@genome-spy/core 0.52.0 → 0.53.1

package/dist/src/utils/cloner.js

@@ -8,12 +8,12 @@
  *
  * @param {T} template The template object that
  * @returns {(function(T):T) & { properties: string[] }}
- * @template T
+ * @template {object} [T=object]
  */
 export default function createCloner(template) {
     // TODO: Check that only properties, not methods get cloned
     const properties = /** @type {string[]} */ (
-        Object.keys(template).filter((k) => typeof k == "string")
+        getAllProperties(template).filter((k) => typeof k == "string")
     );
 
     const cloner = /** @type {(function(T):T) & { properties: string[] }} */ (
@@ -32,3 +32,20 @@ export default function createCloner(template) {
 
     return cloner;
 }
+
+/**
+ * Needed for proxied Apache Arrow tables.
+ *
+ * @param {object} obj
+ */
+export function getAllProperties(obj) {
+    /** @type {string[]} */
+    let props = [];
+    do {
+        props = props.concat(Object.keys(obj));
+        obj = Object.getPrototypeOf(obj);
+    } while (obj && obj !== Object.prototype); // Traverse until the end of the prototype chain
+
+    const uniqueProps = Array.from(new Set(props));
+    return uniqueProps;
+}

package/dist/src/utils/cloner.test.js

@@ -1,10 +1,11 @@
 import { expect, test } from "vitest";
-import createCloner from "./cloner.js";
+import createCloner, { getAllProperties } from "./cloner.js";
 
 const template = {
+    1: "iddqd",
     a: 1,
-    b: "xyzzy",
-    3: "iddqd",
+    c: "xyzzy",
+    b: "idclip",
 };
 
 test("Cloner clones object properly", () => {
@@ -14,11 +15,21 @@ test("Cloner clones object properly", () => {
     expect(makeClone(template)).not.toBe(template);
 
     const another = {
+        1: "hello",
         a: 2,
-        b: "idkfa",
-        3: "hello",
+        c: "idkfa",
+        b: "idclip",
     };
 
     expect(makeClone(another)).toEqual(another);
     expect(makeClone(another)).not.toBe(another);
 });
+
+test("getAllProperties", () => {
+    expect(getAllProperties(template)).toEqual(["1", "a", "c", "b"]);
+
+    const obj = Object.create(template);
+    obj.d = 42;
+
+    expect(getAllProperties(obj)).toEqual(["d", "1", "a", "c", "b"]);
+});

package/dist/src/utils/expression.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"expression.d.ts","sourceRoot":"","sources":["../../../src/utils/expression.js"],"names":[],"mappings":"AA2DA;;;;;;;;;;GAUG;AACH,6CAHW,MAAM,sBACJ,kBAAkB,CAgC9B;;YAvCU,MAAM,EAAE;aACR,MAAM,EAAE;UACR,MAAM;;2CAEO,OAAO,qBAAqB,EAAE,KAAK,KAAK,GAAG"}
+{"version":3,"file":"expression.d.ts","sourceRoot":"","sources":["../../../src/utils/expression.js"],"names":[],"mappings":"AA2DA;;;;;;;;;;GAUG;AACH,6CAHW,MAAM,sBACJ,kBAAkB,CAgC9B;;YAvCU,MAAM,EAAE;aACR,MAAM,EAAE;UACR,MAAM;;iCAEH,CAAC,CAAC,KAAK,CAAC,EAAE,OAAO,qBAAqB,EAAE,KAAK,KAAK,GAAG,CAAC,GAAG,eAAe"}

package/dist/src/utils/ui/tooltip.d.ts

@@ -17,7 +17,7 @@ export default class Tooltip {
     /**
      * @param {boolean} visible
      */
-    set visible(arg: boolean);
+    set visible(visible: boolean);
     get visible(): boolean;
     get enabled(): boolean;
     /**

