before a major refactor

I decide to adopt a new approach of recording and updating item
derivation forests.  Since this affects a lot of things, I decide to
commit before the refactor, so that I can create a branch for that
refactor.

1 files changed, 442 insertions, 27 deletions

diff --git a/chain/src/item/default/mod.rs b/chain/src/item/default/mod.rs
index 1a00368..22069d2 100644
--- a/chain/src/item/default/mod.rs
+++ b/chain/src/item/default/mod.rs
@@ -3,11 +3,13 @@
 
 use super::*;
 use crate::atom::default::DefaultAtom;
-use grammar::{GrammarLabel, GrammarLabelType};
+use grammar::{GrammarLabel, GrammarLabelType, TNT};
 use graph::{
     builder::BuilderMut, labelled::binary::PLGBuilderMut, Graph, LabelGraph, PLGraph, RedirectGraph,
 };
 
+use std::collections::HashSet;
+
 use core::fmt::Display;
 
 /// The type of errors for forest operations.
@@ -30,6 +32,8 @@ pub enum Error {
     LabelConversion(ForestLabelError),
     /// Trying to split a packed node.
     SplitPack(usize),
+    /// A cloned node should have exactly one parent.
+    InvalidClone(usize),
 }
 
 impl Display for Error {
@@ -43,6 +47,9 @@ impl Display for Error {
             Error::NodeNoLabel(n) => write!(f, "node {n} has no labels, but it should have one"),
             Error::LabelConversion(le) => write!(f, "fail to convert labels: {le}"),
             Error::SplitPack(n) => write!(f, "cannot split the packed node {n}"),
+            Error::InvalidClone(n) => {
+                write!(f, "the cloned node {n} should have exactly one parent")
+            }
         }
     }
 }
@@ -68,7 +75,7 @@ impl From<ForestLabelError> for Error {
 /// A default implementation of forest.
 #[derive(Debug, Clone)]
 pub struct DefaultForest<T: GraphLabel> {
-    graph: PLGraph<T>,
+    pub(crate) graph: PLGraph<T>,
     root: Option<usize>,
 }
 
@@ -262,15 +269,14 @@ impl<T: GraphLabel> Forest<T> for DefaultForest<ForestLabel<T>> {
         // the consideration).
 
         let fragment = fragment.borrow();
+        let fragment_nodes_len = fragment.nodes_len();
 
-        let mut frag_stack = Vec::with_capacity(fragment.nodes_len());
+        let mut frag_stack = Vec::with_capacity(fragment_nodes_len);
 
-        let mut self_stack = Vec::with_capacity(fragment.nodes_len());
+        let mut self_stack = Vec::with_capacity(fragment_nodes_len);
 
-        use std::collections::HashSet;
-
-        let mut frag_seen: HashSet<usize> = HashSet::with_capacity(fragment.nodes_len());
-        let mut self_seen: HashSet<usize> = HashSet::with_capacity(fragment.nodes_len());
+        let mut frag_seen: HashSet<usize> = HashSet::with_capacity(fragment_nodes_len);
+        let mut self_seen: HashSet<usize> = HashSet::with_capacity(fragment_nodes_len);
 
         let frag_root = if let Some(root) = fragment.root() {
             root
@@ -294,25 +300,25 @@ impl<T: GraphLabel> Forest<T> for DefaultForest<ForestLabel<T>> {
 
             if fragment.vertex_label(frag_top)? != self.vertex_label(self_top)? {
                 // not a prefix
-                dbg!(
-                    frag_top,
-                    self_top,
-                    fragment.vertex_label(frag_top)?,
-                    self.vertex_label(self_top)?
-                );
+                // dbg!(
+                //     frag_top,
+                //     self_top,
+                //     fragment.vertex_label(frag_top)?,
+                //     self.vertex_label(self_top)?
+                // );
                 return Ok(false);
             }
 
             let self_children = self.children_of(self_top)?;
             let frag_children = fragment.children_of(frag_top)?;
 
