few small fixes of alignment tools, add new orthographic similarity feature for word aligner, final naming of directories, libraries in cdec

1 files changed, 2645 insertions, 0 deletions

diff --git a/decoder/test_data/dummy.3gram.lm b/decoder/test_data/dummy.3gram.lm
new file mode 100644
index 00000000..ae665284
--- /dev/null
+++ b/decoder/test_data/dummy.3gram.lm
@@ -0,0 +1,2645 @@
+
+\data\
+ngram 1=490
+ngram 2=1023
+ngram 3=1119
+
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+-1.533073	predictable factors ,
+-1.533073	outright fantasy had
+-1.533073	the far more
+-2.010194	a few at
+-0.9906404	a few days
+-1.533073	editors finally seized
+-1.533073	information finally available
+-1.533073	was finally placed
+-1.533073	. first ,
+-1.533073	against flesh and
+-1.533073	the following: </s>
+-1.533073	as follows: </s>
+-1.533073	, for we
+-1.533073	asked for an
+-1.533073	church for all
+-1.533073	cocaine for paleoclimatologists
+-1.533073	reason for excluding
+-1.533073	voted for him
+-1.533073	northern forests .
+-1.533073	, from 200–400
+-1.533073	derived from a
+-1.533073	expect from someone
+-1.533073	without fully thinking
+-1.533073	" further along
+-1.533073	much further away
+-1.533073	the further ahead
+-1.533073	. furthermore ,
+-1.533073	the future .
+-1.533073	a generating script
+-1.533073	slowly get the
+-1.533073	to get the
+-1.533073	my ghastly tendency
+-1.533073	was ghostwritten by
+-1.533073	by gil bailie
+-1.533073	but given the
+-1.533073	not going to
+-1.533073	and got used
+-1.533073	a great idea
+-1.533073	your great idea
+-1.533073	keeps growing .
+-1.533073	it grows more
+-1.533073	) had jurisdiction
+-1.533073	fantasy had been
+-1.533073	i had a
+-1.533073	paul had in
+-1.533073	which had a
+-1.533073	and hantemirov and
+-1.533073	by hantemirov and
+-1.533073	in hantemirov and
+-1.533073	be happening deep
+-1.533073	is happening right
+-1.533073	what happens today
+-1.533073	very hard to
+-1.533073	i hardly know
+-1.533073	also has a
+-1.533073	analysis has only
+-1.533073	chronology has always
+-1.533073	it has the
+-1.533073	him hate to
+-2.010194	not have been
+-2.010194	not have similarly
+-2.010194	not have the
+-1.533073	that have relied
+-1.533073	well have been
+-1.533073	will have an
+-1.533073	i haven't read
+-1.533073	, he wrote
+-1.533073	and he is
+-1.533073	said he would
+-1.533073	that he is
+-1.533073	when he made
+-1.533073	observed here prove
+-1.533073	is highly possible
+-1.533073	for him hate
+-1.533073	into him to
+-1.533073	, his initial
+-1.533073	of his comments
+-1.533073	that his precipitous
+-1.533073	by how their
+-0.8145491	. however ,
+-1.533073	enormous hs blade
+-1.533073	unveiled: humanity at
+-2.010194	, i can
+-2.010194	, i noticed
+-2.010194	, i skimmed
+-1.533073	. i haven't
+-1.533073	<s> i hardly
+-1.533073	? i know
+-1.533073	morning i had
+-1.533073	passage i stumbled
+-1.533073	when i checked
+-1.533073	" i'd love
+-1.533073	and i've provided
+-1.834103	great idea ,
+-1.834103	great idea .
