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make explicit
2013-07-11
Florent
A
ngly
More
thoroughl
y
d
ocument
e
d options and de
f
a
u
lts
commit
|
commitdiff
|
tree
2013-07-11
Flo
r
en
t
Angly
Restoring intended
b
ehavi
o
ur
.
.
.
I
th
i
nk
commit
|
commitdiff
|
tree
2013-07-11
F
lor
e
nt An
g
ly
Fixed fa
i
li
n
g DBD test
commit
|
commitdiff
|
tree
2013-02-03
Flore
n
t Ang
l
y
F
ixed POD enco
d
ing is
s
ue
commit
|
commitdiff
|
tree
2012-11-18
F
lore
n
t Angly
Merge branch
'
mast
e
r' of github
.
com
:
bioperl/biope
r
l
.
.
.
commit
|
commitdiff
|
tree
2012-11-17
F
l
oren
t
Angly
Merge branch 'master' i
n
t
o
bug_3390
commit
|
commitdiff
|
tree
2012-11-17
Florent Angl
y
Tigh
t
ene
d
an
d
optim
i
z
ed quali
t
y str
i
ng valid
a
tion
commit
|
commitdiff
|
tree
2012-11-17
Florent
A
ngly
Updated pla
n
ned number of
tes
t
s
commit
|
commitdiff
|
tree
2012-11-17
Florent Angly
'our' is pr
e
fe
r
red ove
r
'u
s
e vars'
commit
|
commitdiff
|
tree
2012-11-17
F
l
orent Angl
y
Test updates (PrimaryQ
u
al mo
s
tl
y
)
commit
|
commitdiff
|
tree
2012-11-17
F
lo
r
ent Angly
P
rim
a
r
ySeq v
a
l
i
dation spee
d
up
commit
|
commitdiff
|
tree
2012-11-16
Floren
t
A
n
gl
y
Instead of closur
e
s, si
m
ply
store attributes in $s
e
lft
commit
|
commitdiff
|
tree
2012-11-15
Florent Angly
Merge br
a
n
c
h 'seqlengt
h
'
commit
|
commitdiff
|
tree
2012-11-09
Flo
r
e
n
t
Angly
Up
d
a
ted number of tests
commit
|
commitdiff
|
tree
2012-11-06
Florent Angly
PrimaryQual validation synch
r
onized with that o
f
Pri
m
a
r
y
S
eq
commit
|
commitdiff
|
tree
2012-11-06
Floren
t
Angly
S
a
m
e
rev
c
om(
)
and length()
approach in
Bio::
D
B::Qua
l
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Florent
An
g
ly
New len
g
th() method neee
d
to consider
stra
n
dedness
commit
|
commitdiff
|
tree
2012-11-06
Florent A
n
g
l
y
Also r
e
ver
t
to old rev
c
om() + test + d
o
c
commit
|
commitdiff
|
tree
2012-11-06
Flor
e
nt Angly
Rev
e
r
t
ed
t
o
previ
o
us behaviour, i
.
e
.
ove
r
r
i
de Prim
a
rySeqI
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Fl
o
rent Angly
Merge
bra
n
ch 'master'
of github
.
