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d2::trans_multi: Add --mi option (useful for debugging multi-alignment
2008-06-01
David Hi
l
vert
d2::trans_mult
i
:
Add --mi optio
n
(us
e
ful
f
o
r deb
u
gging
.
.
.
commit
|
commitdiff
|
tree
2008-05-31
David Hi
l
v
er
t
d
2::align: Mak
e
--lod-pr
e
ferred=
-
3
defaul
t
.
commit
|
commitdiff
|
tree
2008-05-31
David Hilve
r
t
Resolve
c
ompilation iss
u
es
.
commit
|
commitdiff
|
tree
2008-05-31
David Hilvert
d2::ali
g
n::_align(): Don't
c
a
st log2(perturb) to unsigned
.
.
.
commit
|
commitdiff
|
tree
2008-05-31
Dav
i
d H
i
l
v
er
t
d2::ali
g
n::_al
i
g
n
_el
e
ment(
)
: Do
n
'
t
cast log2(
p
er
t
u
rb
.
.
.
commit
|
commitdiff
|
tree
2008-05-31
David Hilvert
d2::align::_align_elem
e
nt():
Scale adj_p for
retaine
d
.
.
.
commit
|
commitdiff
|
tree
2008-05-31
David Hi
l
ve
r
t
d
2
::
a
lign::_al
i
gn_element(): red
u
ce lo
d
a
c
cordi
n
g
t
o
.
.
.
commit
|
commitdiff
|
tree
2008-05-30
David Hi
l
vert
d
2
::align::_
a
lig
n
()
:
Use corre
c
t variables
.
commit
|
commitdiff
|
tree
2008-05-30
David
H
ilvert
d2::align::
_
align(): In
i
tialize
s
teps from lod, n
o
t
.
.
.
commit
|
commitdiff
|
tree
2008-05-30
D
a
vid Hilv
e
rt
d2::al
i
gn::_align(): Initialize a
d
j_p from lod, no
t
.
.
.
commit
|
commitdiff
|
tree
2008-05-30
David H
i
lvert
d2::ali
g
n::_al
i
gn():
Adjust l
e
ve
l
-of-detai
l
to acco
m
modate
.
.
.
commit
|
commitdiff
|
tree
2008-05-30
David Hilver
t
d2::align::_
a
l
i
gn()
:
Replace
ins
t
an
c
es of lod_pr
e
ferred
.
.
.
commit
|
commitdiff
|
tree
2008-05-29
Da
v
id Hilvert
d2::
a
lign:
:
_align: Begin implementa
t
ion of min-dimens
i
o
n
.
.
.
commit
|
commitdiff
|
tree
2008-05-28
D
a
vi
d
H
i
lv
e
rt
d2:
:
al
i
gn: Add new options -
-
l
o
d-preferr
e
d and --min
.
.
.
commit
|
commitdiff
|
tree
2008-05-26
David
H
ilvert
d2
:
:align
:
:_ali
g
n
(): A
n
nou
n
ce alignment steps for each
.
.
.
commit
|
commitdiff
|
tree
2008-05-25
David Hilvert
testsuite/ale
.
0
1/align
.
exp: Revise fo
r
cu
r
re
n
t scrip
t
.
.
.
commit
|
commitdiff
|
tree
2008-05-25
David Hilver
t
ale: Reco
g
n
i
z
e and
skip
-
-trans-{l
o
a
d,save} arguments
.
.
.
commit
|
commitdiff
|
tree
2008-05-25
David Hilve
r
t
ui/ui
.
h
: Atte
m
pted fix for
D
ebian bug #4
8
2765 for sparc
.
.
.
commit
|
commitdiff
|
tree
2008-05-24
Da
v
id Hilve
r
t
ui::ui_l
o
g: Add output for scal
e
c
l
uster reference
.
.
.
commit
|
commitdiff
|
tree
2008-05-19
David Hi
l
vert
Fix compilat
i
on errors
.
commit
|
commitdiff
|
tree
2008-05-14
David H
i
lvert
d2::
r
ender:
:
ipc:
I
n
c
orporate
l
ocal tonal mu
l
t
iplier
.
.
.
commit
|
commitdiff
|
tree
2008-05-14
D
a
vid
H
i
lvert
d2
:
:rend
e
r::
i
pc:
Use local tonal multipliers for simulat
i
ng
.
.
.
commit
|
commitdiff
|
tree
2008-05-14
Dav
i
d Hi
l
vert
d
2
::tra
n
s_*: Add a method for
o
b
t
ainin
g
a tonal mu
l
tip
l
ier
.
.
.
commit
|
commitdiff
|
tree
2008-05-13
David Hilvert
d2::render::incre
m
ental: Ad
j
ust
p
rev_value
a
n
d value
.
.
