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fix filehandle issue for NEXUS parsing
2007-01-16
cjfiel
d
s
fix filehandle
i
ss
u
e for NEXUS p
a
rsin
g
commit
|
commitdiff
|
tree
2007-01-16
cjfields
file
h
andle
tes
t
s (NEX
U
S s
t
ill d
o
esn't wor
k
)
commit
|
commitdiff
|
tree
2007-01-16
cjfields
fix
for filehandle IO
commit
|
commitdiff
|
tree
2007-01-16
c
j
f
i
el
d
s
Bug
2
185
commit
|
commitdiff
|
tree
2007-01-11
c
j
fields
Bug
2
1
82
commit
|
commitdiff
|
tree
2007-01-11
cjfields
revert rnamotif
.
t
c
hanges (committe
d
accidentally along
.
.
.
commit
|
commitdiff
|
tree
2007-01-11
cjf
i
elds
removed extr
a
neous (n
o
w
w
rong) co
m
ment
commit
|
commitdiff
|
tree
2007-01-11
cjfields
Bug 2182
commit
|
commitdiff
|
tree
2007-01-08
cjfields
bug 2172
commit
|
commitdiff
|
tree
2007-01-07
cjfie
l
d
s
sma
l
l changes
commit
|
commitdiff
|
tree
2007-01-07
cjfields
P
O
D
changes
commit
|
commitdiff
|
tree
2006-12-31
cjfields
bug
2167
commit
|
commitdiff
|
tree
2006-12-30
c
jfie
l
ds
small
change re
g
.
HTML::Enti
t
ies
commit
|
commitdiff
|
tree
2006-12-30
cjfields
small
ch
a
n
ges
commit
|
commitdiff
|
tree
2006-12-30
cjfi
e
lds
Bug 2166
commit
|
commitdiff
|
tree
2006-12-30
cjf
i
elds
Removed debu
g
ging
cruf
t
commit
|
commitdiff
|
tree
2006-12-30
c
j
fie
l
ds
tentative f
i
x f
o
r b
u
g
2166
commit
|
commitdiff
|
tree
2006-12-28
cjfields
Mov
i
ng BLAST XML S
A
X
m
eth
o
ds to
separate class
commit
|
commitdiff
|
tree
2006-12-21
cjfields
XML::SAX::Pu
r
e
P
erl works wit
h
older
BLAST XML
report
.
.
.
commit
|
commitdiff
|
tree
2006-12-21
cjfields
add test
s
for 'unisav
e
',
move to Tes
t
:
:M
o
re,
mi
n
or
.
.
.
commit
|
commitdiff
|
tree
2006-12-21
cjf
i
elds
ad
d
ed 'uni
s
a
v
e'
commit
|
commitdiff
|
tree
2006-12-20
cjfield
s
Bug fix
f
or env_proxy
commit
|
commitdiff
|
tree
2006-12-13
cjfields
If parse
r
o
v
erheats, tur
n
off and back sl
o
wly away
.
.
.
commit
|
commitdiff
|
tree
2006-12-13
cjfields
Very exp
e
rimental Infer
n
al
(
cm
s
earch) parser
.
commit
|
commitdiff
|
tree
2006-12-12
cjfield
s
small chang
e
f
or phas
e
test
commit
|
commitdiff
|
tree
2006-12-12
cjfields
Add convenien
c
e parame
t
er '-phase' to
s
p
l
iced_
s
e
q()
commit
|
commitdiff
|
tree
2006-12-12
cjfi
e
lds
spliced
_
seq() phase tests
commit
|
commitdiff
|
tree
2006-12-06
cjf
i
elds
Update f
r
om wiki
commit
|
commitdiff
|
tree
2006-12-06
c
jf
i
elds
Update from wiki
commit
|
commitdiff
|
tree
2006-12-05
c
j
f
i
elds
Grr
.
.
.
refix
B
ug 2159
commit
|
commitdiff
|
tree
2006-12-05
cjfield
s
bug 2159
commit
|
commitdiff
|
tree
2006-12-05
cjfields
Bug 2160
commit
|
commitdiff
|
tree
2006-11-30
cjfiel
d
s
c
hang
e
for blo
c
k to a map
commit
|
commitdiff
|
tree
2006-11-30
cjf
i
elds
Bug 2152
commit
|
commitdiff
|
tree
2006-11-27
c
j
fiel
d
s
throw, not warn, since
t
h
is di
e
s 99
%
of the time anyway
.
