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d2::align: Modify _align() and make_element_nontrivial() to use the method get_pertur...
2007-04-19
D
a
vid Hilvert
d2::align: Modify _align() and ma
k
e_e
l
ement_nontri
v
ial
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
Dav
i
d Hi
l
vert
d2
:
:a
l
ign: Add method get_pertu
r
b_set
(
)
.
commit
|
commitdiff
|
tree
2007-04-17
David Hil
v
ert
Add
f
ile 'VERSION' for cases
w
here th
i
s
doe
s
not exist
.
commit
|
commitdiff
|
tree
2007-04-17
David H
i
lve
r
t
d
2
::t
r
ans_mu
l
t
i
::specifi
c
_rescale():
R
eplace asserti
o
n
.
.
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
Chan
g
elog edits
.
commit
|
commitdiff
|
tree
2007-04-17
Dav
i
d H
i
lver
t
Updat
e
changelog
commit
|
commitdiff
|
tree
2007-04-17
David H
i
lvert
Ad
d
file u
i
_quiet
.
h
.
commit
|
commitdiff
|
tree
2007-04-17
D
a
v
id H
i
lvert
conf
i
gure
.
in: Use contents of file VERSION
for
version
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilv
e
rt
Modify b
l
ack level im
p
lementati
o
n t
o
always apply
t
o
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hil
v
ert
Add 'qui
e
t
'
u
ser
interface type
.
commit
|
commitdiff
|
tree
2007-04-16
David
H
ilvert
Mo
v
e
o
utput identification details to user in
t
e
r
f
a
c
e
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilvert
ui
_
log::ip_step
_
done
(
): 'Fini
s
he
d
frame' --> 'Finish
e
d
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilver
t
Refine
u
i_log::ip_step_done
(
)
.
commit
|
commitdiff
|
tree
2007-04-15
David H
i
l
vert
d
2/ppm
.
h
: Do
n
't set gain v
a
lues if
n
o
n
e are spe
c
ifie
d
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilve
r
t
ui_log: Add separa
t
e output for m
a
tch and mi
s
match
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David H
i
lv
e
r
t
ui_log: Add more lo
g
ging
o
u
t
put
.
commit
|
commitdiff
|
tree
2007-04-15
Da
v
id Hilvert
Add rudimentary l
o
gging interface
.
commit
|
commitdiff
|
tree
2007-04-15
D
avid
Hilvert
ui
:
I
n
dic
a
te when no local alignment d
e
ta
i
l
s
are availa
b
le
.
commit
|
commitdiff
|
tree
2007-04-14
David Hilve
r
t
d2::trans_multi::specific_rescale(
)
: Add an assert
.
.
.
commit
|
commitdiff
|
tree
2007-04-13
D
a
vid
Hilvert
B
e
gin
i
mplementin
g
d2::
a
lign::calcu
l
ate_element_region
(
)
.
commit
|
commitdiff
|
tree
2007-04-13
David
H
ilv
e
r
t
d
2::al
i
gn
:
:_al
i
g
n(): Add cod
e
to
store to and retrieve
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
D
a
vid Hilvert
Ad
d
cod
e
to
r
e
c
alculat
e
each
n
on
-
tr
i
v
ial non-primary
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David
Hilvert
Add local_
a
x_count to th
e
list
of
parameters ta
k
en
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
Davi
d
Hilvert
Change
barre
l
distortion multiplier and ra
t
e o
f
change
.
.
.
commit
|
commitdiff
|
tree
2007-04-08
David H
i
lvert
Add me
t
hods d2::align::
m
ake
_
elem
e
n
t
_no
n
trivial(),
d2
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilver
t
d2::align::follow():
Revert looping over
o
ld_* element
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hil
v
er
t
d2::align
:
:fol
l
ow():
Update element indices of all
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilver
t
d2:
:
tfile
:
Bugfix in
h
a
n
dling of
n
o
n
-primary elements
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
vid Hilvert
Copyright n
o
tice updates
.
commit
|
commitdiff
|
tree
2007-04-03
David Hil
v
e
r
t
Add cod
e
for l
o
ading and savi
n
g non-primary a
l
ignment
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
avid Hilvert
Upd
a
te changelog
.
commit
|
commitdiff
|
tree
2007-04-03
D
avid Hilvert
ui: Modif
y
ma
t
ch format
strin
g
s to provide constant
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
ui_tty
:
Add fi
e
ld width
a
nd precision spec
i
fier
s
to
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David H
i
lvert
Swa
p
argu
m
e
nts to a
l
ignment st
a
t
u
s so that frequent
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
vid
Hil
v
ert
ui_tty
:
Change floating point
formats f
r
o
m
%f to %g
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Dav
i
d Hilvert
d
2
::align: Move
following logic from _
a
lign() t
o
a
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hilve
r
t
Update changelo
g
commit
|
commitdiff
|
tree
2007-04-02
David
H
ilvert
Remove fil
e
'sgauss
.
h' missi
n
g from sg
a
u
s
s patc
h
, as
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
Davi
d
Hilve
r
t
A
d
d missing file from earlier sgauss patch
.
