react-msaview 8.2.0 → 8.4.0

package/dist/rerootTree.js

@@ -0,0 +1,144 @@
+function preorder(root) {
+    const order = [];
+    const parents = new Map();
+    const stack = [root];
+    while (stack.length > 0) {
+        const node = stack.pop();
+        order.push(node);
+        for (const child of (node.children ?? [])) {
+            parents.set(child, node);
+            stack.push(child);
+        }
+    }
+    return { order, parents };
+}
+function hasLengths(order) {
+    return order.some(n => n.length !== undefined);
+}
+// the root's two children make one branch of the unrooted tree, which is the
+// branch a rerooting at either of them splits
+function mergedSibling(root, target) {
+    return root.children?.length === 2
+        ? root.children.find(c => c !== target)
+        : undefined;
+}
+/**
+ * The tree rooted on the branch above `target`, `offset` up from it, or at the
+ * middle of that branch without one. Where the root has two children, their
+ * branches are one branch of the unrooted tree, and `offset` runs across both.
+ *
+ * The nodes between `target` and the old root turn over. A name on one of them
+ * labels the branch above it, which is where a support value sits, so the name
+ * follows that branch to the node now at its lower end. A two-child root has
+ * nothing left to split once one child leaves, so it drops out and its
+ * branches join.
+ */
+export function rerootTree(root, target, offset) {
+    const { order, parents } = preorder(root);
+    if (!parents.has(target)) {
+        return root;
+    }
+    const lengths = hasLengths(order);
+    const sibling = parents.get(target) === root ? mergedSibling(root, target) : undefined;
+    const branch = (target.length ?? 0) + (sibling?.length ?? 0);
+    const at = Math.min(Math.max(offset ?? branch / 2, 0), branch);
+    const length = (n) => (lengths ? n : undefined);
+    const path = [target];
+    for (let n = parents.get(target); n; n = parents.get(n)) {
+        path.push(n);
+    }
+    // Built from the old root down, so the node each turned node now hangs
+    // `above` it already exists. undefined where the old root dropped out.
+    let above;
+    for (let i = path.length - 1; i >= 1; i--) {
+        const node = path[i];
+        const below = path[i - 1];
+        const children = node.children.filter(c => c !== below);
+        if (above) {
+            children.push(above);
+        }
+        if (children.length === 0) {
+            above = undefined;
+        }
+        else if (i === path.length - 1 && children.length === 1) {
+            const only = children[0];
+            above = {
+                ...only,
+                length: length((only.length ?? 0) + (below.length ?? 0) - (i === 1 ? at : 0)),
+            };
+        }
+        else {
+            above = {
+                ...node,
+                name: i === 1 ? undefined : below.name,
+                children,
+                length: length((below.length ?? 0) - (i === 1 ? at : 0)),
+            };
+        }
+    }
+    return {
+        children: [{ ...target, length: length(at) }, ...(above ? [above] : [])],
+    };
+}
+/**
+ * The tree rooted halfway along the longest path between two tips, which is
+ * where a clock would put the root: the usual choice for the unrooted tree
+ * FastTree, IQ-TREE or neighbor joining writes. A tree with no branch lengths
+ * counts branches.
+ */
+export function midpointRoot(root) {
+    const { order, parents } = preorder(root);
+    const tips = order.filter(n => !n.children?.length);
+    if (tips.length < 2) {
+        return root;
+    }
+    const lengths = hasLengths(order);
+    const weight = (n) => (lengths ? (n.length ?? 0) : 1);
+    // distance from `from` to every node over the unrooted tree, and the
+    // neighbor each was reached through
+    function reach(from) {
+        const dist = new Map([[from, 0]]);
+        const via = new Map();
+        const stack = [from];
+        while (stack.length > 0) {
+            const node = stack.pop();
+            const d = dist.get(node);
+            const parent = parents.get(node);
+            if (parent && !dist.has(parent)) {
+                dist.set(parent, d + weight(node));
+                via.set(parent, node);
+                stack.push(parent);
+            }
+            for (const child of (node.children ?? [])) {
+                if (!dist.has(child)) {
+                    dist.set(child, d + weight(child));
+                    via.set(child, node);
+                    stack.push(child);
+                }
+            }
+        }
+        return { dist, via };
+    }
+    function farthest(dist) {
+        return tips.reduce((best, tip) => dist.get(tip) > dist.get(best) ? tip : best);
+    }
+    const a = farthest(reach(tips[0]).dist);
+    const { dist, via } = reach(a);
+    const b = farthest(dist);
+    if (b === a) {
+        return root;
+    }
+    const half = dist.get(b) / 2;
+    let node = b;
+    let next = via.get(node);
+    while (dist.get(next) > half) {
+        node = next;
+        next = via.get(node);
+    }
+    // the midpoint lies on the branch between `node` and `next`, and whichever
+    // of them is the child carries that branch
+    return parents.get(node) === next
+        ? rerootTree(root, node, dist.get(node) - half)
+        : rerootTree(root, next, half - dist.get(next));
+}
+//# sourceMappingURL=rerootTree.js.map

package/dist/rerootTree.js.map

@@ -0,0 +1 @@
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