Struct tskit::TreeSequence

pub struct TreeSequence { /* private fields */ }

A tree sequence.

This is a thin wrapper around the C type tsk_treeseq_t.

When created from a TableCollection, the input tables are moved into the TreeSequence object.

Examples

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.add_node(0, 1.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
tables.add_edge(0., 1000., 0, 1).unwrap();
tables.add_edge(0., 1000., 0, 2).unwrap();

// index
tables.build_index();

// tables gets moved into our treeseq variable:
let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
assert_eq!(treeseq.nodes().num_rows(), 3);
assert_eq!(treeseq.edges().num_rows(), 2);

This type does not std::ops::DerefMut to crate::table_views::TableViews:

assert_eq!(treeseq.nodes_mut().num_rows(), 3);

Implementations

impl TreeSequence

pub fn new<F: Into<TreeSequenceFlags>>(
    tables: TableCollection,
    flags: F
) -> Result<Self, TskitError>

Create a tree sequence from a TableCollection. In general, TableCollection::tree_sequence may be preferred. The table collection is moved/consumed.

Parameters

• tables, a TableCollection

Errors

• TskitError if the tables are not indexed.
• TskitError if the tables are not properly sorted. See TableCollection::full_sort.

Examples

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.build_index();
let tree_sequence = tskit::TreeSequence::try_from(tables).unwrap();

The following may be preferred to the previous example, and more closely mimics the Python tskit interface:

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.build_index();
let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();

The following raises an error because the tables are not indexed:

let mut tables = tskit::TableCollection::new(1000.).unwrap();
let tree_sequence = tskit::TreeSequence::try_from(tables).unwrap();

Note

This function makes no extra copies of the tables. There is, however, a temporary allocation of an empty table collection in order to convince rust that we are safely handling all memory.

Examples found in repository

src/table_collection.rs (line 750)

    pub fn tree_sequence(
        self,
        flags: TreeSequenceFlags,
    ) -> Result<crate::TreeSequence, TskitError> {
        crate::TreeSequence::new(self, flags)
    }

src/trees.rs (line 290)

    pub fn load(filename: impl AsRef<str>) -> Result<Self, TskitError> {
        let tables = TableCollection::new_from_file(filename.as_ref())?;

        Self::new(tables, TreeSequenceFlags::default())
    }

    /// Obtain a copy of the [`TableCollection`].
    /// The result is a "deep" copy of the tables.
    ///
    /// # Errors
    ///
    /// [`TskitError`] will be raised if the underlying C library returns an error code.
    pub fn dump_tables(&self) -> Result<TableCollection, TskitError> {
        let mut inner = crate::table_collection::uninit_table_collection();

        let rv = unsafe {
            ll_bindings::tsk_table_collection_copy((*self.as_ptr()).tables, &mut *inner, 0)
        };

        // SAFETY: we just initialized it.
        // The C API doesn't free NULL pointers.
        handle_tsk_return_value!(rv, unsafe { TableCollection::new_from_mbox(inner)? })
    }

    /// Create an iterator over trees.
    ///
    /// # Parameters
    ///
    /// * `flags` A [`TreeFlags`] bit field.
    ///
    /// # Errors
    ///
    /// # Examples
    ///
    /// ```
    /// // You must include streaming_iterator as a dependency
    /// // and import this type.
    /// use streaming_iterator::StreamingIterator;
    /// // Import this to allow .next_back() for reverse
    /// // iteration over trees.
    /// use streaming_iterator::DoubleEndedStreamingIterator;
    ///
    /// let mut tables = tskit::TableCollection::new(1000.).unwrap();
    /// tables.build_index();
    /// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
    /// let mut tree_iterator = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap();
    /// while let Some(tree) = tree_iterator.next() {
    /// }
    /// ```
    ///
    /// # Warning
    ///
    /// The following code results in an infinite loop.
    /// Be sure to note the difference from the previous example.
    ///
    /// ```no_run
    /// use streaming_iterator::StreamingIterator;
    ///
    /// let mut tables = tskit::TableCollection::new(1000.).unwrap();
    /// tables.build_index();
    /// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
    /// while let Some(tree) = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap().next() {
    /// }
    /// ```
    pub fn tree_iterator<F: Into<TreeFlags>>(&self, flags: F) -> Result<Tree, TskitError> {
        let tree = Tree::new(self, flags)?;

