@jbrowse/bandage-core 9.4.0 → 9.5.0

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

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "9.4.0";
+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-4DEOECM3.js → chunk-T6EGLY2R.js}

@@ -45,7 +45,7 @@ import {
 } from "./chunk-BR25DGIJ.js";
 import {
   version
-} from "./chunk-BIGORSXS.js";
+} from "./chunk-DW4ZNIZH.js";
 import {
   walkRowLabels,
   walkRowsExtent

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-4DEOECM3.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-BIGORSXS.js";
+import "../chunks/chunk-DW4ZNIZH.js";
 import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-4DEOECM3.js";
+} from "./chunks/chunk-T6EGLY2R.js";
 import "./chunks/chunk-UD5FOCI2.js";
 import "./chunks/chunk-WBCOREDZ.js";
 import "./chunks/chunk-4BYTEJGW.js";
@@ -16,7 +16,7 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-OXTR3BVF.js";
 import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-BIGORSXS.js";
+import "./chunks/chunk-DW4ZNIZH.js";
 import "./chunks/chunk-3C5UXR2U.js";
 import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-7GBL7SJY.js";

package/dist/index.js

@@ -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-4DEOECM3.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-BIGORSXS.js";
+} from "./chunks/chunk-DW4ZNIZH.js";
 import {
   walkRowLabels,
   walkRowsExtent

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/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 = "9.4.0";
+export declare const version = "9.5.0";

package/dist/version.js

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

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "9.4.0",
+  "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": {