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Change --gs-mo default to 67%.
2007-04-19
David Hilvert
Change
-
-gs-mo default to 67%
.
commit
|
commitdiff
|
tree
2007-04-19
David
H
ilver
t
u
i: Log output e
n
h
a
n
c
ements
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilver
t
A
llow --g
s
-mo to be specifie
d
as
a
p
ercenta
g
e, make
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
d
2
::align: M
o
dify
_
a
li
g
n
(
) and
make_eleme
n
t_non
t
r
i
vial
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
d2::a
l
ign: A
d
d method get_pert
u
rb_set
(
)
.
commit
|
commitdiff
|
tree
2007-04-17
D
avid Hil
v
ert
Add file 'VERSIO
N
'
for cases where this does
not ex
i
s
t
.
commit
|
commitdiff
|
tree
2007-04-17
Dav
i
d
Hilvert
d2:
:
trans_multi::spec
i
fic_rescal
e
(
)
:
R
e
place assert
i
on
.
.
.
commit
|
commitdiff
|
tree
2007-04-17
D
a
vid
H
ilvert
Changelo
g
edits
.
commit
|
commitdiff
|
tree
2007-04-17
Davi
d
Hilv
e
rt
U
p
dat
e
chan
g
elog
commit
|
commitdiff
|
tree
2007-04-17
D
a
vid Hilv
e
rt
Add
fi
l
e ui
_
quiet
.
h
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
co
n
figure
.
in: Us
e
con
t
ent
s
of fi
l
e VERSI
O
N for ve
r
s
i
on
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
Da
v
i
d
Hilvert
Modify
b
lack level im
p
lementation to always apply to
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hil
v
ert
Add 'quiet' use
r
interface type
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
Move output i
d
ent
i
ficati
o
n de
t
ails to
u
ser inte
r
face
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
u
i
_log::
i
p
_step_don
e
(): '
F
inished frame'
-
->
'Finished
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
Re
f
ine ui
_
log::
i
p_
s
tep_don
e
()
.
commit
|
commitdiff
|
tree
2007-04-15
D
avid Hilvert
d2/ppm
.
h: Don't set g
a
in values if none are specified
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilv
e
rt
ui_log: Add se
p
a
rate outp
u
t
for match and mismatch
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
Dav
i
d Hilvert
ui_log
:
Add more logging output
.
commit
|
commitdiff
|
tree
2007-04-15
Dav
i
d Hilvert
Add rudime
n
tary logging interface
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilver
t
ui: Indicate when no local
a
li
g
nm
e
nt det
a
ils are av
a
ilable
.
commit
|
commitdiff
|
tree
2007-04-14
David Hilvert
d2::trans_
m
ul
t
i:
:
specif
i
c_res
c
ale():
Add an assert
.
.
.
commit
|
commitdiff
|
tree
2007-04-13
D
a
vid Hil
v
ert
Begin im
p
lementing d2::
a
l
i
g
n::calculate_element_region()
.
commit
|
commitdiff
|
tree
2007-04-13
Da
v
id
H
ilve
r
t
d2::align:
:
_
a
li
g
n(): Add code to s
t
ore
to
a
nd retrieve
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David Hi
l
vert
Add co
d
e to reca
l
cula
t
e
each n
o
n
-
trivial non-
p
r
i
m
ary
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David Hilvert
Ad
d
local_a
x
_count t
o
the
l
ist of paramete
r
s take
n
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
Da
v
id Hi
l
ver
t
Change barrel disto
r
tion
m
ultiplier and
rate of change
.
.
.
commit
|
commitdiff
|
tree
2007-04-08
Dav
i
d Hilv
e
rt
A
dd met
h
o
d
s d2::align::make_eleme
n
t_nontrivi
a
l()
,
d2
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hil
v
ert
d2::a
l
ign::follow(): Revert loopi
n
g over old_* element
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Davi
d
Hilve
r
t
d2
:
:ali
g
n::fo
l
low(
)
: U
p
da
t
e element
i
ndices of all
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
d2
:
:tfile: Bugfix in handlin
g
of non-pri
m
a
r
y e
l
e
ments
.
