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more robust parameter handling, matrix is not a required parameter (default of blosum...
2002-11-29
j
aso
n
m
ore robust para
m
e
ter
h
a
n
dling,
mat
r
i
x
is not
a required
.
.
.
commit
|
commitdiff
|
tree
2002-11-29
jaso
n
ne
w
generic
'run' m
e
thod
commit
|
commitdiff
|
tree
2002-11-13
jason
sup
p
ort
-u and -v setti
n
gs, supp
o
rt passing in
fi
l
e
.
.
.
commit
|
commitdiff
|
tree
2002-11-13
jason
f
a
il grac
e
fully
-
r
emove Fugu group Ensem
b
l cruft h
e
re
commit
|
commitdiff
|
tree
2002-11-13
jaso
n
more g
r
a
c
eful exit
i
ng
commit
|
commitdiff
|
tree
2002-11-13
j
a
s
on
add
an Id
head
e
r
commit
|
commitdiff
|
tree
2002-11-13
jason
can run
t
e
s
ts
i
f
we let execut
e
able find
the
e
x
e
commit
|
commitdiff
|
tree
2002-11-13
jaso
n
ah ha
h
, test w
i
l
l
run without
fugu specifi
c
stuf
f
commit
|
commitdiff
|
tree
2002-11-13
jason
Nam
e
of progra
m
is pfsca
n
commit
|
commitdiff
|
tree
2002-11-13
jason
f
a
il gracefully -- and secret message
for
F
ugu guys
.
.
.
commit
|
commitdiff
|
tree
2002-11-13
jason
free res
o
urces
commit
|
commitdiff
|
tree
2002-11-13
j
a
son
use
n
ew A
P
I
commit
|
commitdiff
|
tree
2002-11-13
jason
m
a
k
e sure
res
o
u
r
ce
s
are fr
e
ed
commit
|
commitdiff
|
tree
2002-11-13
ja
s
o
n
c
o
deml --> tcoffee copy
+
paste sillin
e
ss
commit
|
commitdiff
|
tree
2002-11-13
j
a
son
Convert StandAloneBlast to W
r
apperBas
e
(finallyp
e
rl
.
.
.
commit
|
commitdiff
|
tree
2002-11-13
j
a
son
use proper Tools::WrapperBase
n
ow
commit
|
commitdiff
|
tree
2002-11-13
jason
mis
s
ing input files for
S
t
and
A
l
o
neBlast
commit
|
commitdiff
|
tree
2002-11-13
jas
o
n
insure filehandl
e
s are clos
e
d
commit
|
commitdiff
|
tree
2002-11-13
jas
o
n
1
7 t
e
sts
now?
commit
|
commitdiff
|
tree
2002-11-13
j
ason
Brought up t
o
spec with the new
O
bje
c
ts and seqnam
e
.
.
.
commit
|
commitdiff
|
tree
2002-11-13
jason
remov
e
Fug
u
syste
m
stuff
a
nd insure that Fi
l
e
t
mp ha
n
dles
.
.
.
commit
|
commitdiff
|
tree
2002-11-10
jason
fixed
t
o work
with new base object and us
e
bioperl
.
.
.
commit
|
commitdiff
|
tree
2002-11-10
jaso
n
skip
if ret
val i
s
0
commit
|
commitdiff
|
tree
2002-11-10
jason
co
n
sistency
commit
|
commitdiff
|
tree
2002-11-10
jason
co
d
e
b
eautification
commit
|
commitdiff
|
tree
2002-11-10
jason
platform indepen
d
ent filenam
e
commit
|
commitdiff
|
tree
2002-11-09
jason
resp
e
ct the or
i
ginal cwd
commit
|
commitdiff
|
tree
2002-09-18
jason
s
y
no
p
s
is d
o
c
commit
|
commitdiff
|
tree
2002-09-18
jason
defau
l
t
s
hou
l
d be F3X4
commit
|
commitdiff
|
tree
2002-09-18
j
ason
Matthew's Changes co
m
mitte
d
: Add support to save_output
.
.