        Ok(tree)
    }

    /// Get the list of samples as a vector.
    /// # Panics
    ///
    /// Will panic if the number of samples is too large to cast to a valid id.
    #[deprecated(
        since = "0.2.3",
        note = "Please use TreeSequence::sample_nodes instead"
    )]
    pub fn samples_to_vec(&self) -> Vec<NodeId> {
        let num_samples = unsafe { ll_bindings::tsk_treeseq_get_num_samples(self.as_ptr()) };
        let mut rv = vec![];

        for i in 0..num_samples {
            let u = match isize::try_from(i) {
                Ok(o) => NodeId::from(unsafe { *(*self.as_ptr()).samples.offset(o) }),
                Err(e) => panic!("{}", e),
            };
            rv.push(u);
        }
        rv
    }

    /// Get the list of sample nodes as a slice.
    pub fn sample_nodes(&self) -> &[NodeId] {
        let num_samples = unsafe { ll_bindings::tsk_treeseq_get_num_samples(self.as_ptr()) };
        sys::generate_slice(self.as_ref().samples, num_samples)
    }

    /// Get the number of trees.
    pub fn num_trees(&self) -> SizeType {
        self.inner.num_trees().into()
    }

    /// Calculate the average Kendall-Colijn (`K-C`) distance between
    /// pairs of trees whose intervals overlap.
    ///
    /// # Note
    ///
    /// * [Citation](https://doi.org/10.1093/molbev/msw124)
    ///
    /// # Parameters
    ///
    /// * `lambda` specifies the relative weight of topology and branch length.
    ///    See [`TreeInterface::kc_distance`] for more details.
    pub fn kc_distance(&self, other: &TreeSequence, lambda: f64) -> Result<f64, TskitError> {
        self.inner
            .kc_distance(&other.inner, lambda)
            .map_err(|e| e.into())
    }

    // FIXME: document
    pub fn num_samples(&self) -> SizeType {
        self.inner.num_samples().into()
    }

    /// Simplify tables and return a new tree sequence.
    ///
    /// # Parameters
    ///
    /// * `samples`: a slice containing non-null node ids.
    ///   The tables are simplified with respect to the ancestry
    ///   of these nodes.
    /// * `options`: A [`SimplificationOptions`] bit field controlling
    ///   the behavior of simplification.
    /// * `idmap`: if `true`, the return value contains a vector equal
    ///   in length to the input node table.  For each input node,
    ///   this vector either contains the node's new index or [`NodeId::NULL`]
    ///   if the input node is not part of the simplified history.
    pub fn simplify<O: Into<SimplificationOptions>>(
        &self,
        samples: &[NodeId],
        options: O,
        idmap: bool,
    ) -> Result<(Self, Option<Vec<NodeId>>), TskitError> {
        let mut output_node_map: Vec<NodeId> = vec![];
        if idmap {
            output_node_map.resize(usize::try_from(self.nodes().num_rows())?, NodeId::NULL);
        }
        let llsamples = unsafe {
            std::slice::from_raw_parts(samples.as_ptr().cast::<tsk_id_t>(), samples.len())
        };
        let mut inner = self.inner.simplify(
            llsamples,
            options.into().bits(),
            match idmap {
                true => output_node_map.as_mut_ptr().cast::<tsk_id_t>(),
                false => std::ptr::null_mut(),
            },
        )?;
        let views = crate::table_views::TableViews::new_from_tree_sequence(inner.as_mut_ptr())?;
        Ok((
            Self { inner, views },
            match idmap {
                true => Some(output_node_map),
                false => None,
            },
        ))
    }

