@jbrowse/bandage-core 10.2.2 → 10.2.4

package/dist/chunks/chunk-4BYTEJGW.js

@@ -1,44 +0,0 @@
-// src/renderer/canvas.ts
-var MAX_DPR = 2;
-var MAX_CANVAS_DIM_PX = 8192;
-function getDpr() {
-  return typeof devicePixelRatio === "undefined" ? 1 : Math.min(devicePixelRatio, MAX_DPR);
-}
-var warnedCanvasClamp = false;
-function backingPx(cssSize, dpr, axis) {
-  const value = Math.round(cssSize * dpr);
-  if (value > MAX_CANVAS_DIM_PX) {
-    if (!warnedCanvasClamp) {
-      warnedCanvasClamp = true;
-      console.warn(
-        `Canvas ${axis} ${value}px exceeds the safe limit ${MAX_CANVAS_DIM_PX}px and was clamped`
-      );
-    }
-    return MAX_CANVAS_DIM_PX;
-  }
-  return value;
-}
-function syncCanvasSize(canvas, width, height) {
-  const dpr = getDpr();
-  const pw = backingPx(width, dpr, "width");
-  const ph = backingPx(height, dpr, "height");
-  if (canvas.width !== pw || canvas.height !== ph) {
-    canvas.width = pw;
-    canvas.height = ph;
-  }
-  const cssWidth = `${width}px`;
-  const cssHeight = `${height}px`;
-  if (canvas.style.width !== cssWidth) {
-    canvas.style.width = cssWidth;
-  }
-  if (canvas.style.height !== cssHeight) {
-    canvas.style.height = cssHeight;
-  }
-}
-
-export {
-  MAX_DPR,
-  MAX_CANVAS_DIM_PX,
-  getDpr,
-  syncCanvasSize
-};

package/dist/chunks/chunk-7XHHVYG7.js

@@ -1,13 +0,0 @@
-// src/loadBandage.ts
-var cached;
-function loadBandage() {
-  cached ??= import("./bandage-layout-3AR6BCUD.js").then((mod) => mod.default()).catch((e) => {
-    cached = void 0;
-    throw e;
-  });
-  return cached;
-}
-
-export {
-  loadBandage
-};

