@jbrowse/bandage-core 10.2.2 → 10.2.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +6 -7
- package/dist/bubbles/bubbleHalos.js +7 -3
- package/dist/bubbles/bubblesFromGraph.js +4 -2
- package/dist/bubbles/classifyBubble.js +10 -5
- package/dist/bubbles/superbubbles.js +10 -6
- package/dist/chunks/{chunk-N6FECAXP.js → chunk-24WITXQY.js} +17 -8
- package/dist/chunks/{chunk-XTCNEKO5.js → chunk-2QLLQJ72.js} +15 -13
- package/dist/chunks/{chunk-ASSNZXCF.js → chunk-3AOGOCCQ.js} +44 -103
- package/dist/chunks/{chunk-TWRLC3KK.js → chunk-3XSM4OZU.js} +1 -1
- package/dist/chunks/{chunk-WEDZ76AK.js → chunk-4DRQTBBE.js} +1 -1
- package/dist/chunks/{chunk-2LQ5BWT7.js → chunk-4ETPXDO6.js} +1 -1
- package/dist/chunks/{chunk-FP4H7SFT.js → chunk-4HWM3FNK.js} +2 -2
- package/dist/chunks/{chunk-C7MZJSPT.js → chunk-54POIBVC.js} +2 -8
- package/dist/chunks/{chunk-PKFMP65V.js → chunk-5GMFEPWR.js} +1 -1
- package/dist/chunks/{chunk-CDLPYR5O.js → chunk-5I3K4R2G.js} +7 -6
- package/dist/chunks/{chunk-TICYLD5F.js → chunk-7CC7N3XC.js} +35 -78
- package/dist/chunks/{chunk-2CVHXFK7.js → chunk-7SRWJLSC.js} +19 -22
- package/dist/chunks/{chunk-SBMJNRTV.js → chunk-A4PFFC4Q.js} +37 -27
- package/dist/chunks/{chunk-IW6CYVX2.js → chunk-AR4BUBMU.js} +6 -1
- package/dist/chunks/{chunk-IUDJKOLB.js → chunk-B6IW3IRE.js} +15 -33
- package/dist/chunks/{chunk-JUIJI7RC.js → chunk-BAETMD3J.js} +9 -4
- package/dist/chunks/{chunk-L5WF4ZPS.js → chunk-BS4UZ44I.js} +1 -1
- package/dist/chunks/{chunk-HNQPEMYE.js → chunk-CM6LO6OC.js} +0 -1
- package/dist/chunks/{chunk-CLOP7UVD.js → chunk-CQHUZHET.js} +11 -8
- package/dist/chunks/{chunk-R456ME6J.js → chunk-CU6P5RUG.js} +17 -6
- package/dist/chunks/chunk-D5D36ZF6.js +107 -0
- package/dist/chunks/{chunk-AFP3NWSL.js → chunk-DY3JCAMX.js} +1 -1
- package/dist/chunks/{chunk-NRV7R36Q.js → chunk-EFQLEGWM.js} +3 -3
- package/dist/chunks/{chunk-BXEPA4KS.js → chunk-G6UIYQZR.js} +5 -2
- package/dist/chunks/{chunk-NNODIW4U.js → chunk-H2H4Y3TV.js} +1 -0
- package/dist/chunks/{chunk-MVFDSFV2.js → chunk-HNCXR2VS.js} +1 -1
- package/dist/chunks/{chunk-EYK7DJZV.js → chunk-J5FWKGOY.js} +1 -1
- package/dist/chunks/{chunk-PBENCR5L.js → chunk-JBCZIBFC.js} +0 -2
- package/dist/chunks/{chunk-EHUBJDDB.js → chunk-JFY5PWQC.js} +5 -3
- package/dist/chunks/{chunk-5BGP5Z64.js → chunk-JLSJMCDJ.js} +1 -1
- package/dist/chunks/{chunk-DT2GGH4D.js → chunk-JMABOQWL.js} +2 -6
- package/dist/chunks/{chunk-3S3YVOJ7.js → chunk-JSUCGZ6K.js} +1 -1
- package/dist/chunks/{chunk-MLSWIMZO.js → chunk-KBEP7VYK.js} +2 -2
- package/dist/chunks/{chunk-TAMCZHLW.js → chunk-N73TI3VG.js} +2 -2
- package/dist/chunks/chunk-O4EGE27I.js +10 -0
- package/dist/chunks/{chunk-3ZZSX5HN.js → chunk-PTABFYQ7.js} +10 -6
- package/dist/chunks/{chunk-WBCOREDZ.js → chunk-QLWI2PZ3.js} +16 -7
- package/dist/chunks/chunk-RBCE2OQH.js +32 -0
- package/dist/chunks/{chunk-BUBZ32IC.js → chunk-RPRHR56C.js} +4 -8
- package/dist/chunks/{chunk-47DYCZOK.js → chunk-RUCH6ZFL.js} +4 -0
- package/dist/chunks/{chunk-GNTTI6LA.js → chunk-T2PCSAFY.js} +1 -1
- package/dist/chunks/{chunk-XKWD2RY3.js → chunk-URZ3CH2R.js} +3 -10
- package/dist/chunks/{chunk-ALDGONEI.js → chunk-VQC7KELB.js} +1 -1
- package/dist/chunks/{chunk-FLFBYSJO.js → chunk-VQWHMWLF.js} +5 -1
- package/dist/chunks/{chunk-4R6QNG23.js → chunk-WL6ZKUVC.js} +3 -3
- package/dist/chunks/{chunk-CRTD2SBP.js → chunk-WZNPX7Q6.js} +6 -2
- package/dist/chunks/{chunk-FNGIQF43.js → chunk-XA5A27CS.js} +6 -14
- package/dist/chunks/{chunk-DK5P2YOL.js → chunk-XI3ZUTWF.js} +2 -2
- package/dist/chunks/{chunk-ZIUKZUPJ.js → chunk-XL472HHD.js} +1 -1
- package/dist/chunks/{chunk-BPRXQ2SS.js → chunk-XMW266WS.js} +1 -1
- package/dist/chunks/{chunk-DRG4236Y.js → chunk-YN6FDIBT.js} +2 -2
- package/dist/chunks/{chunk-WFB5TXRA.js → chunk-ZY2AFL4Y.js} +13 -31
- package/dist/cli/decodeText.js +6 -0
- package/dist/cli/figure.js +59 -60
- package/dist/cli/fold.js +13 -13
- package/dist/deletionEdges.js +6 -4
- package/dist/el.js +3 -1
- package/dist/figure.js +33 -31
- package/dist/figureData.js +32 -27
- package/dist/figureScene.js +43 -0
- package/dist/figureSettings.js +8 -8
