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Merge commit 'remotes/ctb/doc_alignment' into tutorial
2009-09-02
Ch
r
i
s
topher Lee
Merge commit 'remo
t
e
s
/ctb/
d
o
c
_alignment' into tutorial
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher Lee
revise
d
gff3 code
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er L
e
e
a
dded GFF3 e
x
ample of
gene building
commit
|
commitdiff
|
tree
2009-09-01
C
h
ristopher L
e
e
Mer
g
e commit 'remotes/mkszuba/xmlrpc_tutorial' int
o
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Chri
s
tophe
r
Lee
Merg
e
commit
'
remot
e
s/ctb/doc
_
annotat
i
ons' into
tutorial
commit
|
commitdiff
|
tree
2009-09-01
Chris
t
op
h
er Lee
extracted mater
i
al f
o
r
separa
t
e database tuto
r
ial
commit
|
commitdiff
|
tree
2009-08-29
Christopher Lee
removed unnecessary
s
t
at and shut
i
l import from setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
Christop
h
er Lee
fixe
d
easy_inst
a
ll b
u
g b
y
protecting coordinator
.
Re
s
ourceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christo
p
her Lee
fix
e
d
b
last_test
:
r
e
n
a
med
test_seq_without_db()
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chris
t
ophe
r
L
e
e
Merge com
m
it '
r
emotes/ctb/minor_fixes
'
i
n
t
o minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
sto
p
her
Lee
f
i
x port pa
s
sing in
t
estuti
l
.
T
e
stXMLRPCServer
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
use pair_i
d
entity_tupl
e
() fo
r
b
last_test form
a
tting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chri
s
top
h
er Lee
added Bla
s
tBase
.
tearDo
w
n() to
c
lose seqdbs
a
s the
y
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chri
s
t
opher Lee
Merge commit 'remotes/mkszuba/doc_make
'
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stopher Lee
Mer
g
e c
o
mmit '
r
emotes/mkszuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
C
h
r
i
s
topher
Lee
got rid of BlastMapping
.
warn_about_
s
elf
_
matc
h
es()
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
chang
e
d NLM
S
A pairwiseMode to allow reporting of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christo
p
her Lee
Me
r
ge c
o
mmi
t
'remotes
/
mkszub
a
/debia
n
'
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
retry reading por
t
_file in TestXMLRPCSer
v
er several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christophe
r
Lee
added c
o
mm
e
nts to process_blast(
)
commit
|
commitdiff
|
tree
2009-07-29
C
h
ristoph
e
r Lee
fix proble
m
introdu
c
ed in process_blast
(
) by
c
o
m
mit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christo
p
he
r
Lee
hand
l
e missing WIN
D
IR case on Windows
commit
|
commitdiff
|
tree
2009-07-28
Christoph
e
r L
e
e
added SeqTransl
a
tor
.
__re
p
r
__()
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
M
erge co
m
mit 'remotes/c
t
b/simplef
r
ame_formatdb_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
Merge b
r
anch
'
master' into simpleframe
commit
|
commitdiff
|
tree
2009-07-28
Christopher
Lee
added
S
eqTranslator
.
it
e
r_
f
rames() me
t
h
od, used
i
n
Blast
x
Mapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
h
r
ist
o
p
her Lee
M
e
rg
e
commit
'remotes/ctb
/
simpleframe_doc_align' in
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
C
h
ris
t
oph
e
r
Lee
p
r
otect 2 more tes
t
s usi
n
g blast_ena
b
led() check
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
isto
p
her Lee
fixed s
y
ntax error
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher L
e
e
a
d
d
e
d python 2
.
3 code for Fil
e
P
open to de
t
ect
b
a
d exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
Merge b
r
anch
'
no_edge_db'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
Merge branch 's
i
lencio'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Le
e
added sho
w
FormatdbMess
a
ges o
p
t
ion to BlastMapping
commit
|
commitdiff
|
tree
2009-07-25
Christo
p
her L
e
e
added su
p
port for no-edgeDB
c
ase
i
n mapping
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christopher Lee
added op
t
ion f
o
r l
a
t
e
x o
u
t
put o
f
the reference manual
commit
|
commitdiff
|
tree
2009-07-16
C
hristophe
r
Lee
Me
r
g
e commit 'remotes/ctb/blast_test_rc
'
i
nto simplefram
e
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher Lee
added more d
o
cstrings f
o
r blast
.