package/dist/chunks/chunk-EHUBJDDB.js

@@ -1,135 +0,0 @@
-import {
-  bubbleSegmentIds,
-  classifyBubble,
-  formatBp
-} from "./chunk-XKWD2RY3.js";
-import {
-  svgPath
-} from "./chunk-2CVHXFK7.js";
-import {
-  isBackbone
-} from "./chunk-FYQWPEEY.js";
-
-// src/bubbles/bubbleHalos.ts
-var WHOLE_FRACTION = 0.9;
-function coversGraph(members, nodes) {
-  return members + 2 >= nodes || members >= WHOLE_FRACTION * nodes;
-}
-var SMALL_VARIANT_BP = 50;
-var NAMED_WALKS = 2;
-var MIN_CHIPPED_BP = 1e3;
-function bubbleHalos(graph, bubbles, positions, walkLabel = (name) => name, repeats = []) {
-  const byName = new Map(graph.nodes.map((n) => [n.name, n]));
-  const halos = [];
-  for (const bubble of bubbles) {
-    const parts = [];
-    let minX = Infinity;
-    let maxX = -Infinity;
-    let minY = Infinity;
-    const nodeIds = [];
-    const ends = [];
-    const names = bubbleSegmentIds(bubble);
-    for (const [i, name] of names.entries()) {
-      const node = byName.get(name);
-      const line = node && positions[node.id];
-      if (!node || !line?.length) {
-        continue;
-      }
-      if (bubble.key ? i === 0 || i === names.length - 1 : isBackbone(node) && (node.stable.start < bubble.start || node.stable.start >= bubble.end)) {
-        ends.push(line[Math.floor(line.length / 2)]);
-        continue;
-      }
-      nodeIds.push(node.id);
-      parts.push(svgPath(line.length === 1 ? [line[0], line[0]] : line));
-      for (const p of line) {
-        minX = Math.min(minX, p.x);
-        maxX = Math.max(maxX, p.x);
-        minY = Math.min(minY, p.y);
-      }
-    }
-    if (nodeIds.length === 0) {
-      continue;
-    }
-    const labelAt = { x: (minX + maxX) / 2, y: minY };
-    const anchor = ends.length ? {
-      x: ends.reduce((s, p) => s + p.x, 0) / ends.length,
-      y: ends.reduce((s, p) => s + p.y, 0) / ends.length
-    } : labelAt;
-    const routes = [];
-    for (const [route, own] of ownStretches(bubble)) {
-      let at;
-      let far = -1;
-      for (const id of own) {
-        for (const p of positions[id] ?? []) {
-          const d = Math.hypot(p.x - anchor.x, p.y - anchor.y);
-          if (d > far) {
-            far = d;
-            at = p;
-          }
-        }
-      }
-      if (at) {
-        routes.push({ route, at, text: routeText(route, walkLabel) });
-      }
-    }
-    const whole = bubble.covering === true || coversGraph(nodeIds.length, graph.nodes.length);
-    halos.push({
-      bubble,
-      ...classifyBubble(bubble, repeats),
-      path: parts.join(""),
-      labelAt,
-      members: nodeIds.length,
-      nodeIds,
-      whole,
-      // The drawing's own bubble keeps its name however small. A partial
-      // bubble's lengths are a floor, so it may be no small variant.
-      tick: !whole && !bubble.partial && bubble.longestAlleleLength < SMALL_VARIANT_BP,
-      routes
-    });
-  }
-  return halos;
-}
-var stretches = /* @__PURE__ */ new WeakMap();
-function ownStretches(bubble) {
-  const cached = stretches.get(bubble);
-  if (cached) {
-    return cached;
-  }
-  const chipped = bubble.longestAlleleLength < MIN_CHIPPED_BP ? [] : bubble.routes ?? [];
-  const sharing = /* @__PURE__ */ new Map();
-  chipped.forEach((route, r) => {
-    const counted = /* @__PURE__ */ new Map();
-    for (const id of route.steps) {
-      if (counted.get(id) !== r) {
-        counted.set(id, r);
-        sharing.set(id, (sharing.get(id) ?? 0) + 1);
-      }
-    }
-  });
-  const own = /* @__PURE__ */ new Map();
-  for (const route of chipped) {
-    let rarest = Infinity;
-    for (const id of route.steps) {
-      rarest = Math.min(rarest, sharing.get(id));
-    }
-    const steps = new Set(route.steps.filter((id) => sharing.get(id) === rarest));
-    if (steps.size > 0) {
-      own.set(route, [...steps]);
-    }
-  }
-  stretches.set(bubble, own);
-  return own;
-}
-function routeText(route, walkLabel) {
-  const names = [...new Set(route.walks.map(walkLabel))].sort();
-  const shown = names.slice(0, NAMED_WALKS).join(", ");
-  const more = names.length > NAMED_WALKS ? ` +${names.length - NAMED_WALKS}` : "";
-  return `${shown}${more} \xB7 ${formatBp(route.bp)}`;
-}
-
-export {
-  WHOLE_FRACTION,
-  coversGraph,
-  SMALL_VARIANT_BP,
-  bubbleHalos
-};

package/dist/loadBandage.js

@@ -1,6 +0,0 @@
-import {
-  loadBandage
-} from "./chunks/chunk-7XHHVYG7.js";
-export {
-  loadBandage as default
-};

package/dist/types/bandage/bandage-layout.d.ts

@@ -1,14 +0,0 @@
-import type { LayoutNode } from '../layout/referenceSeeds.js'
-import type { Graph, LayoutResult } from '../types.js'
-
-export interface BandageModule {
-  computeLayout(
-    graph: { nodes: LayoutNode[]; edges: Graph['edges'] },
-    options: Record<string, unknown>,
-  ): LayoutResult
-}
-
-// The vendored Emscripten bundle's default export is a factory that
-// instantiates the wasm module (layout inlined, -sSINGLE_FILE=1).
-declare const createBandageLayoutModule: () => Promise<BandageModule>
-export default createBandageLayoutModule

package/dist/types/loadBandage.d.ts

@@ -1,3 +0,0 @@
-export type { BandageModule } from './bandage/bandage-layout.js';
-import type { BandageModule } from './bandage/bandage-layout.js';
-export default function loadBandage(): Promise<BandageModule>;