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added better iter method
2009-09-05
Chr
i
s
topher Lee
ad
d
ed better i
t
e
r met
h
od
commit
|
commitdiff
|
tree
2009-09-04
C
h
ristopher
L
ee
M
e
rge commi
t
'remot
e
s/ctb
/
xmlrpc_
p
atches
'
commit
|
commitdiff
|
tree
2009-09-04
Christo
p
her Lee
Merge c
o
mmit 're
m
o
te
s
/mkszuba
/
fink'
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher
L
ee
rem
o
ved tests/ol
d
tests
/
n
l
msa_dm2_me
g
at
e
st
.
py
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stop
h
e
r
Lee
Merge
c
o
m
mit 'remotes/mk
s
z
ub
a
/doc
f
ixe
s
'
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher Lee
Mer
g
e commit
'remotes/mksz
u
ba
/
clea
n
up'
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher Lee
Merge commit 'remotes/mkszuba/bsddb_bsddb3'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Le
e
c
o
rrected Cla
s
sicUn
p
i
c
k
l
er refer
e
nce to point to classutil
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christopher L
e
e
re
m
o
ved u
n
used shelve i
m
port
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
r
emoved
unu
s
e
d
import item
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
Merg
e
branc
h
'tut
o
rial'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added argument t
o
make M
a
pView inverse able to reconstitute
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r L
e
e
added test of l
e
n()
method fo
r
S
QLTab
l
e
commit
|
commitdiff
|
tree
2009-09-04
C
h
r
i
stopher
L
ee
added db tutorial
(
mapping)
b
ack to guidelist
table
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r Lee
mapping tutorial just
c
overs mappings, so remove
d
re
f
e
r
en
c
e
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
C
hristopher Lee
ad
d
ed
M
a
p
V
iew
i
nverse examp
l
e
t
o tutorial
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stopher Lee
a
d
d
ed MapView doc
s
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
adde
d
te
s
t for trappi
n
g n
o
n-invertible MapView
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r Lee
added test for __inve
r
t__ m
e
thod to MapView
commit
|
commitdiff
|
tree
2009-09-04
C
hri
s
t
o
pher Lee
a
d
ded __invert
_
_
m
ethod to MapView
commit
|
commitdiff
|
tree
2009-09-04
Christo
p
her
L
ee
add
e
d
material on SQL MapView
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
ad
d
ed
secti
o
ns on m
a
pping to d
i
sk
/ worldbase
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher Lee
changed ti
t
le of xmlrpc tut
o
r
i
al
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
sto
p
her
L
ee
m
inor fixes to gene tutorial
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
stopher Lee
m
o
ved material ou
t
o
f
worldbase
.
rst
t
o
w
o
rldbase2
.
rst
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
i
stophe
r
L
ee
separa
t
e tut
o
rial o
n
s
a
ving da
t
a to wo
r
ldbase
commit
|
commitdiff
|
tree
2009-09-04
Christopher Le
e
mov
e
d
s
c
h
ema material to worldbase2
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
C
h
rist
o
p
h
e
r Lee
ad
d
ed worldbase security warning
commit
|
commitdiff
|
tree
2009-09-03
Christo
p
her Lee
more revisions abou
t
do
w
nloading tuto
r
i
al
commit
|
commitdiff
|
tree
2009-09-03
Christopher
Lee
revisions t
o
d
ow
n
load=True sectio
n
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
ad
d
ed dependency sec
t
i
o
n in
w
orldbase
.
rst tutori
a
l
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
add
e
d worldbase
.
dir
(
)
t
utorial
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stop
h
er Lee
added intro sect
i
on to w
o
rldbas
e
.
rst tut
o
rial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added Purpose to alignment
.
r
s
t
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
more little
c
hang
e
s
t
o
annotation2
.
r
s
t
commit
|
commitdiff
|
tree
2009-09-03
Christopher Le
e
added Purpos
e
and intro to annot
a
t
ions2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Chri
s
topher Lee
moved new basic tutorials to
top
o
f
g
uide list
commit
|
commitdiff
|
tree
2009-09-03
Christopher L
e
e
min
o
r
f
ix to db_basic
.
