@jbrowse/bandage-core 9.3.0 → 9.5.0

package/dist/bubbles/bubbleHalos.js

@@ -3,7 +3,7 @@ import {
   WHOLE_FRACTION,
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-ABOZYAN5.js";
+} from "../chunks/chunk-REM73HCU.js";
 import "../chunks/chunk-XKWD2RY3.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/bubbles/superbubbles.js

@@ -1,9 +1,9 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-ROYHPOYF.js";
+} from "../chunks/chunk-TF7H5LQS.js";
 import "../chunks/chunk-VHW7FDHU.js";
-import "../chunks/chunk-ABOZYAN5.js";
+import "../chunks/chunk-REM73HCU.js";
 import "../chunks/chunk-XKWD2RY3.js";
 import "../chunks/chunk-GOZYKNQ2.js";
 import "../chunks/chunk-FX4RDMDN.js";

package/dist/chunks/{chunk-3FOOZ5VL.js → chunk-DRG4236Y.js}

@@ -21,6 +21,7 @@ var LEGEND_INSET_PX = 6;
 var ROUTE_STACK = 8;
 var GENE_PIN_DROP_PX = 18;
 var GENE_STACK = 2;
+var BUBBLE_STACK = 3;
 var TOPMOST_BASELINE = LABEL_PX + LABEL_PAD;
 function geneCoverageNote(pin) {
   const length = pin.gene.end - pin.gene.start;
@@ -102,10 +103,17 @@ function layoutLabels(m) {
   };
   const byBubble = byExtent(
     m.bubbleHalos.filter((h) => !h.tick),
-    (h) => h.members
+    (h) => h.whole ? -1 : h.members
   );
   const bubbles = placeLabels(
-    byBubble.map((h) => ({ item: h, ...above(h, 6), text: h.label })),
+    byBubble.map((h) => ({
+      item: h,
+      ...above(h, 6),
+      text: h.label,
+      // `0 bp–11 kb superbubble` where `…, 1198 segments, 5 routes` does not fit
+      fallback: h.label.includes(",") ? h.label.split(",")[0] : void 0,
+      stack: BUBBLE_STACK
+    })),
     frame,
     take
   );

package/dist/chunks/{chunk-BTMPPLDF.js → chunk-DW4ZNIZH.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "9.3.0";
+var version = "9.5.0";
 
 export {
   version

package/dist/chunks/{chunk-UNOE2NDN.js → chunk-Q6FRNVDU.js}

@@ -18,6 +18,7 @@ var UNTANGLE_LINKS = 3;
 var UNTANGLE_PUSH = 0.3;
 var SMOOTH_PASSES = 2;
 var MAX_HOPS = 200;
+var REFERENCE_HOPS = 20;
 var EPS = 0.1;
 var WARM = 0.5;
 function flipped(strand, name) {
@@ -238,7 +239,8 @@ function stressLayout(request, opts = {}) {
     let idx = c.indexOf[i];
     let dir = rand() < 0.5 ? -1 : 1;
     let remaining = length;
-    for (let hops = 0; hops < MAX_HOPS; hops++) {
+    const maxHops = refIdx[comp[i]].length >= 2 ? REFERENCE_HOPS : MAX_HOPS;
+    for (let hops = 0; hops < maxHops; hops++) {
       const points = count[chain];
       const step = per[chain];
       const toEnd = (dir > 0 ? points - 1 - idx : idx) * step;

package/dist/chunks/{chunk-ABOZYAN5.js → chunk-REM73HCU.js}

@@ -88,6 +88,7 @@ function bubbleHalos(graph, bubbles, positions, walkLabel = (name) => name, repe
         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),
@@ -95,9 +96,10 @@ function bubbleHalos(graph, bubbles, positions, walkLabel = (name) => name, repe
       labelAt,
       members: nodeIds.length,
       nodeIds,
-      whole: coversGraph(nodeIds.length, graph.nodes.length),
-      // a partial bubble's lengths are a floor, so it may be no small variant
-      tick: !bubble.partial && bubble.longestAlleleLength < SMALL_VARIANT_BP,
+      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
     });
   }

package/dist/chunks/{chunk-TL3TYSCP.js → chunk-T6EGLY2R.js}

@@ -45,7 +45,7 @@ import {
 } from "./chunk-BR25DGIJ.js";
 import {
   version
-} from "./chunk-BTMPPLDF.js";
+} from "./chunk-DW4ZNIZH.js";
 import {
   walkRowLabels,
   walkRowsExtent
@@ -62,7 +62,7 @@ import {
 } from "./chunk-RAKOB6IV.js";
 import {
   geneLabelCandidates
-} from "./chunk-3FOOZ5VL.js";
+} from "./chunk-DRG4236Y.js";
 import {
   nodesUnderBox
 } from "./chunk-FP4H7SFT.js";