com
:
bioper
l
/bi
o
perl
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Florent Angly
Bio::DB::length improvement
commit
|
commitdiff
|
tree
2012-11-06
Florent Angly
Bio::Primar
y
Qual POD update
commit
|
commitdiff
|
tree
2012-11-06
Flore
n
t
A
ngly
More Bio::DB::Qua
l
tests
commit
|
commitdiff
|
tree
2012-11-06
Floren
t
Angl
y
Let PrimarySeqI handle revcom() and trunc()
commit
|
commitdiff
|
tree
2012-11-06
Fl
o
re
n
t
Angly
Test Bio:
:
PrimarySeq
:
:Fasta compliance with
B
i
o
::PrimarySeqI
commit
|
commitdiff
|
tree
2012-11-05
Florent
Angly
More tests
commit
|
commitdiff
|
tree
2012-11-05
Floren
t
Angly
Added
a
t
e
st
commit
|
commitdiff
|
tree
2012-11-05
Florent
A
ngly
Cosmetic changeS
commit
|
commitdiff
|
tree
2012-11-05
F
l
ore
n
t Angly
Redu
n
dant messages
commit
|
commitdiff
|
tree
2012-11-05
Florent Angly
validat
e
_seq() takes a
stri
n
g as
argume
n
t
commit
|
commitdiff
|
tree
2012-11-05
F
lo
r
ent Angly
undef sequence strings ar
e
valid
s
e
quences
commit
|
commitdiff
|
tree
2012-11-05
Florent Ang
l
y
Smal
l
fix
commit
|
commitdiff
|
tree
2012-11-05
F
l
orent Angly
Redu
n
d
a
nt sequence va
l
id
a
tion
commit
|
commitdiff
|
tree
2012-11-05
Florent
Angly
Cosmet
i
c changes, i
n
dentation, e
t
c
commit
|
commitdiff
|
tree
2012-11-05
F
lorent Ang
l
y
Avoid warning
m
essage during testing
commit
|
commitdiff
|
tree
2012-11-01
Florent Angly
Hardening tes
t
commit
|
commitdiff
|
tree
2012-11-01
Florent
Angly
Fix for regr
e
ss
i
on bug #3390
commit
|
commitdiff
|
tree
2012-11-01
Florent A
n
gly
U
p
dated tests for Bio::DB::Fasta
commit
|
commitdiff
|
tree
2012-10-31
Flor
e
nt Angly
Adde
d
test for bug 3
3
90
commit
|
commitdiff
|
tree
2012-10-31
Florent Ang
l
y
Added tests tha
t
use the file() m
e
thod
commit
|
commitdiff
|
tree
2012-10-31
Fl
o
rent Angly
Chang
e
s
file update
commit
|
commitdiff
|
tree
2012-10-31
Fl
o
rent An
g
ly
C
h
anges update
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
-direct
valid o
n
l
y
once
commit
|
commitdiff
|
tree
2012-10-31
F
l
o
r
ent Angly
s
ubseq() speedup
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
More length() tes
t
s and
some POD updat
e
commit
|
commitdiff
|
tree
2012-10-31
Floren
t
Angly
Removed some code redund
a
ncy
commit
|
commitdiff
|
tree
2012-10-31
F
l
orent Angly
Bio::Pr
i
mar
y
Se
q
I speedup
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Cos
m
etic ch
a
ngeS
commit
|
commitdiff
|
tree
2012-10-31
Florent
An
g
l
y
Co
s
metic changes
commit
|
commitdiff
|
tree
2012-10-31
Flor
e
n
t
Angly
Avoid
n
e
w
()
j
u
s
t to
revcom(
)
a sequence
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
en
t
Angly
Su
b
se
q
() optimisation
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
ent Angly
T
e
st
i
n
g subseq() more
thoroughly
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
More te
s
ts
for
v
alidate_seq()
commit
|
commitdiff
|
tree
2012-10-31
F
lor
e
nt
A
ngly
T
esti
n
g val
i
date_seq(
)
and -ref_to_seq
commit
|
commitdiff
|
tree
2012-10-31
Flor
e
n
t
Angly
Constru
c
tor
-
r
e
f_to_seq
f
i
x
commit
|
commitdiff
|
tree
2012-10-31
Floren
t
Angly
Sm
a
ll cha
n
ges in seq() for
c
larity
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
ent Angly
Small
fix in val
i
dation
e
r
ror message
commit
|
commitdiff
|
tree
2012-10-31
Flor
e
n
t
Angly
Prim
a
rySeq::seq
(
) modulariza
t
i
o
n
commit
|
commitdiff
|
tree
2012-10-31
F
loren
t
Angly
Remov
e
d un
n
eede
d
method
commit
|
commitdiff
|
tree
2012-10-31
F
lore
n
t Angly
P
O
D update a
n
d mor
e
con
s
itent variable name
s
commit
|
commitdiff
|
tree
2012-10-30
Fl
o
rent A
n
gly
PrimarySeq direct mode fix/improvement
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Sm
a
ll POD and tests updates
commit
|
commitdiff
|
tree
2012-10-30
Flor
e
n
t
Angly
Doc f
i
xes
commit
|
commitdiff
|
tree
2012-10-30
F
lorent Angly
More
test
s
for Pri
m
a
r
ySeq
commit
|
commitdiff
|
tree
2012-10-30
Florent Ang
l
y
F
ixes
issue in EncodedSe
q
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Cosmetic changes
commit
|
commitdiff
|
tree
2012-10-30
F
lorent An
g
ly
Consiste
n
t
indentatio
n
commit
|
commitdiff
|
tree
2012-10-30
F
l
orent Angly
Se
q
FastaSpeedF
a
c
t
ory
f
i
x
commit
|
commitdiff
|
tree
2012-10-30
Florent Ang
l
y
C
o
nsisten
t
ind
e
ntatio
n
commit
|
commitdiff
|
tree
2012-10-30
Florent A
n
gly
Bio::Prim
a
rySeq::length() optimiz
a
tions
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
More tes
t
s for
B
io::PrimarySeq::length()
commit
|
commitdiff
|
tree
2012-10-30
Flor
e
nt Angly
P
O
D
u
pdated an
d
b
eautific
a
ti
o
n
commit
|
commitdiff
|
tree
2012-10-30
Florent Angl
y
M
o
r
e
t
e
sts for Bi
o
::PrimarySeq::length
(
)
commit
|
commitdiff
|
tree
2012-10-30
Flore
n
t
A
ng
l
y
Add
e
d
t
ests for Bio::PrimarySeq::length()
commit
|
commitdiff
|
tree
2012-10-29
Flo
r
ent Angly
Fix fo
r
b
u
g #3389
commit
|
commitdiff
|
tree
2012-10-29
Floren
t
Angly
PrimarySeq::length() s
p
eedup
commit
|
commitdiff
|
tree
2012-10-10
Flo
r
e
n
t Angly
B
e
tter 0-length sequence su
p
port for
B
io::DB::Qual
.
