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More tests for validate_seq()
2012-10-31
Florent Angly
More tests for v
a
lidate
_
s
e
q()
commit
|
commitdiff
|
tree
2012-10-31
Flor
e
nt
Angly
Testing val
i
date_se
q
()
and -re
f
_to_seq
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
C
o
n
s
tructo
r
-ref_
t
o_s
e
q fix
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Small change
s
in seq()
for
clarity
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
e
n
t
Angly
Small fix in v
a
li
d
a
t
ion
e
r
ror m
e
ssage
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
PrimarySeq::
s
eq() modula
r
ization
commit
|
commitdiff
|
tree
2012-10-31
Florent
A
ngly
Remove
d
unneeded
m
etho
d
commit
|
commitdiff
|
tree
2012-10-31
Fl
o
r
e
nt Angly
POD update an
d
more consitent variable names
commit
|
commitdiff
|
tree
2012-10-30
Floren
t
Angly
Primar
y
Seq dire
c
t mode fix/improvement
commit
|
commitdiff
|
tree
2012-10-30
Florent
A
ngly
Small
P
OD
a
nd
t
ests u
p
date
s
commit
|
commitdiff
|
tree
2012-10-30
Fl
o
rent A
n
gly
Doc
f
i
xes
commit
|
commitdiff
|
tree
2012-10-30
Flo
r
e
n
t Angly
Mor
e
tests for PrimarySeq
commit
|
commitdiff
|
tree
2012-10-30
F
l
ore
n
t Angly
Fixes is
s
ue in
EncodedSeq
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Cosm
e
tic changes
commit
|
commitdiff
|
tree
2012-10-30
Flor
e
n
t
Angly
C
onsi
s
tent indentatio
n
commit
|
commitdiff
|
tree
2012-10-30
Flore
n
t Angly
SeqFastaSp
e
ed
F
ac
t
ory fix
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Consistent indentati
o
n
commit
|
commitdiff
|
tree
2012-10-30
Flore
n
t Angly
B
i
o
::Pr
i
m
arySeq::lengt
h
(
)
o
p
timiz
a
tions
commit
|
commitdiff
|
tree
2012-10-30
Florent Ang
l
y
More tests for Bio:
:
PrimarySeq:
:
length()
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
POD
updated and
b
e
autification
commit
|
commitdiff
|
tree
2012-10-30
F
l
orent An
g
ly
More tes
t
s fo
r
Bio::Primar
y
S
eq::le
n
gth()
commit
|
commitdiff
|
tree
2012-10-30
Fl
o
re
n
t
A
ngly
A
dded
t
ests for Bio::PrimaryS
e
q::len
g
th()
commit
|
commitdiff
|
tree
2012-10-10
F
l
orent Angly
Better 0-length sequence support fo
r
Bio
:
:DB::Qual
.
.
.
commit
|
commitdiff
|
tree
2012-10-10
Flo
r
ent An
g
ly
Better support
f
or 0-length sequences
commit
|
commitdiff
|
tree
2012-09-24
Florent An
g
ly
Merge
b
ranch 'm
a
s
t
er' of github
.
com:bioperl/b
i
operl
.
.
.
commit
|
commitdiff
|
tree
2012-09-24
Flo
r
ent Angly
Fixed an untes
t
ed r
e
gr
e
ssion i
n
Bio::DB:
:
Fasta
commit
|
commitdiff
|
tree
2012-09-10
Florent A
n
gly
Regex
p
to ma
t
ch R
N
A on
r
e
q
u
e
st
o
nly
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Fixed indenta
t
i
on
commit
|
commitdiff
|
tree
2012-09-10
Florent Angl
y
Re
v
ersed problematic commit 8334d175ffba095a9447038d421c
a
c0d
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Flo
r
ent Angly
Merge br
a
nch 'ampli
c
ons
'
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Merge branch 'master' of github
.