.
commit
|
commitdiff
|
tree
2008-05-05
D
a
vid
Hilve
r
t
d
2::trans_mult
i
::set_multi: Use correct se
n
se for the
.
.
.
commit
|
commitdiff
|
tree
2008-05-05
David Hilvert
d2::
a
lign::run::sa
m
ple:
A
ccoun
t
f
or tonal regi
s
tration
.
.
.
commit
|
commitdiff
|
tree
2008-05-05
David Hi
l
vert
d2::align::se
t
_expos
u
re_rati
o
(): Add missin
g
reference
.
.
.
commit
|
commitdiff
|
tree
2008-05-05
David Hilvert
d2:
:
align: Stre
n
gthen conditions
on tonal regist
r
a
tion
.
.
.
commit
|
commitdiff
|
tree
2008-05-05
Davi
d
H
i
lvert
d
2
:
:trans_multi: Use c
u
rrent_el
e
ment by defa
u
lt when
.
.
.
commit
|
commitdiff
|
tree
2008-05-05
David Hi
l
vert
d
2
::align: Add cod
e
for
calculating
tonal regsitration
.
.
.
commit
|
commitdiff
|
tree
2008-05-02
Da
v
id
Hilvert
d2::
t
r
ans_multi, d2::align:
e
n
capsulate bounds scaling
.
.
.
commit
|
commitdiff
|
tree
2008-05-02
D
avid
Hilver
t
d2::tra
n
s_multi::set_
m
ulti(
)
: modify spat
i
o
-
e
l
emental
.
.
.
commit
|
commitdiff
|
tree
2008-05-02
David
H
ilvert
d
2::tra
n
s_*
:
Add code for assi
g
ning,
s
toring, and
r
etrieving
.
.
.
commit
|
commitdiff
|
tree
2008-04-27
David
Hilvert
ui::help::align: Match parenthese
s
.
commit
|
commitdiff
|
tree
2008-04-27
David Hilvert
S
e
t --ma-cert default 0
.
01
.
commit
|
commitdiff
|
tree
2008-04-26
D
a
vid
H
ilvert
d2::ali
g
n::_align():
Limit skipping of
the a
l
ignme
n
t
.
.
.
commit
|
commitdiff
|
tree
2008-04-26
David Hilvert
d2
:
:align: Add method
m
a_
c
ert_satisfied
(
), and use
.
.
.
commit
|
commitdiff
|
tree
2008-04-24
Da
v
id Hilvert
d2::align:
A
dd a st
a
tic variable f
o
r mul
t
i-alignment
.
.
.
commit
|
commitdiff
|
tree
2008-04-23
David Hilvert
ale
:
Count threads when ALE
_
C
OU
N
T
_THREAD
S
=1
.
commit
|
commitdiff
|
tree
2008-04-22
David Hilvert
u
i
/he
l
p
.
h: A
d
d documentat
i
on f
o
r an
--ma-cert option
.
.
.
commit
|
commitdiff
|
tree
2008-04-14
Da
v
id Hil
v
ert
doc/w
e
b: Updat
e
for
0
.
9
.
0
.
commit
|
commitdiff
|
tree
2008-04-14
Davi
d
Hilvert
M
ake --md 100 defaul
t
.
commit
|
commitdiff
|
tree
2008-04-14
David Hil
v
ert
doc: up
d
ates
f
or 0
.
9
.
0
.
commit
|
commitdiff
|
tree
2008-04-12
David Hilvert
d
o
c/web: Place examples section m
o
re
v
isibly
.
commit
|
commitdiff
|
tree
2008-04-12
Davi
d
Hilve
r
t
doc/web:
Revise dis
t
r
ibutio
n
stat
u
s secti
o
n
.
commit
|
commitdiff
|
tree
2008-04-12
David Hilvert
doc/w
e
b: A
d
d
e
x
ample secti
o
n credit
.
commit
|
commitdiff
|
tree
2008-04-12
David Hilvert
d
o
c
/
web:
U
se re
p
o
.
or
.
cz termi
n
ology f
o
r the summary
.
.
.
commit
|
commitdiff
|
tree
2008-04-11
David
H
i
lvert
ui: Modify align
m
ent sta
t
us update to
reduce
t
he number
.
.
.
commit
|
commitdiff
|
tree
2008-04-11
David Hilvert
d
2
::alig
n
: Pe
r
for
m
post-matching usi
n
g trans_multi
.
.
.
commit
|
commitdiff
|
tree
2008-04-10
David H
i
lvert
d2::align: E
n
sur
e
t
h
at the i
s
_default
a
rray
i
s correctly
.
.
.
commit
|
commitdiff
|
tree
2008-04-10
David H
i
lvert
d2::
t
file:
:
tload_n
e
xt(): Correct c
o
unt che
c
k for a
.
