@jbrowse/bandage-core 7.0.0 → 7.2.0

package/dist/chunks/{chunk-EZPBJPK6.js → chunk-3JANT2SW.js}

@@ -12,14 +12,17 @@ import {
 
 // src/layout/walkRowLayout.ts
 var READOUT_ROOM = 1.3;
-function walkRowsExtent(walks) {
+function walkRowsExtent(walks, pitch = {
+  rowPx: ROW_HEIGHT_PX,
+  readouts: true
+}) {
   let longest = walks.reference.bp;
   for (const row of walks.rows) {
     longest = Math.max(longest, row.bp);
   }
   return {
-    maxX: walks.origin + longest * READOUT_ROOM,
-    maxY: walks.rows.length * ROW_HEIGHT_PX
+    maxX: walks.origin + longest * (pitch.readouts ? READOUT_ROOM : 1),
+    maxY: walks.rows.length * pitch.rowPx
   };
 }
 function walkRowLayout(graph, region) {

package/dist/chunks/chunk-6EJIU6IA.js

@@ -0,0 +1,42 @@
+import {
+  stressLayout
+} from "./chunk-UNOE2NDN.js";
+import {
+  loadBandage
+} from "./chunk-7XHHVYG7.js";
+
+// src/layoutEngines.ts
+var LAYOUT_ENGINES = [
+  {
+    value: "fmmm",
+    label: "Bandage (FMMM)",
+    description: "Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm."
+  },
+  {
+    value: "stress",
+    label: "Stress (experimental)",
+    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."
+  }
+];
+var LAYOUT_ENGINE_VALUES = LAYOUT_ENGINES.map((e) => e.value);
+function isLayoutEngineKind(value) {
+  return LAYOUT_ENGINE_VALUES.includes(value);
+}
+var layoutEngine = async (request) => {
+  if (request.options.engine === "stress") {
+    const start2 = performance.now();
+    const result2 = stressLayout(request);
+    return { result: result2, duration: performance.now() - start2 };
+  }
+  const bandage = await loadBandage();
+  const start = performance.now();
+  const result = bandage.computeLayout(request.graph, request.options);
+  return { result, duration: performance.now() - start };
+};
+
+export {
+  LAYOUT_ENGINES,
+  LAYOUT_ENGINE_VALUES,
+  isLayoutEngineKind,
+  layoutEngine
+};

package/dist/chunks/{chunk-6UFS3EWI.js → chunk-EPWYRSHH.js}

@@ -14,7 +14,7 @@ import {
   routeNodes,
   takeRoutes,
   withDeletionRoutes
-} from "./chunk-YZ5CCEDH.js";
+} from "./chunk-JVLURPFW.js";
 import {
   anchorGraph
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-WEMKWLDF.js → chunk-JKXE6CIP.js}

@@ -14,7 +14,7 @@ import {
 } from "./chunk-HNQPEMYE.js";
 import {
   walkRowLayout
-} from "./chunk-EZPBJPK6.js";
+} from "./chunk-3JANT2SW.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-YZ5CCEDH.js → chunk-JVLURPFW.js}

@@ -73,6 +73,7 @@ function takeRoutes(positions, routes) {
 }
 
 export {
+  ROUTE_ID,
   withDeletionRoutes,
   routeNodes,
   takeRoutes

package/dist/chunks/{chunk-MZ7QQRUJ.js → chunk-KREASK3Z.js}

@@ -1,16 +1,14 @@
 import {
   alongRow,
-  boxesGenes
-} from "./chunk-JFNPL4UT.js";
+  boxesGenes,
+  rowPitch
+} from "./chunk-UGD6ZMOF.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";
-import {
-  ROW_HEIGHT_PX
-} from "./chunk-CPMHA4W5.js";
 import {
   el
 } from "./chunk-NNODIW4U.js";
@@ -20,7 +18,6 @@ var PAD_PX = 6;
 var WALK_STRIP_CEILING_PX = 260;
 var LABEL_FONT_PX = 11;
 var MIN_ROW_PX = 3;
-var LABELLED_ROW_PX = 12;
 var READOUT_ROOM = 1.3;
 var MARK_INK = "#111";
 var TICK_PX = 3;
@@ -113,13 +110,11 @@ function walkStripFrame(bars, o) {
   const maxHeight = o.maxHeight ?? WALK_STRIP_CEILING_PX;
   const labelPx = o.labelPx ?? Math.max(...[bars.reference, ...bars.rows].map((r) => r.label.length)) * LABEL_CHAR_PX + 16;
   const count = bars.rows.length + 1;
-  const rowPx = Math.max(
-    MIN_ROW_PX,
-    Math.min(ROW_HEIGHT_PX, Math.floor((maxHeight - 2 * PAD_PX) / count))
+  const { rowPx, barPx, labelled, readouts } = rowPitch(
+    count,
+    maxHeight - 2 * PAD_PX,
+    MIN_ROW_PX
   );
-  const labelled = rowPx >= LABELLED_ROW_PX;
-  const readouts = rowPx >= 14;
-  const barPx = Math.max(2, Math.round(rowPx * 0.6));
   const longest = Math.max(bars.reference.bp, ...bars.rows.map((r) => r.bp), 1);
   const left = labelled ? labelPx : PAD_PX;
   const usable = Math.max(1, o.width - left - PAD_PX);
@@ -194,7 +189,6 @@ function stripGeneGaps(frame, rowGenes, gaps) {
 
 export {
   WALK_STRIP_CEILING_PX,
-  LABELLED_ROW_PX,
   stripMarks,
   segmentAt,
   walkStripFrame,