commit
|
commitdiff
|
tree
2007-04-03
Da
v
id
H
ilvert
C
o
pyri
g
ht no
t
i
ce updates
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
vid H
i
lvert
Add
c
ode
f
o
r loading
and saving no
n
-pri
m
ary
alignment
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David H
i
lvert
Update
c
h
ang
e
lo
g
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
ui: Modif
y
matc
h
fo
r
mat strings to provide
constant
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David
H
ilvert
ui_tt
y
: Add field w
i
d
th and p
r
ecision
s
peci
f
ie
r
s to
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Da
v
id Hil
v
ert
Swap arguments to alignment
s
tatus so that
f
r
equent
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David
Hilvert
ui_tty:
C
hange floating point formats
f
ro
m
%f
to
%g
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
d
2
::al
i
g
n:
M
ov
e
following logic from _align() to a
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Update c
h
angelog
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Remove file
'sgauss
.
h' missing from sgauss patch, as
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hilv
e
rt
Add m
i
s
sing fil
e
from earlier sg
a
uss pat
c
h
.
W
ill be
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
Dav
i
d
Hilv
e
rt
U
p
dat
e
c
h
angelog
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Update change
l
og
commit
|
commitdiff
|
tree
2007-04-02
Davi
d
Hi
l
vert
M
ove the multi-
t
ran
s
f
or
m
ation elemen
t
switching lo
o
p
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Upda
t
e Chang
e
log
commit
|
commitdiff
|
tree
2007-04-02
Da
v
id
Hilvert
d2/a
l
ign
.
h: R
e
calculate
di
f
f statistics
a
f
ter increasing
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David
H
ilvert
Modify han
d
ling of --identity in d2::align so that
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Da
v
id Hil
v
ert
Add methods f
o
r
e
n
a
bli
n
g
and
disabling re
s
tri
c
ted support
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David Hilvert
A
d
d
check for transformati
o
n support t
o
d
2
:
:al
i
gn:
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David
H
ilvert
d2
:
:tran
s
_mu
l
ti
:
Add
method supported() to c
h
eck
for
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
David
Hilv
e
rt
Be
g
in
using non
-
t
r
ivi
a
l multi-transfo
r
mations in d2
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
David Hilvert
d2::tran
s
_multi:
A
d
d get_eleme
n
t()
method
.
commit
|
commitdiff
|
tree
2007-03-27
D
a
vid Hilvert
d2::render
:
:
ipc: Modi
f
y
all
o
cation fo
r
s
u
bdomain
ar
g
uments
.
.
.
commit
|
commitdiff
|
tree
2007-03-24
D
avid Hilvert
d2::align: All
o
cate kept_t with new[]
rather tha
n
mal
l
o
c
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
Da
v
id
H
i
l
vert
Modify sp
e
c
i
f
ic_*() c
a
lls i
n
d2::trans_
m
ulti
t
o call
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilvert
Allocate d2::incre
m
enta
l
::subdomain_args with new[
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David H
i
lvert
Res
o
lv
e
c
er
t
ain compila
t
ion and ru
n
-time
f
ailure
s
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilv
e
rt
d2::trans_mul
t
i: Update methods for
a
tr
i
vial m
u
l
t
i
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilv
e
rt
Initial version of d2/trans
_
mul
t
i
.
h,
t
ak
e
n from t
h
e
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David
Hil
v
ert
Add f
i
l
e
d
2
/trans_single
.
h for impleme
n
ti
n
g singl
e
.
.
.
commit
|
commitdiff
|
tree
2007-03-21
David Hilvert
Mo
v
e
si
n
gle
-
transfo
r
mation cl
a
ss specifics from
d
2
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David Hilvert
d2/trans_abs
t
ract
.
h: In
i
tial
i
mplementat
i
on of an abs
t
r
act
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David Hilve
r
t
d2/tf
i
le
.
h: C
a
ll ungetc() when test for non-primary
.
.
.
commit
|
commitdiff
|
tree
2007-03-15
David H
i
lvert
R
ev
i
se handling of MA elements
.
commit
|
commitdiff
|
tree
2007-03-15
D
avid
H
ilv
e
rt
Modify --ma-c
a
rd
t
o
r
a
n
ge [1,inf) and add cod
e
t
o
iter
a
te
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
Dav
i
d
Hilvert
Add
flags
t
o d2::align:
:
element_t an
d
d
2
:;tfile to
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
David Hilvert
ui/u
i
_tty
.
h
: Rev
i
se upd
a
te() a
n
d updat
e
_l
o
op() so that
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
Dav
i
d Hilvert
ui/ui_tty
.
h: Add a UI up
d
ate th
r
ead
.
commit
|
commitdiff
|
tree
2007-03-13
David
H
ilve
r
t
d2::al
i
gn:
e
xpand and rename the data structure for
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
David Hilvert
d2::a
l
ign: Ma
k
e a structure for follow seman
t
ics variables
.
