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More tests
2012-11-05
Florent Angly
More
t
e
s
t
s
commit
|
commitdiff
|
tree
2012-11-05
Florent Angly
Added
a
test
commit
|
commitdiff
|
tree
2012-11-05
Fl
o
r
ent Angly
Cosmetic changeS
commit
|
commitdiff
|
tree
2012-11-05
Florent A
n
gly
R
e
dunda
n
t m
e
ssages
commit
|
commitdiff
|
tree
2012-11-05
F
lorent Angly
validate_seq() t
a
kes a string
a
s argum
e
nt
commit
|
commitdiff
|
tree
2012-11-05
Florent Angly
u
ndef seque
n
c
e
strings are vali
d
sequ
e
nces
commit
|
commitdiff
|
tree
2012-11-05
Flore
n
t Angly
Sm
a
ll
fix
commit
|
commitdiff
|
tree
2012-11-05
Florent
A
ngly
R
e
dundant se
q
uence vali
d
ation
commit
|
commitdiff
|
tree
2012-11-05
Flor
e
n
t
A
ngly
Cosmetic
c
ha
n
ges, indentation, e
t
c
commit
|
commitdiff
|
tree
2012-11-05
Flore
n
t
Angly
Avoid wa
r
nin
g
me
s
sage dur
i
ng t
e
stin
g
commit
|
commitdiff
|
tree
2012-10-31
Florent
Angly
C
h
anges f
i
l
e update
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
e
n
t A
n
g
ly
Changes upda
t
e
commit
|
commitdiff
|
tree
2012-10-31
Flore
n
t Angly
-dir
e
ct valid only
o
n
ce
commit
|
commitdiff
|
tree
2012-10-31
Fl
o
rent Angly
subseq() spee
d
up
commit
|
commitdiff
|
tree
2012-10-31
Florent A
n
gly
More length() tests and some POD up
d
ate
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Removed some code r
e
dunda
n
c
y
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
B
i
o::PrimarySeqI
spe
e
dup
commit
|
commitdiff
|
tree
2012-10-31
F
lorent Angly
Cosm
e
tic changeS
commit
|
commitdiff
|
tree
2012-10-31
Florent
Angly
Cos
m
eti
c
changes
commit
|
commitdiff
|
tree
2012-10-31
F
lore
n
t
Angly
Avoid ne
w
() just to rev
c
om
(
)
a s
e
quence
commit
|
commitdiff
|
tree
2012-10-31
Florent A
n
gly
Subs
e
q(
)
optimisation
commit
|
commitdiff
|
tree
2012-10-31
Flore
n
t Angl
y
Testin
g
subseq
(
) mo
r
e th
o
r
oughly
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
More tests for validate_seq()
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
ent Ang
l
y
T
e
st
i
ng
validate_seq() and -ref_to_s
e
q
commit
|
commitdiff
|
tree
2012-10-31
Florent
A
n
gly
Cons
t
ructor -ref_
t
o
_seq fix
commit
|
commitdiff
|
tree
2012-10-31
Florent
Angly
S
ma
l
l changes in
seq()
for clari
t
y
commit
|
commitdiff
|
tree
2012-10-31
F
lorent A
n
g
l
y
Small
f
ix in val
i
d
a
ti
o
n
e
rro
r
messa
g
e
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
e
n
t
A
ngly
PrimaryS
e
q
:
:seq() modularization
commit
|
commitdiff
|
tree
2012-10-31
F
l
orent Ang
l
y
Remov
e
d unneeded method
commit
|
commitdiff
|
tree
2012-10-31
F
l
orent Angly
POD upda
t
e a
n
d
mo
r
e consite
n
t
variable names
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Primary
S
eq direct mode fix/
i
mprovement
commit
|
commitdiff
|
tree
2012-10-30
Florent
A
n
gly
