@jbrowse/bandage-core 10.2.3 → 10.2.4

package/README.md

@@ -65,6 +65,8 @@ publishes to npm with trusted publishing.
   JBrowse 2 plugin that browses these graphs by locus
 - [BandageJS](https://github.com/cmdcolin/BandageJS) - standalone page for GFA
   and gbz-base graphs
+- [@jbrowse/graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout) -
+  Bandage's FMMM layout as wasm
 - [@jbrowse/graph-stress-layout](https://github.com/GMOD/graph-stress-layout) -
   stress layout that keeps the reference straight
 - [@gmod/gbz-base](https://github.com/GMOD/gbz-base-js) - range-request reader

package/dist/bubbles/bubbleHalos.js

@@ -3,7 +3,7 @@ import {
   WHOLE_FRACTION,
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-JFY5PWQC.js";
+} from "../chunks/chunk-JA2HJIYS.js";
 import "../chunks/chunk-URZ3CH2R.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-PTABFYQ7.js";

package/dist/bubbles/superbubbles.js

@@ -1,10 +1,10 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-XA5A27CS.js";
+} from "../chunks/chunk-ABUIN5AK.js";
 import "../chunks/chunk-CQHUZHET.js";
 import "../chunks/chunk-T6V4KI2L.js";
-import "../chunks/chunk-JFY5PWQC.js";
+import "../chunks/chunk-JA2HJIYS.js";
 import "../chunks/chunk-URZ3CH2R.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-CM6LO6OC.js";

package/dist/chunks/{chunk-J5FWKGOY.js → chunk-2CHS5LMM.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "10.2.3";
+var version = "10.2.4";
 
 export {
   version

package/dist/chunks/{chunk-XA5A27CS.js → chunk-ABUIN5AK.js}

@@ -9,7 +9,7 @@ import {
 } from "./chunk-T6V4KI2L.js";
 import {
   coversGraph
-} from "./chunk-JFY5PWQC.js";
+} from "./chunk-JA2HJIYS.js";
 import {
   bubbleSegmentIds
 } from "./chunk-URZ3CH2R.js";

package/dist/chunks/{chunk-3AOGOCCQ.js → chunk-GINYTQ43.js}

@@ -24,7 +24,7 @@ import {
 } from "./chunk-RPRHR56C.js";
 import {
   geneLabelCandidates
-} from "./chunk-YN6FDIBT.js";
+} from "./chunk-KC7T5RWG.js";
 import {
   nodesUnderBox
 } from "./chunk-4HWM3FNK.js";
@@ -34,7 +34,7 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   version
-} from "./chunk-J5FWKGOY.js";
+} from "./chunk-2CHS5LMM.js";
 import {
   axisScaleOf
 } from "./chunk-BS4UZ44I.js";

package/dist/chunks/chunk-JA2HJIYS.js

@@ -0,0 +1,71 @@
+import {
+  bubbleSegmentIds,
+  classifyBubble
+} from "./chunk-URZ3CH2R.js";
+import {
+  svgPath
+} from "./chunk-7SRWJLSC.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;
+function bubbleHalos(graph, bubbles, positions, 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 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)) {
+        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 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
+    });
+  }
+  return halos;
+}
+
+export {
+  WHOLE_FRACTION,
+  coversGraph,
+  SMALL_VARIANT_BP,
+  bubbleHalos
+};

package/dist/chunks/{chunk-YN6FDIBT.js → chunk-KC7T5RWG.js}

@@ -18,7 +18,6 @@ import {
 // src/labelLayout.ts
 var HALO_FACTOR = 3.4;
 var LEGEND_INSET_PX = 6;
-var ROUTE_STACK = 8;
 var GENE_PIN_DROP_PX = 18;
 var GENE_STACK = 2;
 var BUBBLE_STACK = 3;
@@ -147,22 +146,6 @@ function layoutLabels(m) {
     version: m.positionsVersion
   }) : { deletions: [], nodes: [] };
   const deletionLabels = placeSizeLabels(sizeCandidates.deletions, take);
-  const routes = placeLabels(
-    byBubble.flatMap(
-      (h) => h.routes.map((route) => {
-        const { x, y } = screen(route.at);
-        return {
-          item: { halo: h, route },
-          x,
-          y: y + 4,
-          text: route.text,
-          stack: ROUTE_STACK
-        };
-      })
-    ),
-    frame,
-    take
-  );
   const nodeLabels = placeSizeLabels(
     sizeCandidates.nodes,
     take,
@@ -172,7 +155,6 @@ function layoutLabels(m) {
     bubbles,
     ticks,
     genes,
-    routes,
     sizes: [...deletionLabels, ...nodeLabels]
   };
 }