- package/dist/foldVariants.js +2 -2
- package/dist/gbzCut.js +1 -1
- package/dist/genes/exonOutline.js +2 -2
- package/dist/genes/geneFiles.js +1 -1
- package/dist/genes/genePins.js +3 -3
- package/dist/gfa/gfaConverter.js +2 -2
- package/dist/gfa-core/gfaParser.js +1 -1
- package/dist/gfa-core/index.js +1 -1
- package/dist/graphLabels.js +4 -4
- package/dist/index.js +72 -73
- package/dist/labelLayout.js +8 -8
- package/dist/layout/forceCache.js +8 -8
- package/dist/layout/mergeRuns.js +2 -2
- package/dist/layout/orderedLayout.js +1 -3
- package/dist/layout/tubeMapLayout.js +6 -6
- package/dist/layout/walkRowDraw.js +11 -11
- package/dist/layout/walkRowLayout.js +3 -1
- package/dist/layout/walkStrip.js +14 -12
- package/dist/layoutEngines.js +1 -2
- package/dist/layoutModes.js +9 -9
- package/dist/nodeWidths.js +1 -3
- package/dist/pathColors.js +5 -5
- package/dist/pipeline.js +7 -7
- package/dist/referenceRampCss.js +9 -9
- package/dist/referenceStrip.js +9 -9
- package/dist/renderer/Canvas2DRenderer.js +2 -2
- package/dist/renderer/GeometryBuilder.js +8 -8
- package/dist/renderer/canvas.js +1 -1
- package/dist/renderer/svgCanvas.js +1 -1
- package/dist/tubeMap/axis.js +5 -5
- package/dist/tubeMap/bundle.js +7 -7
- package/dist/tubeMap/coarsen.js +6 -6
- package/dist/tubeMap/deviations.js +5 -5
- package/dist/tubeMap/draw.js +1 -1
- package/dist/tubeMap/genes.js +6 -6
- package/dist/tubeMap/nodeColors.js +9 -9
- package/dist/types/bubbles/bubblesFromGraph.d.ts +1 -0
- package/dist/types/bubbles/classifyBubble.d.ts +0 -1
- package/dist/types/cli/decodeText.d.ts +1 -0
- package/dist/types/cli/figure.d.ts +4 -15
- package/dist/types/deletionEdges.d.ts +3 -5
- package/dist/types/el.d.ts +1 -0
- package/dist/types/figureData.d.ts +7 -26
- package/dist/types/figureScene.d.ts +31 -0
- package/dist/types/genes/geneFiles.d.ts +2 -1
- package/dist/types/index.d.ts +1 -1
- package/dist/types/layout/deletionRoutes.d.ts +1 -1
- package/dist/types/layout/orderedLayout.d.ts +0 -6
- package/dist/types/layout/walkRowLayout.d.ts +1 -0
- package/dist/types/nodeWidths.d.ts +0 -1
- package/dist/types/renderer/Canvas2DRenderer.d.ts +1 -0
- package/dist/types/renderer/canvas.d.ts +2 -2
- package/dist/types/tubeMap/draw.d.ts +1 -0
- package/dist/types/util/geometry.d.ts +3 -3
- package/dist/types/version.d.ts +1 -1
- package/dist/util/SpatialIndex.js +4 -4
- package/dist/util/edgeCurves.js +3 -3
- package/dist/util/geometry.js +3 -3
- package/dist/util/hitDetection.js +5 -5
- package/dist/version.js +1 -1
- package/dist/viewport.js +8 -8
- package/dist/walkEncoding.js +9 -9
- package/dist/walkHighlight.js +10 -10
- package/dist/walkKey.js +5 -5
- package/package.json +3 -6
- package/dist/chunks/bandage-layout-3AR6BCUD.js +0 -4694
- package/dist/chunks/chunk-4BYTEJGW.js +0 -44
- package/dist/chunks/chunk-7XHHVYG7.js +0 -13
- package/dist/loadBandage.js +0 -6
- package/dist/types/bandage/bandage-layout.d.ts +0 -14
- package/dist/types/loadBandage.d.ts +0 -3
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import {
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layoutGeometryInputs
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import {
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facetLifts,
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walkLift
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buildGeometry,
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computeReferenceRamp
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walkRowsExtent
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import {
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pathLegend,
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walkLabelsOf
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FIGURE_DEFAULTS
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import {
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referenceLabel
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resolveColorScheme
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deletionDrawing,
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deletionEdges
