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Small POD and and error message change
2013-07-12
Fl
o
rent Angly
Small
P
O
D
and and e
r
ror
m
essage
c
hang
e
commit
|
commitdiff
|
tree
2013-07-12
F
l
o
rent Angly
Add
i
ng ar
b
i
t
rary
b
ranch length in Bio::D
B
::Ta
x
onomy
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Florent An
g
l
y
Us
e
a default format
f
o
r as_string
commit
|
commitdiff
|
tree
2013-07-12
Flor
e
nt Angly
Te
s
t u
s
es species,
n
ot int
e
rmediary nod
e
commit
|
commitdiff
|
tree
2013-07-12
Florent
Angly
Avoid use
of an un
d
e
fined valu
e
as a
n
ARRAY refe
r
enc
e
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
U
s
e list cont
e
xt
instead of scalar context to incl
u
de
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
Fixe
d
P
O
D inde
n
tat
i
on
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
Tests for B
i
o::Taxonomy::get_tree
commit
|
commitdiff
|
tree
2013-07-11
Florent
An
g
ly
M
ore thoro
u
ghly docu
m
en
t
e
d optio
n
s
and defaults
commit
|
commitdiff
|
tree
2013-07-11
Florent
Angly
Rest
o
ring i
n
tended be
h
aviour
.
.
.
I t
h
ink
commit
|
commitdiff
|
tree
2013-07-11
Florent Angly
Fixed
failing DBD test
commit
|
commitdiff
|
tree
2013-02-03
Florent An
g
l
y
Fixed
P
O
D encoding issue
commit
|
commitdiff
|
tree
2012-11-18
Florent Ang
l
y
Me
r
ge b
r
anch 'mast
e
r' of gi
t
h
ub
.
com:b
i
operl/biop
e
rl
.
.
.
commit
|
commitdiff
|
tree
2012-11-17
Florent Angly
Merge branc
h
'mast
e
r
' into bug_3390
commit
|
commitdiff
|
tree
2012-11-17
Flore
n
t Angly
Ti
g
htened and optimiz
e
d
q
ual
i
ty string va
l
idat
i
on
commit
|
commitdiff
|
tree
2012-11-17
Flore
n
t An
g
ly
Updated plann
e
d numbe
r
of
t
ests
commit
|
commitdiff
|
tree
2012-11-17
F
l
orent
Angly
'our' is preferred over 'u
s
e vars'
commit
|
commitdiff
|
tree
2012-11-17
Floren
t
Angly
Test updat
e
s (Pri
m
aryQual m
o
stly)
commit
|
commitdiff
|
tree
2012-11-17
Flor
e
n
t
Angly
PrimarySeq validation speedup
commit
|
commitdiff
|
tree
2012-11-16
Florent Angly
Inst
e
ad of c
l
o
s
ur
e
s,
s
i
mply sto
r
e a
t
t
rib
u
tes in $selft
commit
|
commitdiff
|
tree
2012-11-15
Fl
o
rent Angly
Me
r
ge branch
'
seqlength'
commit
|
commitdiff
|
tree
2012-11-09
Flor
e
nt
A
n
gly
Updated number of te
s
t
s
commit
|
commitdiff
|
tree
2012-11-06
Florent An
g
ly
Primar
y
Q
u
al v
a
lidati
o
n synchronized with that of PrimarySeq
commit
|
commitdiff
|
tree
2012-11-06
Florent Angly
Same revcom()
a
n
d length
(
) appr
o
ach
in Bio::DB:
:
Q
u
a
l
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Flor
e
nt Angly
New
l
e
n
gth
(
)
metho
d
neeed t
o
consider
strandedness
commit
|
commitdiff
|
tree
2012-11-06
Florent Ang
l
y
A
l
so r
e
vert to old revco
m
() +
t
est
+
doc
commit
|
commitdiff
|
tree
2012-11-06
Flo
r
ent A
n
g
ly
Reverte
d
to previous
be
h
aviour, i
.
e
.
o
verri
d
e PrimarySeq
I
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Flo
r
e
n
t
A
ngly
Mer
g
e br
a
nch 'master' of github
.
com:bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Fl
o
ren
t
Angl
y
B
io::DB::length
improvement
commit
|
commitdiff
|
tree
2012-11-06
Flor
e
nt
A
ngly
Bio::Prim
a
ryQua
l
POD updat
e
commit
|
commitdiff
|
tree
2012-11-06
Flore
n
t
A
ngly
More Bio::D
B
::Q
u
al tests
commit
|
commitdiff
|
tree
2012-11-06
Fl
o
re
n
t Angly
Let PrimarySe
q
I handle revc
o
m() a
n
d
t
run
c
()
commit
|
commitdiff
|
tree
2012-11-06
Florent Angly
Test Bio::Pr
i
mary
S
eq::F
a
sta
c
ompliance with Bio::PrimarySeqI
commit
|
commitdiff
|
tree
2012-11-05
Florent
A
n
gly
M
ore tests
commit
|
commitdiff
|
tree
2012-11-05
Florent Angly
Added
a test
commit
|
commitdiff
|
tree
2012-11-05
Florent
Angly
Cosmetic
c
ha
n
geS
commit
|
commitdiff
|
tree
2012-11-05
F
l
orent
An
g
ly
R
edundant messa
g
es
commit
|
commitdiff
|
tree
2012-11-05
Florent Angl
y
valid
a
te
_
seq() ta
k
es a
s
tring as argument
commit
|
commitdiff
|
tree
2012-11-05
F
l
orent Angly
u
ndef sequence string
s
are valid sequences
commit
|
commitdiff
|
tree
2012-11-05
Flo
r
ent Angly
Sm
a
l
l fix
commit
|
commitdiff
|
tree
2012-11-05
Florent A
n
g
ly
Redundant
sequence
v
alidat
i
on
commit
|
commitdiff
|
tree
2012-11-05
F
lore
n
t A
n
g
ly
C
osmetic chan
g
es, indentati
o
n, et
c
commit
|
commitdiff
|
tree
2012-11-05
Flore
n
t
Angly
Avoi
d
warning mes
s
ag
e
d
urin
g
t
esting
commit
|
commitdiff
|
tree
2012-11-01
F
l
o
rent Angly
Hardening t
e
st
commit
|
commitdiff
|
tree
2012-11-01
Flore
n
t An
g
ly
F
ix f
o
r reg
r
ession bug
#
3390
commit
|
commitdiff
|
tree
2012-11-01
Flo
r
ent
A
ngly
Updated t
e
sts for Bio::DB::Fasta
commit
|
commitdiff
|
tree
2012-10-31
Flor
e
nt Angly
A
d
ded test for bug
3
3
9
0
commit
|
commitdiff
|
tree
2012-10-31
Floren
t
An
g
ly
Added tests that
use the file()
m
eth
o
d
commit
|
commitdiff
|
tree
2012-10-31
F
l
ore
n
t Angly
Change
s
file upda
t
e
commit
|
commitdiff
|
tree
2012-10-31
F
l
orent Angly
C
hanges upd
a
t
e
commit
|
commitdiff
|
tree
2012-10-31
Florent
Angly
-direct v
a
lid only o
n
ce
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
subseq() speedup
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
ent A
n
gly
More
length()
tests and
s
o
m
e P
O
D update
commit
|
commitdiff
|
tree
2012-10-31
F
lorent Angly
Removed some code redundancy
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Bio::PrimarySeq
I
spee
d
up
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Cosm
e
t
i
c cha
n
geS
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Cosmetic
changes
commit
|
commitdiff
|
tree
2012-10-31
F
l
orent A
n
gl
y
A
v
o
id ne
w
()
ju
s
t to revcom(
)
a sequence
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Subseq() optimisatio
n
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Testing subseq(
)
more thoroughly
commit
|
commitdiff
|
tree
2012-10-31
Florent A
n
gl
y
M
or
e
t
ests for validate_seq()
commit
|
commitdiff
|
tree
2012-10-31
Florent Angl
y
Testing
v
alidate_s
e
q() and -ref_to
_
s
eq
commit
|
commitdiff
|
tree
2012-10-31
F
l
orent
A
n
g
l
y
Cons
t
ru
c
t
o
r -ref_to_seq fix
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Small changes in seq() fo
r
c
l
arity
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Small fix
in valid
a
t
i
on error messag
e
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Prim
