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added better iter method
2009-09-05
Christo
p
her Lee
added better it
e
r method
commit
|
commitdiff
|
tree
2009-09-04
Chri
s
topher Lee
Merge commit 'remote
s
/ctb/xmlrpc
_
patches'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
Merge commit 'remo
t
e
s
/mksz
u
ba/
f
ink'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
removed tests/oldtests/nlmsa_dm2_
m
ega
t
est
.
p
y
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
sto
p
her Le
e
Merge comm
i
t 'remotes/
m
k
s
zub
a
/docf
i
xes
'
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher L
e
e
Merge commit
'remotes
/
mk
s
zuba/clean
u
p'
commit
|
commitdiff
|
tree
2009-09-04
C
hristo
p
h
er Lee
Merge c
o
mmit 'r
e
mote
s
/mkszuba/bsddb_bsd
d
b3'
commit
|
commitdiff
|
tree
2009-09-04
Christop
h
er L
e
e
co
r
rected Cla
s
sicUn
p
ickler r
e
fere
n
ce
t
o poi
n
t to class
u
til
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
re
m
ove
d
unused shelve imp
o
rt
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
r
e
moved un
u
s
e
d import item
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stoph
e
r L
e
e
M
e
r
ge branch
'tuto
r
ial'
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stopher Lee
added argument to make
M
apView
i
n
v
erse a
b
le to rec
o
n
s
titute
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christo
p
her Lee
added test
of len() metho
d
for SQLTable
commit
|
commitdiff
|
tree
2009-09-04
Christop
h
er Lee
added db tutoria
l
(ma
p
ping) back to guid
e
list ta
b
le
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
mapp
i
ng
t
utoria
l
just covers mapp
i
ngs, so removed reference
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher Lee
a
dded MapVie
w
inverse example to tutorial
commit
|
commitdiff
|
tree
2009-09-04
Christophe
r
Le
e
adde
d
MapVi
e
w
d
o
cs
commit
|
commitdiff
|
tree
2009-09-04
Christo
p
her Lee
add
e
d tes
t
f
o
r
t
rappi
n
g n
o
n-invertib
l
e Ma
p
View
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stoph
e
r
L
ee
adde
d
test for __invert__ met
h
od to MapVi
e
w
commit
|
commitdiff
|
tree
2009-09-04
Chris
t
opher
L
ee
added __i
n
vert__ m
e
thod to Ma
p
View
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
s
t
opher Lee
added material on
S
Q
L
Map
V
iew
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
isto
p
her Lee
a
dd
e
d sections on mapping to disk / w
o
r
l
db
a
se
commit
|
commitdiff
|
tree
2009-09-04
Christ
o
p
h
er
L
ee
c
hanged ti
t
le
o
f xmlrpc tutori
a
l
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
s
tophe
r
L
ee
minor fixes to gen
e
tutorial
commit
|
commitdiff
|
tree
2009-09-04
C
hr
i
stopher Lee
moved material
o
u
t of wo
r
ld
b
ase
.
rst to worldbase2
.
rst
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stopher
Lee
separate
t
utorial on saving data to worldbase
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stopher L
e
e
moved sch
e
ma mate
r
ial to worldbase2
.
rst tutori
a
l
commit
|
commitdiff
|
tree
2009-09-03
C
hris
t
oph
e
r Lee
added world
b
ase securit
y
warning
commit
|
commitdiff
|
tree
2009-09-03
Chri
s
topher Lee
more revisions about dow
n
loading tuto
r
i
al
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
opher Lee
revisi
o
ns
t
o
d
ownload=Tr
u
e section
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added
d
ependen
c
y
sec
t
ion in wo
r
ldb
a
s
e
.
r
st tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added worldbase
.
d
ir() tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er Lee
added int
r
o se
c
tio
n
to wo
r
ldba
s
e
.
r
st tutorial
commit
|
commitdiff
|
tree
2009-09-03
C
hri
s
to
p
her Lee
a
d
ded
P
u
r
pose
t
o alignment
.
rst
commit
|
commitdiff
|
tree
2009-09-03
C
hristoph
e
r Lee
more
l
itt
l
e c
h
a
ng
e
s to annotation2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christ
o
pher L
e
e
a
d
d
e
d P
u
rpose and intro to an
n
ot
a
ti
o
ns2
.
