@jbrowse/core 5.0.0-beta.11 → 5.0.0-beta.14

package/esm/util/cellsStep.js

@@ -1,38 +1,16 @@
 // The `cells` step: each row's runs against the reference it was fanned out
 // of, and the texts its walk reads, which the fused identity kernel in
 // cellMatches.ts walks too. Imported by relative path only.
+import { DASH, SPACE, firstDrawn, isGapByte, isUnknownBase, lastDrawn, sameBase, } from './alignedBytes.js';
 import { DerivedTable, numberReaderOf, readerOf, valueAt, } from './featureTable.js';
 import { FannedTable, boundsThrough } from './stepTables.js';
 export const DEFAULT_CELLS_FIELD = 'seq';
-export const DASH = 45;
-export const SPACE = 32;
-const LOWER_BIT = 0x20;
 const CELL_STATES = ['match', 'mismatch', 'gap', 'insertion'];
 export const MATCH = 0;
 export const MISMATCH = 1;
 const GAP = 2;
 const INSERTION = 3;
 export const NO_STATE = 255;
-export function isGapByte(b) {
-    return b === DASH || b === SPACE;
-}
-// The columns carrying the row's own sequence: a gap run reaching either end
-// of the row measures where the block was cut, not the alignment, so it is no
-// cell either.
-export function firstDrawn(bytes, at, len) {
-    let first = 0;
-    while (first < len && isGapByte(bytes[at + first])) {
-        first++;
-    }
-    return first;
-}
-export function lastDrawn(bytes, at, len, first) {
-    let last = len - 1;
-    while (last > first && isGapByte(bytes[at + last])) {
-        last--;
-    }
-    return last;
-}
 // A reference base's cell: no state outside the drawn columns, else the row's
 // gap, or its base matched or not regardless of case.
 export function cellState(refByte, rowByte, drawn) {
@@ -40,10 +18,25 @@ export function cellState(refByte, rowByte, drawn) {
         ? NO_STATE
         : isGapByte(rowByte)
             ? GAP
-            : (refByte | LOWER_BIT) === (rowByte | LOWER_BIT)
+            : sameBase(refByte, rowByte)
                 ? MATCH
                 : MISMATCH;
 }
+// Whether a cell counts toward identity: matched or not against a known
+// reference base.
+export function comparesBase(state, refByte) {
+    return state <= MISMATCH && !isUnknownBase(refByte);
+}
+// What the cells of one run share besides their state: whether they are
+// compared, so a run's `match` is one value.
+export function runKey(state, refByte) {
+    return state <= MISMATCH && isUnknownBase(refByte) ? 1 : 0;
+}
+// A mismatch always starts a run of its own, so each differing base is one
+// instance and a text over `base` letters every one.
+export function opensRun(state, key, runState, openKey) {
+    return state !== runState || key !== openKey || state === MISMATCH;
+}
 // The row a cell step reads against: past any table that only reordered or
 // annotated the rows, the one they were fanned out of.
 function containerOf(table) {
@@ -218,7 +211,11 @@ class CellTable extends DerivedTable {
                     const values = new Float32Array(this.length);
                     for (let i = 0; i < this.length; i++) {
                         const s = this.state[i];
-                        values[i] = s === MATCH ? 1 : s === MISMATCH ? 0 : Number.NaN;
+                        values[i] = comparesBase(s, this.refByte(i))
+                            ? s === MATCH
+                                ? 1
+                                : 0
+                            : Number.NaN;
                     }
                     return { kind: 'number', values, at: undefined, nanIsAbsent: true };
                 });
@@ -254,6 +251,11 @@ class CellTable extends DerivedTable {
             }
         }
     }
+    refByte(i) {
+        const { reference: ref } = this.texts;
+        const f = this.texts.refOf(this.parentOf(i));
+        return ref.bytes[ref.offset[f] + this.textAt[i]];
+    }
     mismatched(i) {
         const { bytes, offset } = this.texts.row;
         const k = this.texts.rowOf(this.parentOf(i));
@@ -342,7 +344,7 @@ class RunLanes {
         const last = lastDrawn(rowBytes, rowAt, rowLen, first);
         let runStart = -1;
         let runState = NO_STATE;
-        let runBase = -1;
+        let openKey = -1;
         let runCol = 0;
         let insertAt = -1;
         for (let col = 0; col < refLen; col++) {
@@ -364,8 +366,8 @@ class RunLanes {
                 insertAt = -1;
             }
             const st = cellState(refByte, rowByte, col >= first && col <= last && col < rowLen);
-            const base = st === MISMATCH ? rowByte : -1;
-            if (st !== runState || base !== runBase) {
+            const key = runKey(st, refByte);
+            if (opensRun(st, key, runState, openKey)) {
                 if (runStart >= 0) {
                     start[n] = runStart;
                     end[n] = pos;
@@ -376,7 +378,7 @@ class RunLanes {
                 }
                 runStart = st === NO_STATE ? -1 : pos;
                 runState = st;
-                runBase = base;
+                openKey = key;
                 runCol = col;
             }
             pos++;