-            if frag_children.len() != self_children.len() {
-                dbg!(
-                    frag_top,
-                    self_top,
-                    fragment.vertex_label(frag_top)?,
-                    self.vertex_label(self_top)?
-                );
+            if frag_children.len() > self_children.len() {
+                // dbg!(
+                //     frag_top,
+                //     self_top,
+                //     fragment.vertex_label(frag_top)?,
+                //     self.vertex_label(self_top)?
+                // );
                 return Ok(false);
             }
 
@@ -320,7 +326,7 @@ impl<T: GraphLabel> Forest<T> for DefaultForest<ForestLabel<T>> {
                 if frag_seen.contains(&frag_child) && self_seen.contains(&self_child) {
                     continue;
                 } else if frag_seen.contains(&frag_child) || self_seen.contains(&self_child) {
-                    dbg!();
+                    // dbg!();
                     return Ok(false);
                 }
 
@@ -352,7 +358,7 @@ impl<T: GraphLabel> Forest<T> for DefaultForest<ForestLabel<T>> {
         let root = if let Some(root) = fragment.root() {
             root
         } else {
-            // Nothing to do to plant an empty forest.
+            // Nothing to plant.
             return Ok(());
         };
 
@@ -393,9 +399,27 @@ impl<T: GraphLabel> Forest<T> for DefaultForest<ForestLabel<T>> {
             return Ok(());
         }
 
-        // First adjoin those nodes and join the edges later.
+        // First adjoin the relevant nodes and join the edges later.
+
+        let mut used_nodes: Vec<bool> = std::iter::repeat(false).take(nodes_len).collect();
+
+        let mut stack = vec![root];
+
+        while let Some(top) = stack.pop() {
+            if used_nodes.get(top).copied() == Some(true) {
+                continue;
+            }
+
+            *used_nodes
+                .get_mut(top)
+                .ok_or(Error::IndexOutOfBounds(top, nodes_len))? = true;
+
+            stack.extend(fragment.children_of(top)?);
+        }
+
+        let used_nodes = used_nodes;
 
-        for node in 0..nodes_len {
+        for node in (0..nodes_len).filter(|node| used_nodes.get(*node).copied() == Some(true)) {
             let label = fragment
                 .vertex_label(node)?
                 .ok_or(Error::NodeNoLabel(node))?;
@@ -582,6 +606,93 @@ impl<T: GraphLabel> PartialEq for DefaultForest<ForestLabel<T>> {
     }
 }
 
+impl<T: GraphLabel> Eq for DefaultForest<ForestLabel<T>> {}
+
+impl<T: GraphLabel> DefaultForest<ForestLabel<T>> {
+    /// A convenient helper function to plant a fragment under a
+    /// node, if it has not been planted yet.
+    ///
+    /// To be precise, this function first checks if the node is
+    /// packed; if so, then it checks every of the cloned children, to
+    /// see if the fragment has already been planted.  If none of the
+    /// clones have the fragment as a prefix, we make a new clone and
+    /// plant the fragment there.
+    ///
+    /// On the other hand, if the node is a plain node, then it checks
+    /// if the fragment is a prefix of the node.  If so, do nothing,
+    /// else clone the node and plant the fragment there, unless the
+    /// node has no children yet, in which case just plant the node
+    /// there.
+    ///
+    /// A special case occurs when the node is the root node, in which
+    /// case we clone it only when its degree is larger than one.
+    ///
+    /// Return either the original node or the cloned node at the end.
+    pub(crate) fn plant_if_needed(
+        &mut self,
+        node: usize,
+        mut fragment: Self,
+    ) -> Result<usize, Error> {
+        if fragment.is_empty() {
+            return Ok(node);
+        }
+
+        let node_label = self.vertex_label(node)?.ok_or(Error::NodeNoLabel(node))?;
+
+        if node_label.is_packed() || node_label.clone_index().is_some() {
+            let mut planted = false;
+
+            let mut node = node;
+
+            if node_label.clone_index().is_some() {
+                let mut parents = self.parents_of(node)?;
+
+                assert_eq!(parents.len(), 1);
+
+                node = parents.next().unwrap().node();
+            }
+
+            for clone in self.children_of(node)? {
+                node = clone;
+
+                if self.is_prefix(clone, &fragment)? {
+                    planted = true;
+
+                    break;
+                }
+            }
+
+            if !planted {
+                let clone = self.clone_node(node, 0, false)?;
+
+                fragment.set_root(1)?;
+
+                self.plant(clone, fragment, false)?;
+
+                return Ok(clone);
+            }
+        } else {
+            let clone_threshold = if self.root == Some(node) { 1 } else { 0 };
+
+            let planted = self.is_prefix(node, &fragment)?;
+
+            fragment.set_root(1)?;
+
+            if !planted && self.degree(node)? > clone_threshold {
+                let clone = self.clone_node(node, 0, false)?;
+
+                self.plant(clone, fragment, false)?;
+
+                return Ok(clone);
+            } else if !planted {
+                self.plant(node, fragment, false)?;
+            }
+        }
+
+        Ok(node)
+    }
+}
+
 pub mod splone;
 