p
y
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher Lee
removed old BlastxM
a
pp
i
ng code
commit
|
commitdiff
|
tree
2009-07-16
C
hristophe
r
Lee
n
ew, greatly si
m
plifi
e
d Blast
x
Mapping
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
p
her Lee
switch
e
d tes
t
_blastx_server to use new Tr
a
nslationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
ad
d
ed read_blast_a
l
ig
n
ment() translateD
e
s
t
option
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
her
Le
e
added NL
M
S
A
.
edges()
method
commit
|
commitdiff
|
tree
2009-07-16
Christophe
r
Lee
switched test_
t
b
l
astn_par
s
er
to us
e
new
T
r
an
s
la
t
ionDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
s
w
itch tblastn to
use new TranslationDB
ap
p
roach
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher Lee
added t
r
anslationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
mo
v
e
d
dbname
d
e
fault into get_bound
_
s
u
bclass()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
m
a
ke Co
o
rdsToInter
v
als / get_interval() u
s
e seq
.
absolute_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
cleaned up SeqPath
.
cla
s
sy
S
lice()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
Merge commit 're
m
ote
s
/mkszuba/nlmsa_no_verbose' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christop
h
er L
e
e
Merge
c
o
mmit 're
m
o
tes/mkszuba/cnestedlist_noti
c
e
'
i
nto
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christop
h
er
L
ee
incom
p
l
e
te
new code for Transla
t
ionDB
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stopher Lee
c
leaned up revers
e
Path co
n
struction
commit
|
commitdiff
|
tree
2009-07-15
C
h
r
istopher L
e
e
add
a
bsolut
e
_slice() method
t
o SeqPath
commit
|
commitdiff
|
tree
2009-07-14
C
h
r
istoph
e
r Lee
Merge commit 'remotes/mkszub
a
/
cnes
t
edlis
t
_l
o
gge
r
' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christopher Lee
Merge bra
n
ch 'master' into
m
egatests
commit
|
commitdiff
|
tree
2009-07-03
Christopher Le
e
Merg
e
b
ranch 'forma
t
db_fail'
commit
|
commitdiff
|
tree
2009-07-03
Christo
p
her Lee
improved whites
p
ace path war
n
ing
commit
|
commitdiff
|
tree
2009-07-03
C
hristop
h
er Lee
added w
a
rning fo
r
w
hitespace in pat
h
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
Me
r
ge comm
i
t 'r
e
m
otes/mkszuba/megatests'
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
use glob
.
glo
b
()
i
nstead of os
.
li
s
tdir(); cleaned
up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Chri
s
t
o
ph
e
r
L
e
e
Merge
c
ommit 'remotes/m
k
szuba/m
i
metext'
commit
|
commitdiff
|
tree
2009-07-01
Chris
t
opher Lee
M
e
rge commit 're
m
otes/mk
s
zub
a
/
d
o
c
fixes'
commit
|
commitdiff
|
tree
2009-07-01
C
h
ristopher Lee
Merge commit 'remotes/mkszuba/h
a
shlib'
commit
|
commitdiff
|
tree
2009-06-26
Christop
h
e
r Lee
fixed c
a
chin
g
bug introduced in commit 8
d
9966 in P
r
e
fixUn
i
on
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christ
o
p
h
er Lee
depreca
t
ed
cursor arg
u
ment
to SQLTable
commit
|
commitdiff
|
tree
2009-06-20
C
hristopher Lee
fixe
d
issue 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
added test for issue
99
commit
|
commitdiff
|
tree
2009-06-20
Ch
r
istopher
L
ee
cleaned up SQ
L
iteServerInfo
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
ad
d
ed DBServerInfo
.
ne
w
_curs
o
r() method
commit
|
commitdiff
|
tree
2009-06-13
Christopher L
e
e
Merge c
o
m
m
it 'remotes/mksz
u
ba/issue97_test' into is
s
ue97_test
commit
|
commitdiff
|
tree
2009-06-13
Ch
r
istop
h
er Lee
removed
redund
a
nt and b
u
ggy rstr
i
p("
.
py
"
)
c
all
f
rom
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
fix pyrex cdef
commit
|
commitdiff
|
tree
2009-06-12
Ch
r
i
stopher Lee
fix is
s
ue97
commit
|
commitdiff
|
tree
2009-06-12
Chri
s
topher Lee
rais
e
d minimum
i
dentity for relaxed
blast tests to 60%
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
replaced
a few remaining refs in th
e
d
ocs
t
o
pyg
r
.
