@jbrowse/bandage-core 9.8.0 → 9.9.0
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/dist/bubbles/popBubble.js +2 -2
- package/dist/bubbles/superbubbles.js +3 -3
- package/dist/chunks/{chunk-75HR3756.js → chunk-2NROXCK3.js} +47 -16
- package/dist/chunks/{chunk-MAUEPAMG.js → chunk-6PYZYBBF.js} +1 -1
- package/dist/chunks/{chunk-VHW7FDHU.js → chunk-A6PSWTLX.js} +1 -1
- package/dist/chunks/{chunk-CG77WIFD.js → chunk-BEMPOHHG.js} +13 -13
- package/dist/chunks/{chunk-7GBL7SJY.js → chunk-EDASNMLY.js} +1 -1
- package/dist/chunks/{chunk-3FVITQAJ.js → chunk-EE37PVQY.js} +2 -2
- package/dist/chunks/{chunk-BOHK5BD3.js → chunk-F4BKWWLS.js} +1 -1
- package/dist/chunks/{chunk-AM3P3WWO.js → chunk-F5BYHLIN.js} +1 -1
- package/dist/chunks/{chunk-ZGRYFUXE.js → chunk-FPTI3WAV.js} +13 -6
- package/dist/chunks/chunk-G45YY72K.js +220 -0
- package/dist/chunks/{chunk-6N7H22SS.js → chunk-HOZI3FBG.js} +2 -2
- package/dist/chunks/{chunk-ST2IBUAN.js → chunk-IGJCTPFB.js} +30 -5
- package/dist/chunks/{chunk-Z7UWHVOM.js → chunk-IJRNMO4D.js} +2 -2
- package/dist/chunks/chunk-IJYFJVIT.js +77 -0
- package/dist/chunks/{chunk-OCMBULGN.js → chunk-J7YKQ5YW.js} +1 -1
- package/dist/chunks/{chunk-VZQ4FKLR.js → chunk-JABM3MUS.js} +1 -1
- package/dist/chunks/{chunk-ZBWMTXTM.js → chunk-KJEMKHVB.js} +1 -1
- package/dist/chunks/{chunk-QMJXHYVQ.js → chunk-MECWJY2R.js} +2 -2
- package/dist/chunks/{chunk-EPREHMKU.js → chunk-P6O4RSOQ.js} +2 -2
- package/dist/chunks/{chunk-373Y3KUJ.js → chunk-RK3MF4FD.js} +1 -1
- package/dist/chunks/{chunk-C55SC5AJ.js → chunk-ROQGMTFB.js} +1 -1
- package/dist/chunks/{chunk-3C5UXR2U.js → chunk-TOVOJNT7.js} +1 -1
- package/dist/chunks/{chunk-JEF73V3A.js → chunk-UVZ56CZX.js} +1 -1
- package/dist/chunks/{chunk-5QOMIEHX.js → chunk-WVBYR6Y7.js} +2 -2
- package/dist/chunks/{chunk-BV64PQ2C.js → chunk-YAN2ZPNV.js} +1 -1
- package/dist/chunks/{chunk-BLRJ6IGK.js → chunk-YGN4KL7W.js} +1 -1
- package/dist/chunks/{chunk-QG5IVMRS.js → chunk-YS7VA5SI.js} +1 -1
- package/dist/chunks/{chunk-XKM5OHQQ.js → chunk-ZBLKAWSD.js} +1 -1
- package/dist/cli/figure.js +19 -18
- package/dist/cli/fold.js +4 -3
- package/dist/figure.js +17 -16
- package/dist/figureSettings.js +5 -4
- package/dist/gfa/gfaConverter.js +2 -2
- package/dist/gfa/gfaTables.js +6 -0
- package/dist/index.js +40 -36
- package/dist/layout/forceCache.js +5 -4
- package/dist/layout/trimToWindow.js +1 -1
- package/dist/layout/tubeMapLayout.js +3 -3
- package/dist/layout/walkRowDraw.js +5 -5
- package/dist/layout/walkRowLayout.js +3 -3
- package/dist/layout/walkRows.js +2 -2
- package/dist/layout/walkStrip.js +6 -6
- package/dist/layoutModes.js +6 -6
- package/dist/pathAnchoring.js +1 -1
- package/dist/pathColors.js +2 -2
- package/dist/pipeline.js +4 -3
- package/dist/referenceRampCss.js +4 -4
- package/dist/referenceStrip.js +4 -4
- package/dist/renderer/GeometryBuilder.js +3 -3
- package/dist/tubeMap/bundle.js +4 -4
- package/dist/tubeMap/coarsen.js +3 -3