package/esm/util/color/index.d.ts

@@ -78,7 +78,7 @@ export declare function relight(color: string, lightnessShift: number, chromaSca
  * once per feature, and what a reader saw was every unlabelled feature in one
  * strong color: a large fake category, drawn over the real ones. Grey says the
  * only true thing about a feature with no value for the attribute you asked to
- * colour by.
+ * color by.
  *
  * @param str - The string to generate a color from
  * @returns A CSS hex color string

package/esm/util/color/index.js

@@ -82,7 +82,7 @@ export { CSS_COLOR_NAMES, isNamedColor, namedColorToHex, } from './cssColorsLeve
 // has to read as "not in a category" beside a palette whose every member is
 // equally light and equally colorful, so it cannot be one more hue.
 export const NO_CATEGORY_COLOR = '#afafaf';
-// What a colour declaration paints where it reads nothing it can colour, so a
+// What a color declaration paints where it reads nothing it can color, so a
 // misconfiguration surfaces rather than passing for the no-category grey.
 export const MISCONFIGURED_COLOR = '#808080';
 const RANDOM_COLOR_TIERS = [
@@ -185,7 +185,7 @@ export function relight(color, lightnessShift, chromaScale = 1) {
  * once per feature, and what a reader saw was every unlabelled feature in one
  * strong color: a large fake category, drawn over the real ones. Grey says the
  * only true thing about a feature with no value for the attribute you asked to
- * colour by.
+ * color by.
  *
  * @param str - The string to generate a color from
  * @returns A CSS hex color string

package/esm/util/color-bits/bit.js

@@ -32,6 +32,6 @@ export function clampByte(n) {
     // against NaN is false, and an unclamped NaN shifts to 0 anyway — silently,
     // one channel at a time. `jexl:alpha(color, get(feature,'opacity'))` on a
     // non-numeric attribute is the reachable one, and it drew the feature at
-    // alpha 0 instead of reaching the invalid-colour sentinel.
+    // alpha 0 instead of reaching the invalid-color sentinel.
     return n > 0 ? (n > 255 ? 255 : n) : 0;
 }