+-1.533073	, if it
+-1.533073	<s> if the
+-1.533073	much illusion and
+-1.533073	an immense energy
+-1.533073	important impact on
+-1.533073	an important impact
+-1.533073	( in a
+-1.533073	. in response
+-1.533073	<s> in one
+-1.533073	acquiesced in this
+-1.533073	begin in terms
+-1.533073	chronology in passing
+-1.533073	described in hantemirov
+-1.533073	had in mind
+-1.533073	patterns in the
+-1.533073	principles in the
+-1.533073	published in any
+-1.533073	refusal in connection
+-1.533073	sat in rev
+-1.533073	set in combination
+-1.533073	subset in briffa
+-2.010194	used in a
+-2.010194	used in briffa's
+-2.010194	used in virtually
+-1.533073	be included with
+-1.533073	, including ,
+-1.533073	while including the
+-1.533073	do indeed see
+-1.533073	224 individual series
+-1.533073	the information finally
+-1.533073	against inhomogeneities ,
+-1.533073	his initial use
+-1.533073	! instead of
+-1.533073	population instead of
+-1.533073	of interannual variability
+-1.533073	deep into the
+-1.533073	projected into him
+-1.533073	bias introduced by
+-1.533073	, is considered
+-1.533073	decline is not
+-1.834103	he is always
+-1.834103	he is doing
+-2.010194	it is ,
+-2.010194	it is highly
+-2.010194	it is within
+-1.533073	obama is that
+-1.533073	selection is derived
+-1.533073	sensitivity is measured
+-1.834103	this is no
+-1.834103	this is the
+-1.533073	versions is related
+-1.533073	what is happening
+-1.834103	, it has
+-1.834103	, it originated
+-1.533073	. it is
+-1.533073	and it was
+-1.533073	as it is
+-1.834103	but it just
+-1.834103	but it looks
+-1.533073	if it grows
+-1.533073	more it is
+-1.533073	read it yet
+-1.834103	, it's like
+-1.834103	, it's very
+-1.533073	but it's not
+-1.533073	where it's much
+-1.533073	with its enormous
+-1.533073	any journal article
+-1.533073	previous journal (
+-1.533073	had jurisdiction .
+-1.533073	due just to
+-1.533073	it just keeps
+-1.533073	not just between
+-1.533073	reposting just one
+-1.533073	, kaufman et
+-1.533073	just keeps growing
+-1.533073	excluding khadyta river
+-1.533073	schweingruber's khadyta river
+-1.533073	also know ,
+-1.533073	hardly know where
+-1.533073	i know !
+-1.533073	readers know ,
+-1.533073	yamal larch sample
+-1.533073	living larches .
+-1.533073	subfossil larches were
+-1.533073	the large-scale "
+-1.533073	it's like trying
+-1.533073	was like crack
+-1.533073	very limited size
+-1.533073	old living larches
+-1.533073	the longest and
+-1.533073	while looking up
+-1.533073	it looks relevant
+-1.533073	i'd love to
+-1.533073	he made that
+-0.8145491	( mag )
+-1.533073	the magnitude of
+-1.533073	by magnus .
+-1.533073	which makes the
+-1.533073	on many multiproxy
+-1.533073	2000 may well
+-1.533073	a mean chronology
+-1.533073	is measured by
+-1.533073	the measurement data
+-1.533073	yamal measurement data
+-1.533073	chronology method that
+-1.533073	corridor method "
+-1.533073	rcs method .
+-1.533073	this method which
+-1.533073	rcs methodology warn
+-1.533073	in mind when
+-1.533073	to mix religion
+-1.533073	far more "
+-1.533073	grows more slowly
+-1.533073	the more it
+-1.533073	this morning i
+-1.533073	, most recently
+-1.533073	and most sensitive
+-1.533073	the most recent
+-1.533073	it's much further
+-1.533073	so much illusion
+-1.533073	the multi-parters ,
+-1.533073	many multiproxy studies
+-1.533073	of mundane politics
+-1.533073	about my ghastly
+-1.533073	catch my attention
+-1.533073	caught my attention
+-1.533073	the national debt
+-1.533073	all-around naughtiness .