package/dist/src/utils/ui/tooltip.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"tooltip.d.ts","sourceRoot":"","sources":["../../../../src/utils/ui/tooltip.js"],"names":[],"mappings":"AAIA,gEAAiE;AAEjE;IACI;;OAEG;IACH,uBAFW,WAAW,EAsBrB;IAnBG,uBAA0B;IAE1B,wBAA4C;IAE5C,kBAAoB;IAGpB,kBAAkB;IAClB,uBADW,GAAG,CACwB;IAEtC,wBAA0B;IAE1B,sBAAsB;IACtB,+BAA+B;IAC/B,aADW,CAAC,MAAM,EAAE,MAAM,CAAC,CACC;IAE5B,sBAAsB;IAK1B;;OAEG;IACH,0BAKC;IAED,uBAEC;IAED,uBAEC;IAED;;OAEG;IACH,0BAFW,OAAO,QAOjB;IAED,wBAEC;IAED;;OAEG;IACH,4BAFW,UAAU,QAkCpB;IA/BG,8BAA0D;IAiC9D,wBAiBC;IAED;;OAEG;IACH,oBAFW,MAAM,GAAG,OAAO,KAAK,EAAE,cAAc,GAAG,WAAW,QAiB7D;IAED,cAGC;IAED;;;;;;;OAOG;IACH,sDAHuB,QAAQ,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAmBlF;IAED,sBAEC;CACJ"}
+{"version":3,"file":"tooltip.d.ts","sourceRoot":"","sources":["../../../../src/utils/ui/tooltip.js"],"names":[],"mappings":"AAIA,gEAAiE;AAEjE;IACI;;OAEG;IACH,uBAFW,WAAW,EAsBrB;IAnBG,uBAA0B;IAE1B,wBAA4C;IAE5C,kBAAoB;IAGpB,kBAAkB;IAClB,uBADW,GAAG,CACwB;IAEtC,wBAA0B;IAE1B,sBAAsB;IACtB,+BAA+B;IAC/B,aADW,CAAC,MAAM,EAAE,MAAM,CAAC,CACC;IAE5B,sBAAsB;IAK1B;;OAEG;IACH,8BAKC;IAED,uBAEC;IAED,uBAEC;IAED;;OAEG;IACH,0BAFW,OAAO,QAOjB;IAED,wBAEC;IAED;;OAEG;IACH,4BAFW,UAAU,QAkCpB;IA/BG,8BAA0D;IAiC9D,wBAiBC;IAED;;OAEG;IACH,oBAFW,MAAM,GAAG,OAAO,KAAK,EAAE,cAAc,GAAG,WAAW,QAiB7D;IAED,cAGC;IAED;;;;;;;OAOG;IACH,sDAHuB,QAAQ,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAmBlF;IAED,sBAEC;CACJ"}

package/dist/src/view/paramMediator.d.ts

@@ -140,7 +140,7 @@ export default class ParamMediator {
  * TODO: The proposed JavaScript signals may provide a better way to implement this.
  * https://github.com/proposal-signals/proposal-signals
  */
-export type ExprRefFunction = ((datum?: import("../data/flowNode.js").Datum) => any) & import("../utils/expression.js").ExpressionProps & {
+export type ExprRefFunction = import("../utils/expression.js").ExpressionFunction & {
     addListener: (listener: () => void) => void;
     invalidate: () => void;
     identifier: () => string;

