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Update changelog
2007-04-21
D
avid Hilver
t
Update changelog
commit
|
commitdiff
|
tree
2007-04-21
David
Hilvert
Set --no-inc t
o
d
efault
.
commit
|
commitdiff
|
tree
2007-04-21
David Hilvert
Ad
d
co
m
ment rega
r
ding removal methods in d2/align
.
h
.
commit
|
commitdiff
|
tree
2007-04-20
David Hilvert
ui_tty:
Add
more updates
;
revise Ir
a
ni-Pel
e
g outpu
t
.
commit
|
commitdiff
|
tree
2007-04-20
David Hilve
r
t
d
2::alig
n
: Select best er
r
or from each c
o
nsecuti
v
e
.
.
.
commit
|
commitdiff
|
tree
2007-04-20
David Hilvert
C
han
g
elog upda
t
e
commit
|
commitdiff
|
tree
2007-04-20
David Hilver
t
Update changelog
commit
|
commitdiff
|
tree
2007-04-20
Dav
i
d Hi
l
v
ert
Fix calcu
l
ation
of global search minimum ove
r
lap
count
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David
H
i
lvert
ui_log: Fix format in set_offset()
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilve
r
t
C
hange --g
s
-
m
o
default to
67
%
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
u
i
: Log outpu
t
enh
a
ncements
.
commit
|
commitdiff
|
tree
2007-04-19
D
avi
d
Hilvert
Allow
-
-gs-mo
to b
e
s
pecified as a percentage, make
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
d2::align:
Modify _align() and
m
ake
_
element_nontrivial
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
D
avid Hilvert
d2::align:
A
dd
m
et
h
od get_pe
r
turb_set()
.
commit
|
commitdiff
|
tree
2007-04-17
D
avid H
i
lvert
Ad
d
file 'VERS
I
ON' for
ca
s
e
s where this does
not
e
x
i
st
.
commit
|
commitdiff
|
tree
2007-04-17
Davi
d
Hilver
t
d2::
t
r
ans_multi::s
p
ecific_rescale(): Replace assertion
.
.
.
commit
|
commitdiff
|
tree
2007-04-17
David H
i
l
v
ert
Changelog edits
.
commit
|
commitdiff
|
tree
2007-04-17
D
a
v
i
d Hilve
r
t
Update changelog
commit
|
commitdiff
|
tree
2007-04-17
Davi
d
H
il
v
ert
A
d
d file ui_quiet
.
h
.
commit
|
commitdiff
|
tree
2007-04-17
David
Hilv
e
rt
configur
e
.
in: Use conten
t
s
of f
i
le VERS
I
O
N
f
or ver
s
ion
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
Da
v
i
d
H
i
lvert
M
o
d
ify black level
implementation
to always a
p
ply to
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hil
v
ert
Add 'quiet' user
int
e
rface t
y
pe
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
M
o
ve outp
u
t id
e
ntif
i
c
a
tion details to u
s
e
r
i
nter
f
ace
.
commit
|
commitdiff
|
tree
2007-04-16
Da
v
i
d Hilvert
ui_log::ip
_
s
t
ep_don
e
(
)
: 'Finishe
d
frame' --> 'Finis
h
ed
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
Refine ui_log::
i
p_step_done()
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilver
t
d2/ppm
.
h: Don't set gain valu
e
s
i
f none are specified
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilvert
u
i_
l
og: Add sep
a
rate o
u
t
put
f
or
match an
d
mi
s
match
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
D
avid Hilvert
ui_log
:
Add more logging
out
p
u
t
.
commit
|
commitdiff
|
tree
2007-04-15
Dav
i
d Hi
l
ver
t
Add rudimentary logging interface
.
commit
|
commitdiff
|
tree
2007-04-15
Davi
d
H
ilvert
ui: Indi
c
ate when no
l
oca
l
alignme
n
t
deta
i
l
s
are
a
v
ailable
.
commit
|
commitdiff
|
tree
2007-04-14
David Hilvert
d2::
t
ra
n
s_multi::specific_rescale(): A
d
d an assert
.
.