package/dist/chunks/{chunk-ROYHPOYF.js → chunk-TF7H5LQS.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-VHW7FDHU.js";
 import {
   coversGraph
-} from "./chunk-ABOZYAN5.js";
+} from "./chunk-REM73HCU.js";
 import {
   bubbleSegmentIds
 } from "./chunk-XKWD2RY3.js";
@@ -259,11 +259,18 @@ function superbubblesFromGraph(graph, span) {
 function graphBubbles(graph, span) {
   const n = graph.nodes.length;
   const reach = bubblesFromGraph(graph);
-  return reach.length === 0 ? superbubblesFromGraph(graph, span) : reach.flatMap(
-    (b) => coversGraph(b.segmentCount - 2, n) ? superbubblesFromGraph(
-      b.segmentCount === n ? graph : bubbleSubgraph(graph, bubbleSegmentIds(b)),
-      b
-    ) : [b]
+  if (reach.length === 0) {
+    const inside = superbubblesFromGraph(graph, span);
+    return span ? [...inside, { ...span, covering: true }] : inside;
+  }
+  return reach.flatMap(
+    (b) => coversGraph(b.segmentCount - 2, n) ? [
+      ...superbubblesFromGraph(
+        b.segmentCount === n ? graph : bubbleSubgraph(graph, bubbleSegmentIds(b)),
+        b
+      ),
+      { ...b, covering: true }
+    ] : [b]
   );
 }
 

package/dist/chunks/{chunk-6EJIU6IA.js → chunk-VK6XMP6B.js}

@@ -1,6 +1,6 @@
 import {
   stressLayout
-} from "./chunk-UNOE2NDN.js";
+} from "./chunk-Q6FRNVDU.js";
 import {
   loadBandage
 } from "./chunk-7XHHVYG7.js";
@@ -14,7 +14,7 @@ var LAYOUT_ENGINES = [
   },
   {
     value: "stress",
-    label: "Stress (experimental)",
+    label: "Stress",
     description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring."
   }
 ];

package/dist/cli/figure.js

@@ -8,8 +8,8 @@ import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind,
   layoutEngine
-} from "../chunks/chunk-6EJIU6IA.js";
-import "../chunks/chunk-UNOE2NDN.js";
+} from "../chunks/chunk-VK6XMP6B.js";
+import "../chunks/chunk-Q6FRNVDU.js";
 import "../chunks/chunk-LYJ4US66.js";
 import {
   LAYOUT_MODES,
@@ -35,7 +35,7 @@ import "../chunks/chunk-LTUWJKHD.js";
 import "../chunks/chunk-WSIFAZU7.js";
 import {
   figureSvg
-} from "../chunks/chunk-TL3TYSCP.js";
+} from "../chunks/chunk-T6EGLY2R.js";
 import "../chunks/chunk-UD5FOCI2.js";
 import "../chunks/chunk-WBCOREDZ.js";
 import "../chunks/chunk-4BYTEJGW.js";
@@ -54,7 +54,7 @@ import "../chunks/chunk-2LQ5BWT7.js";
 import "../chunks/chunk-OXTR3BVF.js";
 import "../chunks/chunk-BR25DGIJ.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-BTMPPLDF.js";
+import "../chunks/chunk-DW4ZNIZH.js";
 import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,
@@ -67,7 +67,7 @@ import {
   graphBackbone,
   refNameBinding
 } from "../chunks/chunk-RAKOB6IV.js";
-import "../chunks/chunk-3FOOZ5VL.js";
+import "../chunks/chunk-DRG4236Y.js";
 import "../chunks/chunk-FP4H7SFT.js";
 import "../chunks/chunk-MLSWIMZO.js";
 import "../chunks/chunk-WFB5TXRA.js";

