gosling.js 0.13.1 → 0.14.0

package/dist/src/exported-utils.d.ts

@@ -1,3 +1,5 @@
 export { getRelativeGenomicPosition, computeChromSizes, getChromInterval, getChromTotalSize, parseGenomicPosition } from './core/utils/assembly';
 export { sanitizeChrName } from './data-fetchers/utils';
+export { convertToFlatTracks as _convertToFlatTracks } from './compiler/spec-preprocess';
+export { spreadTracksByData as _spreadTracksByData } from './core/utils/overlay';
 //# sourceMappingURL=exported-utils.d.ts.map

package/dist/src/exported-utils.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"exported-utils.d.ts","sourceRoot":"","sources":["../../src/exported-utils.ts"],"names":[],"mappings":"AAAA,OAAO,EACH,0BAA0B,EAC1B,iBAAiB,EACjB,gBAAgB,EAChB,iBAAiB,EACjB,oBAAoB,EACvB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAGxD,OAAO,EAAE,mBAAmB,IAAI,oBAAoB,EAAE,MAAM,4BAA4B,CAAC;AACzF,OAAO,EAAE,kBAAkB,IAAI,mBAAmB,EAAE,MAAM,sBAAsB,CAAC"}

package/dist/src/gosling-schema/gosling.schema.d.ts

@@ -323,6 +323,23 @@ interface SingleTrackBase extends CommonTrackDef {
          * @default false
          */
         performanceMode?: boolean;
+        /**
+         * Performance rendering option.
+         * By default, certain marks ('bar', 'line', 'rect', 'area') are stretched when zooming in/out to improve
+         * rendering performance. No marks will be stretched in circular layouts.
+         *
+         * When this option is set to true, all marks will be stretched when zooming in/out.
+         * When this option is set to false, all marks will be rerendered when zooming in/out.
+         *
+         */
+        stretchGraphics?: boolean;
+        /**
+         * Threshold for stretching graphics. If the graphics are scaled larger than the threshold, then the graphic
+         * will be rerendered. If the graphics are scaled smaller than 1/threshold (e.g., 1/2), then the graphic will
+         * be rerendered. This is to prevent the graphics from being stretched too much.
+         * @default 1.5
+         */
+        stretchGraphicsThreshold?: number;
     };
     mark: Mark;
     displacement?: Displacement;