.
.
commit
|
commitdiff
|
tree
2007-03-12
Da
v
i
d Hilv
e
rt
Add
opt
i
on handling for --ma-card and -
-
ma-
c
ont multi
.
.
.
commit
|
commitdiff
|
tree
2007-03-10
D
avid Hilvert
Update chang
e
l
o
g
commit
|
commitdiff
|
tree
2007-03-10
David
H
ilvert
Update help text to reflect new file-scoped options
.
commit
|
commitdiff
|
tree
2007-03-10
David Hilvert
Allow
f
ile-scoped
-
-gs and --gs-
m
o
commit
|
commitdiff
|
tree
2007-03-09
David Hi
l
vert
U
p
dat
e
ch
a
n
gelog
commit
|
commitdiff
|
tree
2007-03-09
David Hilve
r
t
Ignore fex
r
e
gions when
nex
i
s spec
i
fi
e
d
.
commit
|
commitdiff
|
tree
2007-03-09
David
Hilvert
Up
d
ate cha
n
gelog
commit
|
commitdiff
|
tree
2007-03-09
Davi
d
Hilvert
Add --bla
c
k
o
ptio
n
for setting blac
k
l
ev
e
l
.
commit
|
commitdiff
|
tree
2007-03-08
D
a
vid Hil
v
ert
Ad
d
optio
n
--ev for setting exposure
v
alue meta-data
.
commit
|
commitdiff
|
tree
2007-03-08
Davi
d
H
i
lver
t
Disable impli
c
ation for --exp
-
regis
t
er when --cx is
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David Hil
v
ert
Modi
f
y pro
f
i
le local alig
n
men
t
detail outpu
t
to om
i
t
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David Hilvert
Update ch
a
n
g
e
l
o
g
commit
|
commitdiff
|
tree
2007-03-07
Da
v
i
d
H
i
l
vert
Update p
r
o
f
iling
t
i
mers
t
o include timing
details fo
r
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David Hilvert
d2/ppm
.
h: Update error message for n
o
n-PPM fil
e
s to
.
.
.
commit
|
commitdiff
|
tree
2007-03-04
D
a
vid Hilvert
Up
d
ate NEWS
a
n
d
v
ersion numbers f
o
r 0
.
8
.
7 release
.
commit
|
commitdiff
|
tree
2007-03-03
D
a
v
id
H
ilver
t
Update changelog
.
commit
|
commitdiff
|
tree
2007-03-03
Da
v
i
d
Hilvert
M
a
ke --
i
p-no
w
l default
.
commit
|
commitdiff
|
tree
2007-02-25
David Hilvert
Update changelog
.
commit
|
commitdiff
|
tree
2007-02-25
David
H
ilvert
Revise arg
u
ment handli
n
g
f
or ip-
w
l
arguments
.
commit
|
commitdiff
|
tree
2007-02-25
D
avid Hil
v
e
rt
Implement Irani-Pe
l
eg weight limits, and set a default
.
.
.
commit
|
commitdiff
|
tree
2007-02-25
David Hil
v
e
r
t
Update
C
hange
l
og
commit
|
commitdiff
|
tree
2007-02-25
David Hilvert
Ad
d
an incre
m
ental rend
e
r
e
r
mean
i
nvarian
t
weight-limited
.
.
.
commit
|
commitdiff
|
tree
2007-02-24
David Hilver
t
d
2
::filte
r
::
s
caled_
f
ilter::fil
t
er_chan
n
el(): S
l
ightly
.
.
.
commit
|
commitdiff
|
tree
2007-02-24
Dav
i
d Hilver
t
U
pdate cha
n
gelog
commit
|
commitdiff
|
tree
2007-02-24
David Hilvert
d2::imag
e
::de
f
ined
_
scale_by_h
a
lf():
R
eplace incorrect
.
.
.
commit
|
commitdiff
|
tree
2007-02-24
David Hilvert
d
2::image::define
d
_scale_by_half(
)
: U
s
e geom
e
tric mean
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
David Hilvert
d2/filter/scaled_filter
.
h: Clean up
r
ecently
adde
d
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
David Hi
l
v
e
r
t
d2/fi
l
ter
/
scaled
_
f
ilte
r
.
h:
R
e
vise
c
erta
i
nty calculati
o
ns
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
Dav
i
d Hilver
t
NEWS: add 0
.
8
.
6 release i
n
f
or
m
ation
commit
|
commitdiff
|
tree
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