.
commit
|
commitdiff
|
tree
2007-04-13
David Hil
v
ert
Begin implementing d2::align::calculate_element_region
(
)
.
commit
|
commitdiff
|
tree
2007-04-13
Dav
i
d
Hilvert
d2::align::_
a
l
ign(): Add cod
e
to
store to
a
nd retrieve
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David Hilvert
A
dd code to r
e
calculate each n
o
n-trivia
l
n
on-primary
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
Dav
i
d
Hil
v
ert
Add
local_ax_
c
ount
t
o the list of pa
r
ameter
s
t
a
ken
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David Hilvert
Change barrel
dis
t
ortion multip
l
i
e
r and rate
o
f
change
.
.
.
commit
|
commitdiff
|
tree
2007-04-08
David Hilvert
Add
m
ethods d2
:
:
align::make_eleme
n
t_nontrivial(), d2
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
d2::align::follow():
R
evert
l
o
o
p
i
ng ove
r
old_*
element
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
d2::alig
n
::follow(): Update elem
e
nt
i
ndices of all
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David
H
ilvert
d2
:
:tfile
:
Bugfix in hand
l
ing o
f
n
on-primar
y
elements
.
commit
|
commitdiff
|
tree
2007-04-03
Da
v
id Hilv
e
rt
Copyright notice u
p
dates
.
commit
|
commitdiff
|
tree
2007-04-03
David
Hil
v
ert
Add code for load
i
ng and s
a
ving non-primary al
i
gnment
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Dav
i
d Hilvert
Up
d
a
te
c
hangelog
.
commit
|
commitdiff
|
tree
2007-04-03
Da
v
id Hilvert
ui:
M
odi
f
y match format str
i
ngs to provide co
n
stant
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
vid Hilvert
ui_tty: Add field width and p
r
ecisio
n
specifiers to
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
avid Hi
l
vert
Swa
p
a
r
guments to alignme
n
t
s
tatus so
that frequ
e
nt
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
ui_tty: Change floating po
i
nt formats
from %f t
o
%g
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
d2::align: Move fol
l
owing logic fro
m
_al
i
gn() to a
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
Da
v
id Hilvert
U
p
d
a
t
e
chang
e
log
commit
|
commitdiff
|
tree
2007-04-02
David
H
ilv
e
r
t
Re
m
ove file 'sgauss
.
h' missing fro
m
s
g
a
u
ss
p
a
tc
h
,
as
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
D
avi
d
Hilvert
Add missing file fr
o
m
e
arlier sgauss patc
h
.
W
i
ll be
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Update changelog
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Update changelog
commit
|
commitdiff
|
tree
2007-04-02
Da
v
i
d Hilvert
Move the multi-transformation
e
l
em
e
nt switchin
g
loop
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
D
a
vid
H
il
v
e
r
t
Update Changelog
commit
|
commitdiff
|
tree
2007-04-02
David
Hilvert
d2/alig
n
.
h: Rec
a
lculate dif
f
stat
i
sti
c
s
a
fter increasing
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David Hilver
t
Modify hand
l
in
g
of
-
-
i
d
e
ntity in d2::
a
l
i
gn so
t
hat
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David
H
il
v
e
r
t
A
dd methods f
o
r
enabling and disabling
r
estricted support
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Davi
d
Hilvert
Add che
c
k
for transformation sup
p
o
rt
t
o d2::a
l
ign:
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David H
i
l
v
ert
d2::tra
n
s_multi: Add
m
eth
o
d support
e
d() to chec
k
for
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
D
avid Hilv
e
rt
Begin using non-trivial mult
i
-tra
n
sfor
m
ations
in d2
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
David Hi
l
vert
d2::trans_multi: Add
g
e
t
_element
(
) method
.
commit
|
commitdiff
|
tree
2007-03-27
David Hilv
e
rt
d2::render::ipc: Mod
i
fy allocation
f
or subdomain arguments
.
.
.
commit
|
commitdiff
|
tree
2007-03-24
D
a
vid
Hilvert
d2:
:
align:
Allo
c
ate kept_t w
i
t
h new[] rat
h
er th
a
n malloc
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilve
r
t
Modify spec
i
f
i
c_*() calls
in d2::trans_multi to
call
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hil
v
ert
Allo
c
ate d2::
i
ncr
e
mental::subdomain_
a
rgs with new[
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilvert
R
e
solve certain
c
o
m
pil
a
t
ion and run-time
f
ailu
r
es
.
commit
|
commitdiff
|
tree
2007-03-23
David Hi
l
vert
d2::trans_multi: Up
d
ate
m
e
th
o
ds for a
trivial multi
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilvert
I
nitial version of d2/
t
ran
s
_m
u
lti
.
h, taken f
r
om the
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
Dav
i
d Hilvert
Add
file d2/trans_single
.
h for implementing single
.
