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Change --gs-mo default to 67%.
2007-04-19
David
H
ilve
r
t
Cha
n
ge --gs-mo default to
6
7
%
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
ui: Log out
p
ut
e
nha
n
cements
.
commit
|
commitdiff
|
tree
2007-04-19
Dav
i
d
Hilv
e
rt
A
l
l
ow
-
-
gs-mo to
be spe
c
ified as a per
c
e
n
t
age, make
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David H
i
lvert
d2
:
:align: M
o
dify _al
i
gn()
a
nd mak
e
_element_nontrivial
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilve
r
t
d2::align: Add
method get_pertu
r
b_
s
et()
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
Add fi
l
e 'VERS
I
ON' for ca
s
es where this does not exis
t
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
d2::trans_
m
u
lti::specific_rescale(): Replac
e
asse
r
tion
.
.
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
Cha
n
gelog edits
.
commit
|
commitdiff
|
tree
2007-04-17
David
H
i
l
ver
t
Up
d
ate changelog
commit
|
commitdiff
|
tree
2007-04-17
David
Hilvert
Add f
i
le ui_quiet
.
h
.
commit
|
commitdiff
|
tree
2007-04-17
David
Hilvert
config
u
r
e
.
i
n: Use contents of file VER
S
ION
f
or version
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David
Hilvert
Modify black level implementation to always apply
t
o
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
Add 'quiet' u
s
er in
t
erface type
.
commit
|
commitdiff
|
tree
2007-04-16
David
H
ilvert
Move
o
ut
p
ut identification det
a
ils to
u
ser
interface
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
ui
_
log:
:
ip_step_done(): 'Finish
e
d frame'
-
-
> 'Finished
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
Da
v
i
d
Hi
l
vert
Refine
ui
_
log::ip_step_don
e
()
.
commit
|
commitdiff
|
tree
2007-04-15
David
H
ilvert
d2/ppm
.
h: Don't
s
et gain values if none are specified
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
D
a
v
i
d Hilvert
ui_log: Add separate output for match and m
i
smatch
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
D
avid Hilve
r
t
ui_log: Add mo
r
e logging output
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilve
r
t
Add rud
i
mentary
l
o
g
g
ing interface
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilver
t
ui: Indicat
e
when
n
o local alignment details are avail
a
b
le
.
commit
|
commitdiff
|
tree
2007-04-14
Da
v
id Hilvert
d2
:
:trans_m
u
lti::specifi
c
_rescale(): Ad
d
an asse
r
t
.
.
.
commit
|
commitdiff
|
tree
2007-04-13
David Hilvert
Begin i
m
plem
e
nting
d2
:
:al
i
g
n
:
:
calculate_e
l
em
e
nt_region()
.
commit
|
commitdiff
|
tree
2007-04-13
David Hilvert
d2::a
l
ign::_
a
lig
n
()
:
Add c
o
de to s
t
o
r
e
to and
r
e
trieve
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
Da
v
id Hilve
r
t
Ad
d
c
ode t
o
r
ecalculate each non-trivial non
-
primary
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
Dav
i
d Hilvert
Add local_a
x
_co
u
nt to
t
h
e
list of parameters take
n
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David Hi
l
vert
Change barre
l
di
s
tortion multiplier
a
n
d rate of cha
n
ge
.
.
.
commit
|
commitdiff
|
tree
2007-04-08
David Hilver
t
Add metho
d
s d2::align
:
:m
a
ke_ele
m
ent
_
nontriv
i
al()
,
d2
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
avid Hil
v
er
t
d
2
::align::foll
o
w(): Revert looping
o
v
e
r
old_*
e
leme
n
t
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilve
r
t
d2::al
i
gn::follow(): Upda
t
e element
i
n
dice
s
of
a
ll
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hi
l
v
e
r
t
d2::t
f
ile:
B
u
gfix in handlin
g
of non-prim
a
ry elem
e
nts
.
commit
|
commitdiff
|
tree
2007-04-03
D
avi
d
Hilvert
C
o
pyri
g
h
t
notice updates
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
Add code
for
l
oading and s
a
ving non-p
r
i
mary al
i
gn
m
ent
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilve
r
t
Update chan
g
e
l
og
.
commit
|
commitdiff
|
tree
2007-04-03
David Hi
l
vert
ui: Modify ma
t
ch format strings to
p
ro
v
ide constant
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Da
v
id Hilvert
ui_tty:
A
dd field width
a
nd precision specifiers to
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
Swap arguments to alignment status
so that
f
r
equ
e
nt
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Dav
i
d Hi
l
vert
u
i_tty: Change floatin
g
point formats from %f
t
o
%g
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David H
i
lver
t
d2::
a
li
g
n:
Move fo
l
lowing logic fro
m
_al
i
g
n
()
to a
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
D
avid Hilvert
Updat
e
changelog
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Rem
o
ve file 'sg
a
uss
.
h' m
i
ssing from
s
gau
s
s patch, as
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Add
missin
g
file from
earli
e
r sg
a
u
s
s patch
.