    #[cfg(feature = "provenance")]
    #[cfg_attr(doc_cfg, doc(cfg(feature = "provenance")))]
    /// Add provenance record with a time stamp.
    ///
    /// All implementation of this trait provided by `tskit` use
    /// an `ISO 8601` format time stamp
    /// written using the [RFC 3339](https://tools.ietf.org/html/rfc3339)
    /// specification.
    /// This formatting approach has been the most straightforward method
    /// for supporting round trips to/from a [`crate::provenance::ProvenanceTable`].
    /// The implementations used here use the [`humantime`](https://docs.rs/humantime/latest/humantime/) crate.
    ///
    /// # Parameters
    ///
    /// * `record`: the provenance record
    ///
    /// # Examples
    ///
    /// ```
    /// let mut tables = tskit::TableCollection::new(1000.).unwrap();
    /// let mut treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
    /// # #[cfg(feature = "provenance")] {
    /// treeseq.add_provenance(&String::from("All your provenance r belong 2 us.")).unwrap();
    ///
    /// let prov_ref = treeseq.provenances();
    /// let row_0 = prov_ref.row(0).unwrap();
    /// assert_eq!(row_0.record, "All your provenance r belong 2 us.");
    /// let record_0 = prov_ref.record(0).unwrap();
    /// assert_eq!(record_0, row_0.record);
    /// let timestamp = prov_ref.timestamp(0).unwrap();
    /// assert_eq!(timestamp, row_0.timestamp);
    /// use core::str::FromStr;
    /// let dt_utc = humantime::Timestamp::from_str(&timestamp).unwrap();
    /// println!("utc = {}", dt_utc);
    /// # }
    /// ```
    pub fn add_provenance(&mut self, record: &str) -> Result<crate::ProvenanceId, TskitError> {
        if record.is_empty() {
            return Err(TskitError::ValueError {
                got: "empty string".to_string(),
                expected: "provenance record".to_string(),
            });
        }
        let timestamp = humantime::format_rfc3339(std::time::SystemTime::now()).to_string();
        let rv = unsafe {
            ll_bindings::tsk_provenance_table_add_row(
                &mut (*self.inner.as_ref().tables).provenances,
                timestamp.as_ptr() as *mut i8,
                timestamp.len() as ll_bindings::tsk_size_t,
                record.as_ptr() as *mut i8,
                record.len() as ll_bindings::tsk_size_t,
            )
        };
        handle_tsk_return_value!(rv, crate::ProvenanceId::from(rv))
    }

    delegate_table_view_api!();

    /// Build a lending iterator over edge differences.
    ///
    /// # Errors
    ///
    /// * [`TskitError`] if the `C` back end is unable to allocate
    ///   needed memory
    pub fn edge_differences_iter(
        &self,
    ) -> Result<crate::edge_differences::EdgeDifferencesIterator, TskitError> {
        crate::edge_differences::EdgeDifferencesIterator::new_from_treeseq(self, 0)
    }
}

impl TryFrom<TableCollection> for TreeSequence {
    type Error = TskitError;

    fn try_from(value: TableCollection) -> Result<Self, Self::Error> {
        Self::new(value, TreeSequenceFlags::default())
    }

pub fn as_ptr(&self) -> *const tsk_treeseq_t

Pointer to the low-level C type.

Examples found in repository

src/edge_differences.rs (line 37)

    pub fn new_from_treeseq(
        treeseq: &TreeSequence,
        flags: bindings::tsk_flags_t,
    ) -> Result<Self, crate::TskitError> {
        let mut inner = std::mem::MaybeUninit::<bindings::tsk_diff_iter_t>::uninit();
        let code =
            unsafe { bindings::tsk_diff_iter_init(inner.as_mut_ptr(), treeseq.as_ptr(), flags) };
        handle_tsk_return_value!(code, Self(unsafe { inner.assume_init() }))
    }

src/trees.rs (line 67)

    fn new<F: Into<TreeFlags>>(ts: &TreeSequence, flags: F) -> Result<Self, TskitError> {
        let flags = flags.into();

        // SAFETY: this is the type we want :)
        let temp = unsafe {
            libc::malloc(std::mem::size_of::<ll_bindings::tsk_tree_t>())
                as *mut ll_bindings::tsk_tree_t
        };

        // Get our pointer into MBox ASAP
        let nonnull = NonNull::<ll_bindings::tsk_tree_t>::new(temp)
            .ok_or_else(|| TskitError::LibraryError("failed to malloc tsk_tree_t".to_string()))?;

