdiff
|
tree
2009-09-02
Christ
o
ph
e
r Lee
revised se
q
uen
c
e tutorial
intro (fi
r
st part)
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
Merge commit 'remot
e
s/ctb/xmlr
p
c_t
u
torial' into tu
t
orial
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
Merge c
o
mmit 'remotes/ctb/doc_alignment' into tutori
a
l
commit
|
commitdiff
|
tree
2009-09-02
C
h
r
i
stopher
Lee
revised gff
3
code
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istophe
r
Le
e
added
GFF3
e
xample of gene build
i
ng
commit
|
commitdiff
|
tree
2009-09-01
C
h
r
istophe
r
Lee
Merge
commit 'remotes/
m
kszu
b
a/xmlrpc_tutori
a
l' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Christopher Lee
M
er
g
e
c
ommi
t
'
remotes/ctb/do
c
_annotations' into tu
t
orial
commit
|
commitdiff
|
tree
2009-09-01
Chr
i
stopher Lee
extracted materi
a
l for s
e
parate dat
a
base
tutori
a
l
commit
|
commitdiff
|
tree
2009-08-29
C
h
r
is
t
opher Lee
remov
e
d
u
nnecessary stat and
s
hutil import from
setup
.
p
y
commit
|
commitdiff
|
tree
2009-08-14
Chr
i
s
topher Lee
f
ixed easy_install bug by protecting
coordina
t
or
.
R
esourceF
i
l
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher
Lee
fixed bla
s
t_t
e
st: renamed tes
t
_seq_with
o
ut_db()
to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
rist
o
pher
L
ee
Merge commit 'remotes/ctb
/
minor_fixes' into minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
Christ
o
p
her L
e
e
fix
port
pass
i
ng in testuti
l
.
TestXMLR
P
CSer
v
er
commit
|
commitdiff
|
tree
2009-08-04
Christo
p
her Lee
use
pair_identity_tupl
e
() for blast
_
test fo
r
matting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christophe
r
Lee
added B
l
astBas
e
.
tearDown() to close seqdb
s
as
t
h
ey
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christophe
r
L
e
e
Merge co
m
m
it 'remotes/mkszuba/doc_make'
commit
|
commitdiff
|
tree
2009-08-04
C
h
ristopher Lee
Merge c
o
mmit 'remo
t
es/mkszuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
Christ
o
pher Lee
got
rid of BlastM
a
pping
.
warn_abo
u
t
_se
l
f_matc
h
es
(
)
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
c
han
g
ed NLMSA pairw
i
s
e
Mode to al
l
ow
r
eporting
of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christ
o
ph
e
r Lee
Mer
g
e c
o
mmit 'remo
t
es
/
m
ks
z
u
b
a/debian'
commit
|
commitdiff
|
tree
2009-07-29
Chris
t
opher Lee
retry readin
g
port_fil
e
in TestXMLRPCServer several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
ad
d
ed comments to
process_b
l
ast()
commit
|
commitdiff
|
tree
2009-07-29
Chri
s
tophe
r
Lee
fix probl
e
m
i
n
t
r
o
d
u
ced in
p
roce
s
s_blast() by commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Chr
i
stopher Lee
handle
m
issin
g
WINDIR case on
Windows
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
istopher Lee
ad
d
ed S
e
qTranslator
.
__repr__()
commit
|
commitdiff
|
tree
2009-07-28
Chri
s
topher Lee
Merge
c
ommit 'remotes
/
ctb/simpleframe_formatd
b
_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
hrist
o
pher Lee
M
e
rg
e
branch 'mast
e
r
' in
t
o simp
l
eframe
commit
|
commitdiff
|
tree
2009-07-28
C
h
risto
p
her Lee
a
dded
Se
q
T
ranslator
.
i
t
er_fra
m
es() method
,
used in Blastx
M
app
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christop
h
er
L
e
e
Merge co
m
mit 'remot
e
s/ctb/si
m
pleframe_doc_ali
g
n' in
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
istopher
Lee
protect 2 more te
s
ts
u
s
i
n
g blast_enabled(
)
c
heck
commit
|
commitdiff
|
tree
2009-07-27
Chris
t
ophe
r
Lee
fix
e
d syntax error
commit
|
commitdiff
|
tree
2009-07-27
Christopher Le
e
added
p
y
t
hon 2
.
3 code for F
i
lePopen to detect ba
d
e
xit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Le
e
M
erge branch 'no_edge_
d
b'
commit
|
commitdiff
|
tree
2009-07-27
C
hristoph
e
r Lee
Merge
b
ra
n
ch '
s
ilencio'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
a
d
d
e
d show
F
ormat
d
b
M
essa
g
es option t
o
BlastMappi
n
g
commit
|
commitdiff
|
tree
2009-07-25
Christopher Lee
add
e
d
support for no-edgeDB
ca
s
e i
n
mapping
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Ch
r
istopher Lee
a
d
d
ed o
p
tion for
latex output of the reference m
a
nual
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
h
e
r Le
e
Merge commit 'remote
s
/ctb/bl
a
st_
t
est_rc
'
into s
i
m
pleframe
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
pher Le
e
a
dded more docs
t
r
i
ngs f
o
r b
l
ast
.
py
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher Lee
remo
v
ed old Blast
x
M
app
i
ng code
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
new, greatly simplified
B
l
a
stx
M
a
pping
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
oph
e
r
L
ee
swit
c
h
e
d te
s
t_blastx_server to use new Tran
s
l
ationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
i
stophe
r
L
e
e
added r
e
ad_blast_a
l
ignment
(
) translateDest option
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
added N
L
MS
A
.
edges() metho
d
commit
|
commitdiff
|
tree
2009-07-16
Christophe
r
Lee
switched t
e
st_tblastn_parser to
u
se new TranslationD
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
swit
c
h
t
b
l
astn
to
u
se new TranslationD
B
appro
a
ch
commit
|
commitdiff
|
tree
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