package/esm/util/color-bits/parse.js

@@ -9,15 +9,15 @@ const E = 'e'.charCodeAt(0);
 /**
  * Approximative CSS colorspace string pattern, e.g. rgb(), color()
  *
- * **Anchored**, because the whole string has to be a colour for this to be one.
- * Unanchored it matched a colour sitting anywhere inside anything, so
+ * **Anchored**, because the whole string has to be a color for this to be one.
+ * Unanchored it matched a color sitting anywhere inside anything, so
  * `parseCssColor('foo rgb(1,2,3) bar')` answered `[1,2,3]` — and a config slot
- * holding prose, a jexl expression that did not evaluate, or two colours by
- * mistake read as a plausible colour instead of reaching the invalid-colour
+ * holding prose, a jexl expression that did not evaluate, or two colors by
+ * mistake read as a plausible color instead of reaching the invalid-color
  * sentinel. That sentinel is a contract (`colorBits.test.ts`: a broken config
- * reads as magenta, never as a plausible wrong colour), and it was unreachable
+ * reads as magenta, never as a plausible wrong color), and it was unreachable
  * for every such string. Surrounding whitespace is still tolerated: a slot with
- * a trailing space is a formatting slip, not a different colour.
+ * a trailing space is a formatting slip, not a different color.
  */
 const PATTERN = (() => {
     const NAME = String.raw `(\w+)`;
@@ -239,16 +239,27 @@ export function parseColor(color) {
     }
     throw new Error(`Color.parse(): invalid CSS color: "${color}"`);
 }
+/** A channel's leading number, throwing where it has none, as `rgb(a,b,1)`. */
+function parseNumber(value) {
+    const n = Number.parseFloat(value);
+    if (Number.isNaN(n)) {
+        throw new TypeError(`Color.parse(): invalid CSS color channel: "${value}"`);
+    }
+    return n;
+}
 /**
- * Accepts: "50%", "128"
+ * Accepts: "50%", "128", "none"
  * https://developer.mozilla.org/en-US/docs/Web/CSS/color_value/rgb#values
  * @returns a value in the 0 to 255 range
  */
 function parseColorChannel(channel) {
+    if (channel === 'none') {
+        return 0;
+    }
     if (channel.charCodeAt(channel.length - 1) === PERCENT) {
-        return Math.round((Number.parseFloat(channel) / 100) * 255);
+        return Math.round((parseNumber(channel) / 100) * 255);
     }
-    return Math.round(Number.parseFloat(channel));
+    return Math.round(parseNumber(channel));
 }
 /**
  * Accepts: "50%", ".5", "0.5"
@@ -268,9 +279,9 @@ function parseAlphaValue(channel) {
         return 0;
     }
     if (channel.charCodeAt(channel.length - 1) === PERCENT) {
-        return Number.parseFloat(channel) / 100;
+        return parseNumber(channel) / 100;
     }
-    return Number.parseFloat(channel);
+    return parseNumber(channel);
 }
 /**
  * Accepts: "360", "360deg", "400grad", "6.28rad", "1turn", "none"
@@ -302,7 +313,7 @@ function parseAngle(angle) {
             factor = 360;
         }
     }
-    const turns = Number.parseFloat(angle) / factor;
+    const turns = parseNumber(angle) / factor;
     // Hue is periodic, and every caller of this is a hue. `hueToRGB` corrects its
     // argument by at most one turn, so it reads `hsl(-720deg)` as a hue two turns
     // below the wheel rather than as red — folding here is what makes the three
@@ -317,7 +328,7 @@ function parsePercentage(value) {
     if (value.charCodeAt(0) === N) {
         return 0;
     }
-    return Number.parseFloat(value) / 100;
+    return parseNumber(value) / 100;
 }
 /**
  * Accepts: "1.0", "100%", "none"
@@ -328,9 +339,9 @@ function parsePercentageOrValue(value) {
         return 0;
     }
     if (value.charCodeAt(value.length - 1) === PERCENT) {
-        return Number.parseFloat(value) / 100;
+        return parseNumber(value) / 100;
     }
-    return Number.parseFloat(value);
+    return parseNumber(value);
 }
 /**
  * Accepts: "100", "100%", "none"
@@ -341,9 +352,9 @@ function parsePercentageFor(value, range) {
         return 0;
     }
     if (value.charCodeAt(value.length - 1) === PERCENT) {
-        return (Number.parseFloat(value) / 100) * range;
+        return (parseNumber(value) / 100) * range;
     }
-    return Number.parseFloat(value);
+    return parseNumber(value);
 }
 // HSL functions
 function hueToRGB(p, q, t) {

package/esm/util/colorBits.d.ts

@@ -13,12 +13,13 @@ export type { Color } from './color-bits/index.ts';
  * rendering as the magenta invalid-color sentinel. Takes the raw value so it
  * stays dependency-free and directly testable.
  */
-export declare function featureItemRgb(raw: unknown): string | undefined;
+export declare function featureItemRgb(raw: unknown, itemRgbOn?: boolean): string | undefined;
 /**
- * The BED color a feature declares for itself, under either column name, or
- * undefined if it declares none.
+ * The BED color a feature declares for itself, under any column name, or
+ * undefined if it declares none. `itemRgbOn` reads "0,0,0" as black and a
+ * packed integer as UCSC does.
  */
-export declare function featureBedColor(feature: Feature): string | undefined;
+export declare function featureBedColor(feature: Feature, itemRgbOn?: boolean): string | undefined;
 export declare function parseCssColor(color: string | undefined | null): number;
 export declare function cssColorToNormalizedRgb(color: string): [number, number, number];
 export declare function cssColorToRgb(color: string): [number, number, number];
@@ -36,4 +37,14 @@ export declare function abgrRed(c: number): number;
 export declare function abgrGreen(c: number): number;
 export declare function abgrBlue(c: number): number;
 export declare function abgrAlpha(c: number): number;
+/** An ABGR-packed color as lowercase `#rrggbb`, its alpha dropped. */
+export declare function abgrToHex(c: number): string;
+/** Any CSS color as lowercase `#rrggbb`, its alpha dropped. */
+export declare function cssColorToHex(color: string): string;
+/** A 0..1 normalized RGB triple as lowercase `#rrggbb`. */
+export declare function normalizedRgbToHex([r, g, b]: readonly [
+    number,
+    number,
+    number
+]): string;
 export declare function cssColorToNormalizedRgba(color: string): [number, number, number, number];

