react-msaview 9.1.0 → 9.2.0

package/dist/renderToSvg.js.map

@@ -1 +1 @@
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package/dist/rerootTree.d.ts

@@ -12,6 +12,7 @@ export interface TreeNode {
     length?: number;
     children?: TreeNode[];
 }
+export declare function preorder<N extends TreeNode>(root: N, parents?: Map<N, N>): N[];
 /**
  * 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

package/dist/rerootTree.js

@@ -1,16 +1,15 @@
-function preorder(root) {
+export function preorder(root, parents) {
     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);
+            parents?.set(child, node);
             stack.push(child);
         }
     }
-    return { order, parents };
+    return order;
 }
 function hasLengths(order) {
     return order.some(n => n.length !== undefined);
@@ -34,7 +33,8 @@ function mergedSibling(root, target) {
  * branches join.
  */
 export function rerootTree(root, target, offset) {
-    const { order, parents } = preorder(root);
+    const parents = new Map();
+    const order = preorder(root, parents);
     if (!parents.has(target)) {
         return root;
     }
@@ -87,7 +87,8 @@ export function rerootTree(root, target, offset) {
  * counts branches.
  */
 export function midpointRoot(root) {
-    const { order, parents } = preorder(root);
+    const parents = new Map();
+    const order = preorder(root, parents);
     const tips = order.filter(n => !n.children?.length);
     if (tips.length < 2) {
         return root;

package/dist/rerootTree.js.map

@@ -1 +1 @@
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package/dist/schemeResidueColor.d.ts

@@ -0,0 +1,12 @@
+import type { MsaViewModel } from './model.ts';
+/**
+ * A reader for the color the active scheme gives a row's residue, as hex, for a
+ * host that paints another view, such as a structure, with the alignment's own
+ * colors. `seqPos` is 1-based, like `structureResidue`. The reader returns
+ * undefined where the scheme leaves the residue uncolored, the row lacks it, or
+ * its column is hidden.
+ *
+ * Build it inside a reaction: a new scheme, a hidden gap column or a collapsed
+ * clade then re-runs the caller.
+ */
+export declare function schemeResidueColor(model: MsaViewModel): (rowName: string, seqPos: number) => string | undefined;

package/dist/schemeResidueColor.js

@@ -0,0 +1,33 @@
+import { colord } from 'colord';
+import { tileColorFn } from './components/msa/tileColor.js';
+/**
+ * A reader for the color the active scheme gives a row's residue, as hex, for a
+ * host that paints another view, such as a structure, with the alignment's own
+ * colors. `seqPos` is 1-based, like `structureResidue`. The reader returns
+ * undefined where the scheme leaves the residue uncolored, the row lacks it, or
+ * its column is hidden.
+ *
+ * Build it inside a reaction: a new scheme, a hidden gap column or a collapsed
+ * clade then re-runs the caller.
+ */
+export function schemeResidueColor(model) {
+    const colorAt = tileColorFn(model);
+    const { columns } = model;
+    const hexes = new Map();
+    const toHex = (color) => {
+        if (!hexes.has(color)) {
+            const parsed = colord(color);
+            hexes.set(color, parsed.isValid() ? parsed.toHex() : undefined);
+        }
+        return hexes.get(color);
+    };
+    return (rowName, seqPos) => {
+        const col = model.seqPosToVisibleCol(rowName, seqPos - 1);
+        const letter = col === undefined ? undefined : columns.get(rowName)?.[col];
+        const color = col === undefined || letter === undefined
+            ? undefined
+            : colorAt(col, letter);
+        return color === undefined ? undefined : toHex(color);
+    };
+}
+//# sourceMappingURL=schemeResidueColor.js.map

package/dist/schemeResidueColor.js.map

@@ -0,0 +1 @@
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package/dist/similarityColors.d.ts