package/dist/chunks/{chunk-7CC7N3XC.js → chunk-XAWLIU54.js}

@@ -9,7 +9,7 @@ import {
 } from "./chunk-VQWHMWLF.js";
 import {
   version
-} from "./chunk-J5FWKGOY.js";
+} from "./chunk-2CHS5LMM.js";
 import {
   axisScaleOf
 } from "./chunk-BS4UZ44I.js";

package/dist/cli/figure.js

@@ -7,7 +7,7 @@ import {
 } from "../chunks/chunk-G6UIYQZR.js";
 import {
   figureSvg
-} from "../chunks/chunk-3AOGOCCQ.js";
+} from "../chunks/chunk-GINYTQ43.js";
 import "../chunks/chunk-RUCH6ZFL.js";
 import "../chunks/chunk-BAETMD3J.js";
 import {
@@ -19,14 +19,14 @@ import "../chunks/chunk-RBCE2OQH.js";
 import "../chunks/chunk-JSUCGZ6K.js";
 import "../chunks/chunk-RPRHR56C.js";
 import "../chunks/chunk-XL472HHD.js";
-import "../chunks/chunk-YN6FDIBT.js";
+import "../chunks/chunk-KC7T5RWG.js";
 import "../chunks/chunk-4HWM3FNK.js";
 import "../chunks/chunk-KBEP7VYK.js";
 import "../chunks/chunk-H2H4Y3TV.js";
 import {
   laidOutGraph,
   walkLayers
-} from "../chunks/chunk-7CC7N3XC.js";
+} from "../chunks/chunk-XAWLIU54.js";
 import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind
@@ -51,7 +51,7 @@ import {
 } from "../chunks/chunk-VQWHMWLF.js";
 import "../chunks/chunk-Q7LYHGGQ.js";
 import "../chunks/chunk-WSIFAZU7.js";
-import "../chunks/chunk-J5FWKGOY.js";
+import "../chunks/chunk-2CHS5LMM.js";
 import "../chunks/chunk-BS4UZ44I.js";
 import "../chunks/chunk-4ETPXDO6.js";
 import "../chunks/chunk-D5D36ZF6.js";

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-3AOGOCCQ.js";
+} from "./chunks/chunk-GINYTQ43.js";
 import "./chunks/chunk-RUCH6ZFL.js";
 import "./chunks/chunk-BAETMD3J.js";
 import "./chunks/chunk-EFQLEGWM.js";
@@ -9,11 +9,11 @@ import "./chunks/chunk-RBCE2OQH.js";
 import "./chunks/chunk-JSUCGZ6K.js";
 import "./chunks/chunk-RPRHR56C.js";
 import "./chunks/chunk-XL472HHD.js";
-import "./chunks/chunk-YN6FDIBT.js";
+import "./chunks/chunk-KC7T5RWG.js";
 import "./chunks/chunk-4HWM3FNK.js";
 import "./chunks/chunk-KBEP7VYK.js";
 import "./chunks/chunk-H2H4Y3TV.js";
-import "./chunks/chunk-J5FWKGOY.js";
+import "./chunks/chunk-2CHS5LMM.js";
 import "./chunks/chunk-BS4UZ44I.js";
 import "./chunks/chunk-4ETPXDO6.js";
 import "./chunks/chunk-D5D36ZF6.js";

package/dist/figureData.js

@@ -3,7 +3,7 @@ import {
   gfaFigureData,
   laidOutGraph,
   walkLayers
-} from "./chunks/chunk-7CC7N3XC.js";
+} from "./chunks/chunk-XAWLIU54.js";
 import "./chunks/chunk-JMABOQWL.js";
 import "./chunks/chunk-WL6ZKUVC.js";
 import "./chunks/chunk-LOEA5IHZ.js";
@@ -17,7 +17,7 @@ import "./chunks/chunk-RVS2QCOX.js";
 import "./chunks/chunk-VQWHMWLF.js";
 import "./chunks/chunk-Q7LYHGGQ.js";
 import "./chunks/chunk-WSIFAZU7.js";
-import "./chunks/chunk-J5FWKGOY.js";
+import "./chunks/chunk-2CHS5LMM.js";
 import "./chunks/chunk-BS4UZ44I.js";
 import "./chunks/chunk-4ETPXDO6.js";
 import "./chunks/chunk-D5D36ZF6.js";

