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testutil needed new name of get_name_cursor()
2009-09-05
Chri
s
topher
L
e
e
testutil n
e
eded ne
w
name of get_name_cur
s
or()
commit
|
commitdiff
|
tree
2009-09-05
Christopher Lee
made get_nam
e
_cursor()
use
D
BServerInf
o
commit
|
commitdiff
|
tree
2009-09-05
Christ
o
p
her
L
ee
added
i
ter
a
tion test to graph_te
s
t
.
py
commit
|
commitdiff
|
tree
2009-09-05
Christopher Lee
us
e
new iter_ke
y
s(
)
m
e
t
hod
commit
|
commitdiff
|
tree
2009-09-05
Chris
t
opher Lee
a
d
ded better it
e
r metho
d
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
Merge commit 'remot
e
s/
c
tb/xmlr
p
c_patches'
commit
|
commitdiff
|
tree
2009-09-04
Chris
t
op
h
er Lee
Merge c
o
mmit 'remotes/mksz
u
ba/fink'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
rem
o
ved
tests
/
oldtests/nlmsa_dm2_m
e
gatest
.
p
y
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r Lee
Merge commit 'remotes/mkszuba/docfixes
'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
Merge commit 'remotes/mks
z
uba/cleanup'
commit
|
commitdiff
|
tree
2009-09-04
Christo
p
her Lee
Merge com
m
i
t 're
m
ote
s
/
m
kszuba/bsddb
_
b
s
ddb3'
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
i
s
topher Lee
c
orre
c
t
ed Classic
U
npickle
r
r
efere
n
ce
t
o
p
oint to classutil
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
C
h
ri
s
topher Lee
rem
o
ved unused shelv
e
impo
r
t
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
removed
unuse
d
im
p
ort ite
m
commit
|
commitdiff
|
tree
2009-09-04
Ch
r
istopher Lee
Merge branc
h
'tutori
a
l
'
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added
a
rgu
m
ent to make Ma
p
View inver
s
e able to rec
o
nstitute
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Christop
h
er Lee
added
test of le
n
()
m
et
h
o
d for SQLTable
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added db tutorial (mapping) ba
c
k
to guidelist table
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
C
hristop
h
e
r
Lee
mapping tutori
a
l
ju
s
t
co
v
ers mappings, so removed r
e
ference
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
C
h
ristoph
e
r Lee
added MapVi
e
w inverse example to t
u
to
r
ial
commit
|
commitdiff
|
tree
2009-09-04
C
h
ri
s
topher
L
ee
a
dde
d
MapView docs
commit
|
commitdiff
|
tree
2009-09-04
Chris
t
opher
L
ee
ad
d
ed t
e
st for trapping
non-
i
nvertib
l
e MapVi
e
w
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
added
test for
_
_invert__ method
t
o Ma
p
View
commit
|
commitdiff
|
tree
2009-09-04
Christ
o
pher L
e
e
added
__invert__ met
h
od to MapVie
w
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
sto
p
her
Lee
added material on SQ
L
MapVie
w
commit
|
commitdiff
|
tree
2009-09-04
Chr
i
s
t
o
p
he
r
Lee
added sections
on mapping to
disk / wor
l
dbas
e
commit
|
commitdiff
|
tree
2009-09-04
Christopher
L
ee
ch
a
n
ged title of xml
r
pc tutoria
l
commit
|
commitdiff
|
tree
2009-09-04
Christopher Lee
m
inor fixes to gene
tutorial
commit
|
commitdiff
|
tree
2009-09-04
Chris
t
opher Le
e
moved m
a
terial out
of worldbas
e
.
rst to worldbase2
.
rst
commit
|
commitdiff
|
tree
2009-09-04
Christoph
e
r Lee
separate tuto
r
ial on sa
v
i
n
g d
a
ta to w
o
rldb
a
s
e
commit
|
commitdiff
|
tree
2009-09-04
Chri
s
topher Lee
move
d
sche
m
a material to worl
d
base2
.