 impl<T: GraphLabel> DefaultForest<T> {
@@ -596,9 +707,18 @@ impl<T: GraphLabel> DefaultForest<T> {
 
         Self { graph, root }
     }
-}
 
-impl<T: GraphLabel> Eq for DefaultForest<ForestLabel<T>> {}
+    /// Set the root to the given node.
+    pub fn set_root(&mut self, root: usize) -> Result<(), Error> {
+        if root >= self.nodes_len() {
+            return Err(Error::IndexOutOfBounds(root, self.nodes_len()));
+        }
+
+        self.root = Some(root);
+
+        Ok(())
+    }
+}
 
 impl DefaultForest<ForestLabel<GrammarLabel>> {
     /// Prints the forest without nodes that do not have ending
@@ -613,6 +733,8 @@ impl DefaultForest<ForestLabel<GrammarLabel>> {
                 Ok(label) => {
                     if let Some(label) = label {
                         label.label().end().is_none()
+                            || (matches!(self.degree(*node), Ok(0))
+                                && matches!(self.parents_of(*node).map(|iter| iter.len()), Ok(0)))
                     } else {
                         true
                     }
@@ -674,6 +796,299 @@ impl DefaultForest<ForestLabel<GrammarLabel>> {
 
         file.write_all(result.as_bytes())
     }
+
+    /// Remove a node by removing all edges connecting with it.
+    pub fn remove_node(&mut self, node_id: usize) -> Result<(), Error> {
+        let mut builder = PLGBuilderMut::from_graph_mut(&mut self.graph);
+
+        let mut to_remove =
+            Vec::with_capacity(builder.degree(node_id)? + builder.parents_of(node_id)?.len());
+
+        to_remove.extend(
+            builder
+                .children_of(node_id)?
+                .map(|target| (node_id, target)),
+        );
+
+        to_remove.extend(
+            builder
+                .parents_of(node_id)?
+                .map(|parent| (parent.node(), node_id)),
+        );
+
+        for (source, target) in to_remove {
+            builder.remove_edge(source, target, |_| true)?;
+        }
+
+        Ok(())
+    }
+
+    /// Find the last child of the given node whose start and end
+    /// positions contain the given position.  If no such child is
+    /// found, return `Ok(None)`.
+    ///
+    /// The returned tuple is of the form (child, index), where
+    /// `child` is the index of the child node in question, and
+    /// `index` means that the child is the `index`-th child of the
+    /// node.
+    pub(crate) fn position_search(
+        &self,
+        node: usize,
+        pos: usize,
+    ) -> Result<Option<(usize, usize)>, Error> {
+        fn range_contains(label: GrammarLabel, pos: usize) -> bool {
+            let start = label.start();
+
+            if let Some(end) = label.end() {
+                (start..end).contains(&pos)
+            } else {
+                (start..).contains(&pos)
+            }
+        }
+
+        let node_label = self
+            .vertex_label(node)?
+            .ok_or(Error::NodeNoLabel(node))?
+            .label();
+
+        if !range_contains(node_label, pos) {
+            return Ok(None);
+        }
+
+        for (index, child) in self.children_of(node)?.enumerate().rev() {
+            let child_label = self
+                .vertex_label(child)?
+                .ok_or(Error::NodeNoLabel(child))?
+                .label();
+
+            if range_contains(child_label, pos) {
+                return Ok(Some((child, index)));
+            }
+        }
+
+        Ok(None)
+    }
+
+    // /// Check if every child already has an end.
+    // fn every_child_is_completed(&self, node_id: usize, atom: &DefaultAtom) -> Result<bool, Error> {
+    //     let children = self.children_of(node_id)?;
+
+    //     if children.len() == 0 {
+    //         return Ok(true);
+    //     }
+
+    //     let mut pos = self
+    //         .vertex_label(node_id)?
+    //         .ok_or(Error::NodeNoLabel(node_id))?
+    //         .label()