- package/dist/tubeMap/draw.js +4 -1
- package/dist/tubeMap/frame.js +2 -2
- package/dist/tubeMap/nodeColors.js +4 -4
- package/dist/tubeMap/warp.js +1 -1
- package/dist/types/gfa/gfaTables.d.ts +10 -0
- package/dist/types/index.d.ts +1 -0
- package/dist/types/tubeMap/draw.d.ts +2 -1
- package/dist/types/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/viewport.js +5 -4
- package/dist/walkEncoding.js +4 -4
- package/dist/walkHighlight.js +5 -5
- package/package.json +1 -1
- package/dist/chunks/chunk-KQFOCDFY.js +0 -73
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|
endTangent,
|
|
12
12
|
getNodeColor,
|
|
13
13
|
hslToRgb
|
|
14
|
-
} from "../chunks/chunk-
|
|
14
|
+
} from "../chunks/chunk-F4BKWWLS.js";
|
|
15
15
|
import "../chunks/chunk-G2FD7S3C.js";
|
|
16
|
-
import "../chunks/chunk-
|
|
16
|
+
import "../chunks/chunk-EDASNMLY.js";
|
|
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17
|
import "../chunks/chunk-PBENCR5L.js";
|
|
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18
|
import "../chunks/chunk-WFB5TXRA.js";
|
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19
|
import "../chunks/chunk-3ZZSX5HN.js";
|
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20
|
import "../chunks/chunk-AB35TJST.js";
|
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21
|
import "../chunks/chunk-ES2N6V56.js";
|
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-
import "../chunks/chunk-
|
|
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+
import "../chunks/chunk-IGJCTPFB.js";
|
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23
|
import "../chunks/chunk-BPLIXMH7.js";
|
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24
|
import "../chunks/chunk-TAMCZHLW.js";
|
|
25
25
|
import "../chunks/chunk-N6FECAXP.js";
|
package/dist/tubeMap/bundle.js
CHANGED
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
import {
|
|
2
2
|
bundleRoutes
|
|
3
|
-
} from "../chunks/chunk-
|
|
4
|
-
import "../chunks/chunk-
|
|
3
|
+
} from "../chunks/chunk-WVBYR6Y7.js";
|
|
4
|
+
import "../chunks/chunk-HOZI3FBG.js";
|
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5
5
|
import "../chunks/chunk-CWFNEKST.js";
|
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6
|
import "../chunks/chunk-C44YRP5F.js";
|
|
7
|
-
import "../chunks/chunk-
|
|
7
|
+
import "../chunks/chunk-EDASNMLY.js";
|
|
8
8
|
import "../chunks/chunk-3ZZSX5HN.js";
|
|
9
9
|
import "../chunks/chunk-AB35TJST.js";
|
|
10
|
-
import "../chunks/chunk-
|
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10
|
+
import "../chunks/chunk-IGJCTPFB.js";
|
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11
|
import "../chunks/chunk-BPLIXMH7.js";
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12
|
import "../chunks/chunk-TAMCZHLW.js";
|
|
13
13
|
import "../chunks/chunk-N6FECAXP.js";
|
package/dist/tubeMap/coarsen.js
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
import {
|