Will be
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
Up
d
ate changelog
commit
|
commitdiff
|
tree
2007-04-02
David Hilv
e
r
t
Update
c
h
angelog
commit
|
commitdiff
|
tree
2007-04-02
D
avid Hilvert
M
ove the m
u
lti-t
r
ansform
a
tion e
l
ement
switching loo
p
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
Da
v
id
H
ilvert
Up
d
ate
Ch
a
ngelo
g
commit
|
commitdiff
|
tree
2007-04-02
David
H
ilvert
d2/align
.
h: Recalcu
l
ate diff statistics
a
fter increasing
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Dav
i
d Hilvert
Modify handling of --
i
d
entit
y
in d2::alig
n
s
o that
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
David Hilvert
Add m
e
tho
d
s for e
n
ablin
g
and dis
a
bl
i
ng r
e
stri
c
ted s
u
pport
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Dav
i
d Hilvert
Add check f
o
r tr
a
nsform
a
tion su
p
port to d2::a
l
ig
n
:
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Dav
i
d
Hilve
r
t
d
2
:
:tra
n
s_
m
u
l
ti: Add method sup
p
ort
e
d()
to ch
e
ck fo
r
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
Davi
d
H
i
l
ve
r
t
Be
g
in
u
sing n
o
n-
t
rivial
mul
t
i-transform
a
tions
in d2
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
David
Hilvert
d2::trans_multi: Add get_elemen
t
() metho
d
.
commit
|
commitdiff
|
tree
2007-03-27
D
avid Hil
v
ert
d2::render::i
p
c: Modify a
l
loc
a
tion f
o
r subdomain arg
u
ments
.
.
.
commit
|
commitdiff
|
tree
2007-03-24
David Hil
v
e
rt
d2::align: Allocate kept_t with new[] rather than
malloc
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David
H
ilvert
Modify specific_*(
)
calls
i
n d2:
:
trans_m
u
lti to
c
al
l
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David
H
ilvert
A
l
locate
d2::inc
r
emental::subd
o
main_ar
g
s with new[
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
Davi
d
H
ilvert
Re
s
olv
e
ce
r
tain compilation an
d
run-time failures
.
commit
|
commitdiff
|
tree
2007-03-23
D
a
vid Hilver
t
d2::trans_mult
i
: U
p
date metho
d
s for a trivial multi
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
Davi
d
Hilvert
Initia
l
version of d2
/
trans_multi
.
h, taken
from the
.
.
.
commit
|
commitdiff
|
tree
2007-03-23
David Hil
v
ert
Add file d2/trans_singl
e
.
h
for imp
l
em
e
nting single
.
.
.
commit
|
commitdiff
|
tree
2007-03-21
Davi
d
H
ilvert
Mov
e
si
n
gle-transformation
c
las
s
s
p
ecifics from d
2
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David Hilv
e
rt
d2/trans_abstract
.
h: I
n
itial imp
l
eme
n
tation o
f
an abst
r
act
.
.
.
commit
|
commitdiff
|
tree
2007-03-17
David
Hilvert
d2
/
t
file
.
h: Call ung
e
t
c
()
whe
n
te
s
t
f
o
r n
o
n-primary
.
.
.
commit
|
commitdiff
|
tree
2007-03-15
D
a
v
i
d Hi
l
vert
R
e
vis
e
handling
of MA elements
.
commit
|
commitdiff
|
tree
2007-03-15
David
Hilvert
Modify -
-
ma
-
card
t
o r
a
nge [1,
i
nf) and
add c
o
de to i
t
erate
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
David Hilv
e
r
t
A
dd
fla
g
s to d2
:
:align:
:
element_t and
d
2
:
;tfi
l
e
t
o
.
.
.
commit
|
commitdiff
|
tree
2007-03-14
D
avid Hilvert
ui/ui_tty
.
h: Revise update() an
d
update_loop(
)
so that
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
David
H
ilvert
ui/ui_tty
.
h: Ad
d
a UI u
p
d
a
te thread
.
commit
|
commitdiff
|
tree
2007-03-13
D
avi
d
Hilvert
d2::a
l
i
gn
:
expa
n
d and rename
t
he data struct
u
re for
.
.
.
commit
|
commitdiff
|
tree
2007-03-13
David Hilvert
d2::align: M
a
ke
a
s
tructure for follow
s
ema
n
tics varia
b
les
.
.