package/dist/src/gosling-schema/gosling.schema.d.ts.map

@@ -1 +1 @@
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package/dist/src/tracks/gosling-track/gosling-track.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"gosling-track.d.ts","sourceRoot":"","sources":["../../../../src/tracks/gosling-track/gosling-track.ts"],"names":[],"mappings":";AAGA,OAAO,KAAK,EACR,WAAW,EACX,aAAa,EACb,KAAK,EAIL,WAAW,EACX,KAAK,EACR,MAAM,8BAA8B,CAAC;AAGtC,OAAO,KAAK,EAAE,IAAI,IAAI,KAAK,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAK/E,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,wBAAwB,CAAC;AAoChE,eAAO,MAAM,qBAAqB,QAAQ,CAAC;AAgB3C,UAAU,mBAAmB;IACzB;;OAEG;IACH,EAAE,EAAE,MAAM,CAAC;IACX;;OAEG;IACH,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,IAAI,EAAE,WAAW,GAAG,aAAa,CAAC;IAClC,KAAK,EAAE,iBAAiB,CAAC;IACzB,iBAAiB,CAAC,EAAE,OAAO,CAAC;CAC/B;AAED,8CAA8C;AAC9C,UAAU,eAAgB,SAAQ,YAAY;IAC1C,WAAW,EAAE,KAAK,EAAE,CAAC;CACxB;AAED,wFAAwF;AACxF,MAAM,WAAW,IAAK,SAAQ,IAAI,CAAC,KAAK,EAAE,UAAU,CAAC;IACjD,QAAQ,EAAE,QAAQ,GAAG,eAAe,CAAC;CACxC;AAUD,kDAAkD;AAClD,MAAM,WAAW,eAAe;IAC5B,MAAM,EAAE,WAAW,CAAC;IACpB,KAAK,EAAE,KAAK,CAAC;CAChB;;;;;;;;AA01CD,wBAAkD"}
+{"version":3,"file":"gosling-track.d.ts","sourceRoot":"","sources":["../../../../src/tracks/gosling-track/gosling-track.ts"],"names":[],"mappings":";AAGA,OAAO,KAAK,EACR,WAAW,EACX,aAAa,EACb,KAAK,EAIL,WAAW,EACX,KAAK,EACR,MAAM,8BAA8B,CAAC;AAGtC,OAAO,KAAK,EAAE,IAAI,IAAI,KAAK,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAK/E,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,wBAAwB,CAAC;AAoChE,eAAO,MAAM,qBAAqB,QAAQ,CAAC;AAgB3C,UAAU,mBAAmB;IACzB;;OAEG;IACH,EAAE,EAAE,MAAM,CAAC;IACX;;OAEG;IACH,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,IAAI,EAAE,WAAW,GAAG,aAAa,CAAC;IAClC,KAAK,EAAE,iBAAiB,CAAC;IACzB,iBAAiB,CAAC,EAAE,OAAO,CAAC;CAC/B;AAED,8CAA8C;AAC9C,UAAU,eAAgB,SAAQ,YAAY;IAC1C,WAAW,EAAE,KAAK,EAAE,CAAC;CACxB;AAED,wFAAwF;AACxF,MAAM,WAAW,IAAK,SAAQ,IAAI,CAAC,KAAK,EAAE,UAAU,CAAC;IACjD,QAAQ,EAAE,QAAQ,GAAG,eAAe,CAAC;CACxC;AAUD,kDAAkD;AAClD,MAAM,WAAW,eAAe;IAC5B,MAAM,EAAE,WAAW,CAAC;IACpB,KAAK,EAAE,KAAK,CAAC;CAChB;;;;;;;;AA65CD,wBAAkD"}

package/dist/utils.js

@@ -1,12 +1,20 @@
-import { c, b, d, a, p, s } from "./exported-utils-068d7b17.js";
+import { ae, af, c, ab, ac, N, ad, s } from "./exported-utils-d4f1abea.js";
 import "d3-array";
 import "generic-filehandle";
+import "pixi.js";
+import "d3-color";
+import "bezier-js";
+import "d3-scale";
+import "lodash-es";
+import "d3-scale-chromatic";
 export {
+  ae as _convertToFlatTracks,
+  af as _spreadTracksByData,
   c as computeChromSizes,
-  b as getChromInterval,
-  d as getChromTotalSize,
-  a as getRelativeGenomicPosition,
-  p as parseGenomicPosition,
+  ab as getChromInterval,
+  ac as getChromTotalSize,
+  N as getRelativeGenomicPosition,
+  ad as parseGenomicPosition,
   s as sanitizeChrName
 };
 //# sourceMappingURL=utils.js.map

package/dist/utils.js.map

@@ -1 +1 @@
-{"version":3,"file":"utils.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;;"}
+{"version":3,"file":"utils.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;"}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "gosling.js",
   "author": "Sehi L'Yi",
-  "version": "0.13.1",
+  "version": "0.14.0",
   "license": "MIT",
   "repository": {
     "type": "git",
@@ -105,7 +105,6 @@
     "eslint-plugin-prettier": "^4.2.1",
     "eslint-plugin-react": "^7.30.1",
     "fetch-jsonp": "^1.1.3",
-    "gh-pages": "^3.1.0",
     "jsdom": "^19.0.0",
     "jsoncrush": "^1.1.6",
     "knip": "^2.30.0",
@@ -158,8 +157,6 @@
     "coverage": "vitest run --coverage",
     "format": "eslint src/ editor/ --fix && prettier 'editor/**/*.css' --write",
     "schema": "node scripts/generate-schemas.mjs",
-    "predeploy": "pnpm build-editor; echo \"gosling.js.org\" >> build/CNAME",
-    "deploy": "gh-pages -d build",
     "version": "conventional-changelog -p angular -i CHANGELOG.md -s && git add CHANGELOG.md",
     "knip": "knip --config knip.config.json",
     "e2e": "playwright test",

