react-msaview 6.5.0 → 8.0.0

package/dist/rowCoordinateCalculations.d.ts

@@ -1,3 +1,20 @@
+/**
+ * MSA Coordinate Systems:
+ *
+ * 1. **Global Column (globalCol)**: The column index in the full, unfiltered MSA.
+ *    Range: 0 to (MSA width - 1)
+ *    This is the "true" column position before any gap-hiding is applied.
+ *
+ * 2. **Visible Column (visibleCol)**: The column index after hiding gappy columns.
+ *    Range: 0 to (numColumns - 1) where numColumns = MSA width - blanks.length
+ *    This is what the user sees on screen when "Hide columns w/ N% gaps" is enabled.
+ *    When gap hiding is disabled, visibleCol === globalCol.
+ *
+ * 3. **Sequence Position (seqPos)**: The position within a specific row's ungapped sequence.
+ *    Range: 0 to (ungapped sequence length - 1)
+ *    This counts only non-gap characters ('-' and '.' are gaps).
+ *    Each row can have different seqPos values for the same globalCol due to gaps.
+ */
 /**
  * Convert a visible column index to a global column index.
  * This is used when translating mouse/screen coordinates to MSA coordinates.
@@ -21,40 +38,21 @@ export declare function globalColToVisibleCol(blanks: number[], globalCol: numbe
  * that is its own visible index; for a hidden one it is the index of the next
  * visible column, i.e. where the hidden column collapses to.
  *
- * That total answer is what spans want: resolving both ends of a span through
- * globalColToVisibleCol instead loses the whole span whenever either end lands
- * in a hidden column.
+ * Spans use this, since globalColToVisibleCol drops a span whenever either end
+ * lands in a hidden column.
  *
  * @param blanks - Sorted array of global column indices that are hidden
  * @param globalCol - The global column index in the full MSA
  */
 export declare function visibleColsBefore(blanks: number[], globalCol: number): number;
 /**
- * Convert a visible column to a row-specific sequence position.
- * Returns undefined if the position is a gap in the sequence.
+ * The ungapped position a row holds at a global column, or undefined when that
+ * column is a gap in the row or past its end.
  *
- * @param seq - The row's sequence string (including gaps)
- * @param blanks - Sorted array of global column indices that are hidden
- * @param visibleCol - The visible column index
- * @returns The sequence position, or undefined if it's a gap
- */
-export declare function visibleColToSeqPos({ seq, blanks, visibleCol, }: {
-    seq: string;
-    blanks: number[];
-    visibleCol: number;
-}): number | undefined;
-/**
- * Convert a visible column to a row-specific sequence position, with row lookup.
+ * Binary-searches the row's ascending seqPos index; it runs on every mouse
+ * move, and scanning a 30k-column row per event takes the whole frame.
  *
- * @param rowName - The name of the row
- * @param visibleCol - The visible column index
- * @param rowMap - Map from row name to sequence string
- * @param blanks - Sorted array of global column indices that are hidden
- * @returns The sequence position, or undefined if row not found or position is a gap
+ * @param index - The row's seqPos -> global column index (buildSeqPosIndex)
+ * @param globalCol - The global column index in the full MSA
  */
-export declare function visibleColToSeqPosForRow({ rowName, visibleCol, rowMap, blanks, }: {
-    rowName: string;
-    visibleCol: number;
-    rowMap: Map<string, string>;
-    blanks: number[];
-}): number | undefined;
+export declare function seqPosOfGlobalCol(index: Int32Array | undefined, globalCol: number): number | undefined;

