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Update changelog
2007-04-21
Davi
d
Hilvert
Upda
t
e
c
hangelog
commit
|
commitdiff
|
tree
2007-04-21
David Hilvert
S
et --n
o
-in
c
t
o def
a
ult
.
commit
|
commitdiff
|
tree
2007-04-21
David Hilvert
Add comme
n
t regarding remo
v
al methods in d2/ali
g
n
.
h
.
commit
|
commitdiff
|
tree
2007-04-20
David Hilvert
ui
_
tty: Add more updates;
r
e
v
ise Irani-Peleg output
.
commit
|
commitdiff
|
tree
2007-04-20
David Hilvert
d2::align: Select be
s
t
er
r
or
f
rom each conse
c
utive
.
.
.
commit
|
commitdiff
|
tree
2007-04-20
David Hilvert
Changelog update
commit
|
commitdiff
|
tree
2007-04-20
David
H
ilvert
U
pdate chang
e
log
commit
|
commitdiff
|
tree
2007-04-20
Da
v
i
d
Hil
v
ert
Fix calculation of global searc
h
m
i
nimum
o
ver
l
ap count
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
ui_log: Fix fo
r
mat in set_offset()
.
commit
|
commitdiff
|
tree
2007-04-19
Dav
i
d Hilvert
Cha
n
ge
-
-gs-mo def
a
ult t
o
67%
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
ui:
L
o
g output enh
a
nc
e
ments
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilvert
All
o
w --gs
-
mo to
be specif
i
e
d
a
s a perce
n
tage, make
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David Hilve
r
t
d
2
::align: Mo
d
if
y
_al
i
gn()
and make
_
element_nontri
v
ial
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
D
a
v
i
d Hilvert
d2::align:
A
d
d
method get_p
e
rtur
b
_set()
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
Add f
i
l
e
'VERSION' for cases where th
i
s does not exist
.
commit
|
commitdiff
|
tree
2007-04-17
D
a
v
id Hilvert
d2::trans_multi::specific_rescale()
:
Replace assertio
n
.
.
.
commit
|
commitdiff
|
tree
2007-04-17
Davi
d
Hilvert
Change
l
o
g
edits
.
commit
|
commitdiff
|
tree
2007-04-17
David
H
ilvert
U
pdate
c
ha
n
gelog
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
Add file
ui_
q
ui
e
t
.
h
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
c
o
nfig
u
re
.
in: Use
contents o
f
fi
l
e VERSIO
N
for v
e
rsion
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David
Hilvert
Modify black level i
m
plementation
t
o
alwa
y
s apply to
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
Add 'quie
t
' u
s
er interface type
.
commit
|
commitdiff
|
tree
2007-04-16
D
a
vid Hilvert
Move output ident
i
fication
d
etails to
user interfa
c
e
.
commit
|
commitdiff
|
tree
2007-04-16
David H
i
lvert
ui_log:
:
ip_step_done(): 'F
i
n
i
s
he
d
frame' --> 'Finished
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
Dav
i
d
H
ilvert
Refine ui_log::
i
p
_st
e
p_d
o
ne()
.
commit
|
commitdiff
|
tree
2007-04-15
David Hi
l
vert
d
2
/p
p
m
.
h: Don't set gain val
u
es if
non
e
are s
p
eci
f
ied
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilvert
u
i
_log: Add separate outp
u
t fo
r
match and mismatch
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilvert
u
i
_log: Add
more lo
g
gin
g
o
u
tput
.
commit
|
commitdiff
|
tree
2007-04-15
D
avid Hi
l
ve
r
t
Add rudi
m
e
ntary l
o
gging int
e
rface
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilve
r
t
u
i
: Ind
i
c
ate
w
hen no local alignmen
t
details are available
.
commit
|
commitdiff
|
tree
2007-04-14
David Hil
v
ert
d2::t
r
ans_multi::spe
c
ific_rescale(): Ad
d
an assert
.
.
.
commit
|
commitdiff
|
tree
2007-04-13
D
a
v
id Hilvert
Begin
i
mpl
e
menting d
2
::align::calculate_e
l
e
m
e
n
t_region()
.
commit
|
commitdiff
|
tree
2007-04-13
David
H
i
lvert
d2::align::_al
i
gn(): Add code to
store to and retrieve
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David
H
ilvert
Add
c
o
de to
r
e
calculat
e
each non-trivial non-primary
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David
Hil
v
e
rt
Ad
d
l
ocal_ax
_
count
t
o the list of parameters t
a
ken
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
Dav
i
d Hilvert
Change
b
arrel dis
t
ortion
multiplie
r
and rate of change
.