package/dist/exported-utils-068d7b17.js

@@ -1,438 +0,0 @@
-var __defProp = Object.defineProperty;
-var __defNormalProp = (obj, key, value) => key in obj ? __defProp(obj, key, { enumerable: true, configurable: true, writable: true, value }) : obj[key] = value;
-var __publicField = (obj, key, value) => {
-  __defNormalProp(obj, typeof key !== "symbol" ? key + "" : key, value);
-  return value;
-};
-import { bisector } from "d3-array";
-import { RemoteFile as RemoteFile$1 } from "generic-filehandle";
-const CHROM_SIZE_HG38 = {
-  chr1: 248956422,
-  chr2: 242193529,
-  chr3: 198295559,
-  chr4: 190214555,
-  chr5: 181538259,
-  chr6: 170805979,
-  chr7: 159345973,
-  chr8: 145138636,
-  chr9: 138394717,
-  chr10: 133797422,
-  chr11: 135086622,
-  chr12: 133275309,
-  chr13: 114364328,
-  chr14: 107043718,
-  chr15: 101991189,
-  chr16: 90338345,
-  chr17: 83257441,
-  chr18: 80373285,
-  chr19: 58617616,
-  chr20: 64444167,
-  chr21: 46709983,
-  chr22: 50818468,
-  chrX: 156040895,
-  chrY: 57227415
-};
-const CHROM_SIZE_HG19 = {
-  chr1: 249250621,
-  chr2: 243199373,
-  chr3: 198022430,
-  chr4: 191154276,
-  chr5: 180915260,
-  chr6: 171115067,
-  chr7: 159138663,
-  chr8: 146364022,
-  chr9: 141213431,
-  chr10: 135534747,
-  chr11: 135006516,
-  chr12: 133851895,
-  chr13: 115169878,
-  chr14: 107349540,
-  chr15: 102531392,
-  chr16: 90354753,
-  chr17: 81195210,
-  chr18: 78077248,
-  chr19: 59128983,
-  chr20: 63025520,
-  chr21: 48129895,
-  chr22: 51304566,
-  chrX: 155270560,
-  chrY: 59373566,
-  chrM: 16571
-};
-const CHROM_SIZE_HG18 = {
-  chr1: 247249719,
-  chr2: 242951149,
-  chr3: 199501827,
-  chr4: 191273063,
-  chr5: 180857866,
-  chr6: 170899992,
-  chr7: 158821424,
-  chr8: 146274826,
-  chr9: 140273252,
-  chr10: 135374737,
-  chr11: 134452384,
-  chr12: 132349534,
-  chr13: 114142980,
-  chr14: 106368585,
-  chr15: 100338915,
-  chr16: 88827254,
-  chr17: 78774742,
-  chr18: 76117153,
-  chr19: 63811651,
-  chr20: 62435964,
-  chr21: 46944323,
-  chr22: 49691432,
-  chrX: 154913754,
-  chrY: 57772954,
-  chrM: 16571
-};
-const CHROM_SIZE_HG17 = {
-  chr1: 245522847,
-  chr2: 243018229,
-  chr3: 199505740,
-  chr4: 191411218,
-  chr5: 180857866,
-  chr6: 170975699,
-  chr7: 158628139,
-  chr8: 146274826,
-  chr9: 138429268,
-  chr10: 135413628,
-  chr11: 134452384,
-  chr12: 132449811,
-  chr13: 114142980,
-  chr14: 106368585,
-  chr15: 100338915,
-  chr16: 88827254,
-  chr17: 78774742,
-  chr18: 76117153,
-  chr19: 63811651,
-  chr20: 62435964,
-  chr21: 46944323,
-  chr22: 49554710,
-  chrX: 154824264,
-  chrY: 57701691,
-  chrM: 16571
-};
-const CHROM_SIZE_HG16 = {
-  chr1: 246127941,
-  chr2: 243615958,
-  chr3: 199344050,
-  chr4: 191731959,
-  chr5: 181034922,
-  chr6: 170914576,
-  chr7: 158545518,
-  chr8: 146308819,
-  chr9: 136372045,
-  chr10: 135037215,
-  chr11: 134482954,
-  chr12: 132078379,
-  chr13: 113042980,
-  chr14: 105311216,
-  chr15: 100256656,
-  chr16: 90041932,
-  chr17: 81860266,
-  chr18: 76115139,
-  chr19: 63811651,
-  chr20: 63741868,
-  chr21: 46976097,
-  chr22: 49396972,
-  chrX: 153692391,
-  chrY: 50286555,