package/dist/src/view/paramMediator.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"paramMediator.d.ts","sourceRoot":"","sources":["../../../src/view/paramMediator.js"],"names":[],"mappings":"AAoUA;;;GAGG;AACH,6BAHW,GAAG,+CAKb;AAED;;;;;;;GAOG;AACH,oFASC;AAED;;;GAGG;AACH,gJAEC;AAED;;;GAGG;AACH,gMAEC;AAED;;;;;;;;;;GAUG;AACH,mFANW,aAAa,+CAEW,IAAI,KAwCtC;AAED;;;;;;GAMG;AACH,4CAHW,MAAM,GACJ,MAAM,CAUlB;AAED;;;;;;;GAOG;AACH,2CAHW,GAAG,GACD,eAAe,CAW3B;AA9bD;;;;;;;;GAQG;AACH;IA2BI;;;;;OAKG;IACH,2BALW,MAAM,aAAa,EAU7B;IA7BD;;;OAGG;IACH,0BAHU,IAAI,MAAM,EAAE,IAAI,MAAM,IAAI,CAAC,CAAC,CAGvB;IA2Bf;;;OAGG;IACH,wEAzCqB,GAAG,KAAK,IAAI,CAmGhC;IAED;;;;;;;OAOG;IACH,6BANW,MAAM,6BAEN,OAAO,iBACS,IAAI,CAgC9B;IAED;;;OAGG;IACH,qBAFW,MAAM,WAlIc,GAAG,KAAK,IAAI,CA0I1C;IAED;;;OAGG;IACH,oBAFW,MAAM,OAIhB;IAED;;;OAGG;IACH,qBAFW,MAAM,OAKhB;IAED;;OAEG;IACH,kFAIC;IAED;;;;OAIG;IACH,gCAHW,MAAM,GACJ,aAAa,CAQzB;IAID;;;;OAIG;IACH,uBAFW,MAAM,mBA4EhB;IAED;;;;OAIG;IACH,qBAFW,MAAM,OAKhB;IAED;;;;;OAKG;IACH,sBAFa,OAAO,CAiBnB;;CACJ;;;;;;;;;4BAvT4F,MAAM,IAAI,KAAK,IAAI;gBAAc,MAAM,IAAI;gBAAc,MAAM,MAAM"}
+{"version":3,"file":"paramMediator.d.ts","sourceRoot":"","sources":["../../../src/view/paramMediator.js"],"names":[],"mappings":"AAoUA;;;GAGG;AACH,6BAHW,GAAG,+CAKb;AAED;;;;;;;GAOG;AACH,oFASC;AAED;;;GAGG;AACH,gJAEC;AAED;;;GAGG;AACH,gMAEC;AAED;;;;;;;;;;GAUG;AACH,mFANW,aAAa,+CAEW,IAAI,KAwCtC;AAED;;;;;;GAMG;AACH,4CAHW,MAAM,GACJ,MAAM,CAUlB;AAED;;;;;;;GAOG;AACH,2CAHW,GAAG,GACD,eAAe,CAW3B;AA9bD;;;;;;;;GAQG;AACH;IA2BI;;;;;OAKG;IACH,2BALW,MAAM,aAAa,EAU7B;IA7BD;;;OAGG;IACH,0BAHU,IAAI,MAAM,EAAE,IAAI,MAAM,IAAI,CAAC,CAAC,CAGvB;IA2Bf;;;OAGG;IACH,wEAzCqB,GAAG,KAAK,IAAI,CAmGhC;IAED;;;;;;;OAOG;IACH,6BANW,MAAM,6BAEN,OAAO,iBACS,IAAI,CAgC9B;IAED;;;OAGG;IACH,qBAFW,MAAM,WAlIc,GAAG,KAAK,IAAI,CA0I1C;IAED;;;OAGG;IACH,oBAFW,MAAM,OAIhB;IAED;;;OAGG;IACH,qBAFW,MAAM,OAKhB;IAED;;OAEG;IACH,kFAIC;IAED;;;;OAIG;IACH,gCAHW,MAAM,GACJ,aAAa,CAQzB;IAID;;;;OAIG;IACH,uBAFW,MAAM,mBA4EhB;IAED;;;;OAIG;IACH,qBAFW,MAAM,OAKhB;IAED;;;;;OAKG;IACH,sBAFa,OAAO,CAiBnB;;CACJ;;;;;;;;8BAvTY,OAAO,wBAAwB,EAAE,kBAAkB,GAAG;IAAE,WAAW,EAAE,CAAC,QAAQ,EAAE,MAAM,IAAI,KAAK,IAAI,CAAC;IAAC,UAAU,EAAE,MAAM,IAAI,CAAC;IAAC,UAAU,EAAE,MAAM,MAAM,CAAA;CAAC"}

package/dist/src/view/scaleResolution.d.ts

@@ -126,6 +126,15 @@ export default class ScaleResolution implements ScaleResolutionApi {
      * be generalized to other quantitative channels such as color, opacity, size, etc.
      */
     getZoomLevel(): number;
+    /**
+     * Returns the length of the axis in pixels. Chooses the smallest of the views.
+     * They should all be the same, but some exotic configuration might break that assumption.
+     *
+     * This method is needed because positional channels have unit ranges and the
+     * length of the axis is not directly available from the scale. Ideally, ranges would
+     * be configured as pixels, but that is yet to be materialized.
+     */
+    getAxisLength(): number;
     /**
      *
      * @returns {import("../genome/genome.js").default}