Sm
a
ll POD and tests updates
commit
|
commitdiff
|
tree
2012-10-30
Flo
r
ent A
n
gly
Doc fixes
commit
|
commitdiff
|
tree
2012-10-30
F
lorent Angly
More te
s
ts for
Pr
i
marySeq
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
F
i
xes issue in EncodedSe
q
commit
|
commitdiff
|
tree
2012-10-30
Florent An
g
ly
Cosme
t
ic
c
hanges
commit
|
commitdiff
|
tree
2012-10-30
F
l
oren
t
An
g
l
y
Co
n
s
i
stent indentat
i
o
n
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
SeqFastaSpeedFactory fix
commit
|
commitdiff
|
tree
2012-10-30
Fl
o
rent Angly
Consistent indentation
commit
|
commitdiff
|
tree
2012-10-30
Florent
A
ngly
Bio
:
:
P
rima
r
y
S
eq::le
n
gt
h
() opt
i
m
iz
a
tio
n
s
commit
|
commitdiff
|
tree
2012-10-30
F
l
orent A
n
gly
More te
s
ts
f
o
r Bi
o
::Primar
y
Seq::length()
commit
|
commitdiff
|
tree
2012-10-30
Flor
e
nt A
n
gly
P
O
D u
p
dated
a
nd beautif
i
cation
commit
|
commitdiff
|
tree
2012-10-30
F
l
orent A
n
gly
More
tests
for Bio::Primary
S
eq:
:
l
e
ngth()
commit
|
commitdiff
|
tree
2012-10-30
F
l
or
e
nt Angly
Added tests for Bio::Pri
m
arySeq:
:
length()
commit
|
commitdiff
|
tree
2012-10-10
F
lorent
Angly
Better 0-len
g
th seq
u
enc
e
support for Bio::DB::Qua
l
.
.
.
commit
|
commitdiff
|
tree
2012-10-10
Floren
t
Angly
Better sup
p
o
r
t for 0-len
g
th sequences
commit
|
commitdiff
|
tree
2012-09-24
Florent
Angly
Merge branch
'master' of github
.
com:
b
ioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2012-09-24
Flore
n
t Angly
Fi
x
ed an unt
e
sted regressi
o
n in Bio
:
:DB::Fasta
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Regex
p
to
m
atch R
N
A on request only
commit
|
commitdiff
|
tree
2012-09-10
Florent
A
ngly
Fixed indentation
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Reverse
d
problematic
commit 8334d
1
75ffba095a
9
447038d42
1
cac0d
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent Ang
l
y
M
e
rge branch 'amp
l
icons'
commit
|
commitdiff
|
tree
2012-09-10
Flor
e
nt Angly
M
e
rge branch 'maste
r
' of g
i
thub
.
co
m
:bioperl
/
b
i
operl
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Flor
e
nt Angly
R
e
moved
some
comments
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Com
p
ound
ID
can now
i
n
clud the strand
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
B
io
:
:DB::Indexed
B
ase c
o
mpliance wit
h
Bio::DB:Seq
I
and
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Floren
t
Angly
Fixed typo
commit
|
commitdiff
|
tree
2012-09-10
Florent
Angly
Fixed sill
y
error
commit
|
commitdiff
|
tree
2012-09-10
Flo
r
ent Angl
y
Updated Bio::DB::SeqI POD accordin
g
to info in
Bio
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Flor
e
nt
A
ngly
Updated Chang
e
s f
i
le
commit
|
commitdiff
|
tree
2012-09-10
Floren
t
A
ngly
Expl
i
ci
t
var
i
able name instead of Bio/DB/Qual
.