-  chrM: 16571
-};
-const CHROM_SIZE_MM10 = {
-  chr1: 195471971,
-  chr2: 182113224,
-  chr3: 160039680,
-  chr4: 156508116,
-  chr5: 151834684,
-  chr6: 149736546,
-  chr7: 145441459,
-  chr8: 129401213,
-  chr9: 124595110,
-  chr10: 130694993,
-  chr11: 122082543,
-  chr12: 120129022,
-  chr13: 120421639,
-  chr14: 124902244,
-  chr15: 104043685,
-  chr16: 98207768,
-  chr17: 94987271,
-  chr18: 90702639,
-  chr19: 61431566,
-  chrX: 171031299,
-  chrY: 91744698,
-  chrM: 16299
-};
-const CHROM_SIZE_MM9 = {
-  chr1: 197195432,
-  chr2: 181748087,
-  chr3: 159599783,
-  chr4: 155630120,
-  chr5: 152537259,
-  chr6: 149517037,
-  chr7: 152524553,
-  chr8: 131738871,
-  chr9: 124076172,
-  chr10: 129993255,
-  chr11: 121843856,
-  chr12: 121257530,
-  chr13: 120284312,
-  chr14: 125194864,
-  chr15: 103494974,
-  chr16: 98319150,
-  chr17: 95272651,
-  chr18: 90772031,
-  chr19: 61342430,
-  chrX: 166650296,
-  chrY: 15902555,
-  chrM: 16299
-};
-function getRelativeGenomicPosition(absPos, assembly, returnWithinAssembly = false) {
-  const chrSizes = Object.entries(computeChromSizes(assembly).interval);
-  const minPosChr = { chromosome: "unknown", position: Infinity };
-  const maxPosChr = { chromosome: "unknown", position: 0 };
-  for (const chrSize of chrSizes) {
-    const [chromosome, absInterval] = chrSize;
-    const [start, end] = absInterval;
-    if (start <= absPos && absPos < end) {
-      return { chromosome, position: absPos - start };
-    }
-    if (start < minPosChr.position) {
-      minPosChr.chromosome = chromosome;
-      minPosChr.position = start;
-    }
-    if (end > maxPosChr.position) {
-      maxPosChr.chromosome = chromosome;
-      maxPosChr.position = end;
-    }
-  }
-  if (returnWithinAssembly) {
-    if (absPos < minPosChr.position) {
-      return minPosChr;
-    } else {
-      return maxPosChr;
-    }
-  } else {
-    return { chromosome: "unknown", position: absPos };
-  }
-}
-function createChromSizesUrl(chromSizes) {
-  const text = chromSizes.map((d) => d.join("	")).join("\n");
-  const tsv = new Blob([text], { type: "text/tsv" });
-  return URL.createObjectURL(tsv);
-}
-function computeChromSizes(assembly) {
-  if (assembly && typeof assembly === "string" && assembly in CRHOM_SIZES) {
-    return CRHOM_SIZES[assembly];
-  } else if (Array.isArray(assembly) && assembly.length !== 0) {
-    const size = Object.fromEntries(assembly);
-    return {
-      size,
-      interval: getChromInterval(size),
-      total: getChromTotalSize(size),
-      path: createChromSizesUrl(assembly)
-    };
-  } else {
-    return CRHOM_SIZES.hg38;
-  }
-}
-const basePath = (assembly) => `https://s3.amazonaws.com/gosling-lang.org/data/${assembly}.chrom.sizes`;
-const CRHOM_SIZES = Object.freeze({
-  hg38: {
-    size: CHROM_SIZE_HG38,
-    interval: getChromInterval(CHROM_SIZE_HG38),
-    total: getChromTotalSize(CHROM_SIZE_HG38),
-    path: basePath("hg38")
-  },
-  hg19: {
-    size: CHROM_SIZE_HG19,
-    interval: getChromInterval(CHROM_SIZE_HG19),
-    total: getChromTotalSize(CHROM_SIZE_HG19),
-    path: basePath("hg19")
-  },