r
s
t
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
m
o
ved
new basic
t
utorials
t
o top
o
f guide list
commit
|
commitdiff
|
tree
2009-09-03
Christ
o
pher Lee
m
i
n
or
f
ix
to db_
b
asic
.
r
st
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er
Lee
updates to reference/sqlg
r
ap
h
.
r
st docs
commit
|
commitdiff
|
tree
2009-09-03
C
hrist
o
ph
e
r L
e
e
a
dded SQL sa
v
ing
s
e
c
t
ion to
db
tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
b
a
sic
d
a
tabase t
u
to
r
ial
commit
|
commitdiff
|
tree
2009-09-03
Christoph
e
r Le
e
a
dd
e
d ba
c
k __len__(
)
to SQL
T
ableBase
.
How in heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added section on PrefixUnionD
i
ct
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er Lee
added
s
ect
i
on on plugging in
your
ow
n
sequence
parser
commit
|
commitdiff
|
tree
2009-09-02
Christoph
e
r Lee
m
oved old material out to c
o
mpgenomics
.
r
st
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
some minor sequence
tut
o
r
i
a
l
revisions
commit
|
commitdiff
|
tree
2009-09-02
Christopher
Lee
added
t
utorial section on accessing
s
e
quence datab
a
se
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christ
o
pher
Le
e
split up bul
l
et
p
oints to integ
r
ate
i
nto the cod
e
exa
m
p
l
e
commit
|
commitdiff
|
tree
2009-09-02
Christ
o
pher Lee
revised s
e
q
uenc
e
tutori
a
l
intro (
f
irst p
a
rt)
commit
|
commitdiff
|
tree
2009-09-02
Christopher Le
e
Merge commi
t
'remot
e
s
/ctb/xmlrpc_t
u
torial' int
o
tutorial
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
M
e
rge commit
'
r
e
motes/
c
tb/d
o
c
_alig
n
ment' i
n
to tutoria
l
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er L
e
e
revised gff3 code
commit
|
commitdiff
|
tree
2009-09-02
Christopher L
e
e
added G
F
F3 exampl
e
of gene
b
uildi
n
g
commit
|
commitdiff
|
tree
2009-09-01
Christophe
r
Lee
Merg
e
commit 'remotes/mkszuba
/
xmlrpc_tut
o
rial' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Christop
h
e
r Lee
M
erge commit
'remotes/c
t
b
/do
c
_an
n
o
tati
o
ns' into tuto
r
ial
commit
|
commitdiff
|
tree
2009-09-01
Christopher L
e
e
extracted ma
t
e
rial fo
r
separ
a
te database t
u
t
o
rial
commit
|
commitdiff
|
tree
2009-08-29
Ch
r
istopher Lee
rem
o
ved unnecessary stat an
d
shutil im
p
ort fro
m
setu
p
.
py
commit
|
commitdiff
|
tree
2009-08-14
Chris
t
opher Lee
fixed
e
a
sy_insta
l
l bug
b
y protecting coor
d
ina
t
or
.
ResourceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stopher
Lee
fixe
d
blast_test:
ren
a
med tes
t
_
seq_without_db() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
hris
t
opher
L
ee
Merge c
o
mm
i
t 'r
e
mot
e
s
/ctb/minor_fi
x
es' into
minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
fi
x
p
o
rt passing in test
u
til
.
Te
s
tXMLRPC
S
erver
commit
|
commitdiff
|
tree
2009-08-04
Christop
h
er Lee
use pair_identit
y
_tup
l
e() for b
l
ast_t
e
s
t
for
m
at
t
ing
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
st
o
pher
L
ee
added Blast
B
ase
.
tea
r
Down() to close seqdbs as t
h
ey
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Merge commit 'r
e
mote
s
/m
k
szu
b
a/doc_make'
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stopher L
e
e
Merge commit '
r
emotes/mkszuba/
r
pm'
commit
|
commitdiff
|
tree
2009-07-29
Christophe
r
Lee
got rid of B
l
astMapping
.
