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Merge commit 'remotes/mkszuba/cleanup'
2009-09-04
Christo
p
h
er Lee
Me
r
ge commit 'remotes/mkszuba/cleanup
'
commit
|
commitdiff
|
tree
2009-09-04
C
h
ristopher
L
ee
Mer
g
e c
o
mmit 're
m
ote
s
/mksz
u
ba/bsd
d
b_bs
d
db
3
'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
corrected
C
l
assicUnp
i
ckler referenc
e
to
poi
n
t to classu
t
il
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
removed un
u
se
d
shelve import
commit
|
commitdiff
|
tree
2009-09-04
C
h
ri
s
topher Le
e
remo
v
ed unused import
item
commit
|
commitdiff
|
tree
2009-09-04
Christopher Le
e
M
erge branc
h
'tutorial
'
commit
|
commitdiff
|
tree
2009-09-04
Christopher L
e
e
a
d
ded argument
t
o
m
ake
M
apView inverse able
t
o reco
n
stitute
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
C
hri
s
tophe
r
Lee
add
e
d test of len() me
t
hod for
SQLTable
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher Lee
added
d
b
t
utorial (mapping
)
back
to
guidelist tabl
e
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r Lee
m
a
pp
i
ng
t
utoria
l
just covers mappings, so removed reference
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christop
h
e
r
Lee
ad
d
e
d
MapView inverse
e
x
ample
to tutorial
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added MapV
i
ew docs
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added test
f
or trapp
i
ng
n
on-in
v
ertible MapVi
e
w
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
i
stopher
Lee
a
dded
test for __invert__ m
e
thod to
M
apView
commit
|
commitdiff
|
tree
2009-09-04
C
h
ristopher Lee
add
e
d
__invert__
m
ethod to M
a
pView
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added materi
a
l
on SQL MapView
commit
|
commitdiff
|
tree
2009-09-04
C
hristopher Lee
a
d
ded sect
i
ons on mapping
to di
s
k /
w
or
l
d
base
commit
|
commitdiff
|
tree
2009-09-04
C
hristopher Lee
changed t
i
tle of xmlrpc tutorial
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
min
o
r
f
ixes
t
o
gene tutor
i
al
commit
|
commitdiff
|
tree
2009-09-04
C
hristopher Lee
moved mat
e
r
i
a
l
out of worl
d
ba
s
e
.
rst to worldbase
2
.
rst
commit
|
commitdiff
|
tree
2009-09-04
Chri
s
topher Lee
separate tutorial
o
n
s
aving data to worldbase
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
moved
schema
m
a
te
r
ial t
o
worldba
s
e2
.
rst tu
t
o
r
ia
l
commit
|
commitdiff
|
tree
2009-09-03
C
hristop
h
er L
e
e
added w
o
rl
d
base security warning
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
mo
r
e r
e
visions
a
bout
do
w
n
l
oading tutoria
l
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stopher Lee
r
evis
i
ons
to dow
n
load=True sec
t
ion
commit
|
commitdiff
|
tree
2009-09-03
C
h
risto
p
he
r
Lee
ad
d
e
d
d
ependency section in worldbas
e
.
rst t
u
torial
commit
|
commitdiff
|
tree
2009-09-03
Christopher
Lee
added worldbase
.
dir() t
u
torial
commit
|
commitdiff
|
tree
2009-09-03
Christophe
r
Lee
adde
d
intro section to worldbase
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added Purpo
s
e to alignm
e
nt
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
st
o
pher Lee
more
l
ittl
e
changes t
o
annotation
2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christo
p
her Lee
added Purp
o
s
e and intro to annot
a
t
i
ons2
.
r
s
t
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
i
sto
p
he
r
Lee
mo
v
ed new basic tutorial
s
to top o
f
g
u
ide li
s
t
commit
|
commitdiff
|
tree
2009-09-03
C
hristo
p
her L
e
e
minor fix
to db_
b
asic
.
r
st
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
up
d
ates to refer
e
nce/sqlgr
a
ph
.
r
st docs
commit
|
commitdiff
|
tree
2009-09-03
Christopher
L
ee
a
d
d
e
d SQL sa
v
i
ng secti
o
n
to
db tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
b
a
s
ic dat
a
base tutoria
l
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added b
a
c
k
__len__() to SQLTabl
e
Base
.