.
.
commit
|
commitdiff
|
tree
2007-04-08
Dav
i
d
Hilvert
Add methods d2::align::make_el
e
ment_
n
o
n
trivial(), d2
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
d2:
:
align::fol
l
ow():
Revert loop
i
ng ove
r
old_
*
element
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Dav
i
d Hilv
e
rt
d2::align::f
o
llow(): Upd
a
te eleme
n
t indices of al
l
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David
H
ilv
e
rt
d
2
:
:tfile:
Bugf
i
x
in han
d
li
n
g of n
o
n-
p
r
imary elements
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
Copyright notice u
p
dates
.
commit
|
commitdiff
|
tree
2007-04-03
David
Hilver
t
Add
c
ode f
o
r loading and sa
v
ing non-primary
alignment
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
Up
d
ate c
h
angelog
.
commit
|
commitdiff
|
tree
2007-04-03
Dav
i
d
H
ilvert
ui: Mod
i
fy match format strings
t
o provide constant
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
v
id Hilvert
ui
_
tty:
A
dd field
width a
n
d precisio
n
specifiers to
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilv
e
rt
Swap a
r
gume
n
t
s
t
o alignment status
s
o t
h
at
frequent
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Da
v
id Hilvert
u
i_tty:
Ch
a
nge flo
a
ting point
f
ormat
s
fr
o
m %
f
to %g
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
v
i
d
Hilvert
d2::align: Mo
v
e following
l
ogic from _a
l
ign(
)
to a
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hi
l
vert
Upd
a
te
changelog
commit
|
commitdiff
|
tree
2007-04-02
David
Hilvert
Re
m
ove file 'sga
u
s
s
.
h'
m
issing
fro
m
s
gauss patch, as
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
A
d
d
m
issing file
f
rom earlier s
g
auss patch
.
Will be
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hil
v
ert
Updat
e
cha
n
gelog
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
U
pdate cha
n
gelog
commit
|
commitdiff
|
tree
2007-04-02
David
Hilvert
Move th
e
multi-tr
a
nsformatio
n
element switching loop
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David H
i
lver
t
Update Changelog
commit
|
commitdiff
|
tree
2007-04-02
D
avi
d
Hilvert
d2/align
.
h:
Recalcula
t
e di
f
f
statistic
s
a
fte
r
increa
s
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
D
avid Hilvert
Modify
handling of --identity in d2::
a
lign so
t
h
at
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David Hilvert
Add methods for ena
b
ling and disa
b
ling re
s
tricted support
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David H
i
l
vert
Add check for tran
s
formation
support
t
o d2::align:
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Dav
i
d Hilvert
d2::tr
a
ns_multi: Ad
d
method supp
o
rted() to che
c
k fo
r
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
David Hilvert
Begin using non-tr
i
vial multi-
t
ransformation
s
i
n
d2
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
Dav
i
d Hilvert
d2::trans_multi: Add get
_
element() metho
d
.
commit
|
commitdiff
|
tree
2007-03-27
David Hilvert
d2::render:
:
ipc: Modify
allo
c
a
t
i
o
n for su
b
domain arguments
.
.
.
commit
|
commitdiff
|
tree
2007-03-24
Davi
d
Hilvert
d
2
::align: Allo
c
ate kept_t
w
i
t
h new[]
r
a
t
her tha
n
m
a
lloc
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
Da
v
i
d Hilvert
M
odify speci
f
ic_*(
)
calls in d2::trans_multi to call
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilvert
Alloc
a
te d2::incremental::subd
o
main_
a
r
gs
w
ith
new[
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hilv
e
rt
Resolve cer
t
ain compilation and run-time
failures
.
commit
|
commitdiff
|
tree
2007-03-23
David
H
i
l
v
e
rt
d
2::tra
n
s_mu
l
ti:
Update met
h
ods
for a trivi
a
l multi
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
D
a
vid Hilvert
In
i
t
i
a
l
v
er
s
ion of d
2
/trans_multi
.
h, taken from the
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David
Hilvert
Add
f
ile d2/
t
rans_single
.
h for impl
e
m
ent
i
ng single
.
.