package/dist/index.js

@@ -45,7 +45,7 @@ import {
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "./chunks/chunk-XA5A27CS.js";
+} from "./chunks/chunk-ABUIN5AK.js";
 import {
   bubblesFromGraph
 } from "./chunks/chunk-CQHUZHET.js";
@@ -60,7 +60,7 @@ import {
 } from "./chunks/chunk-G6UIYQZR.js";
 import {
   bubbleHalos
-} from "./chunks/chunk-JFY5PWQC.js";
+} from "./chunks/chunk-JA2HJIYS.js";
 import {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
@@ -83,7 +83,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-3AOGOCCQ.js";
+} from "./chunks/chunk-GINYTQ43.js";
 import {
   svgCanvas
 } from "./chunks/chunk-RUCH6ZFL.js";
@@ -151,7 +151,7 @@ import {
   LEGEND_INSET_PX,
   geneCoverageNote,
   layoutLabels
-} from "./chunks/chunk-YN6FDIBT.js";
+} from "./chunks/chunk-KC7T5RWG.js";
 import {
   findHoveredEdge,
   findHoveredNode
@@ -164,7 +164,7 @@ import {
 import {
   figureData,
   gfaFigureData
-} from "./chunks/chunk-7CC7N3XC.js";
+} from "./chunks/chunk-XAWLIU54.js";
 import {
   LAYOUT_ENGINES,
   layoutEngine
@@ -201,7 +201,7 @@ import {
 import "./chunks/chunk-WSIFAZU7.js";
 import {
   version
-} from "./chunks/chunk-J5FWKGOY.js";
+} from "./chunks/chunk-2CHS5LMM.js";
 import {
   axisScaleOf,
   contains,

package/dist/labelLayout.js

@@ -4,7 +4,7 @@ import {
   geneCoverageNote,
   geneLabelCandidates,
   layoutLabels
-} from "./chunks/chunk-YN6FDIBT.js";
+} from "./chunks/chunk-KC7T5RWG.js";
 import "./chunks/chunk-4HWM3FNK.js";
 import "./chunks/chunk-KBEP7VYK.js";
 import "./chunks/chunk-ZY2AFL4Y.js";

package/dist/types/bubbles/bubbleHalos.d.ts

@@ -1,4 +1,4 @@
-import type { BubbleRoute, MinigraphBubble } from './bubbleLine.js';
+import type { MinigraphBubble } from './bubbleLine.js';
 import type { BubbleKind, RepeatSpan } from './classifyBubble.js';
 import type { Graph, NodeSegment } from '../types.js';
 export interface BubbleHalo {
@@ -11,14 +11,8 @@ export interface BubbleHalo {
     nodeIds: string[];
     whole: boolean;
     tick: boolean;
-    routes: RouteLabel[];
-}
-export interface RouteLabel {
-    route: BubbleRoute;
-    at: NodeSegment;
-    text: string;
 }
 export declare const WHOLE_FRACTION = 0.9;
 export declare function coversGraph(members: number, nodes: number): boolean;
 export declare const SMALL_VARIANT_BP = 50;
-export declare function bubbleHalos(graph: Graph, bubbles: MinigraphBubble[], positions: Record<string, NodeSegment[]>, walkLabel?: (name: string) => string, repeats?: readonly RepeatSpan[]): BubbleHalo[];
+export declare function bubbleHalos(graph: Graph, bubbles: MinigraphBubble[], positions: Record<string, NodeSegment[]>, repeats?: readonly RepeatSpan[]): BubbleHalo[];

package/dist/types/labelLayout.d.ts

@@ -1,4 +1,4 @@
-import type { BubbleHalo, RouteLabel } from './bubbles/bubbleHalos.js';
+import type { BubbleHalo } from './bubbles/bubbleHalos.js';
 import type { DeletionEdge } from './deletionEdges.js';
 import type { GenePin } from './genes/genePins.js';
 import type { GraphLabel } from './graphLabels.js';
@@ -47,10 +47,6 @@ export interface LabelLayout {
     bubbles: PlacedLabel<BubbleHalo>[];
     ticks: BubbleTick[];
     genes: PlacedLabel<GenePin>[];
-    routes: PlacedLabel<{
-        halo: BubbleHalo;
-        route: RouteLabel;
-    }>[];
     sizes: GraphLabel[];
 }
 export declare function geneCoverageNote(pin: GenePin): string | undefined;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "10.2.3";
+export declare const version = "10.2.4";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-J5FWKGOY.js";
+} from "./chunks/chunk-2CHS5LMM.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "10.2.3",
+  "version": "10.2.4",
   "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
   "license": "GPL-3.0-or-later",
   "repository": {

package/dist/chunks/chunk-JFY5PWQC.js

@@ -1,137 +0,0 @@
-import {
-  bubbleSegmentIds,
-  classifyBubble
-} from "./chunk-URZ3CH2R.js";
-import {
-  formatBp
-} from "./chunk-PTABFYQ7.js";
-import {
-  svgPath
-} from "./chunk-7SRWJLSC.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
-};