H
o
w in h
e
c
k
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
oph
e
r Lee
added s
e
ction on
P
ref
i
xUnionDict
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher Lee
a
dded
section on plugging in your own seq
u
ence parser
commit
|
commitdiff
|
tree
2009-09-02
C
hrist
o
pher Lee
m
o
ved old material ou
t
to
c
ompgeno
m
ics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
C
h
r
ist
o
pher Lee
s
o
me mi
n
or
s
equence t
u
t
o
rial revis
i
o
n
s
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
added tu
t
orial se
c
tion o
n
acc
e
ssing sequence databas
e
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
C
h
r
istopher Lee
split
u
p bulle
t
p
o
i
n
ts t
o
integrate
into the code exampl
e
commit
|
commitdiff
|
tree
2009-09-02
Chri
s
topher L
e
e
revised se
q
u
e
nce
t
u
to
r
ial intro (first part)
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
s
tophe
r
Lee
M
er
g
e c
o
m
m
it 'remotes/ctb/xmlrpc_tutorial
'
in
t
o
tuto
r
ia
l
commit
|
commitdiff
|
tree
2009-09-02
Christopher
L
e
e
Mer
g
e co
m
m
i
t 'remotes/ctb/doc_alignment' into tutorial
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
revi
s
ed gff3 code
commit
|
commitdiff
|
tree
2009-09-02
Christo
p
her Lee
added GFF3 example
o
f
g
ene building
commit
|
commitdiff
|
tree
2009-09-01
Ch
r
i
stopher Lee
Merge commit 're
m
o
t
es/mk
s
zuba/xmlrpc_tu
t
orial' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
C
hri
s
topher Lee
Mer
g
e
co
m
mit 'rem
o
tes/
c
tb/
d
oc_an
n
otat
i
ons' in
t
o tuto
r
i
al
commit
|
commitdiff
|
tree
2009-09-01
Chris
t
ophe
r
Lee
e
x
tra
c
ted material
for se
p
arate
d
a
t
abase tutorial
commit
|
commitdiff
|
tree
2009-08-29
Christopher
Lee
removed u
n
nec
e
ssary stat and s
h
util impo
r
t from setu
p
.
py
commit
|
commitdiff
|
tree
2009-08-14
Christo
p
h
er
L
ee
fixed easy_in
s
t
all bug by prot
e
cting coordinator
.
R
esourc
e
F
il
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
s
t
o
pher Lee
fixed
b
last_test:
r
enamed test_seq_without_db() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
hr
i
s
t
opher Lee
Merge commit 'remotes/ctb/minor_
f
ixes' into
minor
_
fixes
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
st
o
ph
e
r Lee
fix port passing
i
n testutil
.
TestX
M
LRPCServer
commit
|
commitdiff
|
tree
2009-08-04
C
hristo
p
her Lee
use pair_identity_tupl
e
(
)
for bla
s
t_test format
t
ing
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stopher Lee
a
dded Blas
t
B
a
se
.
tearDown() to close seqd
b
s as t
h
ey
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
M
e
rge commit
'remo
t
e
s
/mkszuba/do
c
_make'
commit
|
commitdiff
|
tree
2009-08-04
C
hristophe
r
Lee
M
erge
c
om
m
it
'
remot
e
s/mkszu
b
a/rpm
'
commit
|
commitdiff
|
tree
2009-07-29
Christo
p
he
r
Lee
got rid of Bla
s
tMapping
.
warn
_
a
bo
u
t_s
e
lf_ma
t
c
he
s
(
)
commit
|
commitdiff
|
tree
2009-07-29
Chr
i
stophe
r
Le
e
changed NLMSA pai
r
w
i
seMode to allow reporting of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Chri
s
tophe
r
Le
e
M
e
rge
commit 'r
e
m
otes/
m
ksz
u
ba/deb
i
an'
commit
|
commitdiff
|
tree
2009-07-29
C
hristo
p
h
e
r Lee
retry reading port_file
in
TestX
M
LRPCServer sev
e
ral
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
C
hristopher Lee
a
d
ded comment
s
to process_b
l
ast()
commit
|
commitdiff
|
tree
2009-07-29
C
h
r
istopher Lee
fix problem introduced in
proc
e
s
s_blas
t
(
) by commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristopher L
e
e
h
andle miss
i
ng WIND
I
R
case on Windows
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
a
d
de
d
SeqTranslator
.