package/dist/src/view/scaleResolution.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scaleResolution.d.ts","sourceRoot":"","sources":["../../../src/view/scaleResolution.js"],"names":[],"mappings":"AAg7BA;;;;;;;;;;GAUG;AACH,6CAFW,OAAO,WAAW,EAAE,OAAO,GAAG,OAAO,WAAW,EAAE,OAAO,EAAE,QA4BrE;AAx6BD,0CAA2C;AAC3C,gCAAiC;AACjC,gCAAiC;AACjC,4BAA6B;AAC7B,4BAA6B;AAE7B;;;;;;;;GAQG;AACH;;;;;;;GAOG;AACH;IAyCI;;OAEG;IACH,2DASC;IARG,8CAAsB;IACtB,yDAAyD;IACzD,SADW,qBAAqB,EAAE,CACjB;IACjB,0FAA0F;IAC1F,MADW,OAAO,oBAAoB,EAAE,IAAI,CAC5B;IAEhB,iEAAiE;IACjE,MADW,MAAM,CACI;IAWzB;;;;;;;OAOG;IACH,4KAEC;IAED;;;OAGG;IACH,+KAEC;IAcD;;;;;OAKG;IACH,qBAFW,qBAAqB,QA4B/B;IA8MD;;;;OAIG;IACH,+DAOC;IAED;;OAEG;IACH,oBAyCC;IAED;;OAEG;IACH;eA5XkC,OAAO,kBAAkB,EAAE,KAAK;MAwajE;IAED,mBAEC;IAED;;OAEG;IACH,oBAFa,mFAA6B,CAOzC;IAED;;;;OAIG;IACH,oBAKC;IAED;;OAEG;IACH,sBAGC;IAUD;;;;;;;OAOG;IACH,kBALW,MAAM,eACN,MAAM,OACN,MAAM,GACJ,OAAO,CAwEnB;IAED;;;;;;OAMG;IACH,eAJW,mFAA6B,aAC7B,OAAO,GAAG,MAAM,iBA0D1B;IAED;;;;OAIG;IACH,qBAcC;IAED;;;;;OAKG;IACH,uBAOC;IA8DD;;;OAGG;IACH,aAFa,OAAO,qBAAqB,EAAE,OAAO,CAajD;IAID;;;;;OAKG;IACH,uBAFW,MAAM,yDAUhB;IAED;;OAEG;IACH,iBAFW,MAAM,yDAKhB;IAED;;;OAGG;IACH,6EAFa,MAAM,CAQlB;IAED;;;OAGG;IACH,mHAFa,MAAM,EAAE,CAOpB;;CACJ;;;;;UAlyBS,OAAO,eAAe,EAAE,OAAO;aAC/B,CAAC;gBACD,OAAO,oBAAoB,EAAE,mBAAmB;qFACd,OAAO,oBAAoB,EAAE,IAAI"}
+{"version":3,"file":"scaleResolution.d.ts","sourceRoot":"","sources":["../../../src/view/scaleResolution.js"],"names":[],"mappings":"AA88BA;;;;;;;;;;GAUG;AACH,6CAFW,OAAO,WAAW,EAAE,OAAO,GAAG,OAAO,WAAW,EAAE,OAAO,EAAE,QA4BrE;AAt8BD,0CAA2C;AAC3C,gCAAiC;AACjC,gCAAiC;AACjC,4BAA6B;AAC7B,4BAA6B;AAE7B;;;;;;;;GAQG;AACH;;;;;;;GAOG;AACH;IAyCI;;OAEG;IACH,2DASC;IARG,8CAAsB;IACtB,yDAAyD;IACzD,SADW,qBAAqB,EAAE,CACjB;IACjB,0FAA0F;IAC1F,MADW,OAAO,oBAAoB,EAAE,IAAI,CAC5B;IAEhB,iEAAiE;IACjE,MADW,MAAM,CACI;IAWzB;;;;;;;OAOG;IACH,4KAEC;IAED;;;OAGG;IACH,+KAEC;IAcD;;;;;OAKG;IACH,qBAFW,qBAAqB,QA4B/B;IA8MD;;;;OAIG;IACH,+DAOC;IAED;;OAEG;IACH,oBAyCC;IAED;;OAEG;IACH;eA5XkC,OAAO,kBAAkB,EAAE,KAAK;MAwajE;IAED,mBAEC;IAED;;OAEG;IACH,oBAFa,mFAA6B,CAOzC;IAED;;;;OAIG;IACH,oBAKC;IAED;;OAEG;IACH,sBAGC;IAUD;;;;;;;OAOG;IACH,kBALW,MAAM,eACN,MAAM,OACN,MAAM,GACJ,OAAO,CAwEnB;IAED;;;;;;OAMG;IACH,eAJW,mFAA6B,aAC7B,OAAO,GAAG,MAAM,iBA0D1B;IAED;;;;OAIG;IACH,qBAcC;IAED;;;;;OAKG;IACH,uBAOC;IAED;;;;;;;OAOG;IACH,wBAoBC;IA8DD;;;OAGG;IACH,aAFa,OAAO,qBAAqB,EAAE,OAAO,CAajD;IAID;;;;;OAKG;IACH,uBAFW,MAAM,yDAUhB;IAED;;OAEG;IACH,iBAFW,MAAM,yDAKhB;IAED;;;OAGG;IACH,6EAFa,MAAM,CAQlB;IAED;;;OAGG;IACH,mHAFa,MAAM,EAAE,CAOpB;;CACJ;;;;;UAh0BS,OAAO,eAAe,EAAE,OAAO;aAC/B,CAAC;gBACD,OAAO,oBAAoB,EAAE,mBAAmB;qFACd,OAAO,oBAAoB,EAAE,IAAI"}

package/dist/src/view/scaleResolution.js

@@ -730,6 +730,36 @@ export default class ScaleResolution {
         return 1.0;
     }
 
