@jbrowse/bandage-core 11.7.3 → 11.8.0
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/README.md +59 -19
- package/dist/bubbles/bubbleHalos.js +6 -6
- package/dist/bubbles/classifyBubble.js +5 -5
- package/dist/bubbles/superbubbles.js +7 -7
- package/dist/chunks/{chunk-ZZZ6NVLW.js → chunk-22ZMVREZ.js} +1 -1
- package/dist/chunks/{chunk-VXKL2ZLR.js → chunk-2H3ALI6L.js} +223 -45
- package/dist/chunks/{chunk-F4CDC72I.js → chunk-2RCKHCF7.js} +1 -1
- package/dist/chunks/{chunk-P276TWPM.js → chunk-3CXZUC2Y.js} +1 -1
- package/dist/chunks/{chunk-VNF236GG.js → chunk-3XYLEK4H.js} +2 -2
- package/dist/chunks/{chunk-PKGPSTRW.js → chunk-4OVIUCSB.js} +2 -2
- package/dist/chunks/{chunk-BLDUBB7X.js → chunk-4YPCUVMC.js} +2 -2
- package/dist/chunks/{chunk-N73RA4DR.js → chunk-6CXLLJ2C.js} +3 -3
- package/dist/chunks/{chunk-4SN7R4UF.js → chunk-6MD4VS2F.js} +1 -1
- package/dist/chunks/{chunk-VACK24HF.js → chunk-735MPLUL.js} +35 -9
- package/dist/chunks/chunk-7GDNDQD7.js +504 -0
- package/dist/chunks/{chunk-2US43KNG.js → chunk-7PEYA3NA.js} +2 -2
- package/dist/chunks/{chunk-XTCIKBWM.js → chunk-AXE3RR7J.js} +1 -1
- package/dist/chunks/{chunk-BXE3SBBN.js → chunk-C3KAPREU.js} +1 -1
- package/dist/chunks/{chunk-QJC63NFR.js → chunk-G3GLGDKV.js} +2 -2
- package/dist/chunks/{chunk-63XWYNID.js → chunk-G4WQBRDS.js} +4 -4
- package/dist/chunks/{chunk-SDI6BVG7.js → chunk-J4PDHWP2.js} +1 -1
- package/dist/chunks/{chunk-GD6RUZU5.js → chunk-JKIAHYAW.js} +14 -8
- package/dist/chunks/{chunk-AJQRKN3X.js → chunk-L2RQV23D.js} +1 -1
- package/dist/chunks/{chunk-EPOPGV5G.js → chunk-LA6JHEVV.js} +1 -1
- package/dist/chunks/{chunk-G7SG4XMK.js → chunk-LODKC7PJ.js} +7 -0
- package/dist/chunks/{chunk-QXBQDHKL.js → chunk-MO4DIRHD.js} +80 -38
- package/dist/chunks/{chunk-IHM43Y7B.js → chunk-N2GAA7RB.js} +1 -1
- package/dist/chunks/{chunk-6RB5ZQ34.js → chunk-N4AJV4GH.js} +25 -14
- package/dist/chunks/{chunk-LH436HS2.js → chunk-NHOXLUIL.js} +2 -2
- package/dist/chunks/{chunk-QLLKALSH.js → chunk-NQWEYJDD.js} +1 -1
- package/dist/chunks/{chunk-AWJJSA7D.js → chunk-OIOAK7BS.js} +1 -1
- package/dist/chunks/{chunk-UTDMFVC7.js → chunk-R3NPBUKT.js} +8 -8
- package/dist/chunks/{chunk-4KOYS5WR.js → chunk-R4XCTRIU.js} +1 -1
- package/dist/chunks/{chunk-XKPXOIWD.js → chunk-S3ICPPXC.js} +3 -3
- package/dist/chunks/{chunk-K4KVAMEF.js → chunk-S4CH434Z.js} +1 -1
- package/dist/chunks/{chunk-HMEAGAGC.js → chunk-S7BCZVRK.js} +2 -2
- package/dist/chunks/{chunk-SG7VQB4F.js → chunk-SDDMV2MM.js} +1 -1
- package/dist/chunks/{chunk-KMLATBNT.js → chunk-SIXFXXRI.js} +3 -3
- package/dist/chunks/{chunk-T3MEG5D3.js → chunk-U6JPSXJ3.js} +90 -21
- package/dist/chunks/{chunk-SENPGW4O.js → chunk-VCUOYVLC.js} +1 -1
- package/dist/chunks/{chunk-33KUO34R.js → chunk-VSRRIFRF.js} +1 -1
- package/dist/chunks/{chunk-BFUS3ENH.js → chunk-X5ULFAMM.js} +2 -2
- package/dist/chunks/{chunk-W5YRBEWQ.js → chunk-XOIYBEU7.js} +1 -1
- package/dist/chunks/{chunk-CL6ELLVF.js → chunk-YEDZ37PH.js} +1 -1
- package/dist/chunks/{chunk-Z4HXW6ZH.js → chunk-YF6T33PU.js} +10 -2
- package/dist/chunks/{chunk-2VMKQKVO.js → chunk-YIWN32ZX.js} +1 -1
- package/dist/chunks/{chunk-2T3V6Z3M.js → chunk-ZKIH2USC.js} +1 -1
- package/dist/cli/figure.js +31 -30
- package/dist/cli/fold.js +6 -6
- package/dist/deletionEdges.js +2 -2