r
s
t tutorial
commit
|
commitdiff
|
tree
2009-09-03
C
h
r
istopher Lee
ad
d
ed worldbase security warning
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er Lee
m
o
r
e revi
s
io
n
s
a
bout dow
n
l
oading tuto
r
i
a
l
commit
|
commitdiff
|
tree
2009-09-03
Chri
s
topher Lee
revisions to
d
ow
n
l
oad=True section
commit
|
commitdiff
|
tree
2009-09-03
Christophe
r
Lee
a
dded
dependency
section
i
n worldbase
.
r
st
tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christo
p
her Lee
added world
b
ase
.
dir() t
u
torial
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er Lee
added i
n
tro section to worldbase
.
r
st t
u
torial
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er Lee
adde
d
Pu
r
pose to alignment
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Chri
s
t
o
pher Lee
m
o
re little chang
e
s to anno
t
ation2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
C
hristopher
Le
e
a
d
de
d
Purpose and intro to annotations2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christopher
Lee
moved new b
a
sic
t
utorials to top of guide list
commit
|
commitdiff
|
tree
2009-09-03
Christophe
r
L
e
e
minor fi
x
to db_b
a
sic
.
r
s
t
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
updates to ref
e
re
n
ce/sqlgraph
.
r
st docs
commit
|
commitdiff
|
tree
2009-09-03
Christopher L
e
e
added SQL sa
v
ing sect
i
on to db tu
t
orial
commit
|
commitdiff
|
tree
2009-09-03
Christopher
L
ee
b
a
sic data
b
ase tut
o
rial
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
sto
p
h
er Lee
added back __len__()
t
o
S
Q
LTabl
e
Base
.
H
o
w in heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
C
h
ristopher Lee
added section on
P
refixUnionDict
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
i
s
topher Lee
a
dded sec
t
ion on plugging i
n
your own
sequence parser
commit
|
commitdiff
|
tree
2009-09-02
C
hristoph
e
r Lee
moved old
mater
i
al out to com
p
g
e
n
o
mic
s
.
rst
commit
|
commitdiff
|
tree
2009-09-02
C
hri
s
topher Lee
s
o
me minor se
q
uence tutorial revisions
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher L
e
e
adde
d
t
u
t
orial s
e
ction on acces
s
ing sequence
database
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Chri
s
top
h
er Lee
split up
b
ullet point
s
to integr
a
te into the code example
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
stopher
L
e
e
re
v
ised sequence tutor
i
al
i
n
t
ro (first part)
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
M
e
rge commit '
r
emotes/ctb/xml
r
pc_
t
uto
r
ia
l
' into tutoria
l
commit
|
commitdiff
|
tree
2009-09-02
Christopher Le
e
Me
r
ge commit 'remo
t
es/ctb/doc
_
alignment' into
tutorial
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristopher Lee
revised gff3 code
commit
|
commitdiff
|
tree
2009-09-02
Chri
s
t
opher
Lee
added GFF3 example of
g
e
ne build
i
ng
commit
|
commitdiff
|
tree
2009-09-01
Christ
o
pher Lee
Mer
g
e commit
're
m
otes/
m
kszuba/xmlrpc_tuto
r
i
a
l'
i
nt
o
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Christopher L
e
e
Merge commit
're
m
o
t
es/ct
b
/doc_ann
o
tat
i
on
s
' into tutor
i
al
commit
|
commitdiff
|
tree
2009-09-01
C
h
ristopher Lee
e
xtracted materia
l
for separate database tutorial
commit
|
commitdiff
|
tree
2009-08-29
Christ
o
pher Lee
removed unnecessary stat and
s
h
uti
l
im
p
ort from
se
t
u
p
.
p
y
commit
|
commitdiff
|
tree
2009-08-14
C
hris
t
o
p
her Lee
fixed
easy_install
b
ug b
y
pro
t
ec
t
ing co
o
rdinator
.
ResourceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
hr
i
stophe
r
Lee
f
ixed
b
l
a
s
t_test: renamed test_
s
eq_
w
ithout_db()
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Merg
e
c
o
m
m
it 'remo
t
es
/
ctb/minor
_
fi
x
e
s' int
o
minor_fix
e
s
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
istopher Le
e
fix port passing
i
n testutil
.
