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remove multi-declaration warning
2013-09-02
Flore
n
t
Angly
Use 'exists',
n
ot 'defined',
to check for existence
.
.
.
commit
|
commitdiff
|
tree
2013-09-02
Floren
t
Angly
Test fixes for Bio::Asse
m
b
ly::Tools::ContigSpectrum
commit
|
commitdiff
|
tree
2013-09-02
F
l
o
r
en
t
A
n
gly
Fixed
some "undefined value" w
a
rnings when taxonomy
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
F
l
orent Angly
Fix
e
d
bug whe
r
e not all nodes i
n
lineage
were merged
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
More t
e
sts
commit
|
commitdiff
|
tree
2013-07-12
Floren
t
Ang
l
y
Better distinguish a
m
bigu
o
u
s
taxon names
commit
|
commitdiff
|
tree
2013-07-12
Flo
r
ent Angly
F
ixed issue
w
here ambi
g
uous taxa names go
t
th
e
s
ame
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Fl
o
rent Angly
Fixed bug whe
r
e
t
axon ra
n
k was missing
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
More Bio::
D
B::Taxonom
y
::
l
ist tests
commit
|
commitdiff
|
tree
2013-07-12
Flor
e
nt
Angly
Bool
e
an return status fo
r
merge_
l
ineage()
commit
|
commitdiff
|
tree
2013-07-12
F
l
orent
An
g
ly
Fixed nu
m
ber of te
s
ts in t/
C
lus
t
erIO/Sequence
F
amily
.
t
commit
|
commitdiff
|
tree
2013-07-12
Florent
An
g
ly
Fix
e
d
use of
u
nin
i
tializ
e
d value $reporttype
commit
|
commitdiff
|
tree
2013-07-12
Flo
r
ent Ang
l
y
F
i
xed redef
i
n
e
d va
r
iable
commit
|
commitdiff
|
tree
2013-07-12
Fl
o
rent
A
ngly
Small POD and
a
nd
error message change
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
A
d
d
i
ng arbitra
r
y branch
length in Bio::DB::Taxonomy
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Florent
Angly
Use
a
d
e
f
ault format fo
r
as_string
commit
|
commitdiff
|
tree
2013-07-12
Flor
e
nt Angly
T
est uses speci
e
s, not in
t
ermediary no
d
e
commit
|
commitdiff
|
tree
2013-07-12
Floren
t
A
n
gly
Avoid use of
a
n undefined
va
l
ue as
a
n
ARRAY reference
commit
|
commitdiff
|
tree
2013-07-12
Florent An
g
ly
Us
e
l
ist
con
t
e
x
t
instead of sca
l
ar
c
onte
x
t to include
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Flo
r
ent Angl
y
Fixed POD
i
ndenta
t
ion
commit
|
commitdiff
|
tree
2013-07-12
F
lorent Angly
Te
s
ts for Bio:
:
Taxonomy::get_tree
commit
|
commitdiff
|
tree
2013-07-11
Florent An
g
ly
Mor
e
thoroug
h
ly documented option
s
and defaults
commit
|
commitdiff
|
tree
2013-07-11
Florent
Angly
Restoring int
e
nded behaviour
.
.
.
I think
commit
|
commitdiff
|
tree
2013-07-11
Florent Angly
Fixed failing DBD te
s
t
commit
|
commitdiff
|
tree
2013-02-03
Florent
A
ngly
F
i
xed POD encodi
n
g issue
commit
|
commitdiff
|
tree
2012-11-18
Florent An
g
ly
Merge bra
n
ch
'
ma
s
t
e
r
'
of
g
ithub
.