rs
t
commit
|
commitdiff
|
tree
2009-09-03
C
h
ris
t
ophe
r
Lee
upda
t
es to
r
eference/sqlgr
a
ph
.
r
st
docs
commit
|
commitdiff
|
tree
2009-09-03
Christopher L
e
e
added SQL
s
a
v
ing section
t
o db tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
basic
d
a
tabase tuto
r
ial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added back __len__() to SQLTableBase
.
How in heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Christopher
Lee
a
dded sec
t
io
n
on
P
refixUnionDict
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er
Lee
added se
c
tion on
p
luggi
n
g in your own
seque
n
ce parser
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
moved o
l
d
m
aterial out t
o
compgenomics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er L
e
e
so
m
e minor
s
eq
u
ence tu
t
o
rial revisions
commit
|
commitdiff
|
tree
2009-09-02
C
hris
t
opher Lee
ad
d
ed tu
t
orial se
c
tion o
n
accessing sequence
database
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
split u
p
bul
l
et points to integrat
e
into t
h
e code example
commit
|
commitdiff
|
tree
2009-09-02
C
hri
s
to
p
her
L
e
e
revi
s
ed sequence tutorial intro (first p
a
rt)
commit
|
commitdiff
|
tree
2009-09-02
Christopher Le
e
Merge commit 'remot
e
s/
c
t
b
/xmlrpc_tutor
i
al' into tutor
i
al
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
Merge commit 'remo
t
es/ctb/doc_alignment' into
t
u
torial
commit
|
commitdiff
|
tree
2009-09-02
Christo
p
her Lee
r
evised
gf
f
3 code
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
i
s
topher Lee
added GFF3
exa
m
ple of gene building
commit
|
commitdiff
|
tree
2009-09-01
Christoph
e
r Lee
Merge co
m
m
it 'remotes/mkszuba/xml
r
p
c_tutorial' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Ch
r
istopher Lee
Merge
c
o
mm
i
t 'remotes/ctb/doc_
a
n
notations
'
into tutoria
l
commit
|
commitdiff
|
tree
2009-09-01
Christopher Lee
extracted materi
a
l for separate database tutoria
l
commit
|
commitdiff
|
tree
2009-08-29
Chris
t
op
h
er Lee
remo
v
ed unne
c
essary stat and shut
i
l
i
mport from
s
etup
.
py
commit
|
commitdiff
|
tree
2009-08-14
Chris
t
oph
e
r Lee
fixed easy_inst
a
ll bu
g
by
protecting coord
i
nator
.
Res
o
urceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher
L
ee
f
i
x
ed bl
a
s
t_te
s
t: renamed test_seq_w
i
thout_db() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stopher Lee
Mer
g
e co
m
mit 'remo
t
es/ctb
/
minor_fixes'
i
n
to min
o
r_fixes
commit
|
commitdiff
|
tree
2009-08-04
Christ
o
p
her Lee
fix port passi
n
g in
t
estutil
.
TestXMLRPCSe
r
v
er
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stopher Lee
us
e
pair_identity
_
tu
p
le() f
o
r blast_test formatting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher
L
ee
added BlastBa
s
e
.
t
e
a
r
Down() to
c
lose seqdbs
as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chris
t
opher Lee
Merg
e
commit '
r
emotes/mkszuba/doc_make'
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
M
e
rge commit
'
remotes/mkszu
b
a/rpm'
commit
|
commitdiff
|
tree
2009-07-29
Ch
r
istopher Lee
got rid
o
f
BlastMappin
g
.
