cm::hybridize Namespace Reference

Functions
BooleanOptionKey const	hybridize ("cm:hybridize")
IntegerVectorOptionKey const	starting_template ("cm:hybridize:starting_template")
BooleanOptionKey const	realign_domains ("cm:hybridize:realign_domains")
BooleanOptionKey const	realign_domains_stage2 ("cm:hybridize:realign_domains_stage2")
IntegerOptionKey const	add_non_init_chunks ("cm:hybridize:add_non_init_chunks")
RealOptionKey const	stage1_increase_cycles ("cm:hybridize:stage1_increase_cycles")
RealOptionKey const	stage2_increase_cycles ("cm:hybridize:stage2_increase_cycles")
RealOptionKey const	stage2min_increase_cycles ("cm:hybridize:stage2min_increase_cycles")
RealOptionKey const	stage1_probability ("cm:hybridize:stage1_probability")
BooleanOptionKey const	skip_stage2 ("cm:hybridize:skip_stage2")
BooleanOptionKey const	no_global_frame ("cm:hybridize:no_global_frame")
BooleanOptionKey const	linmin_only ("cm:hybridize:linmin_only")
IntegerOptionKey const	relax ("cm:hybridize:relax")
RealOptionKey const	frag_weight_aligned ("cm:hybridize:frag_weight_aligned")
IntegerOptionKey const	max_registry_shift ("cm:hybridize:max_registry_shift")
RealOptionKey const	frag_1mer_insertion_weight ("cm:hybridize:frag_1mer_insertion_weight")
RealOptionKey const	small_frag_insertion_weight ("cm:hybridize:small_frag_insertion_weight")
RealOptionKey const	big_frag_insertion_weight ("cm:hybridize:big_frag_insertion_weight")
BooleanOptionKey const	auto_frag_insertion_weight ("cm:hybridize:auto_frag_insertion_weight")
IntegerOptionKey const	stage1_1_cycles ("cm:hybridize:stage1_1_cycles")
IntegerOptionKey const	stage1_2_cycles ("cm:hybridize:stage1_2_cycles")
IntegerOptionKey const	stage1_3_cycles ("cm:hybridize:stage1_3_cycles")
IntegerOptionKey const	stage1_4_cycles ("cm:hybridize:stage1_4_cycles")
RealOptionKey const	stage2_temperature ("cm:hybridize:stage2_temperature")
StringOptionKey const	stage1_4_cenrot_score ("cm:hybridize:stage1_4_cenrot_score")
BooleanOptionKey const	include_loop_ss_chunks ("cm:hybridize:include_loop_ss_chunks")

Function Documentation

add_non_init_chunks()

IntegerOptionKey const cm::hybridize::add_non_init_chunks

(

"cm:hybridize:add_non_init_chunks"

)

References hybridize().

auto_frag_insertion_weight()

BooleanOptionKey const cm::hybridize::auto_frag_insertion_weight

(

"cm:hybridize:auto_frag_insertion_weight"

)

References hybridize().

big_frag_insertion_weight()

RealOptionKey const cm::hybridize::big_frag_insertion_weight

(

"cm:hybridize:big_frag_insertion_weight"

)

References hybridize().

frag_1mer_insertion_weight()

RealOptionKey const cm::hybridize::frag_1mer_insertion_weight

(

"cm:hybridize:frag_1mer_insertion_weight"

)

References hybridize().

frag_weight_aligned()

RealOptionKey const cm::hybridize::frag_weight_aligned

(

"cm:hybridize:frag_weight_aligned"

)

References hybridize().

hybridize()

BooleanOptionKey const cm::hybridize::hybridize

(

"cm:hybridize"

)

Referenced by add_non_init_chunks(), auto_frag_insertion_weight(), big_frag_insertion_weight(), frag_1mer_insertion_weight(), frag_weight_aligned(), include_loop_ss_chunks(), linmin_only(), max_registry_shift(), no_global_frame(), realign_domains(), realign_domains_stage2(), relax(), skip_stage2(), small_frag_insertion_weight(), stage1_1_cycles(), stage1_2_cycles(), stage1_3_cycles(), stage1_4_cenrot_score(), stage1_4_cycles(), stage1_increase_cycles(), stage1_probability(), stage2_increase_cycles(), stage2_temperature(), stage2min_increase_cycles(), and starting_template().

include_loop_ss_chunks()

BooleanOptionKey const cm::hybridize::include_loop_ss_chunks

(

"cm:hybridize:include_loop_ss_chunks"

)

References hybridize().

linmin_only()

BooleanOptionKey const cm::hybridize::linmin_only

(

"cm:hybridize:linmin_only"

)

References hybridize().

max_registry_shift()

IntegerOptionKey const cm::hybridize::max_registry_shift

(

"cm:hybridize:max_registry_shift"

)

References hybridize().

no_global_frame()

BooleanOptionKey const cm::hybridize::no_global_frame

(

"cm:hybridize:no_global_frame"

)

References hybridize().

realign_domains()

BooleanOptionKey const cm::hybridize::realign_domains

(

"cm:hybridize:realign_domains"

)

References hybridize().

realign_domains_stage2()

BooleanOptionKey const cm::hybridize::realign_domains_stage2

(

"cm:hybridize:realign_domains_stage2"

)

References hybridize().

relax()

IntegerOptionKey const cm::hybridize::relax

(

"cm:hybridize:relax"

)

References hybridize().

skip_stage2()

BooleanOptionKey const cm::hybridize::skip_stage2

(

"cm:hybridize:skip_stage2"

)

References hybridize().

small_frag_insertion_weight()

RealOptionKey const cm::hybridize::small_frag_insertion_weight

(

"cm:hybridize:small_frag_insertion_weight"

)

References hybridize().

stage1_1_cycles()

IntegerOptionKey const cm::hybridize::stage1_1_cycles

(

"cm:hybridize:stage1_1_cycles"

)

References hybridize().

stage1_2_cycles()

IntegerOptionKey const cm::hybridize::stage1_2_cycles

(

"cm:hybridize:stage1_2_cycles"

)

References hybridize().

stage1_3_cycles()

IntegerOptionKey const cm::hybridize::stage1_3_cycles

(

"cm:hybridize:stage1_3_cycles"

)

References hybridize().

stage1_4_cenrot_score()

StringOptionKey const cm::hybridize::stage1_4_cenrot_score

(

"cm:hybridize:stage1_4_cenrot_score"

)

References hybridize().

stage1_4_cycles()

IntegerOptionKey const cm::hybridize::stage1_4_cycles

(

"cm:hybridize:stage1_4_cycles"

)

References hybridize().

stage1_increase_cycles()

RealOptionKey const cm::hybridize::stage1_increase_cycles

(

"cm:hybridize:stage1_increase_cycles"

)

References hybridize().

stage1_probability()

RealOptionKey const cm::hybridize::stage1_probability

(

"cm:hybridize:stage1_probability"

)

References hybridize().

stage2_increase_cycles()

RealOptionKey const cm::hybridize::stage2_increase_cycles

(

"cm:hybridize:stage2_increase_cycles"

)

References hybridize().

stage2_temperature()

RealOptionKey const cm::hybridize::stage2_temperature

(

"cm:hybridize:stage2_temperature"

)

References hybridize().

stage2min_increase_cycles()

RealOptionKey const cm::hybridize::stage2min_increase_cycles

(

"cm:hybridize:stage2min_increase_cycles"

)

References hybridize().

starting_template()

IntegerVectorOptionKey const cm::hybridize::starting_template

(

"cm:hybridize:starting_template"

)

References hybridize().