__r
e
pr__
(
)
commit
|
commitdiff
|
tree
2009-07-28
C
hristopher Lee
M
e
rge comm
i
t 'remotes/ctb/si
m
pleframe_formatdb_clean
u
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christ
o
p
h
er Lee
Merge branch
'ma
s
ter'
into
s
impleframe
commit
|
commitdiff
|
tree
2009-07-28
C
hristopher Lee
added
SeqTran
s
lato
r
.
iter_f
r
a
m
es() method, used in Blas
t
x
M
app
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christophe
r
L
ee
M
e
rge commit 'remotes/ctb/simplefram
e
_do
c
_a
l
ign' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
pr
o
tect 2
m
ore tests using blast_enabled
(
) check
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher Lee
fixed s
y
ntax error
commit
|
commitdiff
|
tree
2009-07-27
C
hr
i
sto
p
her
Lee
added
p
ython 2
.
3 code for FilePopen to
d
etect bad exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christoph
e
r Lee
M
e
rge
b
ran
c
h 'no_edge_db'
commit
|
commitdiff
|
tree
2009-07-27
Christopher
L
e
e
M
erge br
a
n
c
h 'silencio'
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
isto
p
h
e
r
L
ee
added s
h
owFormatdbMessa
g
e
s
op
t
ion t
o
B
l
astMapping
commit
|
commitdiff
|
tree
2009-07-25
Chr
i
stopher L
e
e
a
d
ded sup
p
o
r
t for no-ed
g
e
D
B case i
n
mapping
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christo
p
her Lee
adde
d
o
p
ti
o
n for la
t
ex ou
t
p
u
t o
f
the referen
c
e manual
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
isto
p
h
e
r
L
ee
Merge commit 'remotes/ctb/bla
s
t_tes
t
_rc' i
n
to sim
p
lef
r
a
me
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
opher Lee
add
e
d
m
ore
docstr
i
ngs f
o
r blast
.
py
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
removed old Bl
a
stxMappin
g
code
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
topher Lee
new, greatly
simplified Blas
t
xM
a
ppi
n
g
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher Lee
swi
t
ched t
e
st_b
l
astx_se
r
ver to
use new Trans
l
ationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
h
er L
e
e
added re
a
d_blast
_
alignment() translate
D
est option
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
topher Le
e
added NLM
S
A
.
edges() method
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
i
stopher
L
ee
s
wit
c
hed test_tb
l
ast
n
_parser to use new Tr
a
nslat
i
onDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
pher Lee
switch
tblastn
to use
n
ew
Translation
D
B
a
pp
r
oach
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
p
h
er Lee
a
dded
t
ranslati
o
nDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stophe
r
Lee
moved dbname default into get
_
bound_subclass()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
make Coord
s
T
oIntervals / get_interval()
u
se seq
.
abs
o
lu
t
e_
s
li
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
hristo
p
her
L
ee
clean
e
d up SeqPath
.
c
lassySli
c
e
()
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
istophe
r
L
ee
Merge
c
o
mmit 'remotes
/
mks
z
u
ba/nlmsa_no_verbos
e
' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher Lee
Merge co
m
mit 'rem
o
tes/
m
kszuba/cn
e
s
t
edlist_notice' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
istopher Lee
incomplete n
e
w
c
ode
for Tran
s
l
ationDB
commit
|
commitdiff
|
tree
2009-07-15
C
hristopher Lee
cl
e
aned
u
p reversePath c
o
nstruction
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher Lee
add
abs
o
lute_slice()
m
e
thod to SeqPath
commit
|
commitdiff
|
tree
2009-07-14
Christoph
e
r Lee
M
e
rge
commit 'remotes/mkszuba/cnest
e
d
list_logger' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
M
ar
e
k Sz
u
ba
Given exi
s
t
i
ng isolation problem
s
between tests run
.
.
.
commit
|
commitdiff
|
tree
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