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/*! Traits that cover interacting with and manipulating paths in a graph. * [`GraphPaths`] has the basic interface * [`GraphPathNames`] supports retrieving the ID of a path by name, or vice versa * [`MutableGraphPaths`] includes creating and destroying paths, and methods for manipulating the steps on a path * [`PathSequences`] is for going between path step indices and sequence positions * [`GraphPathsRef`] provides a reference to a specific path, which can then be queried using the traits in [`super::path`] * [`IntoPathIds`] provides an iterator on the paths by ID * [`IntoNodeOccurrences`] provides an iterator on the steps that are on a given node */ use crate::handle::Handle; use super::{PathBase, PathId}; /// Trait for iterating through all `PathIds` in a graph. pub trait IntoPathIds { type PathIds: Iterator<Item = PathId>; fn path_ids(self) -> Self::PathIds; } /// Trait for iterating through all the path steps on a handle in a graph. pub trait IntoNodeOccurrences: GraphPaths { /// An iterator through the steps on a path, by `PathId` and `StepIx`. type Occurrences: Iterator<Item = (PathId, Self::StepIx)>; fn steps_on_handle(self, handle: Handle) -> Option<Self::Occurrences>; } /// A handlegraph with embedded paths. The step for any given path is /// indexed by the associated type `StepIx`. /// /// Provides methods for basic querying of the graph's paths, and /// steps on a path. For a more ergonomic way of iterating through the /// steps of a path, see the traits `GraphPathsRef`, and `PathSteps`. pub trait GraphPaths: Sized { type StepIx: Sized + Copy + Eq; /// Return the number of paths in this graph. fn path_count(&self) -> usize; /// Return the number of steps of the path `id`, if it exists. fn path_len(&self, id: PathId) -> Option<usize>; /// Return the circularity of the path `id`, if it exists. fn path_circular(&self, id: PathId) -> Option<bool>; /// Find the handle at step `index` in path `id`, if both the path /// exists, and the step in the path. fn path_handle_at_step( &self, id: PathId, index: Self::StepIx, ) -> Option<Handle>; /// Return the index to the first step of path `id`, if the path /// exists and is not empty. /// /// The resulting `StepIx` should point to the first step of the /// path's `Steps` iterator. fn path_first_step(&self, id: PathId) -> Option<Self::StepIx>; /// Return the index to the last step of path `id`, if the path /// exists and is not empty. /// /// The resulting `StepIx` should point to the last step of the /// path's `Steps` iterator. fn path_last_step(&self, id: PathId) -> Option<Self::StepIx>; /// Return the index to the step after `index` on path `id`, if /// the path exists and `index` both exists on the path, and is /// not the last step of the path. /// /// The resulting `StepIx` should point to the same step as would /// calling `next` on the path's corresponding `Steps` iterator, /// if `index` was the last produced step. fn path_next_step( &self, id: PathId, index: Self::StepIx, ) -> Option<Self::StepIx>; /// Return the index to the step before `index` on path `id`, if /// the path exists and `index` both exists on the path, and is /// not the first step of the path. /// /// The resulting `StepIx` should point to the same step as would /// calling `next_back` on the path's corresponding `Steps` iterator, /// if `index` was the last produced step. fn path_prev_step( &self, id: PathId, index: Self::StepIx, ) -> Option<Self::StepIx>; } /// Trait for retrieving the `PathId` for a path by name, and vice /// versa. /// /// Names are represented as an iterator over `u8`s for flexibility in /// underlying storage. pub trait GraphPathNames: Sized { /// The iterator on the name of a path. type PathName: Iterator<Item = u8>; /// Returns the `PathId` that the provided `name` points to, if /// there exists a path with that name. fn get_path_id(self, name: &[u8]) -> Option<PathId>; /// Returns an iterator that produced the name of the path `id`, /// if that path exists in the graph. fn get_path_name(self, id: PathId) -> Option<Self::PathName>; /// Convenience method for retrieving a path name as a `Vec<u8>`. #[inline] fn get_path_name_vec(self, id: PathId) -> Option<Vec<u8>> { self.get_path_name(id).map(|name| name.collect()) } /// Convenience method for checking whether a path exists by name. #[inline] fn has_path(self, name: &[u8]) -> bool { self.get_path_id(name).is_some() } } /// A handlegraph with embedded paths that can be created, destroyed, /// and otherwise manipulated. pub trait MutableGraphPaths: GraphPaths { /// Create a new path with the given name and return its `PathId`. /// Returns `None` if the path already exists in the graph. fn create_path(&mut self, name: &[u8], circular: bool) -> Option<PathId>; /// Destroy the path with the given `id`. Returns `true` if the /// path was destroyed, `false` if the path did not exist or /// couldn't be destroyed. fn destroy_path(&mut self, id: PathId) -> bool; /// Append a step on the given `handle` to the end of path `id`, /// if the path exists. Returns the index of the new step. fn path_append_step( &mut self, id: PathId, handle: