pub struct Context<'reference, 'query, SubsequenceType: GenomeSequence<Strategies::Alphabet, SubsequenceType> + ?Sized, Strategies: AlignmentStrategySelector> {
pub reference: &'reference SubsequenceType,
pub query: &'query SubsequenceType,
pub reference_name: String,
pub query_name: String,
pub range: AlignmentRange,
pub config: TemplateSwitchConfig<Strategies::Alphabet, Strategies::Cost>,
pub a_star_buffers: AStarBuffers<Box<Node<Strategies>>>,
pub memory: Memory<Strategies>,
pub dynamic_strategies: DynamicStrategies,
/* private fields */
}Fields§
§reference: &'reference SubsequenceType§query: &'query SubsequenceType§reference_name: String§query_name: String§range: AlignmentRange§config: TemplateSwitchConfig<Strategies::Alphabet, Strategies::Cost>§a_star_buffers: AStarBuffers<Box<Node<Strategies>>>§memory: Memory<Strategies>§dynamic_strategies: DynamicStrategiesImplementations§
Source§impl<'reference, 'query, SubsequenceType: GenomeSequence<Strategies::Alphabet, SubsequenceType> + ?Sized, Strategies: AlignmentStrategySelector> Context<'reference, 'query, SubsequenceType, Strategies>
impl<'reference, 'query, SubsequenceType: GenomeSequence<Strategies::Alphabet, SubsequenceType> + ?Sized, Strategies: AlignmentStrategySelector> Context<'reference, 'query, SubsequenceType, Strategies>
pub fn new( reference: &'reference SubsequenceType, query: &'query SubsequenceType, reference_name: &str, query_name: &str, range: AlignmentRange, config: TemplateSwitchConfig<Strategies::Alphabet, Strategies::Cost>, memory: Memory<Strategies>, dynamic_strategies: DynamicStrategies, cost_limit: Option<Strategies::Cost>, memory_limit: Option<usize>, force_label_correcting: bool, ) -> Self
Trait Implementations§
Source§impl<SubsequenceType: GenomeSequence<Strategies::Alphabet, SubsequenceType> + ?Sized, Strategies: AlignmentStrategySelector> AStarContext for Context<'_, '_, SubsequenceType, Strategies>
impl<SubsequenceType: GenomeSequence<Strategies::Alphabet, SubsequenceType> + ?Sized, Strategies: AlignmentStrategySelector> AStarContext for Context<'_, '_, SubsequenceType, Strategies>
Source§fn create_root(&self) -> Self::Node
fn create_root(&self) -> Self::Node
Create the root node of the A* graph.
Source§fn generate_successors(
&mut self,
node: &Self::Node,
opened_nodes_output: &mut impl Extend<Self::Node>,
)
fn generate_successors( &mut self, node: &Self::Node, opened_nodes_output: &mut impl Extend<Self::Node>, )
Generate the successors of this node.
Source§fn is_target(&self, node: &Self::Node) -> bool
fn is_target(&self, node: &Self::Node) -> bool
Returns true if this node is a target node of the A* graph.
Source§fn cost_limit(&self) -> Option<Strategies::Cost>
fn cost_limit(&self) -> Option<Strategies::Cost>
Returns the maximum cost that the target node is allowed to have. Read more
Source§fn memory_limit(&self) -> Option<usize>
fn memory_limit(&self) -> Option<usize>
An approximate memory limit for the aligner in bytes. Read more
Source§fn is_label_setting(&self) -> bool
fn is_label_setting(&self) -> bool
Returns true if the nodes are generated in a label-setting manner. Read more
Source§impl<SubsequenceType: GenomeSequence<Strategies::Alphabet, SubsequenceType> + ?Sized, Strategies: AlignmentStrategySelector> AlignmentContext for Context<'_, '_, SubsequenceType, Strategies>
impl<SubsequenceType: GenomeSequence<Strategies::Alphabet, SubsequenceType> + ?Sized, Strategies: AlignmentStrategySelector> AlignmentContext for Context<'_, '_, SubsequenceType, Strategies>
type AlphabetType = <Strategies as AlignmentStrategySelector>::Alphabet
type AlignmentType = AlignmentType
type SubsequenceType = SubsequenceType
fn reference(&self) -> &Self::SubsequenceType
fn query(&self) -> &Self::SubsequenceType
fn reference_name(&self) -> &str
fn query_name(&self) -> &str
fn range(&self) -> &AlignmentRange
Auto Trait Implementations§
impl<'reference, 'query, SubsequenceType, Strategies> Freeze for Context<'reference, 'query, SubsequenceType, Strategies>where
<<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength as TemplateSwitchMinLengthStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Freeze,
<<Strategies as AlignmentStrategySelector>::Chaining as ChainingStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Freeze,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchCount as TemplateSwitchCountStrategy>::Memory: Freeze,
<<Strategies as AlignmentStrategySelector>::Shortcut as ShortcutStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Freeze,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Freeze,
<Strategies as AlignmentStrategySelector>::Cost: Freeze,
SubsequenceType: ?Sized,
impl<'reference, 'query, SubsequenceType, Strategies> RefUnwindSafe for Context<'reference, 'query, SubsequenceType, Strategies>where
SubsequenceType: RefUnwindSafe + ?Sized,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength as TemplateSwitchMinLengthStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: RefUnwindSafe,
<<Strategies as AlignmentStrategySelector>::Chaining as ChainingStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: RefUnwindSafe,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchCount as TemplateSwitchCountStrategy>::Memory: RefUnwindSafe,
<<Strategies as AlignmentStrategySelector>::Shortcut as ShortcutStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: RefUnwindSafe,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: RefUnwindSafe,
<Strategies as AlignmentStrategySelector>::Cost: RefUnwindSafe,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::IdentifierPrimaryExtraData: RefUnwindSafe,
<Strategies as AlignmentStrategySelector>::NodeOrd: RefUnwindSafe,
<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength: RefUnwindSafe,
<Strategies as AlignmentStrategySelector>::TemplateSwitchCount: RefUnwindSafe,