.
.
commit
|
commitdiff
|
tree
2006-11-27
cjfields
small fixes
for
Annotati
o
n
Fact
o
ry
commit
|
commitdiff
|
tree
2006-11-26
cjfie
l
ds
Bug 2124
commit
|
commitdiff
|
tree
2006-11-26
cjfiel
d
s
Bug 2151
commit
|
commitdiff
|
tree
2006-11-23
cjfields
B
u
g 2146
commit
|
commitdiff
|
tree
2006-11-23
cjfields
Bug
2146
commit
|
commitdiff
|
tree
2006-11-16
cjfields
Co
n
ver
t
to Te
s
t::More
commit
|
commitdiff
|
tree
2006-11-16
cjf
i
e
lds
Convert to Te
s
t::More
commit
|
commitdiff
|
tree
2006-11-16
cjfi
e
l
d
s
B
u
g 214
5
commit
|
commitdiff
|
tree
2006-11-14
c
jfie
l
ds
Add
CVS tags, move dependencies
t
o new file
commit
|
commitdiff
|
tree
2006-11-14
cjfields
N
ew
I
NSTALL
.
WIN doc (from wik
i
)
commit
|
commitdiff
|
tree
2006-11-14
cjfields
Add POD
commit
|
commitdiff
|
tree
2006-11-13
cjfiel
d
s
bug 213
9
; change to T
e
st::More
commit
|
commitdiff
|
tree
2006-11-13
c
jfiel
d
s
B
u
g 2139
commit
|
commitdiff
|
tree
2006-11-13
cj
f
i
e
lds
t
y
po (bug 2141)
commit
|
commitdiff
|
tree
2006-11-13
cjfields
ch
a
n
g
e test f
i
l
e data
commit
|
commitdiff
|
tree
2006-11-11
cjfields
ARP tests
commit
|
commitdiff
|
tree
2006-11-11
cj
f
ields
Simple ARP
par
s
e
r
commit
|
commitdiff
|
tree
2006-11-10
cjfields
use single
q
uotes for system calls to pr
e
vent interpo
l
ati
o
n
commit
|
commitdiff
|
tree
2006-11-10
c
jfields
Change
d
or re
m
oved VERSION
commit
|
commitdiff
|
tree
2006-11-09
cjfield
s
d
e
lete output test
f
i
l
es
commit
|
commitdiff
|
tree
2006-11-09
cjfields
Add xmfa alignm
e
nt te
s
t
s
commit
|
commitdiff
|
tree
2006-11-09
cjfields
add xm
f
a writ
e
_
a
ln() m
e
t
h
od, stk and xmfa file
ex
t
ensions
.
.
.
commit
|
commitdiff
|
tree
2006-11-09
cjfields
using '
o
ur'
commit
|
commitdiff
|
tree
2006-11-09
cjf
i
elds
first pass a
t
x
m
fa parser (next_aln() implemented only
)
commit
|
commitdiff
|
tree
2006-11-09
cjfields
Bug 2134 (change output to
c
o
n
form with rel
.
9 I
D
change
s
)
commit
|
commitdiff
|
tree
2006-11-09
c
j
f
i
elds
Bug 2134 (add
e
d tests for
n
ew swiss fo
r
mat); change
d
.
.
.
commit
|
commitdiff
|
tree
2006-11-09
cjfi
e
ld
s
Bug 2
1
34 (fix parsi
n
g)
commit
|
commitdiff
|
tree
2006-11-09
cjfields
Changed name
commit
|
commitdiff
|
tree
2006-11-08
cjfi
e
lds
B
u
g 2134
commit
|
commitdiff
|
tree
2006-11-08
cjfields
Some modul
e
s don'
t
define VERSION, def
a
ult to 0
commit
|
commitdiff
|
tree
2006-11-08
c
jf
i
elds
Re
m
ove ex
t
r
aneous debuggi
n
g st
a
atements
commit
|
commitdiff
|
tree
2006-11-08
cjfields
t
y
po
commit
|
commitdiff
|
tree
2006-11-08
c
jfields
Using D
B
L
inks for d
a
tabas
e
r
e
fs
commit
|
commitdiff
|
tree
2006-11-07
c
j
f
i
elds
Add
i
tio
n
al
f
un stuff; writ
e
_aln() test ad
d
ed;
may move
.
.
