pub trait StartEndGapParameters {
fn free_start_gap_x(&self) -> bool;
fn free_end_gap_x(&self) -> bool;
fn prob_start_gap_x(&self, i: usize) -> LogProb { ... }
}
Expand description
Trait for parametrization of PairHMM
start and end gap behavior.
This trait can be used to implement global and semiglobal alignments.
- global: methods return
false
andLogProb::ln_zero()
. - semiglobal: methods return
true
andLogProb::ln_one()
.
Required methods
fn free_start_gap_x(&self) -> bool
fn free_start_gap_x(&self) -> bool
Allow free start gap in x.
fn free_end_gap_x(&self) -> bool
fn free_end_gap_x(&self) -> bool
Allow free end gap in x.
Provided methods
fn prob_start_gap_x(&self, i: usize) -> LogProb
fn prob_start_gap_x(&self, i: usize) -> LogProb
Probability to start at x[i]
. This can be left unchanged if you use free_start_gap_x
and
free_end_gap_x
.