a
r
y
S
eq::seq() modula
r
ization
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Removed un
n
eeded method
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
POD update and more con
s
itent v
a
riable names
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
PrimarySeq
d
irect mode
f
ix/improvem
e
n
t
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
S
mall POD and test
s
updat
e
s
commit
|
commitdiff
|
tree
2012-10-30
F
lorent Angly
Doc fixes
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
More tes
t
s
for PrimarySeq
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
F
i
xes
issue in EncodedSeq
commit
|
commitdiff
|
tree
2012-10-30
Flo
r
en
t
Ang
l
y
Cosmeti
c
changes
commit
|
commitdiff
|
tree
2012-10-30
Florent
Angly
Consistent
i
nde
n
tat
i
o
n
commit
|
commitdiff
|
tree
2012-10-30
Florent A
n
gl
y
Se
q
FastaSpeedFactory
fix
commit
|
commitdiff
|
tree
2012-10-30
F
lo
r
ent Ang
l
y
Consisten
t
inde
n
tati
o
n
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Bio::
P
rim
a
ry
S
eq::l
e
ngth() optimi
z
ations
commit
|
commitdiff
|
tree
2012-10-30
Fl
o
rent Angly
More tests
for Bio
:
:PrimarySeq::leng
t
h
()
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
P
OD updated
and beauti
f
icati
o
n
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
More test
s
for B
i
o:
:
P
r
imarySeq::leng
t
h
()
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Added tests f
o
r Bio::
P
rimarySeq::length()
commit
|
commitdiff
|
tree
2012-10-29
Florent Angly
Fix for b
u
g #3389
commit
|
commitdiff
|
tree
2012-10-29
Flore
n
t Angly
Primary
S
e
q
::length(
)
speedup
commit
|
commitdiff
|
tree
2012-10-10
Florent
Ang
l
y
Better 0-length seque
n
ce supp
o
rt for Bi
o
::DB::Qual
.
.
.
commit
|
commitdiff
|
tree
2012-10-10
Flo
r
ent A
n
gly
Better
support for 0-length se
q
uences
commit
|
commitdiff
|
tree
2012-09-24
Florent
Ang
l
y
Me
r
ge branch 'master' of github
.
com:bioperl/
b
ioperl
.
.
.
commit
|
commitdiff
|
tree
2012-09-24
F
l
orent Angly
Fixed an
untested regression in Bi
o
::DB::Fasta
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Rege
x
p t
o
match RNA on r
e
q
uest o
n
ly
commit
|
commitdiff
|
tree
2012-09-10
Florent Angl
y
Fixed in
d
ent
a
tio
n
commit
|
commitdiff
|
tree
2012-09-10
Florent Ang
l
y
Re
v
e
r
sed problematic comm
i
t 8334d175ffba095a9447038
d
421cac0d
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Merge b
r
anch 'ampli
c
ons'
commit
|
commitdiff
|
tree
2012-09-10
F
l
o
r
ent Angly
Me
r
g
e br
a
nch 'master'
o
f gi
t
hub
.
com:bi
o
perl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Fl
o
rent Angly
Removed s
o
m
e
comments
commit
|
commitdiff
|
tree
2012-09-10
Floren
t
Angly
Compound ID
can now inclu
d
the strand
commit
|
commitdiff
|
tree
2012-09-10
F
l
orent An
g
l
y
B
i
o::DB:
:
I
n
dexedBas
e
comp
l
iance w
i
th Bio::
D
B:SeqI and
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Fixed typo
commit
|
commitdiff
|
tree
2012-09-10
F
lo
r
ent Angly
Fixed silly err
o
r
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Updated
Bi
o
::DB::SeqI
P
OD according to info in Bio
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Up
d
ated
C
hanges file
commit
|
commitdiff
|
tree
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