@genome-spy/app 0.51.0 → 0.53.0

package/dist/{long-CYrAUkxh.js → long-D4tVjLLz.js}

@@ -1,4 +1,4 @@
-import { b as Pi } from "./index-C8lYPtq_.js";
+import { b as Pi } from "./index-B5cesONJ.js";
 import { g as Da } from "./_commonjsHelpers-BIiJCwQW.js";
 var re = {};
 (function(e) {
@@ -177,7 +177,7 @@ function aa(e) {
   e.bi_valid > 8 ? Ye(e, e.bi_buf) : e.bi_valid > 0 && (e.pending_buf[e.pending++] = e.bi_buf), e.bi_buf = 0, e.bi_valid = 0;
 }
 function Wa(e, i, t, a) {
-  aa(e), a && (Ye(e, t), Ye(e, ~t)), Ra.arraySet(e.pending_buf, e.window, i, t, e.pending), e.pending += t;
+  aa(e), Ye(e, t), Ye(e, ~t), Ra.arraySet(e.pending_buf, e.window, i, t, e.pending), e.pending += t;
 }
 function Jt(e, i, t, a) {
   var r = i * 2, n = t * 2;
@@ -282,7 +282,7 @@ function Qa(e) {
   ii || (Ga(), ii = !0), e.l_desc = new xt(e.dyn_ltree, ji), e.d_desc = new xt(e.dyn_dtree, Vi), e.bl_desc = new xt(e.bl_tree, Ji), e.bi_buf = 0, e.bi_valid = 0, ia(e);
 }
 function na(e, i, t, a) {
-  C(e, (Ua << 1) + (a ? 1 : 0), 3), Wa(e, i, t, !0);
+  C(e, (Ua << 1) + (a ? 1 : 0), 3), Wa(e, i, t);
 }
 function en(e) {
   C(e, Ki << 1, 3), ee(e, Ht, ne), Xa(e);
@@ -560,7 +560,7 @@ function ua(e, i, t, a, r, n) {
     return ue(e, X);
   a === 8 && (a = 9);
   var f = new Ln();
-  return e.state = f, f.strm = e, f.wrap = h, f.gzhead = null, f.w_bits = a, f.w_size = 1 << f.w_bits, f.w_mask = f.w_size - 1, f.hash_bits = r + 7, f.hash_size = 1 << f.hash_bits, f.hash_mask = f.hash_size - 1, f.hash_shift = ~~((f.hash_bits + S - 1) / S), f.window = new B.Buf8(f.w_size * 2), f.head = new B.Buf16(f.hash_size), f.prev = new B.Buf16(f.w_size), f.lit_bufsize = 1 << r + 6, f.pending_buf_size = f.lit_bufsize * 4, f.pending_buf = new B.Buf8(f.pending_buf_size), f.d_buf = 1 * f.lit_bufsize, f.l_buf = (1 + 2) * f.lit_bufsize, f.level = i, f.strategy = n, f.method = t, _a(e);
+  return e.state = f, f.strm = e, f.wrap = h, f.gzhead = null, f.w_bits = a, f.w_size = 1 << f.w_bits, f.w_mask = f.w_size - 1, f.hash_bits = r + 7, f.hash_size = 1 << f.hash_bits, f.hash_mask = f.hash_size - 1, f.hash_shift = ~~((f.hash_bits + S - 1) / S), f.window = new B.Buf8(f.w_size * 2), f.head = new B.Buf16(f.hash_size), f.prev = new B.Buf16(f.w_size), f.lit_bufsize = 1 << r + 6, f.pending_buf_size = f.lit_bufsize * 4, f.pending_buf = new B.Buf8(f.pending_buf_size), f.d_buf = 1 * f.lit_bufsize, f.l_buf = 3 * f.lit_bufsize, f.level = i, f.strategy = n, f.method = t, _a(e);
 }
 function Rn(e, i) {
   return ua(e, i, vt, pn, xn, gn);
@@ -1036,7 +1036,7 @@ var je = {}, j = {}, it = 30, Gn = 12, Wn = function(i, t) {
   if (i === ui ? (m = Je = f, x = 19) : i === mt ? (m = jn, I -= 257, Je = Vn, Gt -= 257, x = 256) : (m = Jn, Je = Qn, x = -1), z = 0, v = 0, o = d, p = h, w = g, k = 0, T = -1, N = 1 << g, y = N - 1, i === mt && N > oi || i === di && N > _i)
     return 1;
   for (; ; ) {
-    Wt = o - k, f[v] < x ? (Qe = 0, et = f[v]) : f[v] > x ? (Qe = Je[Gt + f[v]], et = m[I + f[v]]) : (Qe = 32 + 64, et = 0), E = 1 << o - k, c = 1 << w, d = c;
+    Wt = o - k, f[v] < x ? (Qe = 0, et = f[v]) : f[v] > x ? (Qe = Je[Gt + f[v]], et = m[I + f[v]]) : (Qe = 96, et = 0), E = 1 << o - k, c = 1 << w, d = c;
     do
       c -= E, n[p + (z >> k) + c] = Wt << 24 | Qe << 16 | et | 0;
     while (c !== 0);

package/dist/remoteFile-BkTxwFub.js

@@ -0,0 +1,90 @@
+import { b as d } from "./index-B5cesONJ.js";
+class b {
+  async getBufferFromResponse(e) {
+    const t = await e.arrayBuffer();
+    return d.Buffer.from(t);
+  }
+  constructor(e, t = {}) {
+    this.baseOverrides = {}, this.url = e;
+    const r = t.fetch || globalThis.fetch.bind(globalThis);