@@ -0,0 +1,11 @@
+import type { ColumnCounts } from './columnCounts.ts';
+/**
+ * The amino acids of a column shaded by BLOSUM62 similarity. Letters the matrix
+ * does not name, such as U, O and J, count for nothing and take no shade.
+ */
+export declare function blosum62ColumnColors(counts: ColumnCounts, col: number): Record<string, string>;
+/**
+ * Nucleotides and anything else without a substitution matrix: a residue's
+ * similarity is the fraction of the rest of its column that equals it.
+ */
+export declare function identityColumnColors(counts: ColumnCounts, col: number): Record<string, string>;

package/dist/similarityColors.js

@@ -0,0 +1,90 @@
+// Similarity shading, after biotite's plot_alignment_similarity_based and
+// Jalview's BLOSUM62 score scheme. Each residue takes a shade of one hue by how
+// similar it is, on average, to the other residues of its column.
+import { BLOSUM62, NUM_SYMBOLS, symbolOfCode } from './blosum62.js';
+import { letterOfResidueSlot, numResidueSlots } from './columnCounts.js';
+const AMINO_ACIDS = 20;
+const HUE = 240;
+const SATURATION = 50;
+const LIGHTEST = 96;
+const DARKEST = 40;
+// BLOSUM62 scaled per row to 0..1 over the twenty amino acids, so a residue's
+// own score is 1 and its worst substitution 0. Not symmetric, like biotite's.
+const normalized = new Float32Array(NUM_SYMBOLS * NUM_SYMBOLS);
+for (let a = 0; a < NUM_SYMBOLS; a++) {
+    let min = Infinity;
+    let max = -Infinity;
+    for (let b = 0; b < AMINO_ACIDS; b++) {
+        const score = BLOSUM62[a * NUM_SYMBOLS + b];
+        min = Math.min(min, score);
+        max = Math.max(max, score);
+    }
+    for (let b = 0; b < NUM_SYMBOLS; b++) {
+        const scaled = (BLOSUM62[a * NUM_SYMBOLS + b] - min) / (max - min);
+        normalized[a * NUM_SYMBOLS + b] = Math.min(Math.max(scaled, 0), 1);
+    }
+}
+// residue slot -> row of the matrix, -1 for a letter the matrix does not name
+const symbolOfSlot = Int8Array.from({ length: numResidueSlots }, (_, slot) => {
+    const letter = letterOfResidueSlot(slot);
+    return letter.length === 1 ? symbolOfCode[letter.charCodeAt(0)] : -1;
+});
+function shade(similarity) {
+    const lightness = Math.round(LIGHTEST - (LIGHTEST - DARKEST) * similarity);
+    return `hsl(${HUE}, ${SATURATION}%, ${lightness}%)`;
+}
+/**
+ * Shades each residue of one column by its mean similarity to the column's
+ * other residues, gaps left out of the mean. A column of fewer than two counted
+ * residues has nothing to compare and colors nothing.
+ */
+function shadeColumn(counts, col, measure) {
+    const { counted, shaded, score } = measure;
+    const present = [];
+    let total = 0;
+    counts.forEachResidue(col, (slot, count) => {
+        if (counted(slot)) {
+            present.push([slot, count]);
+            total += count;
+        }
+    });
+    const colors = {};
+    if (total < 2) {
+        return colors;
+    }
+    for (const [a] of present) {
+        if (shaded(a)) {
+            let sum = -score(a, a);
+            for (const [b, count] of present) {
+                sum += count * score(a, b);
+            }
+            colors[letterOfResidueSlot(a)] = shade(sum / (total - 1));
+        }
+    }
+    return colors;
+}
+const blosum62 = {
+    counted: slot => symbolOfSlot[slot] >= 0,
+    shaded: slot => symbolOfSlot[slot] < AMINO_ACIDS,
+    score: (a, b) => normalized[symbolOfSlot[a] * NUM_SYMBOLS + symbolOfSlot[b]],
+};
+const identity = {
+    counted: () => true,
+    shaded: () => true,
+    score: (a, b) => (a === b ? 1 : 0),
+};
+/**
+ * The amino acids of a column shaded by BLOSUM62 similarity. Letters the matrix
+ * does not name, such as U, O and J, count for nothing and take no shade.
+ */
+export function blosum62ColumnColors(counts, col) {
+    return shadeColumn(counts, col, blosum62);
+}
+/**
+ * Nucleotides and anything else without a substitution matrix: a residue's
+ * similarity is the fraction of the rest of its column that equals it.
+ */
+export function identityColumnColors(counts, col) {
+    return shadeColumn(counts, col, identity);
+}
+//# sourceMappingURL=similarityColors.js.map

package/dist/similarityColors.js.map

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