wa
r
n_abo
u
t
_
self_matches()
commit
|
commitdiff
|
tree
2009-07-29
C
h
ris
t
op
h
er Lee
ch
a
n
g
e
d NL
M
SA pairwiseMod
e
to al
l
ow
reporting of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Chris
t
ophe
r
L
ee
Merge commit
'
r
emotes/m
k
szuba/debian'
commit
|
commitdiff
|
tree
2009-07-29
Christopher Le
e
retry reading
port_fi
l
e
in TestXML
R
P
CServer several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christ
o
pher Lee
added com
m
e
n
ts to p
r
ocess_bla
s
t()
commit
|
commitdiff
|
tree
2009-07-29
C
hristopher Lee
fix pr
o
blem
i
nt
r
oduced in
proces
s
_blast() by commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
handl
e
missing WINDIR case on Window
s
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
added SeqT
r
a
nslat
o
r
.
__
r
e
p
r__()
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristop
h
e
r L
e
e
M
e
rge commit 're
m
ot
e
s/c
t
b/
s
implef
r
ame_
f
ormatdb_clea
n
up
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
Merge br
a
nch
'
master' into simpl
e
frame
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
added SeqTran
s
lator
.
ite
r
_frame
s
() method, used
i
n BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristopher Lee
Merge commit
'
remotes/ct
b
/simplef
r
a
m
e_do
c
_align' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher
Lee
p
r
otect 2 mo
r
e
te
s
ts using bla
s
t_ena
b
l
ed() check
commit
|
commitdiff
|
tree
2009-07-27
C
h
ri
s
topher
L
ee
fixed syntax error
commit
|
commitdiff
|
tree
2009-07-27
Christo
p
her Lee
a
d
ded python 2
.
3
c
ode for FilePopen to detect bad e
x
it
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Chris
t
opher
L
ee
Merge branch 'no_edg
e
_db'
commit
|
commitdiff
|
tree
2009-07-27
C
h
ristopher Lee
Merge
b
ranch 'silencio
'
commit
|
commitdiff
|
tree
2009-07-27
Christ
o
p
h
er Lee
a
d
ded s
h
owF
o
r
matdbMessages op
t
ion to
Blast
M
appi
n
g
commit
|
commitdiff
|
tree
2009-07-25
Chri
s
topher Lee
added supp
o
r
t for no-edgeDB case in mapping
.
G
rap
h
:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christo
p
her L
e
e
ad
d
ed
option for
l
atex outpu
t
of the reference manual
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
Merg
e
commit 're
m
ot
e
s
/
ctb/bl
a
st_test_rc
'
into si
m
plefram
e
commit
|
commitdiff
|
tree
2009-07-16
C
h
rist
o
p
h
er
L
e
e
added more docstrings for blast
.
py
commit
|
commitdiff
|
tree
2009-07-16
C
hristopher Lee
rem
o
ve
d
old Blas
t
xMapping code
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
n
e
w, greatly sim
p
lified
B
last
x
Mapping
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher L
e
e
switche
d
test_b
l
astx_serv
e
r to use n
e
w T
r
anslationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
her Lee
added read_blast
_
alignment
(
) tr
a
nslateDest option
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
her Lee
added NLMSA
.
edge
s
() method
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
swi
t
ched
test_tblast
n
_parser to use
ne
w
T
r
an
s
lati
o
nDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r
Lee
switc
h
t
bl
a
stn to use ne
w
T
r
anslatio
n
DB
a
ppr
o
ach
commit
|
commitdiff
|
tree
2009-07-15
Christopher
L
ee
add
e
d tra
n
s
l
a
tionDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christo
p
her
L
ee
moved db
n
ame
d
efa
u
lt into get_bound_subclass
(
)
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stoph
e
r Le
e
make CoordsToI
n
t
ervals
/
get_in
t
e
rval() use seq
.
abso
l
ute
_
sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
clean
e
d up SeqPath
.
classySlice
(
)
commit
|
commitdiff
|
tree
2009-07-15
Christop
h
er Lee
Merge commit 'remot
e
s/mk
s
z
u
b
a/nlmsa_no_ver
b
ose' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher Lee
Merg
e
c
o
mmit
'
remotes/mkszuba/cn
e
ste
d
list_no
t
ice' into
.
.
.
commit
|
commitdiff
|
tree
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