warn_about_self_mat
c
hes
(
)
commit
|
commitdiff
|
tree
2009-07-29
Chris
t
opher Lee
c
hanged NLMSA pairwiseMode to allow re
p
orting of
s
elf
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christop
h
er
Lee
Me
r
ge co
m
mit 'remo
t
es/mk
s
z
u
ba/deb
i
an'
commit
|
commitdiff
|
tree
2009-07-29
C
hristopher L
e
e
ret
r
y
r
e
ading port_file in TestXMLR
P
CServer several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Chris
t
opher Lee
added comments to pr
o
c
es
s
_
blast()
commit
|
commitdiff
|
tree
2009-07-29
Christopher
L
ee
f
ix
p
roblem in
t
r
oduced in proces
s
_bl
a
st() b
y
com
m
it
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
h
a
ndl
e
mis
s
ing
WINDIR case on Window
s
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristop
h
er L
e
e
adde
d
S
e
q
Translator
.
__repr__
(
)
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristopher Lee
Mer
g
e commit 'r
e
motes/ctb/simpleframe_formatdb_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Chr
i
stopher Lee
Merge b
r
anc
h
'
m
aster' i
n
to
simpleframe
commit
|
commitdiff
|
tree
2009-07-28
C
hri
s
topher Lee
added SeqTranslat
o
r
.
ite
r
_frame
s
() method, used in BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
hr
i
stopher Lee
Merg
e
commit 'remotes/
c
t
b
/simp
l
e
f
rame
_
doc_align' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christop
h
e
r Le
e
prot
e
c
t 2
m
ore tests
u
sing blast_ena
b
led() c
h
eck
commit
|
commitdiff
|
tree
2009-07-27
Christopher
L
ee
fixed sy
n
t
a
x error
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
adde
d
python
2
.
3
c
ode for FilePopen to detect bad exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stoph
e
r
L
ee
Merge branch
'
n
o_edge_
d
b'
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
s
t
o
p
her Lee
Merge branc
h
'silencio'
commit
|
commitdiff
|
tree
2009-07-27
Chris
t
op
h
er L
e
e
adde
d
showFo
r
matdbMe
s
sages option to Bl
a
stMap
p
ing
commit
|
commitdiff
|
tree
2009-07-25
C
h
ris
t
o
p
her
L
ee
a
d
ded
s
upport fo
r
no-
e
dge
D
B case in
mapping
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christ
o
p
h
er Lee
added
o
ption for la
t
ex output of the
r
e
ference manual
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r Lee
Merge commit 'remotes/ctb/
b
last_
t
est_rc' into simp
l
eframe
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
added more d
o
cstrings fo
r
blas
t
.
py
commit
|
commitdiff
|
tree
2009-07-16
C
hristo
p
her Lee
removed old BlastxMapping
c
od
e
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
i
s
topher Lee
new, greatly simpl
i
fied Bla
s
txM
a
pp
i
ng
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher Lee
sw
i
t
c
hed test_blastx_serv
e
r to use new TranslationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher
L
ee
adde
d
read_blast
_
alignment() trans
l
a
teDest option
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
ad
d
ed NLMSA
.
edges() me
t
hod
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
o
p
h
e
r Le
e
s
witched test_tblastn_pa
r
ser t
o
u
s
e ne
w
Tra
n
sla
t
ionDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
pher
L
ee
swi
t
ch tbla
s
tn
to
u
se ne
w
Tra
n
s
l
ationDB a
p
p
roach
commit
|
commitdiff
|
tree
2009-07-15
Christopher
Lee
ad
d
ed
tra
n
slationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christo
p
her Lee
moved dbname default into get_bound_subclass(
)
commit
|
commitdiff
|
tree
2009-07-15
C
h
ristop
h
er Lee
make CoordsTo
I
ntervals / get_inter
v
al() us
e
seq
.
a
bsolute_sl
i
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
is
t
o
pher Lee
cleaned up
SeqPath
.
cl
a
ssySlice()
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stopher L
e
e
M
e
r
ge commit 'remotes/m
k
szuba
/
nlm
s
a_no_verbose' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
Merge commit 'remotes
/
mks
z
uba/cnestedlist_notice' int
o
.
.
.
commit
|
commitdiff
|
tree
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