        // SAFETY: if temp is NULL, we have returned Err already.
        let mut tree = unsafe { mbox::MBox::from_non_null_raw(nonnull) };
        let mut rv =
            unsafe { ll_bindings::tsk_tree_init(tree.as_mut(), ts.as_ptr(), flags.bits()) };
        if rv < 0 {
            return Err(TskitError::ErrorCode { code: rv });
        }
        // Gotta ask Jerome about this one--why isn't this handled in tsk_tree_init??
        if !flags.contains(TreeFlags::NO_SAMPLE_COUNTS) {
            // SAFETY: nobody is null here.
            rv = unsafe {
                ll_bindings::tsk_tree_set_tracked_samples(
                    tree.as_mut(),
                    ts.num_samples().into(),
                    (tree.as_mut()).samples,
                )
            };
        }

        let num_nodes = unsafe { (*(*ts.as_ptr()).tables).nodes.num_rows };
        let api = TreeInterface::new(nonnull, num_nodes, num_nodes + 1, flags);
        handle_tsk_return_value!(
            rv,
            Tree {
                inner: tree,
                current_tree: 0,
                advanced: false,
                api
            }
        )
    }
}

impl streaming_iterator::StreamingIterator for Tree {
    type Item = Tree;
    fn advance(&mut self) {
        let rv = if self.current_tree == 0 {
            unsafe { ll_bindings::tsk_tree_first(self.as_mut_ptr()) }
        } else {
            unsafe { ll_bindings::tsk_tree_next(self.as_mut_ptr()) }
        };
        if rv == 0 {
            self.advanced = false;
            self.current_tree += 1;
        } else if rv == 1 {
            self.advanced = true;
            self.current_tree += 1;
        } else if rv < 0 {
            panic_on_tskit_error!(rv);
        }
    }

    fn get(&self) -> Option<&Tree> {
        match self.advanced {
            true => Some(self),
            false => None,
        }
    }
}

impl streaming_iterator::DoubleEndedStreamingIterator for Tree {
    fn advance_back(&mut self) {
        let rv = if self.current_tree == 0 {
            unsafe { ll_bindings::tsk_tree_last(self.as_mut_ptr()) }
        } else {
            unsafe { ll_bindings::tsk_tree_prev(self.as_mut_ptr()) }
        };
        if rv == 0 {
            self.advanced = false;
            self.current_tree -= 1;
        } else if rv == 1 {
            self.advanced = true;
            self.current_tree -= 1;
        } else if rv < 0 {
            panic_on_tskit_error!(rv);
        }
    }
}

/// A tree sequence.
///
/// This is a thin wrapper around the C type `tsk_treeseq_t`.
///
/// When created from a [`TableCollection`], the input tables are
/// moved into the `TreeSequence` object.
///
/// # Examples
///
/// ```
/// let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// tables.add_node(0, 1.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// tables.add_edge(0., 1000., 0, 1).unwrap();
/// tables.add_edge(0., 1000., 0, 2).unwrap();
///
/// // index
/// tables.build_index();
///
/// // tables gets moved into our treeseq variable:
/// let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
/// assert_eq!(treeseq.nodes().num_rows(), 3);
/// assert_eq!(treeseq.edges().num_rows(), 2);
/// ```
///
/// This type does not [`std::ops::DerefMut`] to [`crate::table_views::TableViews`]:
///
/// ```compile_fail
/// # let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// # tables.add_node(0, 1.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// # tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// # tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// # tables.add_edge(0., 1000., 0, 1).unwrap();
/// # tables.add_edge(0., 1000., 0, 2).unwrap();
///
/// # // index
/// # tables.build_index();
///
/// # // tables gets moved into our treeseq variable:
/// # let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
/// assert_eq!(treeseq.nodes_mut().num_rows(), 3);
/// ```
pub struct TreeSequence {
    pub(crate) inner: sys::LLTreeSeq,
    views: crate::table_views::TableViews,
}