package/esm/util/colorBits.js

@@ -10,13 +10,18 @@ export { alpha, blend, darken, formatHEX, formatHEXA, formatRGBA, getAlpha, getB
 // Returning magenta makes the bad slot visually obvious without breaking the
 // rest of the render.
 const INVALID_COLOR = newColor(255, 0, 255, 255);
-// UCSC's convention is that a color of "0" means "no color specified", and plain
-// BED12 files fill the column with that placeholder (often spelled as the
-// all-zero triple) rather than omitting it — every itemRgb in our own
-// volvox-bed12 fixture is "0,0,0". Honoring those literally would paint an
-// ordinary BED12 track solid black, so read them as absent. A file that really
-// wants black can say so with an explicit `color` slot.
-const BED_TRIPLE_UNSET = /^0(,0,0)?$/;
+// Plain BED12 files fill itemRgb with "0,0,0" rather than omitting it (every
+// itemRgb in the volvox-bed12 fixture is one), and UCSC ignores the column
+// unless trackDb says `itemRgb on`. So the triple reads as absent unless the
+// caller passes `itemRgbOn`. Under it, UCSC also reads a comma-free value as a
+// packed 0xRRGGBB integer, and paints 0 its track color, black by default.
+const BED_TRIPLE_UNSET = '0,0,0';
+function packedRgb(raw) {
+    const n = typeof raw === 'string' && /^\d+$/.test(raw.trim()) ? Number(raw) : raw;
+    return typeof n === 'number' && Number.isInteger(n) && n >= 0 && n <= 0xffffff
+        ? `${n >> 16},${(n >> 8) & 255},${n & 255}`
+        : undefined;
+}
 /**
  * One raw attribute value as a usable BED color, or undefined when it isn't
  * one. Deliberately strict: this feeds an *automatic* coloring path, so a value
@@ -26,11 +31,13 @@ const BED_TRIPLE_UNSET = /^0(,0,0)?$/;
  * rendering as the magenta invalid-color sentinel. Takes the raw value so it
  * stays dependency-free and directly testable.
  */
-export function featureItemRgb(raw) {
+export function featureItemRgb(raw, itemRgbOn = false) {
     const triple = typeof raw === 'string' ? bedTriple(raw) : undefined;
-    return triple !== undefined && !BED_TRIPLE_UNSET.test(triple)
-        ? triple
-        : undefined;
+    return itemRgbOn
+        ? (triple ?? packedRgb(raw))
+        : triple !== BED_TRIPLE_UNSET
+            ? triple
+            : undefined;
 }
 // The names the BED color column goes by, most specific first.
 //
@@ -51,13 +58,14 @@ export function featureItemRgb(raw) {
 // write) keeps working, and can now just be deleted.
 const BED_COLOR_FIELDS = ['itemRgb', 'reserved', 'field8'];
 /**
- * The BED color a feature declares for itself, under either column name, or
- * undefined if it declares none.
+ * The BED color a feature declares for itself, under any column name, or
+ * undefined if it declares none. `itemRgbOn` reads "0,0,0" as black and a
+ * packed integer as UCSC does.
  */
-export function featureBedColor(feature) {
+export function featureBedColor(feature, itemRgbOn = false) {
     let found;
     for (const field of BED_COLOR_FIELDS) {
-        found ??= featureItemRgb(feature.get(field));
+        found ??= featureItemRgb(feature.get(field), itemRgbOn);
     }
     return found;
 }
@@ -144,6 +152,21 @@ export function abgrBlue(c) {
 export function abgrAlpha(c) {
     return (c >>> 24) & 0xff;
 }
+function hexByte(n) {
+    return n.toString(16).padStart(2, '0');
+}
+/** An ABGR-packed color as lowercase `#rrggbb`, its alpha dropped. */
+export function abgrToHex(c) {
+    return `#${hexByte(abgrRed(c))}${hexByte(abgrGreen(c))}${hexByte(abgrBlue(c))}`;
+}
+/** Any CSS color as lowercase `#rrggbb`, its alpha dropped. */
+export function cssColorToHex(color) {
+    return abgrToHex(cssColorToABGR(color));
+}
+/** A 0..1 normalized RGB triple as lowercase `#rrggbb`. */
+export function normalizedRgbToHex([r, g, b]) {
+    return abgrToHex(normalizedRgbToABGR(r, g, b));
+}
 export function cssColorToNormalizedRgba(color) {
     const c = parseCssColor(color);
     return [

