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testutil needed new name of get_name_cursor()
2009-09-05
Ch
r
i
s
t
o
pher Lee
t
estutil needed new
n
a
me o
f
get_name_cursor()
commit
|
commitdiff
|
tree
2009-09-05
Christoph
e
r Lee
made get
_
name_cu
r
so
r
() use D
B
Server
I
nfo
commit
|
commitdiff
|
tree
2009-09-05
Christopher Lee
added
iteration te
s
t
to
g
ra
p
h_test
.
py
commit
|
commitdiff
|
tree
2009-09-05
Christ
o
pher
L
e
e
us
e
n
ew i
t
er
_
k
e
ys() metho
d
commit
|
commitdiff
|
tree
2009-09-05
Christop
h
er
L
e
e
ad
d
e
d better iter
method
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stoph
e
r Lee
Merge commit 're
m
otes/c
t
b
/
xmlrpc_patches'
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stop
h
er Le
e
Me
r
ge commit 'remote
s
/mk
s
zuba/fink'
commit
|
commitdiff
|
tree
2009-09-04
C
hr
i
stophe
r
Le
e
r
e
moved te
s
ts/oldtests/nlms
a
_
dm2_megatest
.
py
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
M
erge commit
'remote
s
/mkszuba/docfixe
s
'
commit
|
commitdiff
|
tree
2009-09-04
Christopher
L
e
e
M
e
rge commi
t
're
m
otes/
m
ks
z
u
b
a/cleanup'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
Merge commit 'remotes/mkszuba/bsddb_bsd
d
b3
'
commit
|
commitdiff
|
tree
2009-09-04
C
hristop
h
er L
e
e
cor
r
ected ClassicUnpickl
e
r reference t
o
po
i
n
t
to classutil
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
remov
e
d unused shelve i
m
port
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher Lee
removed unused im
p
ort item
commit
|
commitdiff
|
tree
2009-09-04
C
hristopher Lee
Mer
g
e bra
n
ch 'tu
t
orial'
commit
|
commitdiff
|
tree
2009-09-04
C
h
ristopher Le
e
added
argument to make M
a
pVie
w
inverse ab
l
e to reconstitute
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added test of len() method
for SQLTable
commit
|
commitdiff
|
tree
2009-09-04
Chris
t
opher
Lee
added
db tutoria
l
(mapping) back to guidelist table
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stopher Lee
mapping tut
o
rial just covers ma
p
pings, s
o
removed re
f
erence
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r Lee
a
d
ded
Map
V
iew inverse
example to tutoria
l
commit
|
commitdiff
|
tree
2009-09-04
Christop
h
er Lee
added MapVi
e
w
d
ocs
commit
|
commitdiff
|
tree
2009-09-04
Christ
o
p
h
e
r
Lee
added te
s
t
f
o
r trapping no
n
-
i
n
vert
i
b
le MapVi
e
w
commit
|
commitdiff
|
tree
2009-09-04
Christ
o
p
h
er Lee
add
e
d test fo
r
__in
v
ert__
m
e
t
ho
d
to MapView
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
a
dd
e
d __inver
t
__ method to MapView
commit
|
commitdiff
|
tree
2009-09-04
C
h
ristopher
Le
e
a
dded material on SQL M
a
p
V
i
e
w
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added sections on
m
apping to dis
k
/ worldbase
commit
|
commitdiff
|
tree
2009-09-04
Christopher
Lee
changed title of xmlrpc
tutorial
commit
|
commitdiff
|
tree
2009-09-04
Christopher
Lee
mino
r
fixes t
o
gene
t
utorial
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r Lee
moved materia
l
out of worldbase
.
rst to world
b
ase2
.
rst
commit
|
commitdiff
|
tree
2009-09-04
C
h
ristoph
e
r Lee
s
eparate tut
o
rial on saving data to worldba
s
e
commit
|
commitdiff
|
tree
2009-09-04
Christopher
Lee
moved schem
a
m
at
e
r
ial to worldbase2
.