.
commit
|
commitdiff
|
tree
2002-09-18
j
a
s
on
handl
e
e
xe
apps
commit
|
commitdiff
|
tree
2002-09-05
jason
SAX
/
Sax
-
>
P
erlSAX
commit
|
commitdiff
|
tree
2002-08-14
jason
for build
i
ng manifest
commit
|
commitdiff
|
tree
2002-08-14
jaso
n
cosme
t
ic code fix
commit
|
commitdiff
|
tree
2002-08-14
j
aso
n
describe the curre
n
t s
t
ate of affair
commit
|
commitdiff
|
tree
2002-07-30
jason
s
k
ip tes
t
s
commit
|
commitdiff
|
tree
2002-07-29
jas
o
n
test file for TCoffee
commit
|
commitdiff
|
tree
2002-07-29
jason
whoops
,
one more time, cleanup tempfiles and d
i
rs
commit
|
commitdiff
|
tree
2002-07-29
j
ason
cleanup of
t
e
m
pfiles wo
r
ks
commit
|
commitdiff
|
tree
2002-07-29
ja
s
o
n
handle bad
r
esult err b
y
skip
p
in
g
tests
commit
|
commitdiff
|
tree
2002-07-29
jason
tes
t
s
u
pda
t
ed to handle missing ex
e
better
commit
|
commitdiff
|
tree
2002-07-29
jason
inherit from Wrapp
e
rBas
e
commit
|
commitdiff
|
tree
2002-07-29
jason
code formatting
commit
|
commitdiff
|
tree
2002-07-29
jas
o
n
API
chan
g
ed a little bit with new parser
commit
|
commitdiff
|
tree
2002-07-29
jas
o
n
handle windows exes
commit
|
commitdiff
|
tree
2002-07-29
j
a
s
o
n
fix test c
o
unt
commit
|
commitdiff
|
tree
2002-07-29
jas
o
n
use ne
w
P
A
ML parser API
commit
|
commitdiff
|
tree
2002-07-27
jason
codeml->protml doc
fixe
s
commit
|
commitdiff
|
tree
2002-07-27
jason
added a
d
d
iti
o
n
s
of
.
exe for on windows, a
l
low alignmen
t
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
jason
br
o
ught in
line with WrapperBase
commit
|
commitdiff
|
tree
2002-07-27
jason
br
o
ugh
t
m
o
dule in
-
li
n
e with new WrapperBa
s
e
commit
|
commitdiff
|
tree
2002-07-27
jason
bump te
s
t
coun
t
commit
|
commitdiff
|
tree
2002-07-27
jason
cop
y
+paste e
r
r
o
r
commit
|
commitdiff
|
tree
2002-07-27
j
a
son
fix internal p
a
ramet
e
r name
commit
|
commitdiff
|
tree
2002-07-27
j
ason
adde
d
P
r
ot
M
L wrapper -
part of M
o
lphy
p
ack
a
ger fo
r
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
jason
te
s
t for protml
r
unni
n
g
commit
|
commitdiff
|
tree
2002-07-25
jason
mig
r
ate from
P
AMLB
a
s
e to WrapperBase
commit
|
commitdiff
|
tree
2002-07-16
jason
pr
i
nt data
to
f
ile rig
h
t away rather than holding array
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
j
a
son
don't redire
c
t
to /dev/null - make
s
ure quiet really
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
jaso
n
more r
o
bust pr
o
gram finding
commit
|
commitdiff
|
tree
2002-07-09
jason
c
h
anged to use PAML template f
o
r
find
executab
l
e insated
.
.
.
commit
|
commitdiff
|
tree
2002-07-06
jason
explicitly closing some filehandl
e
s
appe
a
rs to do a
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
test
s
f
i
nd th
e
mat and data file now,
and will skip
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
j
a
son
n
e
ed
t
o test when
p
eople run Ma
k
e
file
.
PL,
o
therwise
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
j
a
son
pr
o
m
pt
u
s
e
r when Makef
i
le
.