<Strategies as AlignmentStrategySelector>::PrimaryMatch: RefUnwindSafe,
<Strategies as AlignmentStrategySelector>::TemplateSwitchTotalLength: RefUnwindSafe,
<Strategies as AlignmentStrategySelector>::Descendant: RefUnwindSafe,
impl<'reference, 'query, SubsequenceType, Strategies> Send for Context<'reference, 'query, SubsequenceType, Strategies>where
SubsequenceType: Sync + ?Sized,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength as TemplateSwitchMinLengthStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Send,
<<Strategies as AlignmentStrategySelector>::Chaining as ChainingStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Send,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchCount as TemplateSwitchCountStrategy>::Memory: Send,
<<Strategies as AlignmentStrategySelector>::Shortcut as ShortcutStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Send,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Send,
<Strategies as AlignmentStrategySelector>::Cost: Send,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::IdentifierPrimaryExtraData: Send,
<Strategies as AlignmentStrategySelector>::NodeOrd: Send,
<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength: Send,
<Strategies as AlignmentStrategySelector>::TemplateSwitchCount: Send,
<Strategies as AlignmentStrategySelector>::PrimaryMatch: Send,
<Strategies as AlignmentStrategySelector>::TemplateSwitchTotalLength: Send,
<Strategies as AlignmentStrategySelector>::Descendant: Send,
impl<'reference, 'query, SubsequenceType, Strategies> Sync for Context<'reference, 'query, SubsequenceType, Strategies>where
SubsequenceType: Sync + ?Sized,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength as TemplateSwitchMinLengthStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Sync,
<<Strategies as AlignmentStrategySelector>::Chaining as ChainingStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Sync,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchCount as TemplateSwitchCountStrategy>::Memory: Sync,
<<Strategies as AlignmentStrategySelector>::Shortcut as ShortcutStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Sync,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Sync,
<Strategies as AlignmentStrategySelector>::Cost: Sync,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::IdentifierPrimaryExtraData: Sync,
<Strategies as AlignmentStrategySelector>::NodeOrd: Sync,
<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength: Sync,
<Strategies as AlignmentStrategySelector>::TemplateSwitchCount: Sync,
<Strategies as AlignmentStrategySelector>::PrimaryMatch: Sync,
<Strategies as AlignmentStrategySelector>::TemplateSwitchTotalLength: Sync,
<Strategies as AlignmentStrategySelector>::Descendant: Sync,
impl<'reference, 'query, SubsequenceType, Strategies> Unpin for Context<'reference, 'query, SubsequenceType, Strategies>where
<<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength as TemplateSwitchMinLengthStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Unpin,
<<Strategies as AlignmentStrategySelector>::Chaining as ChainingStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Unpin,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchCount as TemplateSwitchCountStrategy>::Memory: Unpin,
<<Strategies as AlignmentStrategySelector>::Shortcut as ShortcutStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Unpin,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: Unpin,
<Strategies as AlignmentStrategySelector>::Cost: Unpin,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::IdentifierPrimaryExtraData: Unpin,
SubsequenceType: ?Sized,
impl<'reference, 'query, SubsequenceType, Strategies> UnsafeUnpin for Context<'reference, 'query, SubsequenceType, Strategies>where
<<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength as TemplateSwitchMinLengthStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: UnsafeUnpin,
<<Strategies as AlignmentStrategySelector>::Chaining as ChainingStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: UnsafeUnpin,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchCount as TemplateSwitchCountStrategy>::Memory: UnsafeUnpin,
<<Strategies as AlignmentStrategySelector>::Shortcut as ShortcutStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: UnsafeUnpin,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: UnsafeUnpin,
<Strategies as AlignmentStrategySelector>::Cost: UnsafeUnpin,
SubsequenceType: ?Sized,
impl<'reference, 'query, SubsequenceType, Strategies> UnwindSafe for Context<'reference, 'query, SubsequenceType, Strategies>where
SubsequenceType: RefUnwindSafe + ?Sized,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength as TemplateSwitchMinLengthStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: UnwindSafe,
<<Strategies as AlignmentStrategySelector>::Chaining as ChainingStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: UnwindSafe,
<<Strategies as AlignmentStrategySelector>::TemplateSwitchCount as TemplateSwitchCountStrategy>::Memory: UnwindSafe,
<<Strategies as AlignmentStrategySelector>::Shortcut as ShortcutStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: UnwindSafe,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::Memory: UnwindSafe,
<Strategies as AlignmentStrategySelector>::Cost: UnwindSafe,
<<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::IdentifierPrimaryExtraData: UnwindSafe,
<Strategies as AlignmentStrategySelector>::NodeOrd: UnwindSafe,
<Strategies as AlignmentStrategySelector>::TemplateSwitchMinLength: UnwindSafe,
<Strategies as AlignmentStrategySelector>::TemplateSwitchCount: UnwindSafe,
<Strategies as AlignmentStrategySelector>::PrimaryMatch: UnwindSafe,
<Strategies as AlignmentStrategySelector>::TemplateSwitchTotalLength: UnwindSafe,
<Strategies as AlignmentStrategySelector>::Descendant: UnwindSafe,
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