com:
b
ioperl/bioper
l
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Floren
t
Angly
Rem
o
ved some comments
commit
|
commitdiff
|
tree
2012-09-10
F
lor
e
nt Angly
C
o
mpound ID can
n
ow
incl
u
d
the
s
trand
commit
|
commitdiff
|
tree
2012-09-10
F
l
o
r
e
nt
A
ng
l
y
Bio::DB::
I
ndexedBase complianc
e
with Bio
:
:DB:SeqI and
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Fix
e
d
t
ypo
commit
|
commitdiff
|
tree
2012-09-10
F
lorent Angl
y
Fi
x
ed si
l
ly err
o
r
commit
|
commitdiff
|
tree
2012-09-10
F
l
o
r
ent Angly
Updated
B
io::DB::SeqI POD
a
ccording to i
n
f
o i
n
Bio
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Up
d
ated
C
hanges fil
e
commit
|
commitdiff
|
tree
2012-09-10
F
l
orent Angly
E
x
pli
c
it va
r
i
abl
e
na
m
e
instea
d
of Bio/DB/Qual
.
pm
commit
|
commitdiff
|
tree
2012-09-10
F
l
ore
n
t
Angly
Hand
l
e R
N
A and
I
UP
A
C characters in Bio::DB::Fas
t
a
commit
|
commitdiff
|
tree
2012-09-10
Floren
t
Angly
Updat
e
d Changes file
commit
|
commitdiff
|
tree
2012-09-10
Florent An
g
ly
Better
alpha
b
et detection method
that h
o
nors
I
UPAC
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Fl
o
rent A
n
gly
Fasta and
Qua
l
only u
s
e t
h
e IndexedBase base
commit
|
commitdiff
|
tree
2012-09-10
F
l
orent Angly
POD update
commit
|
commitdiff
|
tree
2012-09-09
Florent Ang
l
y
P
OD u
p
dat
e
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Fi
x
e
d
bug intr
o
duced
in r
e
cent comm
i
t
commit
|
commitdiff
|
tree
2012-09-09
Fl
o
rent Angly
makeid logic in I
n
dexedBase
commit
|
commitdiff
|
tree
2012-09-09
Flo
r
ent Angly
Adde
d
e
r
ro
r
checks on F
a
sta into Qual
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Sm
a
l
l simp
l
ifica
t
i
osn
commit
|
commitdiff
|
tree
2012-09-09
Fl
o
r
ent A
n
gly
Test -makeid
option
commit
|
commitdiff
|
tree
2012-09-09
Flor
e
nt Angly
More s
t
re
a
mlining
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Support for specifying seque
n
ce strand
commit
|
commitdiff
|
tree
2012-09-09
F
lorent Ang
l
y
Using t
h
e _
p
a
r
se_compound_id() method
commit
|
commitdiff
|
tree
2012-09-09
Flor
e
nt Ang
l
y
Removed a test bec
a
use metho
d
leng
t
h() does
not take
.
.
.
commit
|
commitdiff
|
tree
2012-09-09
Fl
o
ren
t
A
ngly
Storin
g
n
umber of resid
u
es i
n
in
d
ex
f
ile
commit
|
commitdiff
|
tree
2012-09-09
Florent
Angly
Fix t
o
avoid a warning
commit
|
commitdiff
|
tree
2012-09-09
Fl
o
ren
t
Angly
V
a
ri
a
ble
n
ame cha
n
g
es
commit
|
commitdiff
|
tree
2012-09-09
F
l
orent A
n
gly
S
mal
l
ch
a
nges
commit
|
commitdiff
|
tree
2012-09-09
F
l
o
r
ent Angly
Renamed function
more a
p
propriately
commit
|
commitdiff
|
tree
2012-09-09
F
l
orent An
g
ly
Mor
e
methods in IndexedBase
commit
|
commitdiff
|
tree
2012-09-09
F
l
orent Ang
l
y
Misleadi
n
g vari
a
ble name
commit
|
commitdiff
|
tree
2012-09-09
Flore
n
t Angly
Cosm
e
tic cha
n
ge
s
commit
|
commitdiff
|
tree
2012-09-09
Floren
t
Angly
Small c
h
ang
e
s
commit
|
commitdiff
|
tree
2012-09-09
Flore
n
t Angly
F
ixed a couple of
typ
o
s
a
nd worked
o
n consistent indent
