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Merged
sebschmi merged 1 commit into from
May 20, 2025
Merged

Use boxed types in A* data structures. #74

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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
/target
/tsa_config
/*.log
/*.log
/callgrind.out.*
3 changes: 3 additions & 0 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,3 +26,6 @@ compact-genome = "12.3.0"
traitsequence = "8.1.2"
log = "0.4.27"
num-traits = "0.2.19"

[profile.release]
debug = true
28 changes: 28 additions & 0 deletions generic_a_star/src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -579,3 +579,31 @@ impl<NodeIdentifier, Cost> Default for AStarResult<NodeIdentifier, Cost> {
Self::NoTarget
}
}

impl<T: AStarNode> AStarNode for Box<T> {
type Identifier = <T as AStarNode>::Identifier;

type EdgeType = <T as AStarNode>::EdgeType;

type Cost = <T as AStarNode>::Cost;

fn identifier(&self) -> &Self::Identifier {
<T as AStarNode>::identifier(self)
}

fn cost(&self) -> Self::Cost {
<T as AStarNode>::cost(self)
}

fn a_star_lower_bound(&self) -> Self::Cost {
<T as AStarNode>::a_star_lower_bound(self)
}

fn predecessor(&self) -> Option<&Self::Identifier> {
<T as AStarNode>::predecessor(self)
}

fn predecessor_edge_type(&self) -> Option<Self::EdgeType> {
<T as AStarNode>::predecessor_edge_type(self)
}
}
112 changes: 70 additions & 42 deletions lib_tsalign/src/a_star_aligner/template_switch_distance/context.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ pub struct Context<
<Strategies as AlignmentStrategySelector>::Cost,
>>::IdentifierPrimaryExtraData,
>,
Node<Strategies>,
Box<Node<Strategies>>,
>,
pub memory: Memory<Strategies>,

Expand Down Expand Up @@ -102,10 +102,10 @@ impl<
Strategies: AlignmentStrategySelector,
> AStarContext for Context<'_, '_, SubsequenceType, Strategies>
{
type Node = Node<Strategies>;
type Node = Box<Node<Strategies>>;

fn create_root(&self) -> Self::Node {
Self::Node {
Box::new(Node {
node_data: NodeData {
identifier: Identifier::new_primary(self.range.reference_offset(), self.range.query_offset(), 0, GapType::None, <<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::create_root_identifier_primary_extra_data(self)),
predecessor: None,
Expand All @@ -114,7 +114,7 @@ impl<
a_star_lower_bound: Strategies::Cost::zero(),
},
strategies: AlignmentStrategiesNodeMemory::create_root(self),
}
})
}

fn generate_successors(
Expand Down Expand Up @@ -186,12 +186,15 @@ impl<
};

if cost_increment != Strategies::Cost::max_value() {
opened_nodes_output.extend(node.generate_primary_diagonal_successor(
0,
cost_increment,
is_match,
self,
));
opened_nodes_output.extend(
node.generate_primary_diagonal_successor(
0,
cost_increment,
is_match,
self,
)
.map(Into::into),
);
}

if is_match && <<Strategies as AlignmentStrategySelector>::PrimaryMatch as PrimaryMatchStrategy<<Strategies as AlignmentStrategySelector>::Cost>>::always_generate_substitution() {
Expand All @@ -203,7 +206,8 @@ impl<
cost_increment,
false,
self,
));
)
.map(Into::into));
}
}
}
Expand Down Expand Up @@ -232,12 +236,15 @@ impl<
};

if cost_increment != Strategies::Cost::max_value() {
opened_nodes_output.extend(node.generate_primary_diagonal_successor(
flank_index + 1,
cost_increment,
is_match,
self,
));
opened_nodes_output.extend(
node.generate_primary_diagonal_successor(
flank_index + 1,
cost_increment,
is_match,
self,
)
.map(Into::into),
);
}
}
}
Expand All @@ -256,7 +263,8 @@ impl<
.primary_edit_costs
.gap_costs(r.clone(), gap_type != GapType::Deletion),
self,
),
)
.map(Into::into),
);
}

Expand All @@ -271,7 +279,8 @@ impl<
.left_flank_edit_costs
.gap_costs(r, gap_type != GapType::Deletion),
self,
),
)
.map(Into::into),
);
} else if flank_index < 0 {
opened_nodes_output.extend(
Expand All @@ -281,7 +290,8 @@ impl<
.right_flank_edit_costs
.gap_costs(r, gap_type != GapType::Deletion),
self,
),
)
.map(Into::into),
);
}
}
Expand All @@ -300,7 +310,8 @@ impl<
.primary_edit_costs
.gap_costs(q.clone(), gap_type != GapType::Insertion),
self,
),
)
.map(Into::into),
);
}