+    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 ${e} to attempt to work around chrome CORS header caching bug`), r = await this.fetchImplementation(e, {
+          ...t,
+          cache: "reload"
+        });
+      else
+        throw s;
+    }
+    return r;
+  }
+  async read(e, t = 0, r, s = 0, h = {}) {
+    const { headers: n = {}, signal: c, overrides: a = {} } = h;
+    r < 1 / 0 ? n.range = `bytes=${s}-${s + r}` : r === 1 / 0 && s !== 0 && (n.range = `bytes=${s}-`);
+    const l = {
+      ...this.baseOverrides,
+      ...a,
+      headers: {
+        ...n,
+        ...a.headers,
+        ...this.baseOverrides.headers
+      },
+      method: "GET",
+      redirect: "follow",
+      mode: "cors",
+      signal: c
+    }, i = await this.fetch(this.url, l);
+    if (!i.ok)
+      throw new Error(`HTTP ${i.status} ${i.statusText} ${this.url}`);
+    if (i.status === 200 && s === 0 || i.status === 206) {
+      const f = await this.getBufferFromResponse(i), u = f.copy(e, t, 0, Math.min(r, f.length)), w = i.headers.get("content-range"), o = /\/(\d+)$/.exec(w || "");
+      return o != null && o[1] && (this._stat = { size: parseInt(o[1], 10) }), { bytesRead: u, buffer: e };
+    }
+    throw i.status === 200 ? new Error("${this.url} fetch returned status 200, expected 206") : new Error(`HTTP ${i.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: h, overrides: n = {} } = r, c = {
+      headers: s,
+      method: "GET",
+      redirect: "follow",
+      mode: "cors",
+      signal: h,
+      ...this.baseOverrides,
+      ...n
+    }, a = await this.fetch(this.url, c);
+    if (!a)
+      throw new Error("generic-filehandle failed to fetch");
+    if (a.status !== 200)
+      throw Object.assign(new Error(`HTTP ${a.status} fetching ${this.url}`), {
+        status: a.status
+      });
+    if (t === "utf8")
+      return a.text();
+    if (t)
+      throw new Error(`unsupported encoding: ${t}`);
+    return this.getBufferFromResponse(a);
+  }
+  async stat() {
+    if (!this._stat) {
+      const e = d.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
+};

package/dist/style.css

@@ -1 +1 @@
-.genome-spy-app{position:absolute;top:0;bottom:0;left:0;right:0;display:flex;flex-direction:column;font-family:system-ui,Segoe UI,Roboto,Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol;font-size:14px}body>.genome-spy-app{background-color:#fff}.genome-spy-app .genome-spy-container{position:relative;flex-grow:1;overflow:hidden}.gs-toolbar,.gs-toolbar .btn-group{display:flex;flex-direction:row;align-items:center}.gs-toolbar{height:38px;background-color:#6c82ab;box-shadow:0 0 3px #00000080;border-top:1px solid #9dabc7;border-bottom:1px solid #4a5d81}.gs-toolbar .spacer{flex-grow:1}.gs-toolbar .logo{display:block}.gs-toolbar .logo img{vertical-align:middle;width:34px}.gs-toolbar .vis-title,.gs-toolbar .version{color:#fff;font-weight:400;text-shadow:0 1px 2px rgba(0,0,0,.2)}.gs-toolbar .version{text-decoration:none;font-size:80%;opacity:50%}.gs-toolbar .version:visited{color:#fff}.gs-toolbar .search-input{font-size:1em;background-color:#5c74a1;color:#fff;border:1px solid #536991;width:260px;padding:3px 6px;outline:none;position:relative;box-shadow:0 1px 3px #0000001a inset,1px 1px #798db2;text-shadow:0 1px 2px rgba(0,0,0,.3)}.gs-toolbar .search-help{box-sizing:border-box;position:absolute;border:none;background:#f6f6f6;padding:10px;z-index:1000;visibility:hidden;box-shadow:0 3px 14px #00000026;font-size:90%;opacity:0;transition:opacity .2s,transform .2s ease-in-out,visibility .2s;transform:translateY(13px)}.gs-toolbar .search-help>:first-child{margin-top:0}.gs-toolbar .search-help>:last-child{margin-bottom:0}.gs-toolbar .search-help p{margin-bottom:.5em}.gs-toolbar .search-help ul{margin-top:.5em;padding-left:2.5em}.gs-toolbar .search-help li{cursor:pointer}.gs-toolbar .search:focus-within .search-help{opacity:1;visibility:visible;transform:translateY(3px)}.gs-toolbar>*{padding-left:10px}.gs-toolbar>*:last-child{margin-right:10px}.gs-toolbar .tool-btn{padding:0;font-size:1.15em;transition:color .15s;background-color:#7c90b4;background-image:linear-gradient(to bottom,#8698ba,#7288af);color:#fff;height:26px;width:30px;border:1px solid;border-top-color:#9dabc7;border-left-color:#8395b8;border-right-color:#5c74a1;border-bottom-color:#4a5d81;box-shadow:0 1px 1px #00000026;border-radius:2px;margin-left:10px;display:flex;align-items:center;justify-content:center}.gs-toolbar .tool-btn>svg{filter:drop-shadow(0 0 1px rgba(0,0,0,.3))}.gs-toolbar .tool-btn:active>*{position:relative;top:1px}.gs-toolbar .tool-btn:disabled{color:#b6c1d5}.gs-toolbar .tool-btn:hover:not(:disabled){background-image:linear-gradient(to bottom,#8c9ebe,#7c90b4)}.gs-toolbar .tool-btn:hover:not(:disabled)>svg{filter:drop-shadow(0 0 3px rgb(150,200,255))}.gs-toolbar .tool-btn:focus{outline:none}.gs-toolbar .btn-group .tool-btn,.gs-toolbar .dropdown .tool-btn{margin-left:0}.gs-toolbar .dropdown{position:relative}.gs-toolbar .dropdown.show .gs-dropdown-menu{display:block}.gs-toolbar .dropdown.show>button{background-image:linear-gradient(to bottom,#93a3c1,#8698ba)}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu){margin:0;padding:7px 0;background:#f6f6f6;border:#e0e0e0;border-radius:2px;max-height:calc(100vh - 60px);overflow-y:auto;z-index:100;box-shadow:0 3px 15px #00000036;cursor:default;line-height:22px;font-size:13px;font-family:system-ui,Segoe UI,Roboto,Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li{display:block;list-style:none;position:relative;padding:0}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li.active>:is(a:first-child,.submenu-item){background-color:#e8e8e8}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>:is(a:first-child,label,.submenu-item):hover{background-color:#e0e0e0}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>span.disabled-item,:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>a:first-child{display:block}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>span.disabled-item svg:first-child,:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>a:first-child svg:first-child{width:1em;margin-right:.2em}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) .context{font-size:.9em;color:#666}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) .context:before{content:"("}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) .context:after{content:")"}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) .menu-divider{margin:5px 0;border-top:1px solid #e0e0e0}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) .menu-header,:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>:is(span.disabled-item,a:first-child,.submenu-item,label){padding-left:15px;padding-right:15px}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) .menu-header{font-size:12px;color:#666}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>:is(div.submenu-item,.choice-item){display:flex;justify-content:space-between;align-items:center}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>:is(div.submenu-item,.choice-item)>:first-child{flex-grow:1}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>.submenu-item:after{content:"";width:0;height:0;border-top:.4em solid transparent;border-bottom:.4em solid transparent;border-left:.4em solid black;margin-left:1em}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li .kbd-shortcut{color:#666;background-color:#ffffff80;font-size:.9em;border:1px solid #aaa;border-bottom-width:2px;border-radius:3px;padding:3px;line-height:.7em;margin-left:.5em}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li>.disabled-item{color:#999}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) a.menu-ellipsis{padding:0;display:flex;align-items:center;position:absolute;top:0;right:7.5px;height:22px;background-color:#e0e0e0;border-radius:3em;color:#707070}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) a.menu-ellipsis svg{margin:0;width:22px}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) a.menu-ellipsis:hover{background-color:#e9e9e9}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) li:not(:hover) a.menu-ellipsis{display:none}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) .gs-input-binding{margin:0 15px;line-height:normal}:is(.gs-menu,.gs-context-menu,.gs-dropdown-menu) .gs-input-binding .description{margin-bottom:.2em}.provenance-menu .operator{font-size:125%;line-height:.8}.gs-context-menu-backdrop{position:fixed;z-index:100;top:0;right:0;bottom:0;left:0}.gs-context-menu{position:fixed;z-index:100}.gs-dropdown-menu{overflow:auto;position:absolute;display:none;z-index:1;width:max-content}.gs-dropdown-menu ul{padding-left:1.5em;list-style:none}.gs-dropdown-menu>li>ul{padding-left:0}.gs-dropdown-menu.provenance-menu .active-state{background-color:#e0e0e0;border-left:5px solid #c0c0c0;padding-left:10px}.gs-modal{z-index:101;font-family:system-ui,Segoe UI,Roboto,Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol;font-size:14px;position:fixed;top:0;right:0;bottom:0;left:0;display:grid;justify-content:center;align-content:center}.gs-modal *{box-sizing:border-box}.gs-modal .backdrop{position:absolute;top:0;right:0;bottom:0;left:0;background-color:#4b4b4b;opacity:0;transition:opacity .3s ease-in-out}.gs-modal .content{z-index:1;box-shadow:0 3px 15px #00000036;background:white;border-radius:3px;min-width:300px;opacity:0;transform:translateY(-15px);transition:opacity .2s ease-in-out,transform .2s ease-in-out}.gs-modal.visible .backdrop{opacity:.4}.gs-modal.visible .content{transform:translate(0);opacity:1}.gs-modal .modal-body,.gs-modal .modal-title,.gs-modal .modal-buttons{padding:10px}.gs-modal .modal-title{font-weight:700;padding-bottom:0}.gs-modal .modal-body>:first-child{margin-top:0}.gs-modal .modal-body>:last-child{margin-bottom:0}.gs-modal .modal-buttons{display:flex;justify-content:flex-end;gap:10px;border-top:1px solid #d0d0d0}.gs-modal .btn{display:inline-block;padding:4px 12px;margin:0;font-size:1em;line-height:20px;color:#333;text-align:center;text-shadow:0 1px 1px rgba(255,255,255,.75);vertical-align:middle;background-image:linear-gradient(to bottom,#ffffff,#e6e6e6);border:1px solid #cccccc;border-color:rgba(0,0,0,.1) rgba(0,0,0,.1) rgba(0,0,0,.25);border-bottom-color:#b3b3b3;border-radius:4px;box-shadow:inset 0 1px #fff3,0 1px 2px #0000000d;transition:color .15s}.gs-modal .btn:hover:not(:disabled){background-image:linear-gradient(to bottom,#f8f8f8,#d8d8d8)}.gs-modal .btn:active{border-color:rgba(0,0,0,.2) rgba(0,0,0,.2) rgba(0,0,0,.5)}.gs-modal .btn:disabled{color:#a0a0a0}.gs-modal .btn:not(:disabled){cursor:pointer}.gs-modal .btn svg:first-child:not(:last-child){font-size:85%;margin-right:.3em}.gs-modal .btn svg:last-child:not(:first-child){font-size:85%;margin-left:.3em}.gs-modal .btn-group{display:flex;font-size:1.3em;margin-bottom:10px}.gs-modal .btn-group .btn{flex-grow:1}.gs-modal .btn-group .btn:not(:first-child){border-top-left-radius:0;border-bottom-left-radius:0;margin-left:-1px}.gs-modal .btn-group .btn:not(:last-child){border-top-right-radius:0;border-bottom-right-radius:0}.gs-modal .btn-group .btn.chosen{background-image:linear-gradient(to bottom,#f0f0f0,#d8d8d8);box-shadow:inset 0 2px 3px #0000004d}.gs-modal.tour{pointer-events:none;justify-content:right;align-content:end}.gs-modal.tour.visible .backdrop{opacity:1}.gs-modal.tour .backdrop{pointer-events:none;background:linear-gradient(160deg,transparent 70%,rgba(0,0,0,.2))}.gs-modal.tour .content{pointer-events:all;margin:10px;box-shadow:0 3px 15px #00000036,0 2px 5px #00000036}.gs-modal.tour .modal-title{padding-right:3em}.gs-modal.tour .modal-body.markdown img{max-width:350px;display:block;margin:1em auto}.gs-modal .collapse{position:absolute;right:10px;top:10px;background:none;border:none;font-size:1.1em;border-radius:2px;cursor:pointer}.gs-modal .collapse svg{transition:transform .5s}.gs-modal .collapse:hover{background-color:#e8e8e8}.gs-modal:not(.collapsed) .content:not(:hover) .collapse{animation:move .25s .5s 3 linear}@keyframes move{0%{transform:translateY(0)}25%{transform:translateY(-2px)}75%{transform:translateY(2px)}to{transform:translateY(0)}}.gs-modal.collapsed>.content>:not(:is(.modal-title,.collapse)){display:none}.gs-modal.collapsed .modal-title{padding-bottom:10px}.gs-modal.collapsed .collapse svg{transform:rotate(180deg)}.gs-modal a{color:#5570a2;text-decoration:none}.gs-modal a:hover{text-decoration:underline}.gs-checkbox-list-wrapper{position:relative}.gs-checkbox-list-wrapper .search-note{position:absolute;top:0;right:0;bottom:0;left:0;display:grid;justify-content:center;align-content:center;color:gray;font-size:85%;pointer-events:none}.gs-checkbox-list-wrapper .search-note>*{position:relative;top:.7em}.gs-checkbox-list{color:#212529;border:1px solid #ced4da;border-radius:.25em;overflow:auto;max-height:200px;padding:.375em .75em;margin:0}.gs-checkbox-list .color{width:.5em;height:1em;margin-right:.4em}.gs-checkbox-list li{list-style:none}.gs-checkbox-list label.checkbox{margin-bottom:0}.gs-checkbox-list label.checkbox:hover{background-color:#f4f4f4}.gs-checkbox-list .hidden{display:none}.gs-form-group>p:first-child{margin-top:0}.gs-form-group:not(:first-child){margin-top:.5em}.gs-form-group label{display:inline-block;margin-bottom:.5em}.gs-form-group input[type=text],.gs-form-group input[type=number],.gs-form-group select,.gs-form-group textarea{display:block;width:100%;padding:.375em .75em;font-size:1em;font-family:system-ui,Segoe UI,Roboto,Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol;line-height:1.5;color:#212529;background-color:#fff;background-clip:padding-box;border:1px solid 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package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.51.0",
+  "version": "0.53.0",
   "main": "dist/index.js",
   "type": "module",
   "files": [
@@ -29,15 +29,14 @@
     "@fortawesome/fontawesome-free": "^6.4.2",
     "@fortawesome/fontawesome-svg-core": "^6.4.2",
     "@fortawesome/free-solid-svg-icons": "^6.4.2",
-    "@genome-spy/core": "^0.51.0",
+    "@genome-spy/core": "^0.53.0",
     "@reduxjs/toolkit": "^1.8.4",
     "idb": "^7.1.1",
     "lit": "^3.1.2",
     "lz-string": "^1.4.4",
     "mapsort": "^1.0.5",
+    "micromark": "^4.0.0",
     "redux-batched-actions": "^0.5.0",
-    "redux-undo": "^1.0.1",
-    "snarkdown": "^2.0.0"
-  },
-  "gitHead": "c2522b73298c0cc4cf38cca795b35e97c5c292d4"
+    "redux-undo": "^1.0.1"
+  }
 }

package/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2018-2023 Kari Lavikka
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

package/dist/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/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
-};