+    //         .start();
+
+    //     let mut last_child_label = None;
+
+    //     for child in children {
+    //         let child_label = self
+    //             .vertex_label(child)?
+    //             .ok_or(Error::NodeNoLabel(child))?
+    //             .label();
+
+    //         last_child_label = Some(child_label);
+
+    //         if child_label.start() != pos || child_label.end().is_none() {
+    //             return Ok(false);
+    //         }
+
+    //         pos = child_label.end().unwrap();
+    //     }
+
+    //     if let Some(label) = last_child_label {
+    //         if let Some(rule) = label.label().rule() {
+    //             if !atom
+    //                 .is_accepting(2 * rule + 1)
+    //                 .map_err(|_| Error::IndexOutOfBounds(2 * rule + 1, atom.nodes_len()))?
+    //             {
+    //                 return Ok(false);
+    //             }
+    //         }
+    //     }
+
+    //     Ok(true)
+    // }
+
+    // /// Complete the forest by trying to set the ending position of
+    // /// every node that does not have an end, by the ending position
+    // /// of its last child.
+    // pub fn complete(&mut self, atom: &DefaultAtom) -> Result<(), Error> {
+    //     let mut stack: Vec<_> = self
+    //         .nodes()
+    //         .filter(|node| {
+    //             let label = self.vertex_label(*node).unwrap().unwrap().label();
+
+    //             label.label().rule().is_some() && label.end().is_some()
+    //         })
+    //         .collect();
+
+    //     let mut second_stack: Vec<usize> = Vec::new();
+
+    //     let mut pending_candidates: Vec<usize> = Vec::new();
+
+    //     let nodes_len = self.nodes_len();
+
+    //     let mut seen_nodes: HashSet<usize> = HashSet::with_capacity(nodes_len);
+
+    //     while !stack.is_empty() {
+    //         while let Some(mut top) = stack.pop() {
+    //             if seen_nodes.contains(&top) {
+    //                 continue;
+    //             }
+
+    //             seen_nodes.insert(top);
+
+    //             let top_label = self.vertex_label(top)?.unwrap();
+
+    //             if top_label.clone_index().is_some() {
+    //                 let mut top_parents = self.parents_of(top)?;
+
+    //                 if top_parents.len() != 1 {
+    //                     return Err(Error::InvalidClone(top));
+    //                 }
+
+    //                 top = top_parents.next().unwrap().node();
+    //             }
+
+    //             let rule_parents = self.parents_of(top)?;
+
+    //             let candidates = {
+    //                 let mut result = Vec::with_capacity(rule_parents.len());
+
+    //                 for parent in rule_parents {
+    //                     // for parent in self.parents_of(parent.node())? {
+    //                     // if self.degree(parent.node())? <= parent.edge() + 1 {
+    //                     result.push(parent);
+    //                     // }
+    //                     // }
+    //                 }
+
+    //                 result
+    //             };
+
+    //             for candidate in candidates {
+    //                 if matches!(self.vertex_label(candidate.node())?, Some(label) if label.label().end().is_none())
+    //                 {
+    //                     if self.every_child_is_completed(candidate.node(), atom)? {
+    //                         let last_child = self
+    //                             .nth_child(candidate.node(), self.degree(candidate.node())? - 1)?;
+    //                         let end = self
+    //                             .vertex_label(last_child)?
+    //                             .ok_or(Error::NodeNoLabel(last_child))?
+    //                             .label()
+    //                             .end();
+
+    //                         let sploned_node = self.splone(