unsafe impl Send for TreeSequence {}
unsafe impl Sync for TreeSequence {}

impl TreeSequence {
    /// Create a tree sequence from a [`TableCollection`].
    /// In general, [`TableCollection::tree_sequence`] may be preferred.
    /// The table collection is moved/consumed.
    ///
    /// # Parameters
    ///
    /// * `tables`, a [`TableCollection`]
    ///
    /// # Errors
    ///
    /// * [`TskitError`] if the tables are not indexed.
    /// * [`TskitError`] if the tables are not properly sorted.
    ///   See [`TableCollection::full_sort`](crate::TableCollection::full_sort).
    ///
    /// # Examples
    ///
    /// ```
    /// let mut tables = tskit::TableCollection::new(1000.).unwrap();
    /// tables.build_index();
    /// let tree_sequence = tskit::TreeSequence::try_from(tables).unwrap();
    /// ```
    ///
    /// The following may be preferred to the previous example, and more closely
    /// mimics the Python `tskit` interface:
    ///
    /// ```
    /// let mut tables = tskit::TableCollection::new(1000.).unwrap();
    /// tables.build_index();
    /// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
    /// ```
    ///
    /// The following raises an error because the tables are not indexed:
    ///
    /// ```should_panic
    /// let mut tables = tskit::TableCollection::new(1000.).unwrap();
    /// let tree_sequence = tskit::TreeSequence::try_from(tables).unwrap();
    /// ```
    ///
    /// ## Note
    ///
    /// This function makes *no extra copies* of the tables.
    /// There is, however, a temporary allocation of an empty table collection
    /// in order to convince rust that we are safely handling all memory.
    pub fn new<F: Into<TreeSequenceFlags>>(
        tables: TableCollection,
        flags: F,
    ) -> Result<Self, TskitError> {
        let raw_tables_ptr = tables.into_raw()?;
        let mut inner = sys::LLTreeSeq::new(raw_tables_ptr, flags.into().bits())?;
        let views = crate::table_views::TableViews::new_from_tree_sequence(inner.as_mut_ptr())?;
        Ok(Self { inner, views })
    }

    fn as_ref(&self) -> &ll_bindings::tsk_treeseq_t {
        self.inner.as_ref()
    }

    /// Pointer to the low-level C type.
    pub fn as_ptr(&self) -> *const ll_bindings::tsk_treeseq_t {
        self.inner.as_ptr()
    }

    /// Mutable pointer to the low-level C type.
    pub fn as_mut_ptr(&mut self) -> *mut ll_bindings::tsk_treeseq_t {
        self.inner.as_mut_ptr()
    }

    /// Dump the tree sequence to file.
    ///
    /// # Note
    ///
    /// * `options` is currently not used.  Set to default value.
    ///   This behavior may change in a future release, which could
    ///   break `API`.
    ///
    /// # Panics
    ///
    /// This function allocates a `CString` to pass the file name to the C API.
    /// A panic will occur if the system runs out of memory.
    pub fn dump<O: Into<TableOutputOptions>>(&self, filename: &str, options: O) -> TskReturnValue {
        let c_str = std::ffi::CString::new(filename).map_err(|_| {
            TskitError::LibraryError("call to ffi::Cstring::new failed".to_string())
        })?;
        self.inner
            .dump(c_str, options.into().bits())
            .map_err(|e| e.into())
    }

    /// Load from a file.
    ///
    /// This function calls [`TableCollection::new_from_file`] with
    /// [`TreeSequenceFlags::default`].
    pub fn load(filename: impl AsRef<str>) -> Result<Self, TskitError> {
        let tables = TableCollection::new_from_file(filename.as_ref())?;

        Self::new(tables, TreeSequenceFlags::default())
    }

    /// Obtain a copy of the [`TableCollection`].
    /// The result is a "deep" copy of the tables.
    ///
    /// # Errors
    ///
    /// [`TskitError`] will be raised if the underlying C library returns an error code.
    pub fn dump_tables(&self) -> Result<TableCollection, TskitError> {
        let mut inner = crate::table_collection::uninit_table_collection();

        let rv = unsafe {
            ll_bindings::tsk_table_collection_copy((*self.as_ptr()).tables, &mut *inner, 0)
        };

        // SAFETY: we just initialized it.
        // The C API doesn't free NULL pointers.
        handle_tsk_return_value!(rv, unsafe { TableCollection::new_from_mbox(inner)? })
    }