D
ata
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Christo
p
her Lee
Merge commi
t
'remot
e
s/
m
kszuba/deb'
commit
|
commitdiff
|
tree
2009-06-09
C
h
rist
o
p
h
er Lee
M
erge commit 'remotes/
m
k
s
z
ub
a
/renames'
commit
|
commitdiff
|
tree
2009-06-09
Christo
p
he
r
Le
e
Mer
g
e branch 'interval_filters
'
into blast_te
s
ts
commit
|
commitdiff
|
tree
2009-06-09
C
h
r
isto
p
her Lee
relaxed-test
s
h
a
d a b
u
g that ma
d
e them
p
a
ss the c
o
mparison
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chris
t
opher Lee
must clos
e
FilePopen o
b
j
e
ct before ex
i
ting BlastxMapping
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
hristopher L
e
e
m
e
r
g
e
d in ctb/blastx_datab
a
se
commit
|
commitdiff
|
tree
2009-06-04
Christ
o
phe
r
Lee
M
erge commit 'remotes/
c
tb
/
blastx_gen
e
rator' into ctb_t
m
p
commit
|
commitdiff
|
tree
2009-06-04
Chri
s
t
opher Lee
P
E
P8 and whitespace f
i
xes to nlmsa_utils
.
py; no functionalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
converte
d
add_
a
li
g
n
e
d
_interv
a
ls functiona
l
ity into
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher Le
e
clean up Attri
b
u
t
e
I
nterface accordi
n
g to Titus suggestion
s
commit
|
commitdiff
|
tree
2009-06-04
C
hristo
p
her
Lee
Merge com
m
it 'remotes/ctb
/
ctb_int
e
rvals' into interval_
f
ilte
r
s
commit
|
commitdiff
|
tree
2009-06-03
Chr
i
st
o
pher Lee
Merge commi
t
'remotes/c
t
b/ctb_bl
a
s
t
2' into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Christopher Lee
Merge commit
'
r
e
mo
t
es
/
c
t
b/minor_doc_fixes' into
c
t
b_tmp
commit
|
commitdiff
|
tree
2009-06-03
Christo
p
her Lee
merged in
ctb/an
n
otation
commit
|
commitdiff
|
tree
2009-06-03
C
h
risto
p
her Lee
me
r
ge
d
in ctb/blast_ski
p
co
n
flict
w
ith ctb/blast
_
cache
commit
|
commitdiff
|
tree
2009-06-03
Christopher Lee
Merge commit 'r
e
motes/ct
b
/
b
las
t
_c
a
ch
e
'
i
nto
c
t
b_tmp
commit
|
commitdiff
|
tree
2009-05-29
C
hrist
o
pher
Lee
Merge commit 'remot
e
s/ctb
/
n
lmsa_iter_repr'
commit
|
commitdiff
|
tree
2009-05-29
Chri
s
t
o
pher Lee
r
e
moved unneces
s
ary
impor
t
commit
|
commitdiff
|
tree
2009-05-29
Christopher Lee
co
n
verted test_multiblast_s
i
ngle() bac
k
to te
s
t
against
.
.
.
commit
|
commitdiff
|
tree
2009-05-29
Christopher
L
ee
rena
m
e
to avo
i
d false implicati
o
n
t
his test
involves
.
.
.
commit
|
commitdiff
|
tree
2009-05-27
Chr
i
stopher Lee
Merge
c
ommi
t
'remotes
/
mkszuba/trove' into
m
arek_tmp
commit
|
commitdiff
|
tree
2009-05-27
C
h
ristopher
L
ee
added
c
omparison with
single seq b
l
a
s
t in test_multibla
s
t
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
added text file for checkin
g
lon
g
p
a
rser results
commit
|
commitdiff
|
tree
2009-05-27
Christopher
Lee
put close
(
) wit
h
in t
r
y-fin
a
lly as
a
lways
commit
|
commitdiff
|
tree
2009-05-27
Christopher
Lee
Me
r
ge commit 'remo
t
e
s
/
m
ks
z
uba/blast_test' int
o
marek
_
tmp
commit
|
commitdiff
|
tree
next