Expand All @@ -315,7 +326,8 @@ impl<
.left_flank_edit_costs
.gap_costs(q, gap_type != GapType::Insertion),
self,
),
)
.map(Into::into),
);
} else if flank_index < 0 {
opened_nodes_output.extend(
Expand All @@ -325,7 +337,8 @@ impl<
.right_flank_edit_costs
.gap_costs(q, gap_type != GapType::Insertion),
self,
),
)
.map(Into::into),
);
}
}
Expand All @@ -340,7 +353,8 @@ impl<
config.offset_costs.evaluate(&0),
&config.base_cost,
self,
),
)
.map(Into::into),
);
}
}
Expand Down Expand Up @@ -394,7 +408,8 @@ impl<
cost_increment,
template_switch_first_offset + 1,
self,
),
)
.map(Into::into),
)
}
}
Expand All @@ -421,7 +436,8 @@ impl<
cost_increment,
template_switch_first_offset - 1,
self,
),
)
.map(Into::into),
)
}
}
Expand All @@ -443,6 +459,7 @@ impl<
let secondary_root_node: Vec<_> = node
.generate_secondary_root_node(self)
.into_iter()
.map(Box::new)
.collect();
opened_nodes_output = ExtendMap::new(
opened_nodes_direct_output,
Expand Down Expand Up @@ -505,7 +522,8 @@ impl<
.match_or_substitution_cost(p.clone(), s.clone()),
p == s,
self,
),
)
.map(Into::into),
);
}

Expand Down Expand Up @@ -543,7 +561,8 @@ impl<
.secondary_edit_costs(template_switch_direction)
.gap_costs(s, gap_type != GapType::Deletion),
self,
),
)
.map(Into::into),
);
}

Expand All @@ -557,7 +576,8 @@ impl<
.secondary_edit_costs(template_switch_direction)
.gap_costs(p, gap_type != GapType::Insertion),
self,
),
)
.map(Into::into),
);
}
}
Expand All @@ -570,7 +590,8 @@ impl<
let cost_increment = length_cost + length_difference_cost;

opened_nodes_output.extend(
node.generate_initial_template_switch_exit_successor(cost_increment, self),
node.generate_initial_template_switch_exit_successor(cost_increment, self)
.map(Into::into),
)
}
}
Expand Down Expand Up @@ -613,11 +634,14 @@ impl<
assert!(new_cost >= old_cost);
let cost_increment = new_cost - old_cost;

opened_nodes_output.extend(node.generate_template_switch_exit_successor(
cost_increment,
anti_primary_gap + 1,
self,
))
opened_nodes_output.extend(
node.generate_template_switch_exit_successor(
cost_increment,
anti_primary_gap + 1,
self,
)
.map(Into::into),
)
}
}

Expand All @@ -634,11 +658,14 @@ impl<
assert!(new_cost >= old_cost);
let cost_increment = new_cost - old_cost;

opened_nodes_output.extend(node.generate_template_switch_exit_successor(
cost_increment,
anti_primary_gap - 1,
self,
))
opened_nodes_output.extend(
node.generate_template_switch_exit_successor(
cost_increment,
anti_primary_gap - 1,
self,
)
.map(Into::into),
)
}
}

Expand All @@ -652,7 +679,7 @@ impl<
node.generate_primary_reentry_successor(self, anti_primary_gap_cost)
.map(|mut node| {
node.strategies.template_switch_count.increment_count();
node
node.into()
}),
);
}
Expand Down Expand Up @@ -705,7 +732,8 @@ fn generate_output_mapper_function<
<Context<'reference, 'query, SubsequenceType, Strategies> as AStarContext>::Node,
) -> <Context<'reference, 'query, SubsequenceType, Strategies> as AStarContext>::Node {
move |node| {
<Strategies as AlignmentStrategySelector>::Chaining::apply_lower_bound(node, context)
<Strategies as AlignmentStrategySelector>::Chaining::apply_lower_bound(*node, context)
.into()
}
}

Expand Down
2 changes: 1 addition & 1 deletion lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch.rs
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Expand Up @@ -105,7 +105,7 @@ impl<Cost: AStarCost> TemplateSwitchLowerBoundMatrix<Cost> {
),
);
let root_xy = genome_length / 2;
a_star.initialise_with(|context| Node::new_root_at(root_xy, root_xy, context));
a_star.initialise_with(|context| Node::new_root_at(root_xy, root_xy, context).into());
previous_closed_lower_bounds.extend(closed_lower_bounds.drain());

let root_xy_isize = isize::try_from(root_xy).unwrap();
Expand Down
23 changes: 15 additions & 8 deletions lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/shortcut.rs
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Expand Up @@ -88,14 +88,21 @@ impl<Cost: AStarCost> ShortcutStrategy<Cost> for TemplateSwitchLowerBoundShortcu
Identifier::Primary { flank_index, .. }
| Identifier::PrimaryReentry { flank_index, .. } => {
if flank_index == context.config.left_flank_length {
opened_nodes_output.extend(context.memory.shortcut.iter().flat_map(|entry| {
node.generate_template_switch_shortcut_successor(
entry.x(),
entry.y(),
entry.cost(),
context,
)
}));
opened_nodes_output.extend(
context
.memory
.shortcut
.iter()
.flat_map(|entry| {
node.generate_template_switch_shortcut_successor(
entry.x(),
entry.y(),
entry.cost(),
context,
)
})
.map(Into::into),
);
}
}

Expand Down
4 changes: 2 additions & 2 deletions ...lign/src/a_star_aligner/template_switch_distance/strategies/template_switch_min_length.rs
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Expand Up @@ -241,10 +241,10 @@ impl<
Strategies: AlignmentStrategySelector,
> AStarContext for TemplateSwitchMinLengthContext<'_, '_, '_, SubsequenceType, Strategies>
{
type Node = Node<Strategies>;
type Node = Box<Node<Strategies>>;

fn create_root(&self) -> Self::Node {
self.root_node.clone()
self.root_node.clone().into()
}

fn generate_successors(&mut self, node: &Self::Node, output: &mut impl Extend<Self::Node>) {
Expand Down