    /// Create an iterator over trees.
    ///
    /// # Parameters
    ///
    /// * `flags` A [`TreeFlags`] bit field.
    ///
    /// # Errors
    ///
    /// # Examples
    ///
    /// ```
    /// // You must include streaming_iterator as a dependency
    /// // and import this type.
    /// use streaming_iterator::StreamingIterator;
    /// // Import this to allow .next_back() for reverse
    /// // iteration over trees.
    /// use streaming_iterator::DoubleEndedStreamingIterator;
    ///
    /// let mut tables = tskit::TableCollection::new(1000.).unwrap();
    /// tables.build_index();
    /// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
    /// let mut tree_iterator = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap();
    /// while let Some(tree) = tree_iterator.next() {
    /// }
    /// ```
    ///
    /// # Warning
    ///
    /// The following code results in an infinite loop.
    /// Be sure to note the difference from the previous example.
    ///
    /// ```no_run
    /// use streaming_iterator::StreamingIterator;
    ///
    /// let mut tables = tskit::TableCollection::new(1000.).unwrap();
    /// tables.build_index();
    /// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
    /// while let Some(tree) = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap().next() {
    /// }
    /// ```
    pub fn tree_iterator<F: Into<TreeFlags>>(&self, flags: F) -> Result<Tree, TskitError> {
        let tree = Tree::new(self, flags)?;

        Ok(tree)
    }

    /// Get the list of samples as a vector.
    /// # Panics
    ///
    /// Will panic if the number of samples is too large to cast to a valid id.
    #[deprecated(
        since = "0.2.3",
        note = "Please use TreeSequence::sample_nodes instead"
    )]
    pub fn samples_to_vec(&self) -> Vec<NodeId> {
        let num_samples = unsafe { ll_bindings::tsk_treeseq_get_num_samples(self.as_ptr()) };
        let mut rv = vec![];

        for i in 0..num_samples {
            let u = match isize::try_from(i) {
                Ok(o) => NodeId::from(unsafe { *(*self.as_ptr()).samples.offset(o) }),
                Err(e) => panic!("{}", e),
            };
            rv.push(u);
        }
        rv
    }

    /// Get the list of sample nodes as a slice.
    pub fn sample_nodes(&self) -> &[NodeId] {
        let num_samples = unsafe { ll_bindings::tsk_treeseq_get_num_samples(self.as_ptr()) };
        sys::generate_slice(self.as_ref().samples, num_samples)
    }

pub fn as_mut_ptr(&mut self) -> *mut tsk_treeseq_t

Mutable pointer to the low-level C type.

pub fn dump<O: Into<TableOutputOptions>>(
    &self,
    filename: &str,
    options: O
) -> TskReturnValue

Dump the tree sequence to file.

Note

• options is currently not used. Set to default value. This behavior may change in a future release, which could break API.

Panics

This function allocates a CString to pass the file name to the C API. A panic will occur if the system runs out of memory.

pub fn load(filename: impl AsRef<str>) -> Result<Self, TskitError>

Load from a file.

This function calls TableCollection::new_from_file with TreeSequenceFlags::default.

pub fn dump_tables(&self) -> Result<TableCollection, TskitError>

Obtain a copy of the TableCollection. The result is a “deep” copy of the tables.

Errors

TskitError will be raised if the underlying C library returns an error code.

pub fn tree_iterator<F: Into<TreeFlags>>(
    &self,
    flags: F
) -> Result<Tree, TskitError>

Create an iterator over trees.

Parameters

• flags A TreeFlags bit field.

Errors

Examples

// You must include streaming_iterator as a dependency
// and import this type.
use streaming_iterator::StreamingIterator;
// Import this to allow .next_back() for reverse
// iteration over trees.
use streaming_iterator::DoubleEndedStreamingIterator;

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.build_index();
let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
let mut tree_iterator = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap();
while let Some(tree) = tree_iterator.next() {
}

Warning

The following code results in an infinite loop. Be sure to note the difference from the previous example.

use streaming_iterator::StreamingIterator;

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.build_index();
let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
while let Some(tree) = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap().next() {
}

pub fn samples_to_vec(&self) -> Vec<NodeId>

👎Deprecated since 0.2.3: Please use TreeSequence::sample_nodes instead

Get the list of samples as a vector.

Panics

Will panic if the number of samples is too large to cast to a valid id.

pub fn sample_nodes(&self) -> &[NodeId]

Get the list of sample nodes as a slice.

pub fn num_trees(&self) -> SizeType

Get the number of trees.

pub fn kc_distance(
    &self,
    other: &TreeSequence,
    lambda: f64
) -> Result<f64, TskitError>

Calculate the average Kendall-Colijn (K-C) distance between pairs of trees whose intervals overlap.