+    /**
+     * Returns the length of the axis in pixels. Chooses the smallest of the views.
+     * They should all be the same, but some exotic configuration might break that assumption.
+     *
+     * This method is needed because positional channels have unit ranges and the
+     * length of the axis is not directly available from the scale. Ideally, ranges would
+     * be configured as pixels, but that is yet to be materialized.
+     */
+    getAxisLength() {
+        if (this.channel !== "x" && this.channel !== "y") {
+            throw new Error(
+                "Axis length is only defined for x and y channels!"
+            );
+        }
+
+        // Here's a problem: if the view has been hidden, it may have stale coords.
+        // TODO: They should be cleared when the layout is invalidated.
+        // Alternatively, scale ranges could be set in pixels.
+        const lengths = this.members
+            .map(
+                (m) =>
+                    m.view.coords?.[this.channel === "x" ? "width" : "height"]
+            )
+            .filter((len) => len > 0);
+
+        return lengths.length
+            ? lengths.reduce((a, b) => Math.min(a, b), 10000)
+            : 0;
+    }
+
     #getZoomExtent() {
         const props = this.scale.props;
         const zoom = props.zoom;

package/dist/src/view/zoom.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"zoom.d.ts","sourceRoot":"","sources":["../../../src/view/zoom.js"],"names":[],"mappings":"AAkBA,0CAGC;AAgBD;;;;;;GAMG;AACH,yCANW,OAAO,8BAA8B,EAAE,OAAO,UAC9C,OAAO,uBAAuB,EAAE,OAAO,0BAC3B,SAAS,KAAK,IAAI,UAC9B,OAAO,yBAAyB,EAAE,KAAK,aACvC,OAAO,sBAAsB,EAAE,OAAO,QAkJhD;;OA1LS,MAAM;OACN,MAAM;YACN,MAAM;YACN,MAAM;YACN,MAAM"}
+{"version":3,"file":"zoom.d.ts","sourceRoot":"","sources":["../../../src/view/zoom.js"],"names":[],"mappings":"AAkBA,0CAGC;AAgBD;;;;;;GAMG;AACH,yCANW,OAAO,8BAA8B,EAAE,OAAO,UAC9C,OAAO,uBAAuB,EAAE,OAAO,cACvC,CAAC,SAAS,EAAE,SAAS,KAAK,IAAI,UAC9B,OAAO,yBAAyB,EAAE,KAAK,aACvC,OAAO,sBAAsB,EAAE,OAAO,QAkJhD;;OA1LS,MAAM;OACN,MAAM;YACN,MAAM;YACN,MAAM;YACN,MAAM"}

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.52.0",
+  "version": "0.53.1",
   "jsdelivr": "dist/bundle/index.js",
   "unpkg": "dist/bundle/index.js",
   "browser": "dist/bundle/index.js",
@@ -67,5 +67,5 @@
   "devDependencies": {
     "@types/long": "^4.0.1"
   },
-  "gitHead": "aceb97cdd0034ba92528a22687786b25bfee0def"
+  "gitHead": "ad3f36346e1714b5bb9db0d6ff4a068ecfb945a3"
 }