|
2
2
|
pathSteps
|
|
3
|
-
} from "../chunks/chunk-
|
|
3
|
+
} from "../chunks/chunk-HOZI3FBG.js";
|
|
4
4
|
import "../chunks/chunk-CWFNEKST.js";
|
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5
5
|
import "../chunks/chunk-C44YRP5F.js";
|
|
6
|
-
import "../chunks/chunk-
|
|
6
|
+
import "../chunks/chunk-EDASNMLY.js";
|
|
7
7
|
import "../chunks/chunk-3ZZSX5HN.js";
|
|
8
8
|
import "../chunks/chunk-AB35TJST.js";
|
|
9
9
|
import {
|
|
10
10
|
pathOrigin
|
|
11
|
-
} from "../chunks/chunk-
|
|
11
|
+
} from "../chunks/chunk-IGJCTPFB.js";
|
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12
|
import "../chunks/chunk-BPLIXMH7.js";
|
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13
|
import "../chunks/chunk-TAMCZHLW.js";
|
|
14
14
|
import "../chunks/chunk-N6FECAXP.js";
|
package/dist/tubeMap/draw.js
CHANGED
|
@@ -8,10 +8,13 @@ import {
|
|
|
8
8
|
tubeMapMismatchAt,
|
|
9
9
|
tubeMapPicture,
|
|
10
10
|
tubeMapTrackAt
|
|
11
|
-
} from "../chunks/chunk-
|
|
11
|
+
} from "../chunks/chunk-2NROXCK3.js";
|
|
12
12
|
import "../chunks/chunk-XXT2JCAC.js";
|
|
13
13
|
import "../chunks/chunk-CWFNEKST.js";
|
|
14
14
|
import "../chunks/chunk-C44YRP5F.js";
|
|
15
|
+
import "../chunks/chunk-IGJCTPFB.js";
|
|
16
|
+
import "../chunks/chunk-BPLIXMH7.js";
|
|
17
|
+
import "../chunks/chunk-FYQWPEEY.js";
|
|
15
18
|
export {
|
|
16
19
|
drawTubeMap,
|
|
17
20
|
drawTubeMapHighlight,
|
package/dist/tubeMap/frame.js
CHANGED
|
@@ -1,15 +1,15 @@
|
|
|
1
1
|
import {
|
|
2
2
|
tubeMapNodeColors
|
|
3
|
-
} from "../chunks/chunk-
|
|
4
|
-
import "../chunks/chunk-
|
|
3
|
+
} from "../chunks/chunk-KJEMKHVB.js";
|
|
4
|
+
import "../chunks/chunk-F4BKWWLS.js";
|
|
5
5
|
import "../chunks/chunk-G2FD7S3C.js";
|
|
6
|
-
import "../chunks/chunk-
|
|
6
|
+
import "../chunks/chunk-EDASNMLY.js";
|
|
7
7
|
import "../chunks/chunk-PBENCR5L.js";
|
|
8
8
|
import "../chunks/chunk-WFB5TXRA.js";
|
|
9
9
|
import "../chunks/chunk-3ZZSX5HN.js";
|
|
10
10
|
import "../chunks/chunk-AB35TJST.js";
|
|
11
11
|
import "../chunks/chunk-ES2N6V56.js";
|
|
12
|
-
import "../chunks/chunk-
|
|
12
|
+
import "../chunks/chunk-IGJCTPFB.js";
|
|
13
13
|
import "../chunks/chunk-BPLIXMH7.js";
|
|
14
14
|
import "../chunks/chunk-TAMCZHLW.js";
|
|
15
15
|
import "../chunks/chunk-N6FECAXP.js";
|
package/dist/tubeMap/warp.js
CHANGED
|
@@ -0,0 +1,10 @@
|
|
|
1
|
+
import type { GraphTables } from './graphTables.js';
|
|
2
|
+
/**
|
|
3
|
+
* The tables a GFA of S, L and W lines stands for, which `graphFromTables`
|
|
4
|
+
* turns into the Graph `convertGFAToGraph` makes of the text. No string or
|
|
5
|
+
* object is made per walk step: a gbz-base cut of every haplotype is millions
|
|
6
|
+
* of steps, which the text route took seconds over. Undefined for a GFA the
|
|
7
|
+
* tables cannot hold (P or GFA2 records, a segment declared twice, an S tag
|
|
8
|
+
* other than LN/SN/SO/SR), which converts as text instead.