package/dist/rowCoordinateCalculations.js

@@ -1,4 +1,3 @@
-import { isBlank } from './util.js';
 /**
  * MSA Coordinate Systems:
  *
@@ -71,9 +70,8 @@ function countBlanksBefore(blanks, globalCol) {
  * that is its own visible index; for a hidden one it is the index of the next
  * visible column, i.e. where the hidden column collapses to.
  *
- * That total answer is what spans want: resolving both ends of a span through
- * globalColToVisibleCol instead loses the whole span whenever either end lands
- * in a hidden column.
+ * Spans use this, since globalColToVisibleCol drops a span whenever either end
+ * lands in a hidden column.
  *
  * @param blanks - Sorted array of global column indices that are hidden
  * @param globalCol - The global column index in the full MSA
@@ -82,44 +80,20 @@ export function visibleColsBefore(blanks, globalCol) {
     return globalCol - countBlanksBefore(blanks, globalCol);
 }
 /**
- * Convert a visible column to a row-specific sequence position.
- * Returns undefined if the position is a gap in the sequence.
+ * The ungapped position a row holds at a global column, or undefined when that
+ * column is a gap in the row or past its end.
  *
- * @param seq - The row's sequence string (including gaps)
- * @param blanks - Sorted array of global column indices that are hidden
- * @param visibleCol - The visible column index
- * @returns The sequence position, or undefined if it's a gap
+ * Binary-searches the row's ascending seqPos index; it runs on every mouse
+ * move, and scanning a 30k-column row per event takes the whole frame.
+ *
+ * @param index - The row's seqPos -> global column index (buildSeqPosIndex)
+ * @param globalCol - The global column index in the full MSA
  */
-export function visibleColToSeqPos({ seq, blanks, visibleCol, }) {
-    // First convert the visible column to global column
-    const globalCol = visibleColToGlobalCol(blanks, visibleCol);
-    const seqLen = seq.length;
-    // Check if the position in the sequence is a gap
-    if (globalCol < seqLen && isBlank(seq[globalCol])) {
+export function seqPosOfGlobalCol(index, globalCol) {
+    if (!index) {
         return undefined;
     }
-    // Count non-gap characters up to the global position
-    let seqPos = 0;
-    for (let i = 0; i < globalCol && i < seqLen; i++) {
-        if (!isBlank(seq[i])) {
-            seqPos++;
-        }
-    }
-    return globalCol < seqLen ? seqPos : undefined;
-}
-/**
- * Convert a visible column to a row-specific sequence position, with row lookup.
- *
- * @param rowName - The name of the row
- * @param visibleCol - The visible column index
- * @param rowMap - Map from row name to sequence string
- * @param blanks - Sorted array of global column indices that are hidden
- * @returns The sequence position, or undefined if row not found or position is a gap
- */
-export function visibleColToSeqPosForRow({ rowName, visibleCol, rowMap, blanks, }) {
-    const seq = rowMap.get(rowName);
-    return seq !== undefined
-        ? visibleColToSeqPos({ seq, visibleCol, blanks })
-        : undefined;
+    const seqPos = partitionPoint(index.length, i => index[i] >= globalCol);
+    return index[seqPos] === globalCol ? seqPos : undefined;
 }
 //# sourceMappingURL=rowCoordinateCalculations.js.map

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package/dist/scales.d.ts

@@ -0,0 +1,22 @@
+import type { LegendEntry } from './types.ts';
+/** how a channel reads a field: a palette by name, or a color per value */
+export interface ScaleSpec {
+    palette?: string;
+    map?: Record<string, string>;
+}
+export interface ResolvedScale {
+    kind: 'categorical';
+    colorOf: (value: string) => string | undefined;
+    legend: LegendEntry[];
+}
+/**
+ * The scale a channel reads its field through. `values` are the field's values,
+ * in any order and with repeats; the domain is their distinct values sorted, so
+ * a value keeps its color when rows are re-ordered, collapsed or filtered.
+ *
+ * `{map}` colors the values the producer named and leaves the rest uncolored.
+ * `{palette}` takes the colors of a named palette, and a spec with neither
+ * takes the ggplot palette of the domain's size. Every scale is categorical
+ * today; a continuous one waits for a caller.
+ */
+export declare function resolveScale(spec: ScaleSpec | undefined, values: Iterable<string>): ResolvedScale;

package/dist/scales.js

@@ -0,0 +1,30 @@
+import { createPaletteMap } from './createPaletteMap.js';
+import { paletteNamed } from './ggplotPalettes.js';
+/**
+ * The scale a channel reads its field through. `values` are the field's values,
+ * in any order and with repeats; the domain is their distinct values sorted, so
+ * a value keeps its color when rows are re-ordered, collapsed or filtered.
+ *
+ * `{map}` colors the values the producer named and leaves the rest uncolored.
+ * `{palette}` takes the colors of a named palette, and a spec with neither
+ * takes the ggplot palette of the domain's size. Every scale is categorical
+ * today; a continuous one waits for a caller.
+ */
+export function resolveScale(spec, values) {
+    const domain = [...new Set(values)].sort((a, b) => a.localeCompare(b));
+    const { map, palette } = spec ?? {};
+    const colors = map ?? createPaletteMap(domain, paletteNamed(palette));
+    const present = new Set(domain);
+    const labels = map ? Object.keys(map).filter(v => present.has(v)) : domain;
+    return {
+        kind: 'categorical',
+        colorOf: (value) => colors[value],
+        // a categorical value is its own label, and the id a legend keys on
+        legend: labels.map(value => ({
+            id: value,
+            label: value,
+            color: colors[value],
+        })),
+    };
+}
+//# sourceMappingURL=scales.js.map