.
.
commit
|
commitdiff
|
tree
2007-03-21
Davi
d
Hilvert
Mo
v
e single-transformation clas
s
spe
c
ifics from d2
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David Hilvert
d2/trans_abstract
.
h:
I
nitial
im
p
lement
a
tion
of an a
b
stract
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David Hi
l
vert
d2/t
f
ile
.
h: Call unge
t
c() when test for non-primary
.
.
.
commit
|
commitdiff
|
tree
2007-03-15
David Hilvert
Revis
e
ha
n
dl
i
ng of M
A
elements
.
commit
|
commitdiff
|
tree
2007-03-15
Davi
d
Hilve
r
t
Modify --ma-car
d
to range [1,inf) and
a
d
d
cod
e
to iterate
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
Dav
i
d Hil
v
ert
Add
f
lags to
d
2::align::e
l
ement_t and d2:;tfile to
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
Dav
i
d Hilve
r
t
ui/ui_tty
.
h: Revis
e
update(
)
a
nd up
d
a
t
e_loop() so that
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
David Hilvert
u
i
/
u
i
_
tty
.
h: Add a UI update
thread
.
commit
|
commitdiff
|
tree
2007-03-13
David Hi
l
v
e
rt
d2::align: exp
a
nd and rename the data struc
t
u
re for
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
David Hilvert
d2::align:
Make a structure for fol
l
ow semantics variables
.
.
.
commit
|
commitdiff
|
tree
2007-03-12
Da
v
id Hilvert
Add opti
o
n handling for --ma
-
card a
n
d --ma-cont multi
.
.
.
commit
|
commitdiff
|
tree
2007-03-10
David Hilvert
Update chan
g
elog
commit
|
commitdiff
|
tree
2007-03-10
D
avid
Hil
v
ert
Update help t
e
xt to refle
c
t
n
ew
f
i
l
e-sco
p
ed options
.
commit
|
commitdiff
|
tree
2007-03-10
David H
i
lvert
All
o
w file-scoped --g
s
a
n
d --gs-
m
o
commit
|
commitdiff
|
tree
2007-03-09
David Hilvert
Update changelog
commit
|
commitdiff
|
tree
2007-03-09
D
a
vid Hilv
e
rt
Ignore fex regi
o
n
s
when nex is specified
.
commit
|
commitdiff
|
tree
2007-03-09
David H
i
lvert
Update changelog
commit
|
commitdiff
|
tree
2007-03-09
Dav
i
d Hilve
r
t
Add --blac
k
o
ption
for sett
i
ng black l
e
vel
.
commit
|
commitdiff
|
tree
2007-03-08
Da
v
id Hilvert
A
d
d option --e
v
for setting exposure
value meta-data
.
commit
|
commitdiff
|
tree
2007-03-08
David
H
il
v
e
r
t
D
i
s
able implication fo
r
--exp-register when -
-
cx is
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David Hilver
t
Mod
i
fy p
r
o
f
i
l
e local alignment detail
outpu
t
to omit
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David H
i
l
v
ert
Update
changelog
commit
|
commitdiff
|
tree
2007-03-07
David Hilvert
Update
profiling timers to
include
t
imi
n
g de
t
ails
for
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David Hil
v
ert
d
2
/pp
m
.
h
:
Upda
t
e
er
r
or message
f
or
n
on
-
PPM
f
iles to
.
.
.
commit
|
commitdiff
|
tree
2007-03-04
David Hilvert
U
p
date NEWS
and version n
u
mbe
r
s for 0
.
8
.
7 releas
e
.
commit
|
commitdiff
|
tree
2007-03-03
David Hi
l
vert
Upda
t
e changelog
.
commit
|
commitdiff
|
tree
2007-03-03
David Hilvert
M
a
ke --ip-nowl
defaul
t
.
commit
|
commitdiff
|
tree
2007-02-25
Dav
i
d Hilvert
Update ch
a
ngel
o
g
.
commit
|
commitdiff
|
tree
2007-02-25
D
a
v
id Hil
v
e
r
t
Re
v
ise argument handlin
g
for ip-wl a
r
gume
n
ts
.
commit
|
commitdiff
|
tree
2007-02-25
David Hilvert
Implement Irani-Pel
e
g weight
l
imits, and set
a default
.
.
.
commit
|
commitdiff
|
tree
next