+-1.533073	the nettle ,
+-1.533073	was never properly
+-1.533073	<s> next ,
+-1.533073	is no doubt
+-1.533073	the non-robustness observed
+-1.533073	characterizes northern forests
+-1.533073	- not just
+-1.533073	about not struggling
+-1.533073	did not preserve
+-1.533073	does not have
+-1.533073	is not due
+-1.533073	it's not going
+-1.533073	should not be
+-1.533073	were not using
+-0.8145491	would not have
+-1.533073	as noted before
+-1.533073	i noticed that
+-1.533073	, notwithstanding these
+-1.533073	right now ,
+-1.834103	with obama ,
+-1.834103	with obama is
+-1.533073	non-robustness observed here
+-1.533073	, of older
+-1.533073	addition of 17
+-1.533073	all of his
+-1.834103	instead of reposting
+-1.834103	instead of the
+-1.533073	magnitude of interannual
+-1.533073	principalities of darkness
+-1.533073	realm of mundane
+-1.834103	selection of old
+-1.834103	selection of older
+-1.533073	series of subfossil
+-1.533073	shadows of deeper
+-1.533073	terms of commentary
+-1.533073	unrepresentativeness of the
+-1.834103	use of a
+-1.834103	use of this
+-1.533073	virtue of being
+-1.533073	of old trees
+-1.533073	year old living
+-0.8145491	of older trees
+-1.533073	towards older trees
+-1.533073	one oldie ,
+-1.533073	, on average
+-1.533073	article on the
+-1.533073	caveats on rcs
+-1.533073	commentary on this
+-1.533073	impact on many
+-1.533073	play on a
+-1.533073	relied on this
+-1.533073	selected on a
+-1.533073	in one approach
+-1.533073	just one oldie
+-1.533073	recent one .
+-1.533073	placed online .
+-1.533073	has only taken
+-1.533073	( or real
+-1.533073	it originated with
+-1.533073	with osborn and
+-1.533073	prove out (
+-1.533073	and outright fantasy
+-1.533073	briffa's own caveats
+-1.533073	for paleoclimatologists and
+-1.533073	biblical passage i
+-1.533073	in passing and
+-1.533073	the path "
+-1.533073	aging patterns in
+-1.533073	what paul had
+-1.533073	the people that
+-1.533073	, perhaps the
+-1.533073	. perhaps the
+-1.834103	<s> perhaps the
+-1.834103	<s> perhaps there's
+-1.533073	and perhaps they
+-1.533073	( phil trans
+-1.533073	the phil trans
+-1.533073	12 picked cores
+-1.533073	this piece by
+-1.533073	right place .
+-1.533073	finally placed online
+-1.533073	shadow play on
+-1.533073	the point that
+-1.533073	data policy )
+-1.533073	and politics ,
+-1.533073	day politics are
+-1.533073	mundane politics .
+-1.834103	cru population .
+-1.834103	cru population consists
+-2.010194	schweingruber population .
+-2.010194	schweingruber population as
+-2.010194	schweingruber population instead
+-1.533073	the position that
+-1.533073	highly possible and
+-1.533073	about potential bias
+-1.533073	and potential unrepresentativeness
+-1.533073	your power to
+-1.533073	anti-divine powers and
+-1.533073	his precipitous decline
+-1.533073	at precisely the
+-1.533073	usual predictable factors
+-1.533073	2000 presented this
+-1.533073	not preserve centennial-scale
+-1.533073	the previous journal
+-1.533073	and principalities of
+-1.533073	deeper principles in
+-1.533073	a prior selection
+-1.533073	even probable that
+-0.8145491	divergence problem "
+-1.533073	been projected into
+-1.533073	never properly published
+-1.533073	here prove out
+-1.533073	to provide the
+-1.533073	i've provided a
+-1.533073	a provocative thought
+-1.533073	properly published in
+-1.533073	small push at
+-1.533073	a rcs chronology
+-1.533073	on rcs methodology
+-1.533073	the rcs method
+-1.533073	really react to
+-1.533073	haven't read it
+-1.834103	ca readers also
+-1.834103	ca readers know
+-1.533073	worth reading ,
+-1.533073	or real )
+-1.533073	don't really react
+-1.533073	the realm of
+-1.533073	some reason why
+-1.533073	valid reason for
+-1.533073	most recent one
+-1.533073	most recently ,
+-1.533073	until recently ,
+-1.533073	yamal reconstruction .