com:biop
e
rl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2012-11-17
Flor
e
nt Angl
y
Merge branch 'master' into bug
_
3390
commit
|
commitdiff
|
tree
2012-11-17
Fl
o
rent Angly
Tigh
t
ened and
o
ptim
i
zed
quality s
t
ring validation
commit
|
commitdiff
|
tree
2012-11-17
Florent Ang
l
y
U
p
d
a
t
ed planned number
o
f tests
commit
|
commitdiff
|
tree
2012-11-17
Florent
Angly
'our
'
is pr
e
f
e
rred over 'use
v
ars'
commit
|
commitdiff
|
tree
2012-11-17
Flor
e
nt Ang
l
y
Test updates (PrimaryQual mostly)
commit
|
commitdiff
|
tree
2012-11-17
Flo
r
e
n
t Angly
PrimarySeq validation speedup
commit
|
commitdiff
|
tree
2012-11-16
Florent An
g
l
y
Instead of closures,
s
imply store
attributes in $selft
commit
|
commitdiff
|
tree
2012-11-15
Florent Angl
y
M
e
rge b
r
an
c
h 'seqlength
'
commit
|
commitdiff
|
tree
2012-11-09
F
l
orent Angly
Updated number of te
s
ts
commit
|
commitdiff
|
tree
2012-11-06
F
l
orent A
n
g
ly
Prim
a
ryQual validation syn
c
hronized with that of Prim
a
rySeq
commit
|
commitdiff
|
tree
2012-11-06
Flore
n
t Angly
Same revc
o
m
(
) a
n
d length() approach i
n
Bio::
D
B
:
:Qual
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Florent
A
ngly
New
lengt
h
(
)
method neeed
t
o consi
d
er s
t
rande
d
ne
s
s
commit
|
commitdiff
|
tree
2012-11-06
Florent Angly
Als
o
rever
t
to o
l
d re
v
com() + tes
t
+ do
c
commit
|
commitdiff
|
tree
2012-11-06
Floren
t
Angl
y
Reverted
t
o previous beh
a
viour, i
.
e
.
o
v
erride
P
r
i
mar
y
SeqI
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Flor
e
nt Angly
Merge
b
r
anch 'master
'
o
f
gith
u
b
.
com:bio
p
erl/biope
r
l
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Florent
Angly
Bio::
D
B::length improvement
commit
|
commitdiff
|
tree
2012-11-06
Florent A
n
gl
y
Bio::PrimaryQual POD
u
pdate
commit
|
commitdiff
|
tree
2012-11-06
Florent Angly
More Bio::DB
:
:Qu
a
l
tests
commit
|
commitdiff
|
tree
2012-11-06
Flor
e
nt Angly
Let PrimarySeqI handle
revcom() and trunc()
commit
|
commitdiff
|
tree
2012-11-06
Florent An
g
ly
Test Bio::Pr
i
m
aryS
e
q::Fasta compli
a
nce with Bio
:
:Pri
m
arySeqI
commit
|
commitdiff
|
tree
2012-11-05
Florent Angly
More
t
ests
commit
|
commitdiff
|
tree
2012-11-05
Florent Angly
A
d
d
ed
a
test
commit
|
commitdiff
|
tree
2012-11-05
Florent
A
ng
l
y
C
o
smet
i
c ch
a
ngeS
commit
|
commitdiff
|
tree
2012-11-05
Flor
e
nt An
g
ly
R
edundan
t
mes
s
ages
commit
|
commitdiff
|
tree
2012-11-05
Flo
r
ent A
n
gly
va
l
idate_seq(
)
ta
k
e
s
a
st
r
ing as a
r
g
ument
commit
|
commitdiff
|
tree
2012-11-05
Florent Angly
undef sequ
e
nce strings are
valid sequences
commit
|
commitdiff
|
tree
2012-11-05
Florent
A
ng
l
y
Small fix
commit
|
commitdiff
|
tree
2012-11-05
Flo
r
ent Angly
Red
u
ndant sequence validatio
n
commit
|
commitdiff
|
tree
2012-11-05
Flo
r
e
n
t Angly
Cosmet
i
c changes, inde
n
tatio
n
, e
t
c
commit
|
commitdiff
|
tree
2012-11-05
Florent
A
ng
l
y
Avoid w
a
r
n
ing m
e
ssage
d
uring tes
t
ing
commit
|
commitdiff
|
tree
2012-11-01
Flo
r
e
nt Angly
Hardening test
commit
|
commitdiff
|
tree
2012-11-01
F
l
oren
t
Angly
Fix for
r
egression bug #3
3
9
0
commit
|
commitdiff
|
tree
2012-11-01
Florent An
g
ly
Upd
a
ted tests
fo
r
Bio::DB::Fasta
commit
|
commitdiff
|
tree
2012-10-31
Floren
t
Angly
Added test for bug 3390
commit
|
commitdiff
|
tree
2012-10-31
Flore
n
t Angly
Added tests
t
ha
t
u
s
e the file
(
) met
h
od
commit
|
commitdiff
|
tree
2012-10-31
Floren
t
Angly
C
hange
s
file upda
t
e
commit
|