package/dist/bundle/index-Dixm7K89.js

@@ -1,279 +0,0 @@
-import { L as g } from "./__vite-browser-external-C--ziKoh.js";
-import { b as w } from "./index-C8lYPtq_.js";
-import { L as x, u as E } from "./long-CYrAUkxh.js";
-import "./_commonjsHelpers-BIiJCwQW.js";
-const m = 1;
-class _ {
-  constructor({ filehandle: e, path: t }) {
-    if (e)
-      this.filehandle = e;
-    else if (t)
-      this.filehandle = new g(t);
-    else
-      throw new TypeError("either filehandle or path must be defined");
-  }
-  _readLongWithOverflow(e, t = 0, i = !0) {
-    const n = x.fromBytesLE(e.slice(t, t + 8), i);
-    if (n.greaterThan(Number.MAX_SAFE_INTEGER) || n.lessThan(Number.MIN_SAFE_INTEGER))
-      throw new TypeError("integer overflow");
-    return n.toNumber();
-  }
-  _getIndex() {
-    return this.index || (this.index = this._readIndex()), this.index;
-  }
-  async _readIndex() {
-    let e = w.Buffer.allocUnsafe(8);
-    await this.filehandle.read(e, 0, 8, 0);
-    const t = this._readLongWithOverflow(e, 0, !0);
-    if (!t)
-      return [[0, 0]];
-    const i = new Array(t + 1);
-    i[0] = [0, 0];
-    const n = 8 * 2 * t;
-    if (n > Number.MAX_SAFE_INTEGER)
-      throw new TypeError("integer overflow");
-    e = w.Buffer.allocUnsafe(n), await this.filehandle.read(e, 0, n, 8);
-    for (let s = 0; s < t; s += 1) {
-      const r = this._readLongWithOverflow(e, s * 16), a = this._readLongWithOverflow(e, s * 16 + 8);
-      i[s + 1] = [r, a];
-    }
-    return i;
-  }
-  async getLastBlock() {
-    const e = await this._getIndex();
-    if (e.length)
-      return e[e.length - 1];
-  }
-  async getRelevantBlocksForRead(e, t) {
-    const i = t + e;
-    if (e === 0)
-      return [];
-    const n = await this._getIndex(), s = [], r = (h, u) => {
-      const p = h[m], b = u ? u[m] : 1 / 0;
-      return p <= t && b > t ? 0 : p < t ? -1 : 1;
-    };
-    let a = 0, f = n.length - 1, o = Math.floor(n.length / 2), d = r(n[o], n[o + 1]);
-    for (; d !== 0; )
-      d > 0 ? f = o - 1 : d < 0 && (a = o + 1), o = Math.ceil((f - a) / 2) + a, d = r(n[o], n[o + 1]);
-    s.push(n[o]);
-    let c = o + 1;
-    for (; c < n.length && (s.push(n[c]), !(n[c][m] >= i)); c += 1)
-      ;
-    return s[s.length - 1][m] < i && s.push([]), s;
-  }
-}
-class y {
-  constructor({ filehandle: e, path: t, gziFilehandle: i, gziPath: n }) {
-    if (e)
-      this.filehandle = e;
-    else if (t)
-      this.filehandle = new g(t);
-    else
-      throw new TypeError("either filehandle or path must be defined");
-    if (!i && !n && !t)
-      throw new TypeError("either gziFilehandle or gziPath must be defined");
-    this.gzi = new _({
-      filehandle: i,
-      path: !i && !n && t ? n : `${t}.gzi`
-    });
-  }
-  async stat() {
-    const e = await this.filehandle.stat();
-    return Object.assign(e, {
-      size: await this.getUncompressedFileSize(),
-      blocks: void 0,
-      blksize: void 0
-    });
-  }
-  async getUncompressedFileSize() {
-    const [, e] = await this.gzi.getLastBlock(), { size: t } = await this.filehandle.stat(), i = w.Buffer.allocUnsafe(4), { bytesRead: n } = await this.filehandle.read(i, 0, 4, t - 28 - 4);
-    if (n !== 4)
-      throw new Error("read error");
-    const s = i.readUInt32LE(0);
-    return e + s;
-  }
-  async _readAndUncompressBlock(e, [t], [i]) {
-    let n = i;
-    n || (n = (await this.filehandle.stat()).size);
-    const s = n - t;
-    return await this.filehandle.read(e, 0, s, t), await E(e.slice(0, s));
-  }
-  async read(e, t, i, n) {
-    const s = await this.gzi.getRelevantBlocksForRead(i, n), r = w.Buffer.allocUnsafe(32768 * 2);
-    let a = t, f = 0;
-    for (let o = 0; o < s.length - 1; o += 1) {
-      const d = await this._readAndUncompressBlock(r, s[o], s[o + 1]), [, c] = s[o], h = c >= n ? 0 : n - c, u = Math.min(n + i, c + d.length) - c;
-      h >= 0 && h < d.length && (d.copy(e, a, h, u), a += u - h, f += u - h);
-    }
-    return { bytesRead: f, buffer: e };
-  }
-}
-function S(l, e) {
-  return l.offset + l.lineBytes * Math.floor(e / l.lineLength) + e % l.lineLength;
-}
-async function I(l, e) {
-  const t = await l.readFile(e);
-  if (!(t && t.length))
-    throw new Error("No data read from FASTA index (FAI) file");
-  let i = 0, n;
-  const s = t.toString("utf8").split(/\r?\n/).filter((r) => /\S/.test(r)).map((r) => r.split("	")).filter((r) => r[0] !== "").map((r) => ((!n || n.name !== r[0]) && (n = { name: r[0], id: i }, i += 1), {
-    id: n.id,
-    name: r[0],
-    length: +r[1],
-    start: 0,
-    end: +r[1],
-    offset: +r[2],
-    lineLength: +r[3],
-    lineBytes: +r[4]
-  }));
-  return {
