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This still needs an overhaul but fix minor doc bugs in naming the module
2002-11-10
jas
o
n
code beautification
commit
|
commitdiff
|
tree
2002-11-10
j
as
o
n
platfor
m
i
nde
p
e
n
d
ent
fil
e
name
commit
|
commitdiff
|
tree
2002-11-09
j
a
son
respect the ori
g
inal cwd
commit
|
commitdiff
|
tree
2002-09-18
jason
s
yno
p
sis doc
commit
|
commitdiff
|
tree
2002-09-18
jason
defau
l
t sho
u
l
d
be F3
X
4
commit
|
commitdiff
|
tree
2002-09-18
jason
Matthew's
C
hanges committed: Add su
p
p
o
r
t
to save_output
.
.
.
commit
|
commitdiff
|
tree
2002-09-18
jason
handle e
x
e
a
p
ps
commit
|
commitdiff
|
tree
2002-09-05
j
ason
SAX/Sax -> Per
l
S
A
X
commit
|
commitdiff
|
tree
2002-08-14
j
a
son
for bu
i
lding man
i
fest
commit
|
commitdiff
|
tree
2002-08-14
jason
cos
m
etic co
d
e fix
commit
|
commitdiff
|
tree
2002-08-14
jason
d
e
s
crib
e
the curren
t
state of
a
ffai
r
commit
|
commitdiff
|
tree
2002-07-30
j
as
o
n
ski
p
tests
commit
|
commitdiff
|
tree
2002-07-29
jas
o
n
test fi
l
e fo
r
TCoffee
commit
|
commitdiff
|
tree
2002-07-29
jason
whoops,one more time, c
l
ea
n
up temp
f
iles a
n
d dirs
commit
|
commitdiff
|
tree
2002-07-29
jason
c
l
e
anup of tempfile
s
w
o
r
k
s
commit
|
commitdiff
|
tree
2002-07-29
j
aso
n
ha
n
d
l
e bad result err by skipping
t
e
sts
commit
|
commitdiff
|
tree
2002-07-29
jason
tests updated t
o
han
d
le miss
i
n
g
exe
b
etter
commit
|
commitdiff
|
tree
2002-07-29
jason
inher
i
t from WrapperBase
commit
|
commitdiff
|
tree
2002-07-29
jas
o
n
code formatti
n
g
commit
|
commitdiff
|
tree
2002-07-29
ja
s
on
A
PI c
h
anged a little bit wi
t
h
n
e
w pars
e
r
commit
|
commitdiff
|
tree
2002-07-29
jason
handle
windo
w
s
exes
commit
|
commitdiff
|
tree
2002-07-29
jason
fix
t
est
c
ount
commit
|
commitdiff
|
tree
2002-07-29
jas
o
n
u
se new PAML par
s
er API
commit
|
commitdiff
|
tree
2002-07-27
j
ason
codeml->protml doc fixes
commit
|
commitdiff
|
tree
2002-07-27
jason
add
e
d addition
s
o
f
.
exe for on windows, allow alignme
n
t
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
jaso
n
br
o
u
ght
in line with
W
r
apper
B
ase
commit
|
commitdiff
|
tree
2002-07-27
jas
o
n
bro
u
gh
t
module i
n
-line with new WrapperBa
s
e
commit
|
commitdiff
|
tree
2002-07-27
ja
s
on
bu
m
p test
c
ount
commit
|
commitdiff
|
tree
2002-07-27
jason
copy+paste
e
rror
commit
|
commitdiff
|
tree
2002-07-27
j
a
s
on
fix
i
nt
e
rn
a
l
p
aramete
r
na
m
e
commit
|
commitdiff
|
tree
2002-07-27
jason
a
dde
d
ProtM
L
wrappe
r
- part of Molph
y
packager for
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
jason
test
f
o
r
protml r
u
n
n
ing
commit
|
commitdiff
|
tree
2002-07-25
jason
migrate from P
A
MLBase to Wrappe
r
B
a
se
commit
|
commitdiff
|
tree
2002-07-16
j
ason
print d
a
ta
t
o file
r
igh
t
awa
y
r
a
ther
t
han holding array
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
jason
don't
r
edirect to
/
dev/nul
l
-
make sure qu
i
et r
e
a
l
ly
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
jason
more
r
obust progra
m
findi
n
g
commit
|
commitdiff
|
tree
2002-07-09
jason
cha
n
g
ed to u
s
e PAML template for find
e
xecutable insated
.