.
commit
|
commitdiff
|
tree
2006-11-06
cjfields
more Stoc
k
holm tests; skipping two fo
r
no
w
(dr
o
pping
.
.
.
commit
|
commitdiff
|
tree
2006-11-06
cjfields
Add alig
n
ment met
a
s
t
r
ing output
commit
|
commitdiff
|
tree
2006-11-06
cjfields
remove
old
initia
l
ization
p
arameter; will
a
dd builder
.
.
.
commit
|
commitdiff
|
tree
2006-11-06
cjfie
l
ds
Add sequence-ba
s
ed meta o
u
tput
commit
|
commitdiff
|
tree
2006-11-06
cjfi
e
lds
s
t
o
ckh
o
lm
a
lignmen
t
tests
commit
|
commitdiff
|
tree
2006-11-06
cjfields
Add experimental sto
c
kholm writ
e
_a
l
n() support
commit
|
commitdiff
|
tree
2006-11-05
c
jfields
U
s
e Test::More
commit
|
commitdiff
|
tree
2006-11-01
cjfie
l
ds
Im
p
lement
A
nn
o
tatableI (for
a
lignment-spe
c
ific annotation)
commit
|
commitdiff
|
tree
2006-10-31
cjfiel
d
s
r
emove
r
e
dundant sub_L
o
cation_by
_
order(
)
commit
|
commitdiff
|
tree
2006-10-31
cjfields
Bug
2
130
commit
|
commitdiff
|
tree
2006-10-28
cj
f
ields
remo
v
e extraneous use sta
t
ement
commit
|
commitdiff
|
tree
2006-10-26
cjfi
e
lds
Bullet-proof
s
ome tes
t
s
commit
|
commitdiff
|
tree
2006-10-24
cjfields
Bug 20
6
0
commit
|
commitdiff
|
tree
2006-10-24
cjfields
ou
r
$VERSION (perl 5
.
6
.
1-ish)
commit
|
commitdiff
|
tree
2006-10-20
cjfields
Ty
p
o
commit
|
commitdiff
|
tree
2006-10-19
cjfields
Bug 2101 (tentative fix)
commit
|
commitdiff
|
tree
2006-10-17
cjfields
Change
to
Test::More; sk
i
p XM
L
tests
i
f problems aris
e
.
.
.
commit
|
commitdiff
|
tree
2006-10-11
cjfields
Bug 21
2
1
commit
|
commitdiff
|
tree
2006-10-10
cj
f
ields
Bug 2120
commit
|
commitdiff
|
tree
2006-10-05
cjfields
Updat
e
s to POD and egquery (
g
etting
i
t
up
t
o
s
peed)
commit
|
commitdiff
|
tree
2006-10-05
cjfields
Fix
e
s to
g
et EGQuery working
c
or
r
ec
t
ly
commit
|
commitdiff
|
tree
2006-10-04
cjfields
Added tests f
o
r new DocSum methods;
w
ill probab
l
y cut
.
.
.
commit
|
commitdiff
|
tree
2006-10-04
cjf
i
elds
P
O
D
cle
a
n
u
p
(thanks Sendu)
,
remove some debu
g
ging
s
t
u
f
f
.
.
.
commit
|
commitdiff
|
tree
2006-10-04
cjfields
ESummary te
s
ts
commit
|
commitdiff
|
tree
2006-10-04
cjfields
Fixes for
t
est
s
commit
|
commitdiff
|
tree
2006-10-03
c
jfields
Ab
o
ut to add a few tests
for Es
u
mm
a
ry (n
o
t implemented
.
.
.
commit
|
commitdiff
|
tree
2006-10-03
c
j
fields
Add PO
D
commit
|
commitdiff
|
tree
2006-10-03
cjfi
e
lds
Addi
n
g me
t
hods to Doc
S
um and
esummary
(
s
till exp
e
rim
e
ntal)
commit
|
commitdiff
|
tree
2006-10-03
cjfields
Add simple docs
u
m cont
a
ine
r
obje
c
t for esummary
commit
|
commitdiff
|
tree
2006-10-03
cjfie
l
d
s
Setting DB from coo
k
ie is
b
ad
f
or elin
k
;
it sho
u
ld
.
.
.
commit
|
commitdiff
|
tree
2006-10-03
cjf
i
elds
Force IDs to be an arra
y
at a
l
l times
commit
|
commitdiff
|
tree
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