.
commit
|
commitdiff
|
tree
2007-03-21
David H
i
lvert
Mo
v
e sin
g
le-transforma
t
ion class specifics f
r
om
d2
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David Hilver
t
d2/trans_abstra
c
t
.
h: Ini
t
i
a
l
i
mplementation of an abstract
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
D
a
vid
Hilvert
d2/tfile
.
h: Cal
l
ungetc() wh
e
n tes
t
for non-primary
.
.
.
commit
|
commitdiff
|
tree
2007-03-15
D
avid H
i
lvert
Revise handling of MA eleme
n
ts
.
commit
|
commitdiff
|
tree
2007-03-15
David Hi
l
vert
Mod
i
fy --ma-c
a
rd
t
o r
a
n
g
e
[1,inf) an
d
add code to itera
t
e
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
Dav
i
d Hilvert
Ad
d
flags to d2::align::element_t
a
nd d2
:
;
t
file to
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
David H
i
lver
t
ui/
u
i_tty
.
h: Revise update()
a
nd updat
e
_loo
p
() so
t
hat
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
David H
i
lvert
ui/ui
_
tty
.
h: Add
a
UI update thread
.
commit
|
commitdiff
|
tree
2007-03-13
David Hilvert
d2::ali
g
n: expand an
d
rename the
data structure for
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
David Hilvert
d2::ali
g
n:
M
a
k
e
a structu
r
e f
o
r follow
s
emantics
v
ariables
.
.
.
commit
|
commitdiff
|
tree
2007-03-12
D
avid Hil
v
ert
Ad
d
opt
i
on
h
andl
i
ng fo
r
--
m
a
-c
a
r
d
and --ma-
c
on
t
mult
i
.
.
.
commit
|
commitdiff
|
tree
2007-03-10
Da
v
i
d Hi
l
v
e
rt
Update change
l
og
commit
|
commitdiff
|
tree
2007-03-10
Davi
d
Hilvert
Up
d
ate he
l
p text to
refl
e
c
t
new file-s
c
oped opt
i
ons
.
commit
|
commitdiff
|
tree
2007-03-10
David Hilvert
Allow
f
ile-
s
coped --gs a
n
d
-
-
gs-mo
commit
|
commitdiff
|
tree
2007-03-09
D
avid Hilvert
Update
c
hangelo
g
commit
|
commitdiff
|
tree
2007-03-09
D
a
v
id Hi
l
vert
Ignore fex
r
egions when n
e
x is specified
.
commit
|
commitdiff
|
tree
2007-03-09
David
H
ilvert
Update changelo
g
commit
|
commitdiff
|
tree
2007-03-09
David
H
ilvert
Add --bla
c
k optio
n
for setting blac
k
level
.
commit
|
commitdiff
|
tree
2007-03-08
Dav
i
d Hilvert
Add option --ev for setting exposure valu
e
m
e
ta
-
d
ata
.
commit
|
commitdiff
|
tree
2007-03-08
D
avid Hil
v
ert
D
i
s
a
bl
e
impli
c
a
tion for --exp-
r
e
gister when
-
-cx is
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
Da
v
id Hilvert
Modify profile loc
a
l alignment detail output to omit
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
Da
v
id Hilve
r
t
Update c
h
a
n
gelog
commit
|
commitdiff
|
tree
2007-03-07
David
Hilvert
Update
profiling timers to include
tim
i
n
g
d
e
tails for
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
Davi
d
Hilvert
d2/ppm
.
h: U
p
d
a
te
e
rror message for
non-PPM fi
l
e
s t
o
.
.
.
commit
|
commitdiff
|
tree
2007-03-04
David Hilvert
Upda
t
e NEWS and version nu
m
bers
for 0
.
8
.
7 releas
e
.
commit
|
commitdiff
|
tree
2007-03-03
David Hilvert
Update
c
h
a
n
g
e
log
.
commit
|
commitdiff
|
tree
2007-03-03
David
Hi
l
vert
Make
-
-
ip-no
w
l
default
.
commit
|
commitdiff
|
tree
2007-02-25
David
Hilvert
U
pdate changel
o
g
.
commit
|
commitdiff
|
tree
2007-02-25
D
avid Hilvert
Rev
i
se argument handling for ip-wl
a
r
guments
.
commit
|
commitdiff
|
tree
2007-02-25
David
H
ilvert
Im
p
l
e
m
e
nt Irani-
P
e
l
e
g weight limits, and set a default
.
.
.
commit
|
commitdiff
|
tree
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