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function figureScene(graph, layout, o) {
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const region = o.region;
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const rampDomain = o.colorDomain ?? region;
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const rows = o.walkRows;
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const bounds = drawingBounds(layout, {
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region: o.fitToDrawing ? void 0 : region,
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extent: rows && layout.extent ? walkRowsExtent(rows, o.walkRowPitch) : void 0
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// src/renderer/canvas.ts
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var MAX_DPR = 2;
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}
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function syncCanvasSize(canvas, width, height) {
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}
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return dpr;
|
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}
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|
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export {
|
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|
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MAX_CANVAS_DIM_PX,
|
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|
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+
syncCanvasSize
|
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};
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|
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1
1
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import {
|
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2
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polylineSlice
|
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3
|
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} from "./chunk-
|
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+
} from "./chunk-N73TI3VG.js";
|
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import {
|
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5
5
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svgPath
|
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6
|
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} from "./chunk-
|
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|
+
} from "./chunk-7SRWJLSC.js";
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|
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7
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import {
|
|
8
8
|
firstNodeAtOrAfter,
|
|
9
9
|
isAnchored
|
|
@@ -74,12 +74,8 @@ function genePins(graph, genes, positions) {
|
|
|
74
74
|
const distance = Math.abs(pinBp - mid);
|
|
75
75
|
if (distance < atDistance) {
|
|
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76
|
atDistance = distance;
|
|
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|
-
const
|
|
78
|
-
|
|
79
|
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(pinBp - nodeStart) / node.length,
|
|
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|
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(pinBp - nodeStart) / node.length
|
|
81
|
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);
|
|
82
|
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at = p;
|
|
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|
+
const along = node.length ? (pinBp - nodeStart) / node.length : 0;
|
|
78
|
+
at = polylineSlice(line, along, along)[0];
|
|
83
79
|
}
|
|
84
80
|
}
|
|
85
81
|
if (at) {
|
|
@@ -90,6 +90,10 @@ function svgCanvas(width, height) {
|
|
|
90
90
|
out.push(`<path d="${d}" ${paintAttrs("fill", ctx.fillStyle)}/>`);
|
|
91
91
|
}
|
|
92
92
|
},
|
|
93
|
+
// the renderer only ever clears the whole canvas
|
|
94
|
+
clearRect() {
|
|
95
|
+
out.length = 0;
|
|
96
|
+
},
|
|
93
97
|
fillRect(x, y, w, h) {
|
|
94
98
|
out.push(
|
|
95
99
|
`<rect x="${n(x)}" y="${n(y)}" width="${n(w)}" height="${n(h)}" ${paintAttrs("fill", ctx.fillStyle)}/>`