Note

• Citation

Parameters

• lambda specifies the relative weight of topology and branch length. See TreeInterface::kc_distance for more details.

pub fn num_samples(&self) -> SizeType

Examples found in repository

src/trees.rs (line 77)

    fn new<F: Into<TreeFlags>>(ts: &TreeSequence, flags: F) -> Result<Self, TskitError> {
        let flags = flags.into();

        // SAFETY: this is the type we want :)
        let temp = unsafe {
            libc::malloc(std::mem::size_of::<ll_bindings::tsk_tree_t>())
                as *mut ll_bindings::tsk_tree_t
        };

        // Get our pointer into MBox ASAP
        let nonnull = NonNull::<ll_bindings::tsk_tree_t>::new(temp)
            .ok_or_else(|| TskitError::LibraryError("failed to malloc tsk_tree_t".to_string()))?;

        // SAFETY: if temp is NULL, we have returned Err already.
        let mut tree = unsafe { mbox::MBox::from_non_null_raw(nonnull) };
        let mut rv =
            unsafe { ll_bindings::tsk_tree_init(tree.as_mut(), ts.as_ptr(), flags.bits()) };
        if rv < 0 {
            return Err(TskitError::ErrorCode { code: rv });
        }
        // Gotta ask Jerome about this one--why isn't this handled in tsk_tree_init??
        if !flags.contains(TreeFlags::NO_SAMPLE_COUNTS) {
            // SAFETY: nobody is null here.
            rv = unsafe {
                ll_bindings::tsk_tree_set_tracked_samples(
                    tree.as_mut(),
                    ts.num_samples().into(),
                    (tree.as_mut()).samples,
                )
            };
        }

        let num_nodes = unsafe { (*(*ts.as_ptr()).tables).nodes.num_rows };
        let api = TreeInterface::new(nonnull, num_nodes, num_nodes + 1, flags);
        handle_tsk_return_value!(
            rv,
            Tree {
                inner: tree,
                current_tree: 0,
                advanced: false,
                api
            }
        )
    }

pub fn simplify<O: Into<SimplificationOptions>>(
    &self,
    samples: &[NodeId],
    options: O,
    idmap: bool
) -> Result<(Self, Option<Vec<NodeId>>), TskitError>

Simplify tables and return a new tree sequence.

Parameters

• samples: a slice containing non-null node ids. The tables are simplified with respect to the ancestry of these nodes.
• options: A SimplificationOptions bit field controlling the behavior of simplification.
• idmap: if true, the return value contains a vector equal in length to the input node table. For each input node, this vector either contains the node’s new index or NodeId::NULL if the input node is not part of the simplified history.

pub fn add_provenance(
    &mut self,
    record: &str
) -> Result<ProvenanceId, TskitError>

Available on crate feature provenance only.

Add provenance record with a time stamp.

All implementation of this trait provided by tskit use an ISO 8601 format time stamp written using the RFC 3339 specification. This formatting approach has been the most straightforward method for supporting round trips to/from a crate::provenance::ProvenanceTable. The implementations used here use the humantime crate.

Parameters

• record: the provenance record

Examples

let mut tables = tskit::TableCollection::new(1000.).unwrap();
let mut treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
treeseq.add_provenance(&String::from("All your provenance r belong 2 us.")).unwrap();

let prov_ref = treeseq.provenances();
let row_0 = prov_ref.row(0).unwrap();
assert_eq!(row_0.record, "All your provenance r belong 2 us.");
let record_0 = prov_ref.record(0).unwrap();
assert_eq!(record_0, row_0.record);
let timestamp = prov_ref.timestamp(0).unwrap();
assert_eq!(timestamp, row_0.timestamp);
use core::str::FromStr;
let dt_utc = humantime::Timestamp::from_str(&timestamp).unwrap();
println!("utc = {}", dt_utc);

pub fn edges(&self) -> &EdgeTable

Get reference to the EdgeTable.

pub fn individuals(&self) -> &IndividualTable

Get reference to the IndividualTable.

pub fn migrations(&self) -> &MigrationTable

Get reference to the MigrationTable.

pub fn mutations(&self) -> &MutationTable

Get reference to the MutationTable.

pub fn nodes(&self) -> &NodeTable

Get reference to the NodeTable.