-    name: Object.fromEntries(s.map((r) => [r.name, r])),
-    id: Object.fromEntries(s.map((r) => [r.id, r]))
-  };
-}
-class B {
-  constructor({ fasta: e, fai: t, path: i, faiPath: n, chunkSizeLimit: s = 1e6 }) {
-    if (e)
-      this.fasta = e;
-    else if (i)
-      this.fasta = new g(i);
-    else
-      throw new Error("Need to pass filehandle for fasta or path to localfile");
-    if (t)
-      this.fai = t;
-    else if (n)
-      this.fai = new g(n);
-    else if (i)
-      this.fai = new g(`${i}.fai`);
-    else
-      throw new Error("Need to pass filehandle for  or path to localfile");
-    this.chunkSizeLimit = s;
-  }
-  async _getIndexes(e) {
-    return this.indexes || (this.indexes = I(this.fai, e)), this.indexes;
-  }
-  /**
-   * @returns {array[string]} array of string sequence
-   * names that are present in the index, in which the
-   * array index indicates the sequence ID, and the value
-   * is the sequence name
-   */
-  async getSequenceNames(e) {
-    return Object.keys((await this._getIndexes(e)).name);
-  }
-  /**
-   * @returns {array[string]} array of string sequence
-   * names that are present in the index, in which the
-   * array index indicates the sequence ID, and the value
-   * is the sequence name
-   */
-  async getSequenceSizes(e) {
-    const t = {}, i = await this._getIndexes(e), n = Object.values(i.id);
-    for (let s = 0; s < n.length; s += 1)
-      t[n[s].name] = n[s].length;
-    return t;
-  }
-  /**
-   * @returns {array[string]} array of string sequence
-   * names that are present in the index, in which the
-   * array index indicates the sequence ID, and the value
-   * is the sequence name
-   */
-  async getSequenceSize(e, t) {
-    var i;
-    return (i = (await this._getIndexes(t)).name[e]) === null || i === void 0 ? void 0 : i.length;
-  }
-  /**
-   *
-   * @param {string} name
-   * @returns {Promise[boolean]} true if the file contains the given reference sequence name
-   */
-  async hasReferenceSequence(e, t) {
-    return !!(await this._getIndexes(t)).name[e];
-  }
-  /**
-   *
-   * @param {number} seqId
-   * @param {number} min
-   * @param {number} max
-   */
-  async getResiduesById(e, t, i, n) {
-    const s = (await this._getIndexes(n)).id[e];
-    if (s)
-      return this._fetchFromIndexEntry(s, t, i, n);
-  }
-  /**
-   * @param {string} seqName
-   * @param {number} min
-   * @param {number} max
-   */
-  async getResiduesByName(e, t, i, n) {
-    const s = (await this._getIndexes(n)).name[e];
-    if (s)
-      return this._fetchFromIndexEntry(s, t, i, n);
-  }
-  //alias for getResiduesByName
-  async getSequence(e, t, i, n) {
-    return this.getResiduesByName(e, t, i, n);
-  }
-  async _fetchFromIndexEntry(e, t = 0, i, n) {
-    let s = i;
-    if (t < 0)
-      throw new TypeError("regionStart cannot be less than 0");
-    if ((s === void 0 || s > e.length) && (s = e.length), t >= s)
-      return "";
-    const r = S(e, t), a = S(e, s) - r;
-    if (a > this.chunkSizeLimit)
-      throw new Error(`data size of ${a.toLocaleString()} bytes exceeded chunk size limit of ${this.chunkSizeLimit.toLocaleString()} bytes`);
-    const f = Buffer.allocUnsafe(a);
-    return await this.fasta.read(f, 0, a, r, n), f.toString("utf8").replace(/\s+/g, "");
-  }
-}
-class O extends B {
-  constructor({ fasta: e, path: t, fai: i, faiPath: n, gzi: s, gziPath: r, chunkSizeLimit: a }) {
-    super({ fasta: e, path: t, fai: i, faiPath: n, chunkSizeLimit: a }), e && s ? this.fasta = new y({
-      filehandle: e,
-      gziFilehandle: s
-    }) : t && r && (this.fasta = new y({ path: t, gziPath: r }));
-  }
-}
-function L(l) {
-  return l.split(">").filter((e) => /\S/.test(e)).map((e) => {
-    const [t, ...i] = e.split(`
-`), [n, ...s] = t.split(" "), r = i.join("").replace(/\s/g, "");
-    return {
-      id: n,
-      description: s.join(" "),
-      sequence: r
-    };
-  });
-}
-class v {
-  constructor({ fasta: e, path: t }) {
-    if (e)
-      this.fasta = e;
-    else if (t)
-      this.fasta = new g(t);
-    else
-      throw new Error("Need to pass fasta or path");
-    this.data = this.fasta.readFile().then((i) => {
-      const n = i.toString("utf8");
-      return L(n);
-    });
-  }
-  async fetch(e, t, i) {
-    const s = (await this.data).find((a) => a.id === e), r = i - t;
-    if (!s)
-      throw new Error(`no sequence with id ${e} exists`);
-    return s.sequence.substr(t, r);
-  }
-  async getSequenceNames() {
-    return (await this.data).map((t) => t.id);
-  }
-}
-export {
-  O as BgzipIndexedFasta,
-  v as FetchableSmallFasta,
-  B as IndexedFasta,
-  L as parseSmallFasta
-};