|
|
@@ -1,6 +1,9 @@
|
|
|
1
1
|
import {
|
|
2
2
|
SATURATED_PATH_COUNT
|
|
3
3
|
} from "./chunk-FX4RDMDN.js";
|
|
4
|
+
import {
|
|
5
|
+
formatBp
|
|
6
|
+
} from "./chunk-PTABFYQ7.js";
|
|
4
7
|
|
|
5
8
|
// src/bubbles/classifyBubble.ts
|
|
6
9
|
var REPEAT_GROWTH = 10;
|
|
@@ -12,15 +15,6 @@ function coveringRepeat(b, repeats) {
|
|
|
12
15
|
);
|
|
13
16
|
}
|
|
14
17
|
var SUPERBUBBLE_SEGMENTS = 40;
|
|
15
|
-
function formatBp(bp) {
|
|
16
|
-
if (bp >= 1e4) {
|
|
17
|
-
return `${(bp / 1e3).toFixed(0)} kb`;
|
|
18
|
-
}
|
|
19
|
-
if (bp >= 1e3) {
|
|
20
|
-
return `${(bp / 1e3).toFixed(1)} kb`;
|
|
21
|
-
}
|
|
22
|
-
return `${bp} bp`;
|
|
23
|
-
}
|
|
24
18
|
function formatBpRange(shortest, longest) {
|
|
25
19
|
const low = formatBp(shortest);
|
|
26
20
|
const high = formatBp(longest);
|
|
@@ -119,7 +113,6 @@ function bubbleSegmentIds(b) {
|
|
|
119
113
|
}
|
|
120
114
|
|
|
121
115
|
export {
|
|
122
|
-
formatBp,
|
|
123
116
|
classifyBubble,
|
|
124
117
|
BUBBLE_KIND_COLORS,
|
|
125
118
|
BUBBLE_KIND_NAMES,
|
|
@@ -25,7 +25,11 @@ function parseRegion(text) {
|
|
|
25
25
|
);
|
|
26
26
|
}
|
|
27
27
|
const n = (s) => Number(s.replaceAll(",", ""));
|
|
28
|
-
|
|
28
|
+
const region = { refName: m[1], start: n(m[2]), end: n(m[3]) };
|
|
29
|
+
if (region.end <= region.start) {
|
|
30
|
+
throw new Error(`"${text}" ends at or before it starts`);
|
|
31
|
+
}
|
|
32
|
+
return region;
|
|
29
33
|
}
|
|
30
34
|
async function openGbz(db, index) {
|
|
31
35
|
const base = await GBZBase.open({ source: db, haplotypeIndex: index });
|
|
@@ -6,16 +6,16 @@ import {
|
|
|
6
6
|
hasTubeMapPaths,
|
|
7
7
|
tubeMapLayout,
|
|
8
8
|
tubeMapReferenceLayout
|
|
9
|
-
} from "./chunk-
|
|
9
|
+
} from "./chunk-XI3ZUTWF.js";
|
|
10
10
|
import {
|
|
11
11
|
anchoredLayout
|
|
12
12
|
} from "./chunk-L3O7AWLI.js";
|
|
13
13
|
import {
|
|
14
14
|
orderedLayout
|
|
15
|
-
} from "./chunk-
|
|
15
|
+
} from "./chunk-CM6LO6OC.js";
|
|
16
16
|
import {
|
|
17
17
|
walkRowLayout
|
|
18
|
-
} from "./chunk-
|
|
18
|
+
} from "./chunk-54POIBVC.js";
|
|
19
19
|
import {
|
|
20
20
|
isBackbone,
|
|
21
21
|
isOffReference
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import {
|
|
2
2
|
engineKey,
|
|
3
3
|
forceLayout
|
|
4
|
-
} from "./chunk-
|
|
4
|
+
} from "./chunk-2QLLQJ72.js";
|
|
5
5
|
|
|
6
6
|
// src/layout/forceCache.ts
|
|
7
7
|
var DEFAULT_SIZE = 4;
|
|
@@ -33,7 +33,11 @@ function createForceLayoutCache(size = DEFAULT_SIZE) {
|
|
|
33
33
|
return { ...r, duration: r.duration || performance.now() - started };
|
|
34
34
|
})
|
|
35
35
|
};
|
|
36
|
-
entry.run.catch(() =>
|
|
36
|
+
entry.run.catch(() => {
|
|
37
|
+
if (cache.get(key) === entry) {
|
|
38
|
+
cache.delete(key);
|
|
39
|
+
}
|
|
40
|
+
});
|
|
37
41
|
cache.set(key, entry);
|
|
38
42
|
return entry.run;
|
|
39
43
|
},
|
|
@@ -1,23 +1,21 @@
|
|
|
1
1
|
import {
|
|
2
2
|
bubblesFromGraph,
|
|
3
|
+
relax,
|
|
3
4
|
walkIndexOf,
|
|
4
5
|
walkRoutes
|
|
5
|
-
} from "./chunk-
|
|
6
|
+
} from "./chunk-CQHUZHET.js";
|
|
6
7
|
import {
|
|
7
8
|
bubbleSubgraph
|
|
8
9
|
} from "./chunk-T6V4KI2L.js";
|
|
9
10
|
import {
|
|
10
11
|
coversGraph
|
|
11
|
-
} from "./chunk-
|
|
12
|
+
} from "./chunk-JFY5PWQC.js";
|
|
12
13
|
import {
|
|
13
14
|
bubbleSegmentIds
|
|
14
|
-
} from "./chunk-
|
|
15
|
-
import {
|
|
16
|
-
SATURATED_PATH_COUNT
|
|
17
|
-
} from "./chunk-FX4RDMDN.js";
|
|
15
|
+
} from "./chunk-URZ3CH2R.js";
|
|
18
16
|
import {
|
|
19
17
|
strandSides
|
|
20
|
-
} from "./chunk-
|
|
18
|
+
} from "./chunk-7SRWJLSC.js";
|
|
21
19
|
import {
|
|
22
20
|
isBackbone
|
|
23
21
|
} from "./chunk-FYQWPEEY.js";
|
|
@@ -196,13 +194,7 @@ function routesThrough(nodes, offset, next, f) {
|
|
|
196
194
|
}
|
|
197
195
|
for (let p = offset[k]; p < offset[k + 1]; p++) {
|
|
198
196
|
const u = next[p] >> 1;
|
|
199
|
-
|
|
200
|
-
const prev = best.get(u);
|
|
201
|
-
best.set(u, {
|
|
202
|
-
min: Math.min(prev?.min ?? Infinity, cur.min + add),
|
|
203
|
-
max: Math.max(prev?.max ?? -Infinity, cur.max + add),
|
|
204
|
-