p
m
commit
|
commitdiff
|
tree
2012-09-10
Florent An
g
ly
Handle R
N
A and IUPAC c
h
aracters in
B
io:
:
DB::
F
asta
commit
|
commitdiff
|
tree
2012-09-10
Fl
o
ren
t
A
n
gly
Updated C
h
ange
s
fil
e
commit
|
commitdiff
|
tree
2012-09-10
Flore
n
t Angly
Better a
l
ph
a
b
et
d
etection
method that honors IUP
A
C
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
F
l
o
rent Angly
Fasta and
Q
u
al only use the Indexed
B
ase base
commit
|
commitdiff
|
tree
2012-09-10
F
l
orent An
g
ly
POD
u
p
d
ate
commit
|
commitdiff
|
tree
2012-09-09
Florent
A
ngly
POD
update
commit
|
commitdiff
|
tree
2012-09-09
Flor
e
n
t
Angly
F
ix
e
d bug intr
o
duce
d
i
n recent commit
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
mak
e
i
d log
i
c in
IndexedBase
commit
|
commitdiff
|
tree
2012-09-09
F
lorent Angly
Added erro
r
checks
o
n Fa
s
ta into Qual
commit
|
commitdiff
|
tree
2012-09-09
Flore
n
t Angly
Small si
m
plificatiosn
commit
|
commitdiff
|
tree
2012-09-09
Florent
A
ngly
Test -makeid
option
commit
|
commitdiff
|
tree
2012-09-09
Flo
r
ent A
n
gly
More streamlining
commit
|
commitdiff
|
tree
2012-09-09
Florent Angl
y
Suppo
r
t
f
o
r specif
y
ing sequence strand
commit
|
commitdiff
|
tree
2012-09-09
F
lorent
A
ngly
Using the _parse_compound_id() method
commit
|
commitdiff
|
tree
2012-09-09
F
lorent A
n
gly
Removed a test because me
t
hod le
n
g
th() does not take
.
.
.
commit
|
commitdiff
|
tree
2012-09-09
Florent Ang
l
y
Storing num
b
e
r
of residues in index fi
l
e
commit
|
commitdiff
|
tree
2012-09-09
Flo
r
ent Ang
l
y
Fix to avoid a
w
a
rni
n
g
commit
|
commitdiff
|
tree
2012-09-09
F
l
ore
n
t Angly
Variable name changes
commit
|
commitdiff
|
tree
2012-09-09
Flor
e
n
t
A
ngl
y
Sm
a
ll c
h
anges
commit
|
commitdiff
|
tree
2012-09-09
Florent
Angly
Renamed function more approp
r
iately
commit
|
commitdiff
|
tree
2012-09-09
Florent
A
n
g
ly
Mor
e
m
e
thod
s
in IndexedBase
commit
|
commitdiff
|
tree
2012-09-09
Flor
e
nt
A
ngly
Misleading var
i
ab
l
e
name
commit
|
commitdiff
|
tree
2012-09-09
F
lore
n
t Angly
Cos
m
et
i
c
changes
commit
|
commitdiff
|
tree
2012-09-09
Florent
A
ng
l
y
Sma
l
l
c
ha
n
ges
commit
|
commitdiff
|
tree
2012-09-09
Fl
o
rent A
n
gly
Fixed a c
o
uple of typ
o
s and worked on
c
onsistent in
d
en
t
aion
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Sub to
p
ar
s
e compound IDs
commit
|
commitdiff
|
tree
2012-09-08
Fl
o
ren
t
A
n
gly
Fixe
d
bug affectin
g
B
i
o::
D
B:
:
SeqFeature
commit
|
commitdiff
|
tree
2012-09-08
Florent Angly
Fixing some failing
tests
commit
|
commitdiff
|
tree
2012-09-08
Florent
A
ngly
Renamed tes
t
files
for
c
onsi
s
tency
commit
|
commitdiff
|
tree
2012-09-08
Floren
t
A
n
gly
PO
D
reorgani
z
at
i
on
commit
|
commitdiff
|
tree
2012-09-08
Florent Angly
Fixe
d
test
commit
|
commitdiff
|
tree
2012-09-08
Flo
r
ent A
n
gly
POD u
p
date
commit
|
commitdiff
|
tree
2012-09-08
Fl
o
rent Angly
Te
s
t he
a
der()
commit
|
commitdiff
|
tree
2012-09-08
Florent Angly
fh(
)
moved to _
f
h() in IndexedBase
commit
|
commitdiff
|
tree
2012-09-08
Floren
t
Angly
POD update
commit
|
commitdiff
|
tree
2012-09-08
F
lor
e
nt Angly
POD update
commit
|
commitdiff
|
tree
2012-09-08
Florent An
g
ly
POD update
commit
|
commitdiff
|
tree
2012-09-08
F
lorent Angly
Imp
r
oved
te
s
ts
commit
|
commitdiff
|
tree
2012-09-07
Florent Angly
PO
D
u
p
date
commit
|
commitdiff
|
tree
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