+-1.533073	this refusal in
+-1.533073	staunchly refused to
+-1.533073	is related to
+-1.533073	looks relevant ,
+-1.533073	have relied on
+-1.533073	mix religion and
+-1.533073	data remained unarchived
+-1.533073	commenter remarked that
+-1.533073	of reposting just
+-1.533073	, requiring briffa
+-1.533073	in response to
+-1.533073	the resulting yamal
+-1.533073	in rev .
+-1.533073	happening right now
+-1.834103	the right place
+-1.834103	the right time
+-1.533073	were right .
+-1.533073	between ring widths
+-1.533073	17 ring-width series
+-0.8145491	khadyta river ,
+-1.533073	conservatives said he
+-1.533073	the same bias
+-1.533073	larch sample should
+-1.533073	and sat in
+-1.533073	similar schweingruber data
+-0.1249387	the schweingruber population
+-1.533073	why schweingruber's khadyta
+-1.533073	. science (
+-1.533073	a science article
+-1.533073	and science (
+-1.533073	generating script )
+-1.533073	can see the
+-1.533073	indeed see the
+-1.533073	you see ,
+-1.533073	finally seized the
+-1.834103	were selected .
+-1.834103	were selected on
+-1.533073	biased selection of
+-1.533073	cru selection is
+-1.533073	prior selection of
+-1.533073	most sensitive series
+-1.533073	where sensitivity is
+-1.533073	individual series of
+-1.533073	ring-width series ,
+-1.533073	sensitive series ,
+-1.533073	data set in
+-1.533073	. several things
+-1.533073	a shadow play
+-1.533073	the shadows of
+-1.533073	these shadows .
+-2.010194	and shiyatov 2002
+-2.010194	and shiyatov themselves
+-2.010194	and shiyatov would
+-1.533073	sample should not
+-1.533073	a similar schweingruber
+-1.533073	have similarly affected
+-1.533073	, since this
+-1.533073	limited size and
+-1.533073	i skimmed this
+-1.533073	more slowly ,
+-1.533073	way slowly get
+-1.533073	a small push
+-1.533073	because so much
+-1.533073	there's some reason
+-1.533073	from someone whose
+-1.533073	to start today
+-1.533073	cru staunchly refused
+-1.533073	not struggling against
+-1.533073	multiproxy studies that
+-1.533073	subsequent study ,
+-1.533073	this study .
+-1.533073	i stumbled upon
+-1.533073	of subfossil larches
+-1.533073	the subfossil collection
+-1.533073	yamal subfossil data
+-1.533073	every subsequent study
+-1.533073	this subset in
+-1.533073	" success .
+-1.533073	taymir supplement .