n: Math.min(SATURATED_PATH_COUNT, cur.n + (prev?.n ?? 0))
|
|
205
|
-
});
|
|
197
|
+
relax(best, u, cur, u === sink ? 0 : nodes[u].length);
|
|
206
198
|
}
|
|
207
199
|
}
|
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208
200
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return best.get(sink) ?? { min: 0, max: 0, n: 0 };
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@@ -6,14 +6,14 @@ import {
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6
6
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import {
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7
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pathCssColor,
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8
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pathGreyCssColor
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9
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-
} from "./chunk-
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9
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+
} from "./chunk-3XSM4OZU.js";
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import {
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11
11
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pathOrigin
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12
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} from "./chunk-M6LK4GII.js";
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import {
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14
14
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ownStrand,
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15
15
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strandSides
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16
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-
} from "./chunk-
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16
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+
} from "./chunk-7SRWJLSC.js";
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import {
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18
18
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isBackbone
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} from "./chunk-FYQWPEEY.js";
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@@ -1,12 +1,12 @@
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1
1
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import {
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2
2
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nodesUnderBox
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3
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-
} from "./chunk-
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3
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+
} from "./chunk-4HWM3FNK.js";
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4
4
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import {
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5
5
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nodeLabelBudget,
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6
6
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placeSizeLabels,
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7
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rowLabelBox,
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8
8
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sizeLabelCandidates
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9
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-
} from "./chunk-
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9
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+
} from "./chunk-PTABFYQ7.js";
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10
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import {
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11
11
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LABEL_CHAR_PX,
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12
12
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LABEL_PAD,
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