bio 3.0.0

//! Interval tree, a data structure for efficiently storing and searching intervals.
//!
//! This implementation is based on the sorted array version as described/given in
//! https://github.com/lh3/cgranges / https://github.com/lh3/cgranges/blob/master/cpp/IITree.h
//!
//! It uses the same conventions as `crate::data_structures::interval_tree::IntervalTree`.
//! Note that if you do not use the `ArrayBackedIntervalTree::from_iter` constructor, you have to call `index(&mut self)`
//! first before `find()`-ing overlaps.
//!
//! # Example
//! ```
//! use bio::data_structures::interval_tree::ArrayBackedIntervalTree;
//! use bio::utils::Interval;
//! use std::iter::FromIterator;
//!
//! let mut tree = ArrayBackedIntervalTree::new();
//! tree.insert(12..34, 0);
//! tree.insert(0..23, 1);
//! tree.insert(34..56, 2);
//! // since we did at least one manual insert, we have to index the tree
//! tree.index();
//! let i1 = &tree.find(22..25)[0];
//! assert_eq!(i1.interval().start, 0);
//! assert_eq!(i1.interval().end, 23);
//! assert_eq!(i1.data(), &1u32);
//!
//! let tree =
//!     ArrayBackedIntervalTree::from_iter(vec![(12..34, 0), (0..23, 1), (34..56, 2)].into_iter());
//! // no call to `index` needed here, since that happens in `from_iter` already
//! let i2 = &tree.find(22..25)[1];
//! assert_eq!(i2.interval().start, 12);
//! assert_eq!(i2.interval().end, 34);
//! assert_eq!(i2.data(), &0u32);
//! ```

use crate::utils::Interval;
use std::cmp::min;
use std::iter::FromIterator;

/// A `find` query on the interval tree does not directly return references to the intervals in the
/// tree but wraps the fields `interval` and `data` in an `Entry`.
#[derive(Clone, Eq, PartialEq, Hash, Debug, Serialize, Deserialize)]
struct InternalEntry<N: Ord + Clone + Copy, D> {
    data: D,
    interval: Interval<N>,
    max: N,
}

/// A `find` query on the interval tree does not directly return references to the nodes in the tree, but
/// wraps the fields `interval` and `data` in an `Entry`.
#[derive(Copy, Clone, Eq, PartialEq, Hash, Debug, Serialize)]
pub struct Entry<'a, N: Ord + Clone, D> {
    data: &'a D,
    interval: &'a Interval<N>,
}

impl<'a, N: Ord + Clone + 'a, D: 'a> Entry<'a, N, D> {
    /// Get a reference to the data for this entry
    pub fn data(&self) -> &'a D {
        self.data
    }

    /// Get a reference to the interval for this entry
    pub fn interval(&self) -> &'a Interval<N> {
        self.interval
    }
}

impl<N: Ord + Clone + Copy, D> Default for ArrayBackedIntervalTree<N, D> {
    fn default() -> Self {
        ArrayBackedIntervalTree {
            entries: vec![],
            max_level: 0,
            indexed: false,
        }
    }
}

#[derive(Clone, Eq, PartialEq, Hash, Debug, Serialize, Deserialize)]
pub struct ArrayBackedIntervalTree<N: Ord + Clone + Copy, D> {
    entries: Vec<InternalEntry<N, D>>,
    max_level: usize,
    indexed: bool,
}

impl<N, D, V> FromIterator<(V, D)> for ArrayBackedIntervalTree<N, D>
where
    V: Into<Interval<N>>,
    N: Ord + Clone + Copy,
    D: Clone,
{
    fn from_iter<T: IntoIterator<Item = (V, D)>>(iter: T) -> Self {
        let mut tree = Self::new();
        iter.into_iter()
            .for_each(|(interval, data)| tree.insert(interval, data));
        tree.index();
        tree
    }
}

impl<N: Ord + Clone + Copy, D: Clone> ArrayBackedIntervalTree<N, D> {
    pub fn new() -> Self {
        Default::default()
    }

    pub fn insert<I: Into<Interval<N>>>(&mut self, interval: I, data: D) {
        let interval = interval.into();
        let max = interval.end;
        self.entries.push(InternalEntry {
            interval,
            data,
            max,
        });
        self.indexed = false;
    }

    pub fn index(&mut self) {
        if !self.indexed {
            self.entries.sort_by_key(|e| e.interval.start);
            self.index_core();
            self.indexed = true;
        }
    }

    fn index_core(&mut self) {
        let a = &mut self.entries;
        if a.is_empty() {
            return;
        }

        let n = a.len();
        let mut last_i = 0;
        let mut last_value = a[0].max;
        (0..n).step_by(2).for_each(|i| {
            last_i = i;
            a[i].max = a[i].interval.end;
            last_value = a[i].max;
        });
        let mut k = 1;
        while (1 << k) <= n {
            // process internal nodes in the bottom-up order
            let x = 1 << (k - 1);
            let i0 = (x << 1) - 1; // i0 is the first node
            let step = x << 2;
            for i in (i0..n).step_by(step) {
                // traverse all nodes at level k
                let end_left = a[i - x].max; // max value of the left child
                let end_right = if i + x < n { a[i + x].max } else { last_value }; // max value of the right child
                let end = max3(a[i].interval.end, end_left, end_right);
                a[i].max = end;
            }
            last_i = if (last_i >> k & 1) > 0 {
                last_i - x
            } else {
                last_i + x
            };
            if last_i < n && a[last_i].max > last_value {
                last_value = a[last_i].max
            }
            k += 1;
        }
        self.max_level = k - 1;
    }