Handle, ) -> Option<Self::StepIx>; /// Prepend a step on the given `handle` to the beginning of path /// `id`, if the path exists. Returns the index of the new step. fn path_prepend_step( &mut self, id: PathId, handle: Handle, ) -> Option<Self::StepIx>; /// Insert a step on the given `handle` into path `id`, after the /// step at `index`. Returns the index of the new step if it was /// successfully inserted, or `None` if either the path or the /// step does not exist. fn path_insert_step_after( &mut self, id: PathId, index: Self::StepIx, handle: Handle, ) -> Option<Self::StepIx>; /// Remove the step at `index` from path `id`. Returns the index /// of the removed step if it existed and was removed. fn path_remove_step( &mut self, id: PathId, index: Self::StepIx, ) -> Option<Self::StepIx>; /// Flip the orientation of the handle on step at `index` on path /// `id`, if it exists. fn path_flip_step( &mut self, id: PathId, index: Self::StepIx, ) -> Option<Self::StepIx>; /// Replace the steps starting from the step at `from` (inclusive) /// until the step `to` (exclusive) with steps on the `Handle`s in /// `new_segment`. Returns a pair where the first entry is the /// pointer to the step corresponding to the first handle in /// `new_segment`, and the second entry, the step corresponding to /// the last handle. /// /// Depending on the graph implementation, if `to` denotes a step /// beyond the path, all steps beginning at `from` will be removed /// and replaced. If `new_segment` is empty, the range will simply /// be deleted, contracting the path. In that case, which pointers /// are returned depend on the implementation. /// /// The step `from` must come before `to` in the path, but it's up /// to implementations to choose how to handle it if that's not /// the case -- potentially panicking. fn path_rewrite_segment( &mut self, id: PathId, from: Self::StepIx, to: Self::StepIx, new_segment: &[Handle], ) -> Option<(Self::StepIx, Self::StepIx)>; /// Set the circularity of path `id`. fn path_set_circularity( &mut self, id: PathId, circular: bool, ) -> Option<()>; } /// A handlegraph with embedded paths whose steps are associated with /// the sequence positions and lengths of their nodes. pub trait PathSequences: GraphPaths { /// Return the length of path `id` in nucleotides, if it exists. fn path_bases_len(&self, id: PathId) -> Option<usize>; /// Return the index of the step at sequence position `pos` along /// path `id`, or `None` if either the path doesn't exist, or if /// the path is shorter than `pos` bases. fn path_step_at_base(&self, id: PathId, pos: usize) -> Option<Self::StepIx>; /// Return the sequence offset of the step at `index` in path /// `id`, if it exists. fn path_step_base_offset( &self, id: PathId, index: Self::StepIx, ) -> Option<usize>; } /// A handlegraph that can produce references to specific paths. pub trait GraphPathsRef: GraphPaths { type PathRef: PathBase<StepIx = Self::StepIx>; fn get_path_ref(self, id: PathId) -> Option<Self::PathRef>; } pub trait GraphPathsSteps: GraphPathsRef { type Step: super::path::PathStep; type Steps: DoubleEndedIterator<Item = Self::Step>; fn path_steps(self, id: PathId) -> Option<Self::Steps>; fn path_steps_range( self, id: PathId, from: Self::StepIx, to: Self::StepIx, ) -> Option<Self::Steps>; } pub trait GraphPathsRefMut: GraphPaths { type PathMut: PathBase<StepIx = Self::StepIx>; fn get_path_mut_ref<'a>( &'a mut self, id: PathId, ) -> Option<&'a mut Self::PathMut>; } impl<'a, T> GraphPaths for &'a T where T: GraphPaths, { type StepIx = T::StepIx; fn path_count(&self) -> usize { T::path_count(self) } fn path_len(&self, id: PathId) -> Option<usize> { T::path_len(self, id) } fn path_circular(&self, id: PathId) -> Option<bool> { T::path_circular(self, id) } fn path_handle_at_step( &self, id: PathId, index: Self::StepIx, ) -> Option<Handle> { T::path_handle_at_step(self, id, index) } fn path_first_step(&self, id: PathId) -> Option<Self::StepIx> { T::path_first_step(self, id) } fn path_last_step(&self, id: PathId) -> Option<Self::StepIx> { T::path_last_step(self, id) } fn path_next_step( &self, id: PathId, step: Self::StepIx, ) -> Option<Self::StepIx> { T::path_next_step(self, id, step) } fn path_prev_step( &self, id: PathId, step: Self::StepIx, ) -> Option<Self::StepIx> { T::path_prev_step(self, id, step) } } impl<'a, T> GraphPaths for &'a mut T where T: GraphPaths, { // type Step = T::Step; type StepIx = T::StepIx; fn path_count(&self) -> usize { T::path_count(self) } fn path_len(&self, id: PathId) -> Option<usize> { T::path_len(self, id) } fn path_circular(&self, id: PathId) -> Option<bool> { T::path_circular(self, id) } fn path_handle_at_step( &self, id: PathId, index: Self::StepIx, ) -> Option<Handle> { T::path_handle_at_step(self, id, index) } fn path_first_step(&self, id: PathId) -> Option<Self::StepIx> { T::path_first_step(self, id) } fn path_last_step(&self, id: PathId) -> Option<Self::StepIx> { T::path_last_step(self, id) } fn path_next_step( &self, id: PathId, step: Self::StepIx, ) -> Option<Self::StepIx> { T::path_next_step(self, id, step) } fn path_prev_step( &self, id: PathId, step: Self::StepIx, ) -> Option<Self::StepIx> { T::path_prev_step(self, id, step) } }