|
|
9
|
+
*/
|
|
10
|
+
export declare function gfaTables(text: string): GraphTables | undefined;
|
package/dist/types/index.d.ts
CHANGED
|
@@ -93,6 +93,7 @@ export { LABEL_CHAR_PX, LABEL_PAD, LABEL_PX } from './overlayLabels.js';
|
|
|
93
93
|
export type { Graph, GraphEdge, GraphNode, LayoutResult, NodeSegment, } from './types.js';
|
|
94
94
|
export { cutWindowGFA, haplotypeWanted, referencePathQuery, referenceSamplesOf, resolveReferenceSample, } from './gbzWindow.js';
|
|
95
95
|
export type { GbzWindowOptions } from './gbzWindow.js';
|
|
96
|
+
export { gfaTables } from './gfa/gfaTables.js';
|
|
96
97
|
export { graphFromTables, graphTablesGFA } from './gfa/graphTables.js';
|
|
97
98
|
export type { GraphTables } from './gfa/graphTables.js';
|
|
98
99
|
export { engineKey } from './pipeline.js';
|
|
@@ -34,6 +34,7 @@ interface Filled {
|
|
|
34
34
|
color: string;
|
|
35
35
|
id: number;
|
|
36
36
|
haplotype: boolean;
|
|
37
|
+
reference: boolean;
|
|
37
38
|
x0: number;
|
|
38
39
|
x1: number;
|
|
39
40
|
}
|
|
@@ -60,7 +61,7 @@ export interface TubeMapPicture {
|
|
|
60
61
|
mismatches: TubeMapMismatch[];
|
|
61
62
|
}
|
|
62
63
|
export declare function trackColors(layout: TubeMapLayout, pathColors: readonly string[]): ReadonlyMap<number, string>;
|
|
63
|
-
export declare function tubeMapPicture({ layout, pathColors, }: Pick<TubeMapDrawing, 'layout' | 'pathColors'>): TubeMapPicture;
|
|
64
|
+
export declare function tubeMapPicture({ layout, pathColors, graph, }: Pick<TubeMapDrawing, 'layout' | 'pathColors'> & Partial<Pick<TubeMapDrawing, 'graph'>>): TubeMapPicture;
|
|
64
65
|
export interface TubeMapFrame extends TubeMapTransform {
|
|
65
66
|
width: number;
|
|
66
67
|
highlightNode?: string | null;
|
package/dist/types/version.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
export declare const version = "9.
|
|
1
|
+
export declare const version = "9.9.0";
|
package/dist/version.js
CHANGED
package/dist/viewport.js
CHANGED
|
@@ -5,17 +5,18 @@ import {
|
|
|
5
5
|
screenToLayout,
|
|
6
6
|
viewportOf,
|
|
7
7
|
zoomAbout
|
|
8
|
-
} from "./chunks/chunk-
|
|
9
|
-
import "./chunks/chunk-
|
|
8
|
+
} from "./chunks/chunk-ZBLKAWSD.js";
|
|
9
|
+
import "./chunks/chunk-FPTI3WAV.js";
|
|
10
10
|
import "./chunks/chunk-PUG7LXDF.js";
|
|
11
11
|
import "./chunks/chunk-IGVV37VI.js";
|
|
12
|
-
import "./chunks/chunk-
|
|
12
|
+
import "./chunks/chunk-J7YKQ5YW.js";
|
|
13
|
+
import "./chunks/chunk-G45YY72K.js";
