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Match parentheses.
2007-04-22
David
H
ilvert
Match pa
r
entheses
.
commit
|
commitdiff
|
tree
2007-04-22
D
a
vi
d
Hilver
t
d2/align
.
h:
E
n
c
apsula
t
e
reliability
c
h
e
ck
withi
n
i
s
_reliable
.
.
.
commit
|
commitdiff
|
tree
2007-04-22
Dav
i
d Hilvert
Change -
-
mcd-r
e
moval default
t
o 1
.
commit
|
commitdiff
|
tree
2007-04-22
David
H
i
lv
e
r
t
Var
i
ous changes and bugfixes
f
or dynami
c
monte c
a
rlo
.
.
.
commit
|
commitdiff
|
tree
2007-04-22
D
avid
Hilve
r
t
d2/align
.
h: prior
to chan
g
in
g
perturbat
i
o
n
step size
.
.
.
commit
|
commitdiff
|
tree
2007-04-21
Da
v
id
H
ilv
e
rt
Up
d
ate changelog
commit
|
commitdiff
|
tree
2007-04-21
David Hilv
e
rt
Update changelog
commit
|
commitdiff
|
tree
2007-04-21
Dav
i
d Hilvert
Set --
n
o
-
inc t
o
default
.
commit
|
commitdiff
|
tree
2007-04-21
David H
i
lvert
Add comment rega
r
ding re
m
oval methods i
n
d2/
a
lig
n
.
h
.
commit
|
commitdiff
|
tree
2007-04-20
Davi
d
H
ilvert
ui_tty
:
Add more
u
p
dates; revis
e
Ir
a
ni-Peleg ou
t
put
.
commit
|
commitdiff
|
tree
2007-04-20
David Hil
v
ert
d2
:
:
a
lign:
S
elec
t
b
es
t
error from each consecut
i
ve
.
.
.
commit
|
commitdiff
|
tree
2007-04-20
Davi
d
Hilvert
Changelog
update
commit
|
commitdiff
|
tree
2007-04-20
David Hilvert
U
p
da
t
e
c
h
ang
e
l
o
g
commit
|
commitdiff
|
tree
2007-04-20
Dav
i
d Hilvert
F
ix calculation of global
s
earch min
i
mum ove
r
l
a
p
c
ount
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David Hil
v
ert
ui_l
o
g: Fix f
o
rma
t
in
s
et_off
s
et()
.
commit
|
commitdiff
|
tree
2007-04-19
Da
v
id Hilvert
Change
--
g
s-mo default to
6
7
%
.
commit
|
commitdiff
|
tree
2007-04-19
Dav
i
d Hilvert
u
i
:
L
o
g ou
t
put enhancem
e
nts
.
commit
|
commitdiff
|
tree
2007-04-19
Da
v
id Hilv
e
rt
Allow --gs-m
o
to
be sp
e
cified as
a
percentage, make
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
d2::align: Mo
d
ify _align()
a
nd mak
e
_eleme
n
t_n
o
ntr
i
vial
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
d
2
:
:
ali
g
n:
Add method get_pert
u
rb_set()
.
commit
|
commitdiff
|
tree
2007-04-17
David Hi
l
vert
Add file '
V
ERSI
O
N' for cases where this does not exist
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
d2::trans
_
mu
l
ti::
s
pecific_resca
l
e(): Replac
e
asser
t
ion
.
.
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
Changelog ed
i
ts
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
Update changelo
g
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
Add
file ui_quiet
.
h
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilv
e
rt
configure
.
in
:
Use co
n
tents of file VE
R
SION for version
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
Mo
d
ify
black lev
e
l implementat
i
on to always
a
p
ply
t
o
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
A
dd 'qu
i
et' user i
n
t
e
r
face
type
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
M
ove output identification det
a
ils to user interface
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
ui
_
log::ip_st
e
p_don
e
(): 'F
i
nished frame' -->
'
Finished
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
D
a
vid Hilvert
Refine ui_log::
i
p_step_
d
one()
.
commit
|
commitdiff
|
tree
2007-04-15
D
a
vid Hilv
e
r
t
d2/ppm
.
h
:
Don't set
g
ain
values
i
f none
a
re s
p
e
cified
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David
H
ilve
r
t
u
i
_l
o
g: Add sepa
r
ate output for match
a
nd m
i
s
m
atch
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilvert
u
i
_log:
A
dd
m
ore logging output
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilvert
Add
r
udimentary logging interfa
c
e
.
commit
|
commitdiff
|
tree
2007-04-15
David
H
i
l
v
ert
u
i: Indicate when no local al
i
gn
m
ent details
ar
e
avai
l
able
.
commit
|
commitdiff
|
tree
2007-04-14
Dav
i
d
Hilv
e
r
t
d2:
:
trans_multi:
:
specific
_
rescale():
Ad
d
a
n
assert
.