Will be
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
Davi
d
Hilvert
Update c
h
angel
o
g
commit
|
commitdiff
|
tree
2007-04-02
D
a
v
id
H
ilvert
U
p
d
a
te chan
g
elo
g
commit
|
commitdiff
|
tree
2007-04-02
D
avid H
i
lver
t
Move the
m
ul
t
i-transformatio
n
element s
w
itching loop
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David
H
ilvert
Update Ch
a
ngelog
commit
|
commitdiff
|
tree
2007-04-02
David
H
ilvert
d
2/al
i
gn
.
h: Recalculate diff
s
ta
t
istic
s
af
t
er inc
r
eas
i
ng
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David H
i
lvert
M
od
i
fy handli
n
g of --identit
y
in
d2::
a
l
i
gn so that
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Dav
i
d Hi
l
vert
Add
m
eth
o
d
s
for enab
l
ing and disabli
n
g restricted suppo
r
t
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David Hilv
e
rt
Ad
d
check for tr
a
nsformation s
u
pport to d2::align:
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David Hilvert
d2::tra
n
s_mult
i
:
A
dd method s
u
pporte
d
() to c
h
e
ck for
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
David Hil
v
ert
Beg
i
n usin
g
n
o
n-trivi
a
l mu
l
ti-tr
a
n
sfo
r
mations i
n
d
2
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
Dav
i
d Hilvert
d
2
::trans_mult
i
: Add get_element() method
.
commit
|
commitdiff
|
tree
2007-03-27
David Hilvert
d2::ren
d
er::ipc: Mo
d
ify
a
lloca
t
ion for sub
d
oma
i
n argu
m
en
t
s
.
.
.
commit
|
commitdiff
|
tree
2007-03-24
D
a
vid H
i
lvert
d
2
::align: All
o
cate kept_t with new[] rath
e
r t
h
an mal
l
oc
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
Da
v
id Hilvert
Modify
spe
c
ific_*() calls
in d2::trans_mul
t
i to call
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
Davi
d
Hilvert
Allocate d2:
:
incremental::subdomain_arg
s
w
ith new[
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
D
avid H
i
lvert
R
e
s
olve
certain c
o
mpil
a
tion and ru
n
-
t
ime failures
.
commit
|
commitdiff
|
tree
2007-03-23
D
a
vid
H
i
l
ve
r
t
d2::tran
s
_multi: Update methods for a trivial mult
i
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
D
avid Hilvert
Initial version of d2/trans_multi
.
h, taken from th
e
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilvert
Add
f
ile d2/trans_
s
ingle
.
h for im
p
le
m
e
nting single
.
.
.
commit
|
commitdiff
|
tree
2007-03-21
David Hilv
e
r
t
Mo
v
e s
i
ngl
e
-transformati
o
n class specif
i
cs
from d2
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David
H
ilver
t
d2/t
r
ans_abstract
.
h
:
Initial implement
a
tion of
an abstract
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David Hilvert
d2
/
tfi
l
e
.
h: Call ungetc() when test for non-p
r
imar
y
.
.
.
commit
|
commitdiff
|
tree
2007-03-15
Dav
i
d H
i
lve
r
t
R
e
vis
e
handling of MA ele
m
ents
.
commit
|
commitdiff
|
tree
2007-03-15
D
a
vid Hilvert
Modify --m
a
-c
a
rd to r
a
nge [1,inf) and add code to iterate
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
David H
i
lvert
Add flags to d2::align::element
_
t and d2:;tfi
l
e to
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
David Hil
v
er
t
ui/u
i
_tty
.
h: Revi
s
e
up
d
ate() and u
p
date_loop() so t
h
at
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
Da
v
id Hilvert
ui/u
i
_tty
.
h: Add a
UI u
p
date thread
.
commit
|
commitdiff
|
tree
2007-03-13
David Hilver
t
d
2::al
i
gn:
e
xp
a
nd and rename t
h
e data
s
t
r
uctu
r
e fo
r
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
D
a
vid
Hi
l
ver
t
d2::align: Make a structure f
o
r foll
o
w sema
n
ti
c
s
v
ariables
.