|
|
13
14
|
import "./chunks/chunk-OA7RIMZ2.js";
|
|
14
15
|
import "./chunks/chunk-QYBZZI5H.js";
|
|
15
16
|
import "./chunks/chunk-CDLPYR5O.js";
|
|
16
17
|
import "./chunks/chunk-JVLURPFW.js";
|
|
17
18
|
import "./chunks/chunk-ES2N6V56.js";
|
|
18
|
-
import "./chunks/chunk-
|
|
19
|
+
import "./chunks/chunk-IGJCTPFB.js";
|
|
19
20
|
import "./chunks/chunk-BPLIXMH7.js";
|
|
20
21
|
import "./chunks/chunk-TAMCZHLW.js";
|
|
21
22
|
import "./chunks/chunk-UVBGRJQX.js";
|
package/dist/walkEncoding.js
CHANGED
|
@@ -9,16 +9,16 @@ import {
|
|
|
9
9
|
schemeColor,
|
|
10
10
|
schemeCss,
|
|
11
11
|
schemeRgb
|
|
12
|
-
} from "./chunks/chunk-
|
|
13
|
-
import "./chunks/chunk-
|
|
12
|
+
} from "./chunks/chunk-F5BYHLIN.js";
|
|
13
|
+
import "./chunks/chunk-F4BKWWLS.js";
|
|
14
14
|
import "./chunks/chunk-G2FD7S3C.js";
|
|
15
|
-
import "./chunks/chunk-
|
|
15
|
+
import "./chunks/chunk-EDASNMLY.js";
|
|
16
16
|
import "./chunks/chunk-PBENCR5L.js";
|
|
17
17
|
import "./chunks/chunk-WFB5TXRA.js";
|
|
18
18
|
import "./chunks/chunk-3ZZSX5HN.js";
|
|
19
19
|
import "./chunks/chunk-AB35TJST.js";
|
|
20
20
|
import "./chunks/chunk-ES2N6V56.js";
|
|
21
|
-
import "./chunks/chunk-
|
|
21
|
+
import "./chunks/chunk-IGJCTPFB.js";
|
|
22
22
|
import "./chunks/chunk-BPLIXMH7.js";
|
|
23
23
|
import "./chunks/chunk-TAMCZHLW.js";
|
|
24
24
|
import "./chunks/chunk-N6FECAXP.js";
|
package/dist/walkHighlight.js
CHANGED
|
@@ -2,17 +2,17 @@ import {
|
|
|
2
2
|
facetLifts,
|
|
3
3
|
walkHighlight,
|
|
4
4
|
walkLift
|
|
5
|
-
} from "./chunks/chunk-
|
|
6
|
-
import "./chunks/chunk-
|
|
7
|
-
import "./chunks/chunk-
|
|
5
|
+
} from "./chunks/chunk-EE37PVQY.js";
|
|
6
|
+
import "./chunks/chunk-F5BYHLIN.js";
|
|
7
|
+
import "./chunks/chunk-F4BKWWLS.js";
|
|
8
8
|
import "./chunks/chunk-G2FD7S3C.js";
|
|
9
|
-
import "./chunks/chunk-
|
|
9
|
+
import "./chunks/chunk-EDASNMLY.js";
|
|
10
10
|
import "./chunks/chunk-PBENCR5L.js";
|
|
11
11
|
import "./chunks/chunk-WFB5TXRA.js";
|
|
12
12
|
import "./chunks/chunk-3ZZSX5HN.js";
|
|
13
13
|
import "./chunks/chunk-AB35TJST.js";
|
|
14
14
|
import "./chunks/chunk-ES2N6V56.js";
|
|
15
|
-
import "./chunks/chunk-
|
|
15
|
+
import "./chunks/chunk-IGJCTPFB.js";
|
|
16
16
|
import "./chunks/chunk-BPLIXMH7.js";
|
|
17
17
|
import "./chunks/chunk-TAMCZHLW.js";
|
|
18
18
|
import "./chunks/chunk-N6FECAXP.js";
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/bandage-core",
|
|
3
|
-
"version": "9.