Examples found in repository

src/trees.rs (line 433)

    pub fn simplify<O: Into<SimplificationOptions>>(
        &self,
        samples: &[NodeId],
        options: O,
        idmap: bool,
    ) -> Result<(Self, Option<Vec<NodeId>>), TskitError> {
        let mut output_node_map: Vec<NodeId> = vec![];
        if idmap {
            output_node_map.resize(usize::try_from(self.nodes().num_rows())?, NodeId::NULL);
        }
        let llsamples = unsafe {
            std::slice::from_raw_parts(samples.as_ptr().cast::<tsk_id_t>(), samples.len())
        };
        let mut inner = self.inner.simplify(
            llsamples,
            options.into().bits(),
            match idmap {
                true => output_node_map.as_mut_ptr().cast::<tsk_id_t>(),
                false => std::ptr::null_mut(),
            },
        )?;
        let views = crate::table_views::TableViews::new_from_tree_sequence(inner.as_mut_ptr())?;
        Ok((
            Self { inner, views },
            match idmap {
                true => Some(output_node_map),
                false => None,
            },
        ))
    }

pub fn populations(&self) -> &PopulationTable

Get reference to the PopulationTable.

pub fn sites(&self) -> &SiteTable

Get reference to the SiteTable.

pub fn provenances(&self) -> &ProvenanceTable

Available on crate feature provenance only.

Get reference to the ProvenanceTable

pub fn individuals_iter(&self) -> impl Iterator<Item = IndividualTableRow> + '_

Return an iterator over the individuals.

pub fn nodes_iter(&self) -> impl Iterator<Item = NodeTableRow> + '_

Return an iterator over the nodes.

pub fn edges_iter(&self) -> impl Iterator<Item = EdgeTableRow> + '_

Return an iterator over the edges.

pub fn migrations_iter(&self) -> impl Iterator<Item = MigrationTableRow> + '_

Return an iterator over the migrations.

pub fn mutations_iter(&self) -> impl Iterator<Item = MutationTableRow> + '_

Return an iterator over the mutations.

pub fn populations_iter(&self) -> impl Iterator<Item = PopulationTableRow> + '_

Return an iterator over the populations.

pub fn sites_iter(&self) -> impl Iterator<Item = SiteTableRow> + '_

Return an iterator over the sites.

pub fn provenances_iter(&self) -> impl Iterator<Item = ProvenanceTableRow> + '_

Available on crate feature provenance only.

Return an iterator over provenances

pub fn samples_as_vector(&self) -> Vec<NodeId>

Obtain a vector containing the indexes (“ids”) of all nodes for which crate::TSK_NODE_IS_SAMPLE is true.

The provided implementation dispatches to crate::NodeTable::samples_as_vector.

pub fn create_node_id_vector(
    &self,
    f: impl FnMut(&NodeTableRow) -> bool
) -> Vec<NodeId>

Obtain a vector containing the indexes (“ids”) of all nodes satisfying a certain criterion.

The provided implementation dispatches to crate::NodeTable::create_node_id_vector.

Parameters

• f: a function. The function is passed the current table collection and each crate::node_table::NodeTableRow. If f returns true, the index of that row is included in the return value.

Examples

Get all nodes with time > 0.0:

let mut tables = tskit::TableCollection::new(100.).unwrap();
tables
    .add_node(tskit::TSK_NODE_IS_SAMPLE, 0.0, tskit::PopulationId::NULL,
    tskit::IndividualId::NULL)
    .unwrap();
tables
    .add_node(tskit::TSK_NODE_IS_SAMPLE, 1.0, tskit::PopulationId::NULL,
    tskit::IndividualId::NULL)
    .unwrap();
let samples = tables.create_node_id_vector(
    |row: &tskit::NodeTableRow| row.time > 0.,
);
assert_eq!(samples[0], 1);

pub fn edge_differences_iter(
    &self
) -> Result<EdgeDifferencesIterator, TskitError>

Build a lending iterator over edge differences.

Errors

• TskitError if the C back end is unable to allocate needed memory

Trait Implementations

impl TryFrom<TableCollection> for TreeSequence

type Error = TskitError

The type returned in the event of a conversion error.

fn try_from(value: TableCollection) -> Result<Self, Self::Error>

Performs the conversion.

impl Send for TreeSequence

impl Sync for TreeSequence