.
.
commit
|
commitdiff
|
tree
2007-04-13
Da
v
id Hilvert
Begin
i
mplementing d2::al
i
gn::calculat
e
_
e
l
e
ment_
r
egio
n
()
.
commit
|
commitdiff
|
tree
2007-04-13
David Hilvert
d2::align::_a
l
ign(): Add code to stor
e
to and r
e
trieve
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
D
a
vid Hilvert
Add
c
ode to recalcul
a
t
e
each non-triv
i
al non-primary
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
Da
v
id H
i
lver
t
Add local_ax
_
count
t
o th
e
list
of paramet
e
r
s tak
e
n
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David Hilvert
Ch
a
n
ge bar
r
el
disto
r
tio
n
multiplier
a
nd r
a
te of change
.
.
.
commit
|
commitdiff
|
tree
2007-04-08
David
Hi
l
vert
Add metho
d
s
d2::
a
lign::
m
ake_element_nontrivia
l
(
)
,
d
2
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
d2::al
i
gn:
:
follow(
)
: Reve
r
t
l
oo
p
ing
o
ve
r
old_* e
l
ement
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
d2::
a
lign::fol
l
o
w(): Update el
e
me
n
t indices o
f
a
ll
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
av
i
d
Hilv
e
r
t
d2::tfile: Bugfix in
handling of non
-
prima
r
y el
e
ments
.
commit
|
commitdiff
|
tree
2007-04-03
David Hil
v
ert
Copy
r
igh
t
notice updates
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
Add code for load
i
ng
and saving no
n
-primary alignment
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Da
v
id Hilvert
Up
d
a
t
e chan
g
elog
.
commit
|
commitdiff
|
tree
2007-04-03
Davi
d
Hilvert
ui: Modify match format strings to provide constant
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David
Hilvert
ui_tty
:
Add
field width and
p
recision specifiers
to
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David
Hilvert
Swap ar
g
u
ments t
o
a
l
ignment
status
s
o
t
h
at frequ
e
n
t
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
avid Hilvert
ui_
t
ty:
Change f
l
oatin
g
point formats fr
o
m %f to %g
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Dav
i
d Hilvert
d
2
:
:
align: M
o
v
e followi
n
g logic from _align() to
a
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David H
i
lve
r
t
Upda
t
e
changelog
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Remove file 'sgauss
.
h'
m
i
ssing f
r
om sgaus
s
patch, a
s
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hilver
t
Add missing
f
ile from
e
a
rl
i
er sgauss
pat
c
h
.
Will be
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
Da
v
id
Hilv
e
r
t
Upda
t
e changelog
commit
|
commitdiff
|
tree
2007-04-02
David
H
i
lv
e
rt
Update changelog
commit
|
commitdiff
|
tree
2007-04-02
D
a
vid Hilvert
Mov
e
the multi-transf
o
rmation element swi
t
c
hing loop
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
Davi
d
Hilvert
Upd
a
te Changelog
commit
|
commitdiff
|
tree
2007-04-02
David
Hilve
r
t
d2/alig
n
.
h: Re
c
alculate diff stat
i
stics
a
f
ter increasing
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David
Hilvert
M
o
dify handling of -
-
identity in d
2
:
:align so that
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Davi
d
Hilve
r
t
Add methods for enabling an
d
d
isa
b
li
n
g restricted support
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David H
i
lvert
Add check for
transform
a
tion sup
p
ort to d2::
a
lign:
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David
H
ilvert
d2::
t
ra
n
s_multi: Add met
h
o
d
supp
o
rted() to check
for
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
D
avid Hilvert
Begin using
non-
t
rivial multi-tr
a
n
s
f
o
r
ma
t
ion
s
in d2
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
Davi
d
Hil
v
ert
d2::trans
_
multi: Ad
d
get
_
e
l
ement() met
h
od
.
commit
|
commitdiff
|
tree
2007-03-27
David
Hilvert
d
2:
:
r
ender::ipc: Modi
f
y a
l
loca
t
ion for
s
ubdom
a
i
n arguments
.
.