package/dist/bundle/remoteFile-1_eCK3VV.js

@@ -1,96 +0,0 @@
-import { b as u } from "./index-C8lYPtq_.js";
-const h = typeof window < "u" ? window : typeof self < "u" ? self : { fetch: void 0 };
-class b {
-  async getBufferFromResponse(e) {
-    if (typeof e.buffer == "function")
-      return e.buffer();
-    if (typeof e.arrayBuffer == "function") {
-      const t = await e.arrayBuffer();
-      return u.Buffer.from(t);
-    } else
-      throw new TypeError("invalid HTTP response object, has no buffer method, and no arrayBuffer method");
-  }
-  constructor(e, t = {}) {
-    this.baseOverrides = {}, this.url = e;
-    const r = t.fetch || h.fetch && h.fetch.bind(h);
-    if (!r)
-      throw new TypeError("no fetch function supplied, and none found in global environment");
-    t.overrides && (this.baseOverrides = t.overrides), this.fetchImplementation = r;
-  }
-  async fetch(e, t) {
-    let r;
-    try {
-      r = await this.fetchImplementation(e, t);
-    } catch (s) {
-      if (`${s}`.includes("Failed to fetch"))
-        console.warn(`generic-filehandle: refetching ${e} to attempt to work around chrome CORS header caching bug`), r = await this.fetchImplementation(e, {
-          ...t,
-          cache: "reload"
-        });
-      else
-        throw s;
-    }
-    return r;
-  }
-  async read(e, t = 0, r, s = 0, o = {}) {
-    const { headers: i = {}, signal: f, overrides: n = {} } = o;
-    r < 1 / 0 ? i.range = `bytes=${s}-${s + r}` : r === 1 / 0 && s !== 0 && (i.range = `bytes=${s}-`);
-    const l = {
-      ...this.baseOverrides,
-      ...n,
-      headers: {
-        ...i,
-        ...n.headers,
-        ...this.baseOverrides.headers
-      },
-      method: "GET",
-      redirect: "follow",
-      mode: "cors",
-      signal: f
-    }, a = await this.fetch(this.url, l);
-    if (!a.ok)
-      throw new Error(`HTTP ${a.status} ${a.statusText} ${this.url}`);
-    if (a.status === 200 && s === 0 || a.status === 206) {
-      const d = await this.getBufferFromResponse(a), w = d.copy(e, t, 0, Math.min(r, d.length)), m = a.headers.get("content-range"), c = /\/(\d+)$/.exec(m || "");
-      return c && c[1] && (this._stat = { size: parseInt(c[1], 10) }), { bytesRead: w, buffer: e };
-    }
-    throw a.status === 200 ? new Error("${this.url} fetch returned status 200, expected 206") : new Error(`HTTP ${a.status} fetching ${this.url}`);
-  }
-  async readFile(e = {}) {
-    let t, r;
-    typeof e == "string" ? (t = e, r = {}) : (t = e.encoding, r = e, delete r.encoding);
-    const { headers: s = {}, signal: o, overrides: i = {} } = r, f = {
-      headers: s,
-      method: "GET",
-      redirect: "follow",
-      mode: "cors",
-      signal: o,
-      ...this.baseOverrides,
-      ...i
-    }, n = await this.fetch(this.url, f);
-    if (!n)
-      throw new Error("generic-filehandle failed to fetch");
-    if (n.status !== 200)
-      throw Object.assign(new Error(`HTTP ${n.status} fetching ${this.url}`), {
-        status: n.status
-      });
-    if (t === "utf8")
-      return n.text();
-    if (t)
-      throw new Error(`unsupported encoding: ${t}`);
-    return this.getBufferFromResponse(n);
-  }
-  async stat() {
-    if (!this._stat) {
-      const e = u.Buffer.allocUnsafe(10);
-      if (await this.read(e, 0, 10, 0), !this._stat)
-        throw new Error(`unable to determine size of file at ${this.url}`);
-    }
-    return this._stat;
-  }
-  async close() {
-  }
-}
-export {
-  b as R
-};