-  hg18: {
-    size: CHROM_SIZE_HG18,
-    interval: getChromInterval(CHROM_SIZE_HG18),
-    total: getChromTotalSize(CHROM_SIZE_HG18),
-    path: basePath("hg18")
-  },
-  hg17: {
-    size: CHROM_SIZE_HG17,
-    interval: getChromInterval(CHROM_SIZE_HG17),
-    total: getChromTotalSize(CHROM_SIZE_HG17),
-    path: basePath("hg17")
-  },
-  hg16: {
-    size: CHROM_SIZE_HG16,
-    interval: getChromInterval(CHROM_SIZE_HG16),
-    total: getChromTotalSize(CHROM_SIZE_HG16),
-    path: basePath("hg16")
-  },
-  mm10: {
-    size: CHROM_SIZE_MM10,
-    interval: getChromInterval(CHROM_SIZE_MM10),
-    total: getChromTotalSize(CHROM_SIZE_MM10),
-    path: basePath("mm10")
-  },
-  mm9: {
-    size: CHROM_SIZE_MM9,
-    interval: getChromInterval(CHROM_SIZE_MM9),
-    total: getChromTotalSize(CHROM_SIZE_MM9),
-    path: basePath("mm9")
-  },
-  // `unknown` assembly contains only one chromosome with max length
-  unknown: {
-    size: { chr: Number.MAX_VALUE },
-    interval: { chr: [0, Number.MAX_VALUE] },
-    total: Number.MAX_VALUE,
-    path: basePath("hg38")
-    // just to ensure this does not make crash
-  }
-});
-function getAutoCompleteId(assembly) {
-  switch (assembly) {
-    case "hg19":
-      return "OHJakQICQD6gTD7skx4EWA";
-    case "mm10":
-      return "QDutvmyiSrec5nX4pA5WGQ";
-    case "mm9":
-      return "GUm5aBiLRCyz2PsBea7Yzg";
-    case "hg38":
-    default:
-      return "P0PLbQMwTYGy-5uPIQid7A";
-  }
-}
-function getChromInterval(chromSize) {
-  const interval = {};
-  Object.keys(chromSize).reduce((sum, k) => {
-    interval[k] = [sum, sum + chromSize[k]];
-    return sum + chromSize[k];
-  }, 0);
-  return interval;
-}
-function getChromTotalSize(chromSize) {
-  return Object.values(chromSize).reduce((sum, current) => sum + current, 0);
-}
-function parseGenomicPosition(position) {
-  const [chromosome, intervalString] = position.split(":");
-  if (intervalString) {
-    const [start, end] = intervalString.split("-").map((s) => +s.replace(/,/g, ""));
-    if (!Number.isNaN(start) && !Number.isNaN(end)) {
-      return { chromosome, start, end };
-    }
-  }
-  return { chromosome };
-}
-class GenomicPositionHelper {
-  constructor(chromosome, start, end) {
-    this.chromosome = chromosome;
-    this.start = start;
-    this.end = end;
-  }
-  static fromString(str) {
-    const result = parseGenomicPosition(str);
-    return new GenomicPositionHelper(result.chromosome, result.start, result.end);
-  }
-  toAbsoluteCoordinates(assembly, padding = 0) {
-    const info = computeChromSizes(assembly);
-    const size = info.size[this.chromosome];
-    const interval = info.interval[this.chromosome];
-    if (size === void 0 || interval === void 0) {
-      throw new Error(`Chromosome name ${this.chromosome} is not valid`);
-    }
-    let { start, end } = this;
-    if (start === void 0 || end === void 0) {
-      [start, end] = [1, size];
-    }
-    const offset = interval[0];
-    return [start + offset - padding, end + offset + padding];
-  }
-}
-function filterUsingGenoPos(data, [minX, maxX], config) {
-  const { x, xe, x1, x1e } = config;