.
.
commit
|
commitdiff
|
tree
2012-10-10
Florent Angly
Better support for 0-
l
ength
sequen
c
es
commit
|
commitdiff
|
tree
2012-09-24
Florent Angly
Merge b
r
anch 'mast
e
r' of github
.
com:bioper
l
/
biope
r
l
.
.
.
commit
|
commitdiff
|
tree
2012-09-24
Fl
o
rent Angly
Fixed an unte
s
ted
r
eg
r
e
ssi
o
n i
n
Bio::DB::Fasta
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Regexp
to match R
N
A on request onl
y
commit
|
commitdiff
|
tree
2012-09-10
Flore
n
t Ang
l
y
F
i
xed inde
n
tati
o
n
commit
|
commitdiff
|
tree
2012-09-10
Florent An
g
ly
Rev
e
rsed probl
e
mat
i
c
c
ommit 83
3
4d1
7
5f
f
ba0
9
5a94470
3
8d421cac0d
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Merge br
a
nch 'amp
l
icons'
commit
|
commitdiff
|
tree
2012-09-10
Flor
e
nt Ang
l
y
Merge br
a
nch 'master
'
o
f
g
ith
u
b
.
com:bioperl/bioper
l
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent
Angly
Re
m
oved some comments
commit
|
commitdiff
|
tree
2012-09-10
F
l
orent An
g
ly
Compou
n
d ID can now inc
l
ud the strand
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Bi
o
::DB::IndexedBas
e
co
m
pliance with
Bio
:
:DB:Se
q
I and
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Flore
n
t
Angly
Fixed
t
ypo
commit
|
commitdiff
|
tree
2012-09-10
F
loren
t
Angly
F
ixed
sil
l
y e
r
ror
commit
|
commitdiff
|
tree
2012-09-10
Fl
o
ren
t
Angly
Updated Bi
o
::DB::SeqI POD accordi
n
g
t
o info in Bio
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Floren
t
Angl
y
Update
d
Changes fi
l
e
commit
|
commitdiff
|
tree
2012-09-10
Flo
r
ent Angly
Exp
l
i
cit variable
name instead of Bio/DB/Qual
.
pm
commit
|
commitdiff
|
tree
2012-09-10
F
l
orent
A
ngly
Hand
l
e
RN
A
and IUPAC charac
t
er
s
i
n
Bio::DB::Fasta
commit
|
commitdiff
|
tree
2012-09-10
F
lo
r
ent
A
ngly
Updated Ch
a
nges file
commit
|
commitdiff
|
tree
2012-09-10
Florent Ang
l
y
B
etter al
p
hab
e
t
detection met
h
od that honors
IUPA
C
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Fasta
a
nd Qual o
n
ly
u
se the Indexe
d
Base ba
s
e
commit
|
commitdiff
|
tree
2012-09-10
F
lor
e
nt Angly
P
O
D update
commit
|
commitdiff
|
tree
2012-09-09
Florent
A
ngly
POD u
p
d
a
te
commit
|
commitdiff
|
tree
2012-09-09
Floren
t
Angly
F
i
x
ed
b
ug in
t
rodu
c
ed i
n
recen
t
commit
commit
|
commitdiff
|
tree
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