package/dist/scales.js.map

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

@@ -2,9 +2,8 @@
  * The global column of every ungapped sequence position in a row, i.e.
  * index[seqPos] is the column holding the seqPos-th non-gap character.
  *
- * A row is indexed once and then answers seqPos -> column by lookup, which is
- * what makes the domain overlay affordable: it resolves one position per feature
- * per row on every redraw, and scanning the row for each would be quadratic.
+ * The domain overlay resolves one position per feature per row on every redraw,
+ * and scanning the row for each would be quadratic.
  *
  * @example
  * // Row: "A-TG-C" (A at 0, T at 2, G at 3, C at 5)

package/dist/seqPosToGlobalCol.js

@@ -2,9 +2,8 @@
  * The global column of every ungapped sequence position in a row, i.e.
  * index[seqPos] is the column holding the seqPos-th non-gap character.
  *
- * A row is indexed once and then answers seqPos -> column by lookup, which is
- * what makes the domain overlay affordable: it resolves one position per feature
- * per row on every redraw, and scanning the row for each would be quadratic.
+ * The domain overlay resolves one position per feature per row on every redraw,
+ * and scanning the row for each would be quadratic.
  *
  * @example
  * // Row: "A-TG-C" (A at 0, T at 2, G at 3, C at 5)
@@ -19,6 +18,8 @@ export function buildSeqPosIndex(row) {
             index[n++] = col;
         }
     }
-    return index.subarray(0, n);
+    // slice, not subarray: a subarray keeps the whole row-length buffer alive,
+    // and a gappy alignment's indexes are held for as long as the parse is
+    return index.slice(0, n);
 }
 //# sourceMappingURL=seqPosToGlobalCol.js.map

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package/dist/sequenceLogo.d.ts

@@ -12,17 +12,12 @@ export declare function maxBitsFor(sequenceType: 'dna' | 'rna' | 'amino'): numbe
  * stack bottom-up in array order.
  *
  * Heights follow Schneider & Stephens: the column's information content is
- * `log2(alphabet) - H` bits, and each residue takes the share of that its own
- * frequency earns. Frequencies come from the non-gap residues only, so a column
- * of two residues and eight gaps is read as a two-way choice rather than a
- * ten-way one -- otherwise every gappy column would look uninformative for the
- * wrong reason.
+ * `log2(alphabet) - H` bits, split among residues by frequency. Frequencies
+ * count non-gap residues only, so two residues and eight gaps form a two-way
+ * choice.
  *
- * The whole stack is then scaled by the non-gap fraction, which plain WebLogo
- * does not do. Here it earns its place: the track sits directly under an
- * alignment where the gaps are visible, and a column that is 90% gap drawing a
- * full-height stack off its one remaining pair of residues reads as a conserved
- * site. Scaling makes stack height mean "how much this column tells you about
- * the family", matching what the conservation track above it already plots.
+ * Unlike plain WebLogo, the stack is then scaled by the non-gap fraction, so a
+ * 90%-gap column with one conserved pair does not draw a full-height stack, and
+ * stack height matches the conservation track.
  */
 export declare function columnLogoStack(colStats: ColumnCounts, col: number, maxBits: number): LogoLetter[];

package/dist/sequenceLogo.js

@@ -9,18 +9,13 @@ export function maxBitsFor(sequenceType) {
  * stack bottom-up in array order.
  *
  * Heights follow Schneider & Stephens: the column's information content is
- * `log2(alphabet) - H` bits, and each residue takes the share of that its own
- * frequency earns. Frequencies come from the non-gap residues only, so a column
- * of two residues and eight gaps is read as a two-way choice rather than a
- * ten-way one -- otherwise every gappy column would look uninformative for the
- * wrong reason.
+ * `log2(alphabet) - H` bits, split among residues by frequency. Frequencies
+ * count non-gap residues only, so two residues and eight gaps form a two-way
+ * choice.
  *
- * The whole stack is then scaled by the non-gap fraction, which plain WebLogo
- * does not do. Here it earns its place: the track sits directly under an
- * alignment where the gaps are visible, and a column that is 90% gap drawing a
- * full-height stack off its one remaining pair of residues reads as a conserved
- * site. Scaling makes stack height mean "how much this column tells you about
- * the family", matching what the conservation track above it already plots.
+ * Unlike plain WebLogo, the stack is then scaled by the non-gap fraction, so a
+ * 90%-gap column with one conserved pair does not draw a full-height stack, and
+ * stack height matches the conservation track.
  */
 export function columnLogoStack(colStats, col, maxBits) {
     const total = colStats.total(col);