PL is run
commit
|
commitdiff
|
tree
2002-07-05
ja
s
on
update
t
est count
commit
|
commitdiff
|
tree
2002-07-03
j
aso
n
makefile
commit
|
commitdiff
|
tree
2002-07-02
jason
added
codeml data
commit
|
commitdiff
|
tree
2002-07-02
jason
removed run wrappers tests
f
ro
m
core - th
e
y have been
.
.
.
commit
|
commitdiff
|
tree
2002-06-26
jason
readme for run wrappers
commit
|
commitdiff
|
tree
2002-06-21
jaso
n
t
estfile renamed
commit
|
commitdiff
|
tree
2002-06-21
jas
o
n
remove debug
c
opyfi
l
e
commit
|
commitdiff
|
tree
2002-06-21
jason
shorten
f
ilename to
avoid
p
ossible windows long filename
s
.
.
.
commit
|
commitdiff
|
tree
2002-06-19
j
ason
doc fix
commit
|
commitdiff
|
tree
2002-06-18
jason
use the determined pa
t
h
to RP when attempting
to find
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
j
ason
return the va
l
ues as hash of
hashes as they
are al
l
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
jason
small doc tweaks and added runna
b
le s
y
nopsis
commit
|
commitdiff
|
tree
2002-06-17
jas
o
n
yn00 wra
p
per
for P
A
ML
commit
|
commitdiff
|
tree
2002-06-15
ja
s
on
quiete
r
t
e
sts unless BIO
P
ER
L
DEBUG env variable is set
commit
|
commitdiff
|
tree
2002-06-14
jason
set v
e
r
bose to -
1
commit
|
commitdiff
|
tree
2002-06-14
ja
s
o
n
PAML packag
e
--
c
odeml w
r
a
pper and test committe
d
commit
|
commitdiff
|
tree
2002-05-31
jason
doc fix
commit
|
commitdiff
|
tree
2002-05-31
jas
o
n
handle c
a
se
w
he
n
PHYLIP i
s
installed but not clust
a
l
w
commit
|
commitdiff
|
tree
2002-05-30
jas
o
n
han
d
le s
o
m
e
w
e
i
rd boundary ca
s
es
commit
|
commitdiff
|
tree
2002-05-21
jason
update
some of the d
o
cs
commit
|
commitdiff
|
tree
2002-05-21
ja
s
on
t
e
st value fo
r
protdist
commit
|
commitdiff
|
tree
2002-04-22
j
aso
n
fixes to remove warnings
commit
|
commitdiff
|
tree
2002-04-22
j
a
son
fix
war
n
ings
commit
|
commitdiff
|
tree
2002-04-18
jason
POD fix
commit
|
commitdiff
|
tree
2002-03-22
jason
up
d
ated tests for v 1
.
22 problems on main tru
n
k
commit
|
commitdiff
|
tree
2002-03-21
j
a
son
s
i
m
p
le align has o
v
erall perce
n
t id meth
o
d
commit
|
commitdiff
|
tree
2002-03-19
j
ason
cl
e
a
n
up be
f
ore ea
c
h
r
un of
a
n
a
pplicat
i
on
commit
|
commitdiff
|
tree
2002-03-15
jas
o
n
m
e
r
ge from branch
commit
|
commitdiff
|
tree
2002-03-15
j
a
son
merge change
s
from branch
commit
|
commitdiff
|
tree
2002-03-15
jason
up
d
at
e
d to
han
d
le tests
w
ith SearchIO
o
bject returned
.
.
.
commit
|
commitdiff
|
tree
2002-03-15
jas
o
n
better synops
i
s
and
d
oc
update
commit
|
commitdiff
|
tree
2002-03-14
j
a
son
io cl
e
an
u
p called at outset of an analyses
-
- from
.
.
.
commit
|
commitdiff
|
tree
2002-03-14
jason
merged exe checking fr
o
m
b
ranch
commit
|
commitdiff
|
tree
2002-03-14
ja
s
o
n
s
k
ip nic
e
ly, hand
l
e case
w
here
serve
r
is d
o
wn
commit
|
commitdiff
|
tree
2002-03-11
j
ason
use SearchIO n
o
t Tools::Blast
commit
|
commitdiff
|
tree
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