.
.
commit
|
commitdiff
|
tree
2002-07-06
jason
explicitly closi
n
g some fileh
a
ndles appears to do a
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
tests f
i
nd the mat and data f
i
le now, and wi
l
l skip
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
need to t
e
st when peop
l
e run Makefile
.
PL,
othe
r
wise
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
ja
s
on
prompt user when Makefile
.
PL
i
s
run
commit
|
commitdiff
|
tree
2002-07-05
jason
update test c
o
unt
commit
|
commitdiff
|
tree
2002-07-03
jason
makefile
commit
|
commitdiff
|
tree
2002-07-02
jason
added code
m
l
data
commit
|
commitdiff
|
tree
2002-07-02
jason
removed r
u
n wrappers
t
ests
f
rom cor
e
- they
h
a
v
e been
.
.
.
commit
|
commitdiff
|
tree
2002-06-26
jason
r
e
a
d
me for run wrappers
commit
|
commitdiff
|
tree
2002-06-21
jason
testfile rena
m
ed
commit
|
commitdiff
|
tree
2002-06-21
jason
rem
o
ve de
b
ug copyf
i
le
commit
|
commitdiff
|
tree
2002-06-21
jas
o
n
sho
r
ten
f
ilename t
o
a
void possible windows long
filena
m
es
.
.
.
commit
|
commitdiff
|
tree
2002-06-19
j
a
s
o
n
doc fix
commit
|
commitdiff
|
tree
2002-06-18
j
a
s
o
n
use th
e
det
e
r
mined path to RP when at
t
em
p
ting to
f
ind
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
jason
r
e
turn th
e
v
alues a
s
h
ash o
f
h
a
sh
e
s as they are all
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
jason
s
m
all
doc tweak
s
a
n
d
a
dded r
u
n
n
abl
e
synopsis
commit
|
commitdiff
|
tree
2002-06-17
jason
yn00 wrapp
e
r
for P
A
ML
commit
|
commitdiff
|
tree
2002-06-15
jason
q
u
ie
t
er tests unless BIOPERLDEBUG env va
r
iabl
e
is
s
et
commit
|
commitdiff
|
tree
2002-06-14
jason
set verbose
t
o
-
1
commit
|
commitdiff
|
tree
2002-06-14
jason
P
AML package --
c
od
e
ml
wr
a
p
p
er and test committe
d
commit
|
commitdiff
|
tree
2002-05-31
jason
doc
f
i
x
commit
|
commitdiff
|
tree
2002-05-31
jason
handle case when PH
Y
LIP is
i
nstalled but not clustalw
commit
|
commitdiff
|
tree
2002-05-30
jaso
n
handle some
weird boundary cas
e
s
commit
|
commitdiff
|
tree
2002-05-21
jason
u
pdate some of the docs
commit
|
commitdiff
|
tree
2002-05-21
jason
test value
f
o
r
protdist
commit
|
commitdiff
|
tree
2002-04-22
jason
fixes to
r
emove warnings
commit
|
commitdiff
|
tree
2002-04-22
jason
f
i
x
warni
n
gs
commit
|
commitdiff
|
tree
2002-04-18
jason
P
OD fix
commit
|
commitdiff
|
tree
2002-03-22
j
as
o
n
updated tests
for
v
1
.
22 proble
m
s
o
n main trunk
commit
|
commitdiff
|
tree
2002-03-21
j
a
son
sim
p
l
e
alig
n
has overall per
c
en
t
id me
t
hod
commit
|
commitdiff
|
tree
2002-03-19
jason
cleanup before e
a
ch ru
n
of an appl
i
c
ation
commit
|
commitdiff
|
tree
2002-03-15
j
a
so
n
merg
e
from branc
h
commit
|
commitdiff
|
tree
2002-03-15
j
ason
me
r
ge c
h
ang
e
s from branch
commit
|
commitdiff
|
tree
2002-03-15
j
ason
upd
a
te
d
to handle test
s
with Searc
h
IO o
b
ject ret
u
rne
d
.
