lib_tsalign::config

Struct TemplateSwitchConfig

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pub struct TemplateSwitchConfig<AlphabetType, Cost> {
Show 14 fields
    pub left_flank_length: isize,
    pub right_flank_length: isize,
    pub template_switch_min_length: usize,
    pub base_cost: BaseCost<Cost>,
    pub primary_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>,
    pub secondary_forward_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>,
    pub secondary_reverse_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>,
    pub left_flank_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>,
    pub right_flank_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>,
    pub offset_costs: CostFunction<isize, Cost>,
    pub length_costs: CostFunction<usize, Cost>,
    pub length_difference_costs: CostFunction<isize, Cost>,
    pub forward_anti_primary_gap_costs: CostFunction<isize, Cost>,
    pub reverse_anti_primary_gap_costs: CostFunction<isize, Cost>,

}

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§left_flank_length: isize§right_flank_length: isize§template_switch_min_length: usize§base_cost: BaseCost<Cost>§primary_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>§secondary_forward_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>§secondary_reverse_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>§left_flank_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>§right_flank_edit_costs: GapAffineAlignmentCostTable<AlphabetType, Cost>§offset_costs: CostFunction<isize, Cost>§length_costs: CostFunction<usize, Cost>§length_difference_costs: CostFunction<isize, Cost>§forward_anti_primary_gap_costs: CostFunction<isize, Cost>§reverse_anti_primary_gap_costs: CostFunction<isize, Cost>

Implementations§

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impl<AlphabetType: Alphabet, Cost: AStarCost> TemplateSwitchConfig<AlphabetType, Cost>

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pub fn read_plain(reader: impl Read) -> Result<Self>

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impl<AlphabetType, Cost: Bounded + Ord> TemplateSwitchConfig<AlphabetType, Cost>

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pub fn verify(&self) -> Result<()>

Returns an error if any cost function is malformed.

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impl<AlphabetType, Cost> TemplateSwitchConfig<AlphabetType, Cost>

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pub fn secondary_edit_costs( &self, direction: TemplateSwitchDirection, ) -> &GapAffineAlignmentCostTable<AlphabetType, Cost>

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pub fn anti_primary_gap_costs( &self, direction: TemplateSwitchDirection, ) -> &CostFunction<isize, Cost>

Trait Implementations§

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impl<AlphabetType: Alphabet, Cost: Clone> Clone for TemplateSwitchConfig<AlphabetType, Cost>

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fn clone(&self) -> Self

Returns a duplicate of the value. Read more
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fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source. Read more
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impl<AlphabetType: Debug, Cost: Debug> Debug for TemplateSwitchConfig<AlphabetType, Cost>

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fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter. Read more
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impl<AlphabetType: Alphabet, Cost: AStarCost> Default for TemplateSwitchConfig<AlphabetType, Cost>

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fn default() -> Self

Returns the “default value” for a type. Read more
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impl<AlphabetType: Alphabet, Cost: AStarCost> Display for TemplateSwitchConfig<AlphabetType, Cost>

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fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter. Read more
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impl<AlphabetType: PartialEq, Cost: PartialEq> PartialEq for TemplateSwitchConfig<AlphabetType, Cost>

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fn eq(&self, other: &TemplateSwitchConfig<AlphabetType, Cost>) -> bool

Tests for self and other values to be equal, and is used by ==.
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fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.
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impl<AlphabetType: Eq, Cost: Eq> Eq for TemplateSwitchConfig<AlphabetType, Cost>

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impl<AlphabetType, Cost> StructuralPartialEq for TemplateSwitchConfig<AlphabetType, Cost>

Auto Trait Implementations§

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impl<AlphabetType, Cost> Freeze for TemplateSwitchConfig<AlphabetType, Cost>
where Cost: Freeze,

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impl<AlphabetType, Cost> RefUnwindSafe for TemplateSwitchConfig<AlphabetType, Cost>
where Cost: RefUnwindSafe, AlphabetType: RefUnwindSafe,

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impl<AlphabetType, Cost> Send for TemplateSwitchConfig<AlphabetType, Cost>
where Cost: Send, AlphabetType: Send,

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impl<AlphabetType, Cost> Sync for TemplateSwitchConfig<AlphabetType, Cost>
where Cost: Sync, AlphabetType: Sync,

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impl<AlphabetType, Cost> Unpin for TemplateSwitchConfig<AlphabetType, Cost>
where Cost: Unpin, AlphabetType: Unpin,

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impl<AlphabetType, Cost> UnwindSafe for TemplateSwitchConfig<AlphabetType, Cost>
where Cost: UnwindSafe, AlphabetType: UnwindSafe,

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