    /// Find overlapping intervals in the index.
    /// Returns a vector of entries, consisting of the interval and its associated data.
    ///
    /// # Arguments
    ///
    /// * `interval` - The interval for which overlaps are to be found in the index. Can also be a `Range`.
    ///
    /// # Panics
    ///
    /// Panics if this `IITree` instance has not been indexed yet.
    pub fn find<I: Into<Interval<N>>>(&self, interval: I) -> Vec<Entry<N, D>> {
        let mut buf = Vec::with_capacity(512);
        self.find_into(interval, &mut buf);
        buf
    }

    /// Find overlapping intervals in the index
    ///
    /// # Arguments
    ///
    /// * `interval` - The interval for which overlaps are to be found in the index. Can also be a `Range`.
    /// * `results` - A reusable buffer vector for storing the results.
    ///
    /// # Panics
    ///
    /// Panics if this `IITree` instance has not been indexed yet.
    pub fn find_into<'b, 'a: 'b, I: Into<Interval<N>>>(
        &'a self,
        interval: I,
        results: &'b mut Vec<Entry<'a, N, D>>,
    ) {
        if !self.indexed {
            panic!("This IITree has not been indexed yet. Call `index()` first.")
        }

        let interval = interval.into();
        let (start, end) = (interval.start, interval.end);
        let n = self.entries.len();
        let a = &self.entries;
        results.clear();
        let mut stack = [StackCell::empty(); 64];
        // push the root; this is a top down traversal
        stack[0].k = self.max_level;
        stack[0].x = (1 << self.max_level) - 1;
        stack[0].w = false;
        let mut t = 1;
        while t > 0 {
            t -= 1;
            let StackCell { k, x, w } = stack[t];
            if k <= 3 {
                // we are in a small subtree; traverse every node in this subtree
                let i0 = x >> k << k;
                let i1 = min(i0 + (1 << (k + 1)) - 1, n);
                for (i, node) in a.iter().enumerate().take(i1).skip(i0) {
                    if node.interval.start >= end {
                        break;
                    }
                    if start < node.interval.end {
                        // if overlap, append to `results`
                        results.push(Entry {
                            interval: &self.entries[i].interval,
                            data: &self.entries[i].data,
                        });
                    }
                }
            } else if !w {
                // if left child not processed
                let y = x - (1 << (k - 1)); // the left child of x; NB: y may be out of range (i.e. y>=n)
                stack[t].k = k;
                stack[t].x = x;
                stack[t].w = true; // re-add node x, but mark the left child having been processed
                t += 1;
                if y >= n || a[y].max > start {
                    // push the left child if y is out of range or may overlap with the query
                    stack[t].k = k - 1;
                    stack[t].x = y;
                    stack[t].w = false;
                    t += 1;
                }
            } else if x < n && a[x].interval.start < end {
                // need to push the right child
                if start < a[x].interval.end {
                    results.push(Entry {
                        interval: &self.entries[x].interval,
                        data: &self.entries[x].data,
                    });
                }
                stack[t].k = k - 1;
                stack[t].x = x + (1 << (k - 1));
                stack[t].w = false;
                t += 1;
            }
        }
    }
}

fn max3<T: Ord>(a: T, b: T, c: T) -> T {
    a.max(b.max(c))
}

#[derive(Clone, Copy)]
struct StackCell {
    // node
    x: usize,
    // level
    k: usize,
    // false if left child hasn't been processed
    w: bool,
}

impl StackCell {
    fn empty() -> Self {
        Self {
            x: 0,
            k: 0,
            w: false,
        }
    }
}

#[cfg(test)]
mod tests {
    use proptest::prelude::*;

    use super::*;

    #[test]
    fn test_example() {
        let mut tree = ArrayBackedIntervalTree::new();
        tree.insert(12..34, 0);
        tree.insert(0..23, 1);
        tree.insert(34..56, 2);
        tree.index();
        let overlap = tree.find(22..25);

        let e1 = Entry {
            interval: &(0..23).into(),
            data: &1,
        };
        let e2 = Entry {
            interval: &(12..34).into(),
            data: &0,
        };
        let expected = vec![e1, e2];
        assert_eq!(overlap, expected);
    }

    /// Regression test: catch a scenario where the `max` value of an entry
    /// wasn't extended to take into account all of the leaf nodes it contained
    /// when indexing
    #[test]
    fn test_disjoint_two_element_search() {
        let mut tree = ArrayBackedIntervalTree::new();
        tree.insert(12..34, 0);
        tree.insert(40..56, 1);
        tree.index();
        let overlap = tree.find(40..41);

        let e1 = Entry {
            interval: &(40..56).into(),
            data: &1,
        };
        let expected = vec![e1];
        assert_eq!(overlap, expected);
    }

    proptest! {
        /// Given a query interval in the format `(start, len)` and a sequence
        /// of intervals `(start, len)` to index, assert that
        /// `ArrayBackedIntervalTree::find` returns all the intervals which
        /// overlap the query.
        #[test]
        fn find_arbitrary(
            query in (0u32..1001, 0u32..1001),
            intervals in prop::collection::vec((0u32..1000, 0u32..1000), 0..1000)
        ) {
            let tree = ArrayBackedIntervalTree::from_iter(
                intervals
                    .into_iter()
                    .enumerate()
                    .map(|(i, (start, len))| (start..start + len, i)),
            );

            let (start, len) = query;
            let end = start + len;

            let expected: Vec<_> = tree
                .entries
                .iter()
                .filter_map(|internal| {
                    if internal.interval.start < end && start < internal.interval.end {
                        Some(Entry {
                            interval: &internal.interval,
                            data: &internal.data,
                        })
                    } else {
                        None
                    }
                })
                .collect();

            prop_assert_eq!(
                tree.find(start..end),
                expected,
                "{:?} in {:?}",
                start..end,
                tree.entries
            );
        }
    }
}