|
|
3
|
+
"version": "9.9.0",
|
|
4
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",
|
|
5
5
|
"license": "GPL-3.0-or-later",
|
|
6
6
|
"repository": {
|
|
@@ -1,73 +0,0 @@
|
|
|
1
|
-
// src/tubeMap/warp.ts
|
|
2
|
-
var MAX_GAP_PX = 24;
|
|
3
|
-
var isReal = (c) => c.bp1 > c.bp0;
|
|
4
|
-
function referenceKnots(columns, bpToScreen) {
|
|
5
|
-
const real = columns.filter(isReal);
|
|
6
|
-
if (real.length === 0) {
|
|
7
|
-
const first = columns[0];
|
|
8
|
-
return first ? [{ tx: first.x0, sx: bpToScreen(first.bp0) }] : [];
|
|
9
|
-
}
|
|
10
|
-
const screen = real.map((c) => ({
|
|
11
|
-
c,
|
|
12
|
-
s0: bpToScreen(c.bp0),
|
|
13
|
-
s1: bpToScreen(c.bp1),
|
|
14
|
-
trimLeft: 0,
|
|
15
|
-
trimRight: 0
|
|
16
|
-
}));
|
|
17
|
-
for (let i = 0; i + 1 < screen.length; i++) {
|
|
18
|
-
const left = screen[i];
|
|
19
|
-
const right = screen[i + 1];
|
|
20
|
-
const demand = Math.min(right.c.x0 - left.c.x1, MAX_GAP_PX);
|
|
21
|
-
const short = demand - (right.s0 - left.s1);
|
|
22
|
-
if (short > 0) {
|
|
23
|
-
const capLeft = (left.s1 - left.s0) / 2;
|
|
24
|
-
const capRight = (right.s1 - right.s0) / 2;
|
|
25
|
-
let fromLeft = Math.min(short / 2, capLeft);
|
|
26
|
-
const fromRight = Math.min(short - fromLeft, capRight);
|
|
27
|
-
fromLeft = Math.min(short - fromRight, capLeft);
|
|
28
|
-
left.trimRight = fromLeft;
|
|
29
|
-
right.trimLeft = fromRight;
|
|
30
|
-
}
|
|
31
|
-
}
|
|
32
|
-
const knots = [];
|
|
33
|
-
for (const { c, s0, s1, trimLeft, trimRight } of screen) {
|
|
34
|
-
knots.push(
|
|
35
|
-
{ tx: c.x0, sx: s0 + trimLeft },
|
|
36
|
-
{ tx: c.x1, sx: s1 - trimRight }
|
|
37
|
-
);
|
|
38
|
-
}
|
|
39
|
-
return knots;
|
|
40
|
-
}
|
|
41
|
-
function warpX(knots, tx) {
|
|
42
|
-
const n = knots.length;
|
|
43
|
-
if (n === 0) {
|
|
44
|
-
return tx;
|
|
45
|
-
}
|
|
46
|
-
const first = knots[0];
|
|
47
|
-
const last = knots[n - 1];
|
|
48
|
-
if (tx <= first.tx) {
|
|
49
|
-
return first.sx + (tx - first.tx);
|
|
50
|
-
}
|
|
51
|
-
if (tx >= last.tx) {
|
|
52
|
-
return last.sx + (tx - last.tx);
|
|
53
|
-
}
|
|
54
|
-
let lo = 0;
|
|
55
|
-
let hi = n - 1;
|
|
56
|
-
while (hi - lo > 1) {
|
|
57
|
-
const mid = lo + hi >> 1;
|
|
58
|
-
if (knots[mid].tx <= tx) {
|
|
59
|
-
lo = mid;
|
|
60
|
-
} else {
|
|
61
|
-
hi = mid;
|
|
62
|
-
}
|
|
63
|
-
}
|
|
64
|
-
const a = knots[lo];
|
|
65
|
-
const b = knots[hi];
|
|
66
|
-
const span = b.tx - a.tx;
|
|
67
|
-
return span > 0 ? a.sx + (tx - a.tx) / span * (b.sx - a.sx) : a.sx;
|
|
68
|
-
}
|
|
69
|
-
|
|
70
|
-
export {
|
|
71
|
-
referenceKnots,
|
|
72
|
-
warpX
|
|
73
|
-
};
|