+-1.533073	were supplemented by
+-1.533073	a surface ,
+-1.533073	would take an
+-1.533073	only taken a
+-1.834103	the taymir data
+-1.834103	the taymir supplement
+-1.533073	and temperature ,
+-1.533073	ghastly tendency to
+-1.533073	in terms of
+-1.533073	trees than the
+-1.533073	" that characterizes
+-1.533073	admit that the
+-1.533073	and that way
+-1.533073	is that he
+-1.533073	made that wise
+-1.533073	method that they
+-1.533073	noticed that the
+-1.533073	people that voted
+-1.533073	point that his
+-1.533073	position that the
+-1.533073	probable that the
+-1.533073	remarked that "
+-1.533073	studies that have
+-1.533073	things that cast
+-1.533073	" the trouble
+-2.010194	, the more
+-2.010194	, the resulting
+-2.010194	, the yamal
+-1.533073	. the cru
+-1.834103	<s> the subfossil
+-1.834103	<s> the yamal
+-1.533073	affected the "
+-1.533073	along the path
+-2.010194	and the people
+-2.010194	and the phil
+-2.010194	and the right
+-1.533073	archive the data
+-1.533073	at the crossroads
+-0.8145491	between the two
+-1.533073	but the further
+-1.834103	by the addition
+-1.834103	by the magnitude
+-1.533073	combine the multi-parters
+-1.533073	control the national
+-0.8145491	get the arkive
+-1.533073	given the use
+-1.533073	has the virtue
+-1.533073	have the same
+-1.533073	if the non-robustness
+-1.834103	in the realm
+-1.834103	in the schweingruber
+-1.533073	including the taymir
+-1.533073	into the future
+-1.533073	is the most
+-1.533073	makes the point
+-0.8145491	of the 12
+-1.533073	on the trouble
+-2.010194	perhaps the biased
+-2.010194	perhaps the day
+-2.010194	perhaps the difference
+-1.533073	precisely the right
+-1.533073	provide the measurement
+-1.834103	see the far
+-1.834103	see the shadows
+-1.533073	seized the nettle
+-1.533073	than the schweingruber
+-2.135133	that the conservatives
+-2.135133	that the cru
+-2.135133	that the previous
+-2.135133	that the yamal
+-1.533073	through the very
+-2.135133	to the back-and-forth
+-2.135133	to the cru
+-2.135133	to the large-scale
+-2.135133	to the usual
+-1.533073	took the position
+-1.533073	up the biblical
+-1.533073	used the chronology
+-1.533073	using the schweingruber
+-1.533073	were the longest
+-1.533073	what the conservatives
+-1.533073	while the yamal
+-2.135133	with the information
+-2.135133	with the rcs
+-2.135133	with the taymir
+-2.135133	with the yamal
+-1.533073	wrote the following:
+-1.533073	how their cores
+-1.533073	shiyatov themselves ,
+-1.533073	they themselves were
+-1.533073	perhaps there's some
+-1.834103	. these data
+-1.834103	. these were
+-1.533073	cast these shadows
+-1.533073	notwithstanding these warnings
+-1.533073	and they can
+-1.533073	did they expect
+-1.533073	perhaps they don't
+-1.533073	that they themselves
+-1.533073	) things that
+-1.533073	several things caught
+-1.533073	to think up
+-1.533073	fully thinking through
+-2.010194	, this analysis
+-2.010194	, this chronology
+-2.010194	, this will
+-1.834103	. this bias
+-1.834103	. this is
+-1.533073	<s> this morning
+-1.533073	but this is
+-1.533073	earlier this year
+-1.533073	in this refusal
+-1.533073	of this subset
+-1.834103	on this difference
+-1.834103	on this study
+-1.533073	presented this chronology
+-1.533073	since this method
+-1.533073	skimmed this article
+-1.533073	upon this piece
+-1.533073	all those years
+-1.533073	to those "
+-1.533073	provocative thought .
+-1.533073	a thousand ,
+-1.533073	thinking through the
+-1.533073	a time ,
+-1.533073	right time and
+-1.533073	approach to constructing
+-1.533073	are to those
+-1.533073	briffa to archive
+-1.533073	but to what
+-1.533073	compared to the
+-1.533073	day to day
+-1.533073	down to about
+-1.533073	exception to the
+-1.533073	going to start
+-1.533073	hard to think
+-1.533073	hate to admit
+-1.533073	him to begin
+-1.533073	just to the
+-1.533073	love to get
+-1.533073	power to change
+-1.533073	react to what
+-1.533073	refused to provide
+-1.533073	related to different
+-1.533073	response to the
+-1.533073	tendency to mix
+-1.533073	trying to control
+-1.533073	where to begin
+-1.533073	happens today would
+-1.533073	start today .