-  const definedXFields = [x, xe, x1, x1e].filter((f) => f);
-  return data.filter((d) => {
-    if (definedXFields.length === 0) {
-      return true;
-    } else if (definedXFields.length === 1) {
-      const value = +d[definedXFields[0]];
-      return typeof value === "number" && minX < value && value <= maxX;
-    } else {
-      const values = definedXFields.map((f) => +d[f]).filter((v) => !isNaN(v));
-      const minValue = Math.min(...values);
-      const maxValue = Math.max(...values);
-      return minX <= maxValue && minValue <= maxX;
-    }
-  });
-}
-bisector((d) => d.pos).left;
-function sanitizeChrName(chrName, assembly, chromosomePrefix) {
-  if (Array.isArray(assembly)) {
-    return chrName;
-  }
-  if (chromosomePrefix) {
-    chrName = chrName.replace(chromosomePrefix, "chr");
-  } else if (!chrName.includes("chr")) {
-    chrName = `chr${chrName}`;
-  }
-  return chrName;
-}
-class RemoteFile extends RemoteFile$1 {
-  constructor() {
-    super(...arguments);
-    // Overrides `read` to eagerly read 200 or 206 response
-    // from https://github.com/GMOD/generic-filehandle/blob/0e8209be25e3097307bd15e964edd8c017e808d7/src/remoteFile.ts#L100-L162
-    __publicField(this, "read", async (buffer, offset = 0, length, position = 0, opts = {}) => {
-      const { headers = {}, signal, overrides = {} } = opts;
-      if (length < Infinity) {
-        headers.range = `bytes=${position}-${position + length}`;
-      } else if (length === Infinity && position !== 0) {
-        headers.range = `bytes=${position}-`;
-      }
-      const args = {
-        // @ts-expect-error private property
-        ...this.baseOverrides,
-        ...overrides,
-        headers: {
-          ...headers,
-          ...overrides.headers,
-          // @ts-expect-error private property
-          ...this.baseOverrides.headers
-        },
-        method: "GET",
-        redirect: "follow",
-        mode: "cors",
-        signal
-      };
-      const response = await this.fetch(this.url, args);
-      if (!response.ok) {
-        throw new Error(`HTTP ${response.status} ${response.statusText} ${this.url}`);
-      }
-      if (response.status === 200 || response.status === 206) {
-        const responseData = await this.getBufferFromResponse(response);
-        const bytesCopied = responseData.copy(buffer, offset, 0, Math.min(length, responseData.length));
-        const res = response.headers.get("content-range");
-        const sizeMatch = /\/(\d+)$/.exec(res || "");
-        if (sizeMatch && sizeMatch[1]) {
-          this._stat = { size: parseInt(sizeMatch[1], 10) };
-        }
-        return { bytesRead: bytesCopied, buffer };
-      }
-      throw new Error(`HTTP ${response.status} fetching ${this.url}`);
-    });
-  }
-}
-export {
-  GenomicPositionHelper as G,
-  RemoteFile as R,
-  getRelativeGenomicPosition as a,
-  getChromInterval as b,
-  computeChromSizes as c,
-  getChromTotalSize as d,
-  filterUsingGenoPos as f,
-  getAutoCompleteId as g,
-  parseGenomicPosition as p,
-  sanitizeChrName as s
-};
-//# sourceMappingURL=exported-utils-068d7b17.js.map