.
.
commit
|
commitdiff
|
tree
2002-03-15
jas
o
n
bette
r
s
y
n
opsis and doc update
commit
|
commitdiff
|
tree
2002-03-14
jason
i
o
cleanup cal
l
ed at outse
t
of an analyses -- fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2002-03-14
ja
s
on
merge
d
exe c
h
ecking f
r
om branch
commit
|
commitdiff
|
tree
2002-03-14
j
as
o
n
skip
nicely, h
a
n
d
le case where server
i
s down
commit
|
commitdiff
|
tree
2002-03-11
jason
use Sea
r
chIO not
Tools::Blas
t
commit
|
commitdiff
|
tree
2002-03-09
ja
s
on
turn of clu
s
talw debugging
commit
|
commitdiff
|
tree
2002-03-05
jason
unlink test file
o
utput
commit
|
commitdiff
|
tree
2002-03-04
jas
o
n
added abil
i
ty
t
o
dump
a
l
ignments as w
e
ll as
s
e
q
u
ences
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
jas
o
n
added
e
xample docu
m
entation to the POD
commit
|
commitdiff
|
tree
2002-02-18
jason
t
est for c
m
d
lin
e
argument where
value i
s
a Bio::P
r
imarySe
q
I
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
jason
han
d
le cmd line argum
e
nts pointing to a B
i
o::Primar
y
S
eqI
.
.
.
commit
|
commitdiff
|
tree
2002-02-06
jason
params should
be appended not ov
e
rwritin
g
commit
|
commitdiff
|
tree
2002-01-30
j
ason
verbosity=-1 is
s
a
m
e
a
s
quiet
(
)
commit
|
commitdiff
|
tree
2002-01-11
ja
s
on
debug
message now uses t
h
e debug method
commit
|
commitdiff
|
tree
2002-01-09
jas
o
n
warn
a
bout no
t
using old
c
lustalw
commit
|
commitdiff
|
tree
2002-01-09
jas
o
n
us
e
the u
p
dated PROGRAM exe locatio
n
in
f
orm
a
ti
o
n to
.
.
.
commit
|
commitdiff
|
tree
2002-01-09
j
a
s
o
n
check to
i
nsure defined obje
c
t before ca
l
ling ISA
commit
|
commitdiff
|
tree
2001-12-14
jason
s
kip msg updated due
to clustal 1
.
81 b
u
g
commit
|
commitdiff
|
tree
2001-12-14
jason
n
ice message
p
rinting when blast is not
r
unnable
commit
|
commitdiff
|
tree
2001-12-14
jason
more quiet
w
arning
s
o t
e
sts are
l
ess chatty
commit
|
commitdiff
|
tree
2001-12-14
jason
issue nice messa
g
e
when skipping EM
B
OSS te
s
ts
commit
|
commitdiff
|
tree
2001-12-14
ja
s
on
s
kip can print a
nic
e
message about
w
hy it skippe
d
commit
|
commitdiff
|
tree
2001-12-14
jason
emboss fact
o
ry beh
a
ves more quiet
l
y w
h
en EMBOSS is
.
.
.
commit
|
commitdiff
|
tree
2001-11-19
jason
EM
B
OSS more run
n
able and w/ test
s
commit
|
commitdiff
|
tree
2001-08-10
j
a
son
don't
hav
e
clus
t
a
l
w tes
t
s fail for 0
.
9 r
e
le
a
s
e
commit
|
commitdiff
|
tree
2001-08-07
jason
documen
t
atio
n
for ret
r
ieve_blas
t
m
e
th
o
d
commit
|
commitdiff
|
tree
2001-06-15
jason
min
i
u
m identity s
c
ore required i
n
stead
of ha
r
d value
.
.
.
commit
|
commitdiff
|
tree
2001-06-14
jason
sta
t
us set to inva
l
id on a failed retrieval
commit
|
commitdiff
|
tree
2001-06-12
j
ason
using priva
t
e state outside of class
,
must cha
n
ge
the
.
.
.
commit
|
commitdiff
|
tree
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