package/esm/util/colorRamp.d.ts

@@ -17,7 +17,7 @@ export declare const VIRIDIS_STOPS: readonly ColorRampStop[];
 export declare function darkAtLowEnd(scheme: ColorSchemeName): boolean;
 /**
  * #api
- * The domain a continuous colour scale spans: each end `min` or `max` pins,
+ * The domain a continuous color scale spans: each end `min` or `max` pins,
  * else the extent's, ascending, since a span has no direction and `reverse`
  * is the ramp's. An open end stops at a pinned one rather than crossing it,
  * and an extent holding no value (`[Infinity, -Infinity]`) spans [0, 1].
@@ -25,7 +25,7 @@ export declare function darkAtLowEnd(scheme: ColorSchemeName): boolean;
 export declare function rampDomain(min: number | undefined, max: number | undefined, extent: readonly [number, number]): [number, number];
 /**
  * #api
- * The stops a continuous colour scale samples: `range`'s CSS colours where it
+ * The stops a continuous color scale samples: `range`'s CSS colors where it
  * lists any, else the named `scheme`, viridis while that is unset, turned
  * round under `reverse`.
  */
@@ -53,7 +53,7 @@ export declare function sampleColorRamp(stops: readonly ColorRampStop[], t: numb
 export declare function buildColorRampLut(stops: readonly ColorRampStop[]): Uint8Array<ArrayBuffer>;
 /**
  * #api
- * A continuous colour scale's ramp as a config declares it.
+ * A continuous color scale's ramp as a config declares it.
  */
 export interface RampDeclaration {
     range?: readonly string[];

package/esm/util/colorRamp.js

@@ -90,6 +90,22 @@ const PURPLEORANGE_STOPS = [
     [179, 88, 6, 255],
     [127, 59, 8, 255],
 ];
+const REDGREYBLUE_STOPS = [
+    [199, 67, 56, 255],
+    [140, 140, 140, 255],
+    [47, 102, 176, 255],
+];
+const BLUEYELLOWRED_STOPS = [
+    [69, 117, 180, 255],
+    [116, 173, 209, 255],
+    [171, 217, 233, 255],
+    [224, 243, 248, 255],
+    [255, 255, 191, 255],
+    [254, 224, 144, 255],
+    [253, 174, 97, 255],
+    [244, 109, 67, 255],
+    [215, 48, 39, 255],
+];
 const SCHEME_STOPS = {
     viridis: VIRIDIS_STOPS,
     juicebox: JUICEBOX_STOPS,
@@ -101,6 +117,8 @@ const SCHEME_STOPS = {
     cividis: stopsFromHex(CIVIDIS_HEX_SPEC),
     redblue: REDBLUE_STOPS,
     purpleorange: PURPLEORANGE_STOPS,
+    redgreyblue: REDGREYBLUE_STOPS,
+    blueyellowred: BLUEYELLOWRED_STOPS,
 };
 function luminanceOverWhite([r, g, b, a]) {
     const over = (c) => 255 + (c - 255) * (a / 255);
@@ -118,7 +136,7 @@ export function darkAtLowEnd(scheme) {
 const EMPTY_EXTENT_DOMAIN = [0, 1];
 /**
  * #api
- * The domain a continuous colour scale spans: each end `min` or `max` pins,
+ * The domain a continuous color scale spans: each end `min` or `max` pins,
  * else the extent's, ascending, since a span has no direction and `reverse`
  * is the ramp's. An open end stops at a pinned one rather than crossing it,
  * and an extent holding no value (`[Infinity, -Infinity]`) spans [0, 1].
@@ -138,7 +156,7 @@ export function rampDomain(min, max, extent) {
 }
 /**
  * #api
- * The stops a continuous colour scale samples: `range`'s CSS colours where it
+ * The stops a continuous color scale samples: `range`'s CSS colors where it
  * lists any, else the named `scheme`, viridis while that is unset, turned
  * round under `reverse`.
  */