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-TL3TYSCP.js";
+} from "./chunks/chunk-T6EGLY2R.js";
 import "./chunks/chunk-UD5FOCI2.js";
 import "./chunks/chunk-WBCOREDZ.js";
 import "./chunks/chunk-4BYTEJGW.js";
@@ -16,13 +16,13 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-OXTR3BVF.js";
 import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-BTMPPLDF.js";
+import "./chunks/chunk-DW4ZNIZH.js";
 import "./chunks/chunk-3C5UXR2U.js";
 import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-RAKOB6IV.js";
-import "./chunks/chunk-3FOOZ5VL.js";
+import "./chunks/chunk-DRG4236Y.js";
 import "./chunks/chunk-FP4H7SFT.js";
 import "./chunks/chunk-MLSWIMZO.js";
 import "./chunks/chunk-WFB5TXRA.js";

package/dist/index.js

@@ -42,7 +42,7 @@ import {
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "./chunks/chunk-ROYHPOYF.js";
+} from "./chunks/chunk-TF7H5LQS.js";
 import {
   bubbleSubgraph
 } from "./chunks/chunk-VHW7FDHU.js";
@@ -54,7 +54,7 @@ import {
 } from "./chunks/chunk-BXEPA4KS.js";
 import {
   bubbleHalos
-} from "./chunks/chunk-ABOZYAN5.js";
+} from "./chunks/chunk-REM73HCU.js";
 import {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
@@ -74,10 +74,10 @@ import {
 import {
   LAYOUT_ENGINES,
   layoutEngine
-} from "./chunks/chunk-6EJIU6IA.js";
+} from "./chunks/chunk-VK6XMP6B.js";
 import {
   stressLayout
-} from "./chunks/chunk-UNOE2NDN.js";
+} from "./chunks/chunk-Q6FRNVDU.js";
 import "./chunks/chunk-LYJ4US66.js";
 import {
   FORCE_LAYOUT_LABEL,
@@ -119,7 +119,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-TL3TYSCP.js";
+} from "./chunks/chunk-T6EGLY2R.js";
 import {
   WALK_STRIP_CEILING_PX,
   cutsWholeWalks,
@@ -219,7 +219,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-BTMPPLDF.js";
+} from "./chunks/chunk-DW4ZNIZH.js";
 import {
   walkRowLabels,
   walkRowsExtent
@@ -255,7 +255,7 @@ import {
   LEGEND_INSET_PX,
   geneCoverageNote,
   layoutLabels
-} from "./chunks/chunk-3FOOZ5VL.js";
+} from "./chunks/chunk-DRG4236Y.js";
 import {
   findHoveredEdge,
   findHoveredNode

package/dist/labelLayout.js

@@ -4,7 +4,7 @@ import {
   geneCoverageNote,
   geneLabelCandidates,
   layoutLabels
-} from "./chunks/chunk-3FOOZ5VL.js";
+} from "./chunks/chunk-DRG4236Y.js";
 import "./chunks/chunk-FP4H7SFT.js";
 import "./chunks/chunk-MLSWIMZO.js";
 import "./chunks/chunk-WFB5TXRA.js";

package/dist/layout/stressEngine.js

@@ -1,7 +1,7 @@
 import {
   chains,
   stressLayout
-} from "../chunks/chunk-UNOE2NDN.js";
+} from "../chunks/chunk-Q6FRNVDU.js";
 import "../chunks/chunk-LYJ4US66.js";
 import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-FYQWPEEY.js";

package/dist/layoutEngines.js

@@ -3,8 +3,8 @@ import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind,
   layoutEngine
-} from "./chunks/chunk-6EJIU6IA.js";
-import "./chunks/chunk-UNOE2NDN.js";
+} from "./chunks/chunk-VK6XMP6B.js";
+import "./chunks/chunk-Q6FRNVDU.js";
 import "./chunks/chunk-LYJ4US66.js";
 import "./chunks/chunk-7XHHVYG7.js";
 import "./chunks/chunk-JVLURPFW.js";

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

@@ -14,6 +14,7 @@ export interface MinigraphBubble {
     routes?: BubbleRoute[];
     key?: string;
     offReference?: true;
+    covering?: true;
 }
 export interface BubbleRoute {
     steps: string[];

package/dist/types/layoutEngines.d.ts

@@ -5,7 +5,7 @@ export declare const LAYOUT_ENGINES: readonly [{
     readonly description: "Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm.";
 }, {
     readonly value: "stress";
-    readonly label: "Stress (experimental)";
+    readonly label: "Stress";
     readonly description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring.";
 }];
 export type LayoutEngineKind = (typeof LAYOUT_ENGINES)[number]['value'];

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "9.3.0";
+export declare const version = "9.5.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-BTMPPLDF.js";
+} from "./chunks/chunk-DW4ZNIZH.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "9.3.0",
+  "version": "9.5.0",
   "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": {