.
.
commit
|
commitdiff
|
tree
2007-03-12
David H
i
lvert
Add opt
i
on handli
n
g
f
or --
m
a-
c
ard a
n
d --ma-cont multi
.
.
.
commit
|
commitdiff
|
tree
2007-03-10
David Hilvert
Update changelog
commit
|
commitdiff
|
tree
2007-03-10
David Hi
l
vert
Update hel
p
text
t
o reflect new file-s
c
op
e
d options
.
commit
|
commitdiff
|
tree
2007-03-10
D
a
vid Hilvert
A
l
lo
w
file-sc
o
pe
d
--gs and --gs-
m
o
commit
|
commitdiff
|
tree
2007-03-09
D
avid Hil
v
er
t
Update changelog
commit
|
commitdiff
|
tree
2007-03-09
Dav
i
d Hilvert
Ignore fex
r
eg
i
ons when nex is specified
.
commit
|
commitdiff
|
tree
2007-03-09
David Hilvert
Upda
t
e
c
h
a
ngelog
commit
|
commitdiff
|
tree
2007-03-09
David Hilvert
A
dd --b
l
ack op
t
ion f
o
r
s
e
tting black
l
evel
.
commit
|
commitdiff
|
tree
2007-03-08
David Hilve
r
t
Add option --ev fo
r
s
etting expos
u
re
v
alue
meta-data
.
commit
|
commitdiff
|
tree
2007-03-08
David Hilvert
Disable implication for
--exp-register
w
hen --cx is
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David Hil
v
ert
M
odify prof
i
le
local a
l
ignment detail outpu
t
to omit
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
Davi
d
Hilvert
Update changelog
commit
|
commitdiff
|
tree
2007-03-07
David Hilver
t
Update
p
rofiling tim
e
r
s to
i
n
clude timing detail
s
for
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
D
a
vid
Hi
l
ve
r
t
d2
/
ppm
.
h: Update error messa
g
e f
o
r non-
P
PM files to
.
.
.
commit
|
commitdiff
|
tree
2007-03-04
David Hilvert
Update NEWS and version
numbers fo
r
0
.
8
.
7 release
.
commit
|
commitdiff
|
tree
2007-03-03
David Hilver
t
Update changelog
.
commit
|
commitdiff
|
tree
2007-03-03
D
a
v
id Hilvert
Make -
-
ip-nowl default
.
commit
|
commitdiff
|
tree
2007-02-25
David
H
i
lvert
Update cha
n
g
e
log
.
commit
|
commitdiff
|
tree
2007-02-25
Da
v
id
Hilvert
Revi
s
e argument
h
andling for
ip
-
wl a
r
guments
.
commit
|
commitdiff
|
tree
2007-02-25
D
a
vi
d
H
i
l
v
ert
Impl
e
ment
I
ran
i
-Peleg we
i
ght
l
imit
s
,
and se
t
a default
.
.
.
commit
|
commitdiff
|
tree
2007-02-25
Dav
i
d Hilvert
Upda
t
e Cha
n
ge
l
og
commit
|
commitdiff
|
tree
2007-02-25
David Hilvert
Add an inc
r
emental rend
e
rer mean invariant we
i
g
ht-li
m
ited
.
.
.
commit
|
commitdiff
|
tree
2007-02-24
Da
v
i
d Hilvert
d2::filter::sca
l
ed_fi
l
ter::filter_channel(): Slightly
.
.
.
commit
|
commitdiff
|
tree
2007-02-24
Davi
d
Hi
l
v
ert
Update
c
hange
l
og
commit
|
commitdiff
|
tree
2007-02-24
David
H
ilvert
d
2
:
:
image::defined_scale_by_half(): Replace incorrect
.
.
.
commit
|
commitdiff
|
tree
2007-02-24
Da
v
id Hilvert
d2::imag
e
::defined_sc
a
le_b
y
_
h
alf(): Use geomet
r
i
c
me
a
n
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
David Hi
l
vert
d2/filter/
s
caled
_
fi
l
ter
.
h: Clean
u
p rece
n
tly
added
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
David Hi
l
ver
t
d2/filter/scaled_filt
e
r
.
h: Revis
e
certa
i
n
t
y calculatio
n
s
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
Da
v
id Hilver
t
NEWS: add 0
.
8
.
6 r
e
lease information
commit
|
commitdiff
|
tree
next