.
commit
|
commitdiff
|
tree
2007-03-24
Dav
i
d
Hilv
e
rt
d
2
::align
:
Allocate kept_
t
wi
t
h
new
[
] rather than malloc
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
D
a
vid Hilvert
Mod
i
f
y
specific_*() calls
i
n d2::trans_mul
t
i to call
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
D
avid
H
ilve
r
t
Allocate d2::incremental:
:
su
b
domai
n
_args
with
n
ew[
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilvert
Resolve certain co
m
p
ilation
a
nd run-time failur
e
s
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilvert
d2::trans_mult
i
:
U
pdate met
h
ods for a trivia
l
mu
l
ti
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
Da
v
id H
i
lvert
Initial version of d2/trans_multi
.
h, taken f
r
o
m
the
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilvert
Add file d2/
t
rans_singl
e
.
h
for implementing single
.
.
.
commit
|
commitdiff
|
tree
2007-03-21
Dav
i
d
Hilve
r
t
Move si
n
gle-transformatio
n
class specif
i
cs from d2
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David
Hilve
r
t
d2/trans_abstr
a
ct
.
h
: In
i
tial implement
a
ti
o
n of an abstract
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David Hilv
e
rt
d2/tfile
.
h
:
Call ungetc() when test for non-primary
.
.
.
commit
|
commitdiff
|
tree
2007-03-15
Dav
i
d
Hilv
e
rt
Revise handling of MA element
s
.
commit
|
commitdiff
|
tree
2007-03-15
D
a
v
id Hilve
r
t
Modif
y
--ma-card to ran
g
e [
1
,
i
nf) a
n
d add code to iterate
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
D
avi
d
Hilv
e
r
t
Add
f
lags t
o
d2::ali
g
n::elem
e
nt_t and d2:;tf
i
l
e t
o
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
Dav
i
d Hilve
r
t
u
i
/u
i
_
tty
.
h:
R
e
v
i
se update
(
) and update_loop() so
that
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
David Hi
l
vert
ui
/
ui_tt
y
.
h
:
A
dd
a UI update thread
.
commit
|
commitdiff
|
tree
2007-03-13
Dav
i
d Hil
v
ert
d2::a
l
ign: expand and rename the data structure for
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
David Hilvert
d
2::
a
lign: Make a struct
u
re for follow se
m
antics variabl
e
s
.
.
.
commit
|
commitdiff
|
tree
2007-03-12
David Hilvert
Add option hand
l
in
g
f
o
r --ma-card and --ma-cont multi
.
.
.
commit
|
commitdiff
|
tree
2007-03-10
David Hi
l
v
ert
Update c
h
angelog
commit
|
commitdiff
|
tree
2007-03-10
David Hilvert
Up
d
a
t
e he
l
p
t
ext to reflect new
f
ile-scop
e
d option
s
.
commit
|
commitdiff
|
tree
2007-03-10
David Hilvert
Allow file-scop
e
d --g
s
a
nd
--gs-mo
commit
|
commitdiff
|
tree
2007-03-09
David Hilve
r
t
Up
d
ate chan
g
el
o
g
commit
|
commitdiff
|
tree
2007-03-09
David Hilvert
Ignore
f
e
x
regi
o
ns when nex
is sp
e
c
if
i
ed
.
commit
|
commitdiff
|
tree
2007-03-09
David Hilv
e
rt
U
pd
a
te chang
e
log
commit
|
commitdiff
|
tree
2007-03-09
David Hilver
t
Add --
b
lack
option
f
or
s
etting bl
a
ck l
e
vel
.
commit
|
commitdiff
|
tree
2007-03-08
D
a
vid Hilvert
Add o
p
ti
o
n --ev for sett
i
ng exp
o
s
ure value me
t
a
-
d
ata
.
commit
|
commitdiff
|
tree
2007-03-08
Dav
i
d
Hilvert
Disable i
m
plicati
o
n f
o
r --exp-regist
e
r when --cx is
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
D
avid Hilvert
Modify
prof
i
le local alig
n
m
e
n
t detail ou
t
put to omit
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David
H
il
v
ert
Update changelog
commit
|
commitdiff
|
tree
2007-03-07
David Hil
v
ert
Updat
e
profiling timers to include timing details for
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
Dav
i
d Hi
l
v
e
rt
d2/ppm
.
h: Upda
t
e error
message fo
r
n
on-PPM files
to
.
.
.
commit
|
commitdiff
|
tree
next