.
.
commit
|
commitdiff
|
tree
2008-04-10
Da
v
id
H
i
l
vert
d2::file::tload_ne
x
t()
:
Add code
to
a
utomatically s
k
ip
.
.
.
commit
|
commitdiff
|
tree
2008-04-10
Davi
d
Hil
v
ert
d2::tfi
l
e: Add multi-coordinate indices to
t
h
e tail
.
.
.
commit
|
commitdiff
|
tree
2008-04-10
David
Hilvert
D
i
sable
mult
i
-a
l
ignm
e
nt for -
-
md 0
.
commit
|
commitdiff
|
tree
2008-04-10
Dav
i
d Hi
l
vert
d2::alig
n
::astate_t: p
r
ovide for changes in the
s
ize
.
.
.
commit
|
commitdiff
|
tree
2008-04-09
David Hi
l
ve
r
t
d2:
:
ali
g
n: U
p
date fo
l
l
o
wi
n
g to
fi
x
s
e
ma
n
tics a
n
d to
.
.
.
commit
|
commitdiff
|
tree
2008-04-04
David Hi
l
v
ert
doc/
w
eb
/
index:
M
ake
di
s
tribution
d
escript
i
ons more
.
.
.
commit
|
commitdiff
|
tree
2008-04-04
Dav
i
d
H
ilve
r
t
doc/web/inde
x
: Add section for d
i
s
tribu
t
ion
sta
t
us
.
commit
|
commitdiff
|
tree
2008-03-28
David Hilve
r
t
doc/web/index
.
txt
:
Add
'
GUI' s
e
ction with an entry
.
.
.
commit
|
commitdiff
|
tree
2008-03-26
David
H
i
lvert
d2:
:
align::_align_e
l
em
e
nt: Move UI
output
code in the
.
.
.
commit
|
commitdiff
|
tree
2008-03-24
D
avid Hilvert
d2::t
r
an
s
_ab
s
tract::bd: Rem
o
ve fa
i
ling
a
s
ser
t
ion
.
commit
|
commitdiff
|
tree
2008-03-24
David Hilve
r
t
d2::tr
a
ns_multi:
Fix bugs in spatio-elemental map a
s
s
ignment
.
commit
|
commitdiff
|
tree
2008-03-23
David Hilvert
d2
:
:
tr
a
ns_multi: Add support
f
o
r
a
l
ignment in
t
he
case
.
.
.
commit
|
commitdiff
|
tree
2008-03-22
Dav
i
d Hi
l
vert
d2:
:
align:
S
et transf
o
rmation default
s
and
r
esca
l
e
.
.
.
commit
|
commitdiff
|
tree
2008-03-22
Da
v
id
H
ilvert
doc/we
b
/
i
ndex/
E
xamples: Add a
l
i
nk t
o
Gr
e
gory Max
w
ell
.
.
.
commit
|
commitdiff
|
tree
2008-03-21
D
a
v
id Hilvert
ui_log: Fix typo
.
commit
|
commitdiff
|
tree
2008-03-21
David Hilvert
web/in
d
ex
:
U
pdate 'Image Galleri
e
s' to the more
g
ene
r
i
c
.
.
.
commit
|
commitdiff
|
tree
2008-03-21
David Hilve
r
t
u
i_log: Add
m
ethod start_mul
t
i_
a
lignment_elem
e
nt()
.
.
.
commit
|
commitdiff
|
tree
2008-03-20
David Hilvert
ui::ui_log: Don't record
e
ntire m
u
lt
i
-alignme
n
t
s
tr
u
c
tures
.
.
.
commit
|
commitdiff
|
tree
2008-03-19
Da
v
id Hi
l
v
e
rt
d
o
c/web/man
u
als/index
.
t
xt: Encode
manuals page as AsciiDoc
.
commit
|
commitdiff
|
tree
2008-03-18
Dav
i
d Hilvert
doc/web/foo
t
er-html
.
txt: Leave more padding
a
b
o
v
e
f
ooter
.
commit
|
commitdiff
|
tree
2008-03-17
David Hil
v
e
r
t
ui::u
i
_tt
y
:
During a
l
ignment, sta
r
t a new line when
.
.
.
commit
|
commitdiff
|
tree
2008-03-17
D
a
v
i
d
Hilver
t
d2:
:
align
:
Remove certain de
b
uggin
g
output
.
commit
|
commitdiff
|
tree
2008-03-17
David Hilvert
Document a method for disabling --thresh
o
l
d, a
n
d disab
l
e
.
.
.
commit
|
commitdiff
|
tree
2008-03-17
D
a
v
i
d Hilvert
doc:
U
p
date A
s
ciiDoc HTML f
o
o
ter fo
r
'wi
t
hout an
y
wa
r
ranty
.