rst
tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added wo
r
ldbase se
c
uri
t
y warn
i
ng
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er Lee
m
o
r
e revisions about
d
ownloading tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
r
e
visions to download=True s
e
ction
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added dependency section in worl
d
base
.
rst tutor
i
al
commit
|
commitdiff
|
tree
2009-09-03
Christopher Le
e
adde
d
worldbase
.
di
r
() tutorial
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stopher
Lee
added intro s
e
ction
t
o worldbase
.
rst tu
t
o
ria
l
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added Purpose to alignment
.
r
st
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
m
ore li
t
tle chan
g
es to
ann
o
tation2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
ist
o
pher
L
ee
a
dded Pu
r
p
o
s
e
and
intro to annot
a
ti
o
n
s2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Chri
s
tophe
r
Lee
moved new
b
as
i
c tuto
r
ials t
o
to
p
o
f guide list
commit
|
commitdiff
|
tree
2009-09-03
Christo
p
her Lee
minor
f
ix to db_basic
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stopher Lee
u
pdates to reference/sq
l
graph
.
rst docs
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
o
pher Le
e
add
e
d SQL savi
n
g section to db t
u
t
or
i
al
commit
|
commitdiff
|
tree
2009-09-03
Christophe
r
L
e
e
basic d
a
tabase tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added back __len__(
)
to S
Q
LTable
B
ase
.
How in
heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added section on Pre
f
i
x
U
nio
n
Dic
t
commit
|
commitdiff
|
tree
2009-09-02
Christopher
L
ee
added secti
o
n on plugging in you
r
own
sequ
e
nce parser
commit
|
commitdiff
|
tree
2009-09-02
C
hristopher
L
e
e
m
o
ved old m
a
terial out to compgenomics
.
r
st
commit
|
commitdiff
|
tree
2009-09-02
Christopher
L
ee
s
o
me mi
n
or
s
e
q
ue
n
c
e t
u
torial revisions
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
e
r
Le
e
adde
d
tutorial section o
n
acces
s
ing sequence database
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er L
e
e
split up bulle
t
p
o
ints
t
o inte
g
rate into th
e
code example
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istophe
r
Lee
re
v
ised
sequence
tutorial in
t
ro
(
f
irst
p
ar
t
)
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
Merge c
o
mmit 'remot
e
s/c
t
b/xmlrpc_tutorial' into tutorial
commit
|
commitdiff
|
tree
2009-09-02
Christ
o
p
h
er Lee
Merge commit 'r
e
motes/ctb/d
o
c
_alig
n
ment' into tutorial
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristopher Lee
revised gff3 code
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
stopher
Lee
added GFF3 ex
a
m
ple of gene bu
i
lding
commit
|
commitdiff
|
tree
2009-09-01
Christopher
L
ee
Merge
commit 'remotes/mkszuba/xmlrp
c
_tutorial' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Chri
s
topher Lee
Merge commi
t
'remotes/ctb/doc_annotations' i
n
t
o t
u
t
orial
commit
|
commitdiff
|
tree
2009-09-01
Christopher Lee
extracted mat
e
rial fo
r
sepa
r
ate d
a
t
a
b
a
s
e
tu
t
o
rial
commit
|
commitdiff
|
tree
2009-08-29
Chr
i
stopher Lee
removed unnec
e
s
s
ary stat a
n
d s
h
util
i
mport from setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
Chri
s
top
h
er Lee
fixed
e
asy_install bug b
y
prot
e
cti
n
g
coordinator
.
ResourceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Le
e
fixed blas
t
_
test: rename
d
test_seq_w
i
thout_db() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Merge
c
o
m
mit 'remotes/ct
b
/mi
n
o
r
_fixes' into
minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
C
h
ristopher Lee
fix po
r
t passi
n
g
i
n
t
e
s
tutil
.