package/dist/sequenceLogo.js.map

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

@@ -2,20 +2,13 @@ import type { IAnyType, IOptionalIType, OptionalDefaultValueOrFunction } from '@
 /**
  * `types.stripDefault`, degrading to `types.optional` on hosts that lack it.
  *
- * stripDefault keeps defaulted properties out of snapshots, but it exists only
- * in the mobx-state-tree that ships with unreleased @jbrowse/core. This package
- * declares `@jbrowse/mobx-state-tree: ^5.0.0`, and inside jbrowse-web the host
- * supplies its own copy at runtime -- the plugin bundle externalizes it -- so we
- * genuinely do not know which version we are calling until we are running.
+ * stripDefault keeps defaulted properties out of snapshots, and only the
+ * mobx-state-tree in unreleased @jbrowse/core has it. The plugin bundle
+ * externalizes mobx-state-tree, so the host's copy is known only at runtime, and
+ * calling a missing stripDefault during model construction makes PluginLoader
+ * reject and the whole app show its error page.
  *
- * Calling it where it is absent throws while the model is being constructed,
- * which in a plugin bundle means PluginLoader rejects and the entire app renders
- * its error page. Losing minimal snapshots is a far better failure than losing
- * the session, so this degrades instead.
- *
- * The two signatures are identical, so behaviour differs only in that defaults
- * reappear in snapshots on older hosts (bigger session snapshots and shared
- * URLs, nothing incorrect). stripDefaultSnapshot.test.ts still pins the stripped
- * behaviour, since dev runs against a version that has it.
+ * The signatures are identical; on older hosts, defaults reappear in snapshots
+ * and shared URLs. stripDefaultSnapshot.test.ts pins the stripped behaviour.
  */
 export declare function stripDefault<IT extends IAnyType>(type: IT, defaultValue: OptionalDefaultValueOrFunction<IT>): IOptionalIType<IT, [undefined]>;

package/dist/stripDefault.js

@@ -2,21 +2,14 @@ import { types } from '@jbrowse/mobx-state-tree';
 /**
  * `types.stripDefault`, degrading to `types.optional` on hosts that lack it.
  *
- * stripDefault keeps defaulted properties out of snapshots, but it exists only
- * in the mobx-state-tree that ships with unreleased @jbrowse/core. This package
- * declares `@jbrowse/mobx-state-tree: ^5.0.0`, and inside jbrowse-web the host
- * supplies its own copy at runtime -- the plugin bundle externalizes it -- so we
- * genuinely do not know which version we are calling until we are running.
+ * stripDefault keeps defaulted properties out of snapshots, and only the
+ * mobx-state-tree in unreleased @jbrowse/core has it. The plugin bundle
+ * externalizes mobx-state-tree, so the host's copy is known only at runtime, and
+ * calling a missing stripDefault during model construction makes PluginLoader
+ * reject and the whole app show its error page.
  *
- * Calling it where it is absent throws while the model is being constructed,
- * which in a plugin bundle means PluginLoader rejects and the entire app renders
- * its error page. Losing minimal snapshots is a far better failure than losing
- * the session, so this degrades instead.
- *
- * The two signatures are identical, so behaviour differs only in that defaults
- * reappear in snapshots on older hosts (bigger session snapshots and shared
- * URLs, nothing incorrect). stripDefaultSnapshot.test.ts still pins the stripped
- * behaviour, since dev runs against a version that has it.
+ * The signatures are identical; on older hosts, defaults reappear in snapshots
+ * and shared URLs. stripDefaultSnapshot.test.ts pins the stripped behaviour.
  */
 export function stripDefault(type, defaultValue) {
     return typeof types.stripDefault === 'function'

package/dist/stripDefault.js.map

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