+-1.533073	) took the
+-1.533073	bias towards older
+-1.834103	phil trans b
+-1.834103	phil trans editors
+-1.533073	old trees described
+-2.010194	older trees .
+-2.010194	older trees an
+-2.010194	older trees than
+-0.8145491	the trouble with
+-1.533073	being true ,
+-1.533073	like trying to
+-0.8145491	the two versions
+-1.533073	remained unarchived .
+-1.533073	arkive under control
+-1.533073	an unintentional bias
+-1.533073	potential unrepresentativeness of
+-1.533073	, until recently
+-1.533073	violence unveiled: humanity
+-1.533073	looking up the
+-1.533073	think up a
+-1.533073	stumbled upon this
+-1.533073	initial use of
+-1.533073	the use of
+-1.533073	" used by
+-1.533073	briffa used the
+-1.533073	data used in
+-1.533073	got used in
+-1.533073	was used in
+-1.533073	, using the
+-1.533073	not using .
+-1.533073	the usual predictable
+-1.533073	a valid reason
+-1.533073	centennial-scale variability and
+-1.533073	interannual variability .
+-1.834103	two versions .
+-1.834103	two versions is
+-1.533073	it's very hard
+-1.533073	the very limited
+-1.533073	. violence unveiled:
+-1.533073	in virtually every
+-1.533073	the virtue of
+-1.533073	that voted for
+-1.533073	methodology warn against
+-1.533073	these warnings ,
+-1.533073	blade was like
+-1.533073	book was ghostwritten
+-1.533073	chronology was used
+-1.533073	data was finally
+-1.533073	it was never
+-1.533073	that way slowly
+-1.533073	for we do
+-1.533073	may well have
+-1.533073	conservatives were right
+-1.533073	cores were selected
+-1.533073	data were supplemented
+-1.533073	larches were selected
+-1.533073	themselves were not
+-1.533073	these were the
+-1.533073	. what did
+-1.533073	<s> what a
+-1.533073	changing what happens
+-1.533073	doubt what paul
+-1.533073	exactly what the
+-1.834103	to what is
+-1.834103	to what will
+-1.533073	. what's your
+-1.834103	, when combined
+-1.834103	, when i
+-1.533073	mind when he
+-1.533073	, where sensitivity
+-1.533073	case where it's
+-1.533073	know where to
+-1.533073	( which had
+-1.834103	, which ,
+-1.834103	, which makes
+-1.533073	method which did
+-1.533073	( while looking
+-1.533073	, while including
+-1.533073	. while the
+-1.533073	someone whose book
+-1.533073	reason why schweingruber's
+-1.533073	ring widths and
+-1.533073	this will have
+-1.533073	what will be
+-1.533073	that wise crack
+-1.533073	. with the
+-1.533073	begin with .
+-1.533073	change with a
+-1.533073	chronology with its
+-1.533073	combination with the
+-1.533073	combined with the
+-1.533073	connection with osborn
+-1.533073	included with the
+-1.533073	originated with briffa
+-0.8145491	trouble with obama
+-1.533073	is within your
+-1.533073	done without fully
+-1.533073	always worth reading
+-1.533073	bias would not
+-1.533073	he would do
+-1.533073	shiyatov would not
+-1.533073	today would take
+-1.533073	. wright's church
+-1.533073	he wrote the
+-1.533073	, yamal larch
+-1.533073	briffa's yamal reconstruction
+-1.533073	resulting yamal chronology
+-1.212489	the yamal chronology
+-2.232043	the yamal data
+-2.232043	the yamal measurement
+-2.232043	the yamal subfossil
+-1.533073	200–400 year old
+-1.533073	this year ,
+-1.533073	those years ?
+-1.533073	' yes ,
+-1.533073	back-and-forth yesterday about
+-1.533073	it yet ,
+-1.533073	ahead you see
+-1.533073	what's your great
+-1.533073	within your power
+
+\end\