TestXMLRPCS
e
rver
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
use pair_identity_tuple() for blast_test forma
t
tin
g
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
ris
t
op
h
er Lee
added BlastBa
s
e
.
tearDown
(
) to close seqdbs
as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christo
p
h
er Lee
Merge commit 'r
e
motes/mkszuba/doc_make'
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
sto
p
her Le
e
Mer
g
e commit 'rem
o
tes
/
mkszuba/r
p
m'
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
got rid of BlastMapping
.
warn
_
about
_
self_matches()
commit
|
commitdiff
|
tree
2009-07-29
Christoph
e
r Lee
changed NLMSA
p
airwi
s
eMod
e
to allo
w
re
p
orting of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
M
erge commit 're
m
otes/mkszu
b
a/debian'
commit
|
commitdiff
|
tree
2009-07-29
Christo
p
her Lee
retry readi
n
g
p
o
r
t_file in Test
X
MLRPCServer several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher L
e
e
add
e
d co
m
ments to process_blast()
commit
|
commitdiff
|
tree
2009-07-29
Chris
t
opher Lee
fix problem introd
u
c
ed i
n
process_blast(
)
by co
m
mit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
ha
n
dle mis
s
ing
W
INDIR
cas
e
on Windo
w
s
commit
|
commitdiff
|
tree
2009-07-28
Christo
p
her Lee
added
SeqTran
s
lator
.
__repr__()
commit
|
commitdiff
|
tree
2009-07-28
Christo
p
her Lee
Merge commit 'remo
t
es/
c
tb/simplefra
m
e_formatdb_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christ
o
pher Lee
Merge branc
h
'master
'
into simplefram
e
commit
|
commitdiff
|
tree
2009-07-28
Christopher Le
e
added SeqTranslator
.
iter_fra
m
e
s
() method, used in Blast
x
Mapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christophe
r
Lee
Merge commit 'remote
s
/ctb/simpleframe_do
c
_align' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
istophe
r
Lee
p
r
o
tect 2 more tests using
blast_enabl
e
d(
)
c
h
e
ck
commit
|
commitdiff
|
tree
2009-07-27
Chris
t
opher Lee
fixed synt
a
x erro
r
commit
|
commitdiff
|
tree
2009-07-27
Chri
s
toph
e
r Lee
a
d
d
ed python 2
.
3 code f
o
r File
P
open t
o
de
t
ect bad
exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
Merg
e
b
r
anch 'no_edge_db'
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher
L
ee
Merge
b
ranch
'silen
c
io'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
added showFormatdbMessages
option to
Blast
M
a
ppin
g
commit
|
commitdiff
|
tree
2009-07-25
C
hristoph
e
r
Lee
added suppor
t
for
n
o-edgeDB case in mapp
i
ng
.
Graph
:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christopher Lee
added op
t
i
on
for latex
o
utput
o
f the reference ma
n
ual
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r Lee
M
erge c
o
mmi
t
'r
e
motes/ctb/blast_test_rc' int
o
s
imple
f
r
ame
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
added more docstrings
f
or bl
a
s
t
.
py
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
o
pher Lee
r
emoved ol
d
B
lastxMapping code
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stophe
r
Lee
new, great
l
y simplified Blastx
M
apping
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristoph
e
r Lee
switched test_bla
s
tx_s
e
rver t
o
u
s
e new Translat
i
onDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christop
h
er Le
e
a
d
ded read_bl
a
st_alig
n
ment() translate
D
est option
commit
|
commitdiff
|
tree
2009-07-16
C
h
ri
s
top
h
er Lee
added NLMSA
.
edges() m
e
thod
commit
|
commitdiff
|
tree
2009-07-16
C
hristopher
Le
e
switc
h
ed
t
est
_
tblastn_parser to
u
s
e
new Translation
D
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
switch t
b
la
s
tn to u
s
e new Tr
a
nsl
a
tion
D
B appro
a
ch
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
added tr
a
nsla
t
ionDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher Lee
moved
d
bna
m
e default
into get_bound_su
b
c
lass()
commit
|
commitdiff
|
tree
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