+    //                             candidate.node(),
+    //                             end,
+    //                             self.degree(candidate.node())? - 1,
+    //                             true,
+    //                         )?;
+
+    //                         second_stack.push(sploned_node);
+    //                     } else {
+    //                         pending_candidates.push(candidate.node());
+    //                     }
+    //                 } else {
+    //                     second_stack.push(candidate.node());
+    //                 }
+    //             }
+
+    //             let mut new_pending = Vec::with_capacity(pending_candidates.len());
+
+    //             while let Some(node) = pending_candidates.pop() {
+    //                 if self.every_child_is_completed(node, atom)? {
+    //                     let last_edge = self.degree(node)? - 1;
+    //                     let last_child = self.nth_child(node, last_edge)?;
+    //                     let end = self
+    //                         .vertex_label(last_child)?
+    //                         .ok_or(Error::NodeNoLabel(last_child))?
+    //                         .label()
+    //                         .end();
+
+    //                     let sploned_node = self.splone(node, end, last_edge, true)?;
+
+    //                     second_stack.push(sploned_node);
+    //                 } else {
+    //                     new_pending.push(node);
+    //                 }
+    //             }
+
+    //             std::mem::swap(&mut pending_candidates, &mut new_pending);
+    //         }
+
+    //         std::mem::swap(&mut stack, &mut second_stack);
+    //     }
+
+    //     Ok(())
+    // }
+
+    // /// Unconditionally set the label of the node to be the new label.
+    // ///
+    // /// # Warning
+    // ///
+    // /// Use with caution: it does not do anything special, so it is
+    // /// the responsibility of the caller to ensure this operation is
+    // /// legal.
+    // #[allow(dead_code)]
+    // pub(crate) fn set_label(&mut self, node: usize, label: GrammarLabel) -> Result<(), Error> {
+    //     let status = self
+    //         .vertex_label(node)?
+    //         .ok_or(Error::NodeNoLabel(node))?
+    //         .status;
+
+    //     let label = ForestLabel::new(label, status);
+
+    //     let mut builder = PLGBuilderMut::from_graph_mut(&mut self.graph);
+
+    //     builder.set_label(node, label)?;
+
+    //     Ok(())
+    // }
+
+    /// Set the position of every node.
+    pub(crate) fn set_pos(&mut self, pos: usize) -> Result<(), Error> {
+        let mut builder = PLGBuilderMut::from_graph_mut(&mut self.graph);
+
+        for node in 0..builder.nodes_len() {
+            let label = builder
+                .vertex_label(node)?
+                .ok_or(Error::NodeNoLabel(node))?;
+
+            let mut label_label = label.label();
+
+            label_label.set_start(pos);
+
+            if matches!(label_label.label().tnt(), Some(TNT::Ter(_))) {
+                label_label.set_end(pos + 1);
+            } else if builder.degree(node)? == 1 && label_label.label().rule().is_some() {
+                let child = builder.children_of(node)?.next().unwrap();
+
+                if matches!(
+                    builder
+                        .vertex_label(child)?
+                        .ok_or(Error::NodeNoLabel(child))?
+                        .label()
+                        .label()
+                        .tnt(),
+                    Some(TNT::Ter(_))
+                ) {
+                    label_label.set_end(pos + 1);
+                }
+            }
+
+            let new_label = ForestLabel::new(label_label, label.status);
+
+            builder.set_label(node, new_label)?;
+        }
+
+        Ok(())
+    }
 }
 
 /// Print the labels found in the forest, so that we can easily