commitdiff
|
tree
2012-10-31
Floren
t
A
ngl
y
Chan
g
e
s
updat
e
commit
|
commitdiff
|
tree
2012-10-31
F
l
or
e
nt Angly
-
d
ire
c
t valid only o
n
ce
commit
|
commitdiff
|
tree
2012-10-31
Florent Angl
y
subs
e
q() sp
e
edup
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
M
o
re length() te
s
ts and some
POD u
p
date
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Remove
d
some
code
redundancy
commit
|
commitdiff
|
tree
2012-10-31
Florent A
n
gly
Bio::PrimaryS
e
qI speedup
commit
|
commitdiff
|
tree
2012-10-31
Florent Ang
l
y
Cosm
e
t
ic changeS
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
en
t
Angly
C
osmeti
c
changes
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Av
o
id new() just to revcom() a s
e
quence
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
ent
Angly
Subseq(
)
optimisation
commit
|
commitdiff
|
tree
2012-10-31
Florent Ang
l
y
Testi
n
g subs
e
q() m
o
re thoroughly
commit
|
commitdiff
|
tree
2012-10-31
Fl
o
re
n
t Angly
More t
e
s
ts for validat
e
_seq()
commit
|
commitdiff
|
tree
2012-10-31
F
lo
r
en
t
Angly
Test
i
n
g
vali
d
ate_seq() and -ref_to_seq
commit
|
commitdiff
|
tree
2012-10-31
Flore
n
t Angl
y
C
onst
r
uctor -r
e
f_to
_
s
eq fix
commit
|
commitdiff
|
tree
2012-10-31
Fl
o
r
ent Angly
Small cha
n
ges in s
e
q() for clarity
commit
|
commitdiff
|
tree
2012-10-31
Fl
o
rent
A
ngly
Small fix i
n
va
l
idation
error message
commit
|
commitdiff
|
tree
2012-10-31
Florent Angl
y
PrimarySeq::se
q
()
modularization
commit
|
commitdiff
|
tree
2012-10-31
F
l
orent Angly
R
e
moved u
n
needed me
t
hod
commit
|
commitdiff
|
tree
2012-10-31
Florent A
n
gly
POD upd
a
te and more consitent variable
n
ames
commit
|
commitdiff
|
tree
2012-10-30
Florent
Angly
PrimarySeq direct
mode fi
x
/improvement
commit
|
commitdiff
|
tree
2012-10-30
Flor
e
n
t Angly
Small P
O
D
a
nd tests updates
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Doc fixes
commit
|
commitdiff
|
tree
2012-10-30
Florent An
g
ly
Mo
r
e tests for
Pr
i
marySeq
commit
|
commitdiff
|
tree
2012-10-30
Fl
o
rent Angly
Fixes issue
in
E
ncod
e
dSeq
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Cosmetic chang
e
s
commit
|
commitdiff
|
tree
2012-10-30
F
l
o
rent Angly
Consi
s
tent
indentation
commit
|
commitdiff
|
tree
2012-10-30
Florent Angl
y
SeqFastaS
p
e
edFactor
y
fi
x
commit
|
commitdiff
|
tree
2012-10-30
Fl
o
rent Angly
Consiste
n
t ind
e
ntati
o
n
commit
|
commitdiff
|
tree
2012-10-30
F
lorent Angly
Bio::PrimarySeq::length() optimizations
commit
|
commitdiff
|
tree
2012-10-30
Floren
t
Angly
More tests f
o
r Bio::PrimarySeq::length()
commit
|
commitdiff
|
tree
2012-10-30
Florent An
g
ly
P
O
D updated and beautif
i
cation
commit
|
commitdiff
|
tree
2012-10-30
Flor
e
n
t
Angly
More tests for Bio::PrimarySeq
:
:
l
en
g
th()
commit
|
commitdiff
|
tree
2012-10-30
Florent
Angly
Ad
d
ed te
s
ts for
B
io::Prim
a
r
ySeq:
:
le
n
g
t
h()
commit
|
commitdiff
|
tree
2012-10-29
F
l
o
rent Angly
Fix fo
r
bug
#3389
commit
|
commitdiff
|
tree
2012-10-29
Flore
n
t An
g
ly
P
r
i
marySeq::len
g
th() spee
d
up
commit
|
commitdiff
|
tree
2012-10-10
Fl
o
r
e
nt Angly
Better 0-length sequence
s
upport
f
o
r
Bio::DB::Qual
.
.
.
commit
|
commitdiff
|
tree
2012-10-10
Floren
t
Angly
Bet
t
er
s
upport for 0-length sequences
commit
|
commitdiff
|
tree
2012-09-24
Florent An
g
ly
M
erge branch 'mast
e
r' of gith
u
b
.
com
:
biop
e
rl/
b
ioperl
.
.
.
commit
|
commitdiff
|
tree
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