Te
s
t
XM
L
RPC
S
erv
e
r
commit
|
commitdiff
|
tree
2009-08-04
Christo
p
h
e
r Lee
u
se pair_i
d
e
n
t
ity_tupl
e
() for b
l
ast_test forma
t
ting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stoph
e
r Lee
added
Blas
t
Base
.
t
e
arDown() t
o
close seqd
b
s as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Mer
g
e
commit 're
m
otes/
m
kszuba/do
c
_make'
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Merge comm
i
t 'remot
e
s
/
mkszuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
C
hristopher Lee
got rid of BlastMapping
.
warn_about_self_matche
s
()
commit
|
commitdiff
|
tree
2009-07-29
Chris
t
opher
Lee
change
d
NLMSA pairwiseMode to allow
reporting of
s
elf
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
Merg
e
commit 'remotes
/
m
k
szuba/d
e
bian'
commit
|
commitdiff
|
tree
2009-07-29
Chri
s
topher Lee
retry readin
g
port_file
i
n Tes
t
XMLRPC
S
erver se
v
e
r
a
l
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
C
hristopher Lee
added comments t
o
process_blas
t
()
commit
|
commitdiff
|
tree
2009-07-29
C
h
rist
o
phe
r
Lee
f
ix problem i
n
t
rod
u
c
ed in
p
rocess_blas
t
()
by commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
h
ris
t
o
p
h
er Lee
ha
n
dle
m
issing WINDIR case
o
n W
i
ndo
w
s
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristopher Lee
add
e
d SeqT
r
ansl
a
tor
.
__repr__()
commit
|
commitdiff
|
tree
2009-07-28
Christopher
L
ee
Mer
g
e comm
i
t 'remotes/ctb/s
i
m
plefram
e
_format
d
b_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Chris
t
o
p
her L
e
e
Merge
b
ranch 'master' into simpl
e
f
r
ame
commit
|
commitdiff
|
tree
2009-07-28
C
h
r
istopher Lee
added
S
e
q
T
ranslator
.
iter_fram
e
s
(
)
meth
o
d, used
i
n BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
h
ris
t
opher Lee
M
erge commit
'remotes/ctb/simple
f
rame_doc_align'
i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
protec
t
2 more
t
e
s
ts using blast
_
e
n
able
d
() check
commit
|
commitdiff
|
tree
2009-07-27
Christoph
e
r Lee
fi
x
e
d
syntax err
o
r
commit
|
commitdiff
|
tree
2009-07-27
Christo
p
her Lee
added python 2
.
3
code for
F
ilePopen
to det
e
ct b
a
d exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
Merge br
a
nch 'no_edge_db
'
commit
|
commitdiff
|
tree
2009-07-27
C
h
ristopher Lee
M
e
rg
e
branc
h
'si
l
encio'
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
istopher
L
e
e
added show
F
orm
a
tdbMessages opt
i
on to Bl
a
s
tMapping
commit
|
commitdiff
|
tree
2009-07-25
Christopher Lee
added support for
no-edgeDB
c
ase
i
n mapping
.
G
raph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christ
o
pher Le
e
adde
d
o
pti
o
n for l
a
te
x
output
of the
r
eference manual
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
s
t
opher Lee
Merge commit 'remo
t
es/ctb/blast_te
s
t_rc'
i
nto simpleframe
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
s
t
op
h
er
L
e
e
add
e
d more docstrings for b
l
ast
.
py
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
o
pher Le
e
remo
v
ed old Blastx
M
appin
g
code
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
n
ew, gr
e
at
l
y simplified B
l
astxMappin
g
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
swi
t
ch
e
d test_blastx_ser
v
e
r
to
u
se new Translation
D
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r Lee
added
read_blast_alignment() translateDes
t
o
ptio
n
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
i
s
tophe
r
Lee
a
dded
N
L
MSA
.
edges
(
) metho
d
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
opher Lee
switched test_tblastn_par
s
er
t
o us
e
n
e
w Tr
a
nslationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
i
stop
h
er L
e
e
switch tblastn to use ne
w
T
r
a
nslationD
B
ap
p
roach
commit
|
commitdiff
|
tree
2009-07-15
Christopher Le
e
added translationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
moved dbname default int
o
g
et_bo
u
nd_subclas
s
(
)
commit
|
commitdiff
|
tree
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