.
commit
|
commitdiff
|
tree
2007-03-12
David Hi
l
ve
r
t
Add
o
p
t
ion
hand
l
i
ng fo
r
--ma-card and --ma-cont multi
.
.
.
commit
|
commitdiff
|
tree
2007-03-10
D
a
vid Hilvert
Update
changelog
commit
|
commitdiff
|
tree
2007-03-10
David Hilver
t
Update
h
elp text to reflect new file-s
c
oped
opti
o
ns
.
commit
|
commitdiff
|
tree
2007-03-10
Da
v
id Hilvert
Allow fil
e
-
s
c
o
ped --g
s
and --gs-mo
commit
|
commitdiff
|
tree
2007-03-09
D
a
vid Hilv
e
rt
Upd
a
te cha
n
gelog
commit
|
commitdiff
|
tree
2007-03-09
David Hilvert
Ignore
f
ex regions when n
e
x
i
s
s
p
ecified
.
commit
|
commitdiff
|
tree
2007-03-09
Dav
i
d Hi
l
vert
Update
c
han
g
elog
commit
|
commitdiff
|
tree
2007-03-09
David H
i
lve
r
t
Add -
-
black opt
i
on for
s
etting black l
e
vel
.
commit
|
commitdiff
|
tree
2007-03-08
David Hilvert
Add option -
-
ev for
setting exposure
v
a
lue meta-da
t
a
.
commit
|
commitdiff
|
tree
2007-03-08
Dav
i
d Hilvert
Di
s
able implication
f
o
r -
-
exp-
r
egist
e
r
w
h
en --cx is
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David Hilvert
M
odify profile local alignment d
e
tail output t
o
o
m
it
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
Da
v
id
H
ilver
t
Update changelog
commit
|
commitdiff
|
tree
2007-03-07
D
avid Hil
v
ert
Upd
a
te
profiling timers
to includ
e
timing details for
.
.
.
commit
|
commitdiff
|
tree
2007-03-07
David Hilve
r
t
d2/ppm
.
h: Update error mess
a
g
e
f
o
r non-P
P
M files to
.
.
.
commit
|
commitdiff
|
tree
2007-03-04
Davi
d
Hi
l
vert
Update NEWS
a
nd v
e
rsion numbers for 0
.
8
.
7 re
l
e
a
se
.
commit
|
commitdiff
|
tree
2007-03-03
David Hi
l
vert
Update changelog
.
commit
|
commitdiff
|
tree
2007-03-03
David Hilvert
M
a
k
e --ip-nowl default
.
commit
|
commitdiff
|
tree
2007-02-25
David
H
ilv
e
rt
Update
c
hangelog
.
commit
|
commitdiff
|
tree
2007-02-25
David Hilvert
Re
v
ise
a
rgument handling fo
r
i
p
-
w
l
arguments
.
commit
|
commitdiff
|
tree
2007-02-25
David Hilvert
I
mplement Ira
n
i
-
Peleg weight limits,
a
n
d set
a
d
e
fault
.
.
.
commit
|
commitdiff
|
tree
2007-02-25
Davi
d
Hil
v
ert
Updat
e
Cha
n
gelo
g
commit
|
commitdiff
|
tree
2007-02-25
David Hilvert
Add an incremental render
e
r mean invariant weight-limited
.
.
.
commit
|
commitdiff
|
tree
2007-02-24
David Hilvert
d2::filter::scale
d
_f
i
lter:
:
filter_channe
l
(
)
: Slightly
.
.
.
commit
|
commitdiff
|
tree
2007-02-24
Davi
d
Hilvert
U
pdate ch
a
ngelo
g
commit
|
commitdiff
|
tree
2007-02-24
David Hilve
r
t
d2::image::defined_
s
cale_by_h
a
lf(): Replace inco
r
rect
.
.
.
commit
|
commitdiff
|
tree
2007-02-24
David
H
ilvert
d2::i
m
age::defined_
s
cale_by_ha
l
f(): Use
g
e
ometric mea
n
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
David Hilvert
d2
/
filter/scaled_filter
.
h: Clean up recently added
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
David Hilvert
d2/filter/scaled_filter
.
h: Revi
s
e
certainty c
a
l
c
ulation
s
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
Dav
i
d Hilver
t
NEWS:
a
dd 0
.
8
.
6 release information
commit
|
commitdiff
|
tree
2007-02-17
David
Hil
v
ert
Upd
a
t
e
changelog for 0
.
8
.
6 releas
e
d
a
te
.
commit
|
commitdiff
|
tree
2007-02-17
David Hilvert
doc: R
e
n
a
me 'localhos
t
' subdire
c
tory to m
o
re relevant
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
Dav
i
d Hilvert
bootstr
a
p:
R
e
move c
o
de to pru
n
e documentation
commit
|
commitdiff
|
tree
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