.
.
commit
|
commitdiff
|
tree
2008-03-17
D
a
v
i
d Hil
v
ert
doc
:
Revise
f
ron
t
-
p
a
ge example f
i
le
.
commit
|
commitdiff
|
tree
2008-03-17
David Hilver
t
doc
:
Add
an asciidoc ge
n
erator
s
cript a
n
d exampl
e
f
iles
.
.
.
commit
|
commitdiff
|
tree
2008-03-13
David
H
i
l
vert
d2:
:
al
i
gn::_align: Don't
s
et the zeroth element alignment
.
.
.
commit
|
commitdiff
|
tree
2008-03-12
David H
i
lve
r
t
Occasi
o
nally wr
i
te multi-al
i
gnent s
t
r
uctures
i
n full
.
.
.
commit
|
commitdiff
|
tree
2008-03-09
Davi
d
Hilv
e
rt
d2::align::_align: Resc
a
le multi
-
alignment transformation
.
.
.
commit
|
commitdiff
|
tree
2008-03-09
Da
v
id H
i
lvert
d2::align:
Fur
t
her updates
f
or migra
t
ion to single
.
.
.
commit
|
commitdiff
|
tree
2008-03-06
D
avid Hilvert
d2::align: Begin
m
igration
to using sin
g
le-transfo
r
mati
o
n
.
.
.
commit
|
commitdiff
|
tree
2008-02-14
David Hilvert
d2:
:
align: Set o
r
ig
i
n
al
b
ou
n
ds
before align
i
ng the
.
.
.
commit
|
commitdiff
|
tree
2008-02-14
D
a
vid Hilvert
d2::align: Imple
m
ent f
u
rther change
s
fo
r
mult
i
-alignme
n
t
.
commit
|
commitdiff
|
tree
2008-02-13
Davi
d
Hilve
r
t
d
2
::align: Further m
o
difications for multi-a
l
ignme
n
t
.
commit
|
commitdiff
|
tree
2008-02-13
Davi
d
Hilv
e
rt
B
e
gin mo
d
ifica
t
ion
o
f d2
:
:
a
lign for mu
l
ti
-
alignment
.
commit
|
commitdiff
|
tree
2008-02-13
Da
v
i
d
Hi
l
vert
R
e
so
l
ve c
o
mpiler warn
i
n
g
s
.
commit
|
commitdiff
|
tree
2008-02-13
David
H
ilvert
d2::tran
s
_m
u
lti: I
m
plement mul
t
i-
a
l
i
gnment
pe() and
.
.
.
commit
|
commitdiff
|
tree
2008-02-13
D
a
vi
d
Hilvert
d2::
t
ra
n
s
_
multi::use_mult
i
: Check coordinate ag
a
in
s
t
.
.
.
commit
|
commitdiff
|
tree
2008-02-12
David H
i
lvert
d2::t
r
ans_mul
t
i: Fix
c
omp
i
lation bug
s
.
commit
|
commitdiff
|
tree
2008-02-12
D
a
vid
H
ilvert
d2::
t
rans_multi::use_multi: Add
c
ode t
o
gene
r
ate spat
i
o
.
.
.
commit
|
commitdiff
|
tree
2008-02-12
David H
i
lve
r
t
d2::tran
s
_multi::se
t
_current_bounds: Change loop for
.
.
.
commit
|
commitdiff
|
tree
2008-02-12
David Hil
v
er
t
d
2
::trans_
m
ulti: Modify c
e
rtain unsigne
d
int t
o
ind
e
x_t
.
commit
|
commitdiff
|
tree
2008-02-02
David
Hilvert
d2::trans_multi: Change
t
he sort orde
r
on the element
.
.
.
commit
|
commitdiff
|
tree
2008-02-01
David Hilvert
d2::trans_multi: c
l
ean-up edi
t
.
commit
|
commitdiff
|
tree
2008-01-31
David Hilvert
Resolve compilatio
n
fail
u
res
.
commit
|
commitdiff
|
tree
2008-01-29
David Hilver
t
d2::
t
rans_multi: Continue
i
mpleme
n
ta
t
ion of the
f
ixed
.
.
.
commit
|
commitdiff
|
tree
2008-01-27
David Hilve
r
t
d2::trans_mu
l
ti: Change offs
e
t sto
r
age to poi
n
t
data
.
.
.
commit
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commitdiff
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tree
2008-01-27
David Hil
v
ert
d2:
:
trans_mu
l
ti: Add sto
r
a
g
e
for o
f
fs
e
t values
.
commit
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commitdiff
|
tree
2008-01-26
David Hilvert
Fi
x
com
p
i
l
ation failures
a
ri
s
ing from
t
he priv
a
ti
z
ation
.
.
.
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