a
i
o
n
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Sub to parse compou
n
d IDs
commit
|
commitdiff
|
tree
2012-09-08
F
lorent A
n
gly
F
i
x
ed bug af
f
e
c
ting Bio::DB::SeqFeature
commit
|
commitdiff
|
tree
2012-09-08
F
l
o
r
ent Angly
F
i
xing
s
ome failing
t
ests
commit
|
commitdiff
|
tree
2012-09-08
Flor
e
nt An
g
l
y
R
e
named test file
s
f
o
r consis
t
e
n
c
y
commit
|
commitdiff
|
tree
2012-09-08
Flor
e
nt Ang
l
y
P
O
D reorganization
commit
|
commitdiff
|
tree
2012-09-08
Florent Angl
y
Fixed test
commit
|
commitdiff
|
tree
2012-09-08
Floren
t
Ang
l
y
POD up
d
ate
commit
|
commitdiff
|
tree
2012-09-08
F
lo
r
ent Angly
T
est head
e
r
(
)
commit
|
commitdiff
|
tree
2012-09-08
Florent Angly
fh() moved to _fh() i
n
Ind
e
x
e
dBase
commit
|
commitdiff
|
tree
2012-09-08
Flor
e
nt A
n
gly
POD up
d
a
te
commit
|
commitdiff
|
tree
2012-09-08
Floren
t
Angly
POD upd
a
te
commit
|
commitdiff
|
tree
2012-09-08
Flore
n
t Angly
POD
upd
a
te
commit
|
commitdiff
|
tree
2012-09-08
F
l
orent Angly
Improved t
e
sts
commit
|
commitdiff
|
tree
2012-09-07
Florent
A
n
g
ly
POD
u
pda
t
e
commit
|
commitdiff
|
tree
2012-09-07
Flo
r
ent Angly
Big PO
D
update
commit
|
commitdiff
|
tree
2012-09-07
Florent A
n
gl
y
New option to remove index file
whe
n
done
commit
|
commitdiff
|
tree
2012-09-07
Florent Angly
More im
p
ro
v
em
e
nts
commit
|
commitdiff
|
tree
2012-09-07
Flore
n
t Angly
Some
m
ore
streamlinin
g
commit
|
commitdiff
|
tree
2012-09-07
Florent Angly
Mo
v
ed get_seq_
s
tream to IndexedBase
commit
|
commitdiff
|
tree
2012-09-07
Florent Angly
Migra
t
ing more code
t
o IndexedBase
commit
|
commitdiff
|
tree
2012-09-07
Florent
A
ngly
Code simplification
commit
|
commitdiff
|
tree
2012-09-07
Flore
n
t
Angly
Small
P
OD ch
a
nge
commit
|
commitdiff
|
tree
2012-09-07
F
lorent
Angly
Misc cha
n
ges
commit
|
commitdiff
|
tree
2012-09-07
Florent A
n
gly
User
can
supply an arbitrary name for the index file
commit
|
commitdiff
|
tree
2012-09-06
F
lorent
A
ngly
Suppor
t
i
n
dexin
g
an arbi
t
ra
r
y se
t
of files
commit
|
commitdiff
|
tree
2012-09-06
Florent Angly
Better erro
r
che
c
k
ing
commit
|
commitdiff
|
tree
2012-09-06
F
lorent Angly
S
li
g
h
t
code
rea
r
r
angeme
n
t
commit
|
commitdiff
|
tree
2012-09-06
Florent Angly
Support for indexing multiple files
commit
|
commitdiff
|
tree
2012-09-06
Florent Ang
l
y
More mo
d
ularity
a
n
d cod
e
re
u
se
commit
|
commitdiff
|
tree
2012-09-06
Flore
n
t Angl
y
Remov
e
d some
temporary
code
commit
|
commitdiff
|
tree
2012-09-06
Flo
r
e
nt Angly
Small cha
n
ges
commit
|
commitdiff
|
tree
2012-09-06
Florent
A
n
g
l
y
Removed unneeded pragmas
commit
|
commitdiff
|
tree
2012-09-06
Florent Angl
y
Mor
e
IndexedBase work
commit
|
commitdiff
|
tree
2012-09-06
Florent An
g
ly
Packin
g
metho
d
s
inside IndexedBase
commit
|
commitdiff
|
tree
2012-09-06
Flore
n
t Angly
More IndexedBase wo
r
k
commit
|
commitdiff
|
tree
2012-09-06
Florent Angly
M
ore DB buildi
n
g
c
ode in In
d
e
x
edBase
commit
|
commitdiff
|
tree
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