- package/dist/figure.js +27 -26
- package/dist/figureData.js +25 -24
- package/dist/figureScene.js +18 -17
- package/dist/figureSettings.js +6 -6
- package/dist/foldVariants.js +2 -2
- package/dist/genes/genePins.js +3 -3
- package/dist/graphLabels.js +4 -4
- package/dist/index.js +45 -44
- package/dist/labelLayout.js +8 -8
- package/dist/layout/forceCache.js +6 -6
- package/dist/layout/mergeRuns.js +2 -2
- package/dist/layout/orientToReference.js +2 -2
- package/dist/layout/tubeMapLayout.js +9 -9
- package/dist/layout/walkRowDraw.js +9 -8
- package/dist/layout/walkRowLayout.js +3 -3
- package/dist/layout/walkRowRuns.js +1 -1
- package/dist/layout/walkRows.js +2 -2
- package/dist/layout/walkStrip.js +13 -12
- package/dist/layoutModes.js +11 -11
- package/dist/pathColors.js +5 -5
- package/dist/pipeline.js +5 -5
- package/dist/referenceStrip.js +9 -8
- package/dist/renderer/GeometryBuilder.js +8 -7
- package/dist/renderer/walkLanes.js +44 -0
- package/dist/tubeMap/axis.js +5 -5
- package/dist/tubeMap/bundle.js +10 -10
- package/dist/tubeMap/coarsen.js +10 -10
- package/dist/tubeMap/deviations.js +11 -11
- package/dist/tubeMap/draw.js +5 -5
- package/dist/tubeMap/genes.js +6 -6
- package/dist/tubeMap/nodeColors.js +9 -8
- package/dist/tubeMap/reads.js +2 -2
- package/dist/types/figureData.d.ts +22 -0
- package/dist/types/renderer/types.d.ts +20 -0
- package/dist/types/renderer/walkLanes.d.ts +60 -0
- package/dist/types/util/geometry.d.ts +13 -1
- package/dist/types/version.d.ts +1 -1
- package/dist/types/walkEncoding.d.ts +7 -5
- package/dist/types/walkHighlight.d.ts +3 -0
- package/dist/util/SpatialIndex.js +4 -4
- package/dist/util/edgeCurves.js +3 -3
- package/dist/util/geometry.js +7 -1
- package/dist/util/hitDetection.js +5 -5
- package/dist/version.js +1 -1
- package/dist/viewport.js +6 -6
- package/dist/walkEncoding.js +9 -8
- package/dist/walkHighlight.js +10 -9
- package/dist/walkKey.js +5 -5
- package/package.json +1 -1
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import {
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layoutModeByValue
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genePins
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version
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axisScaleOf
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import {
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figureScene
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import {
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encodingStops
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import {
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laneSlideAt,
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passesKey,
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threadsPasses
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} from "./chunk-7GDNDQD7.js";
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import {
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abgrBlue,
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import {
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FIGURE_DEFAULTS
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import {
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engineSettingsOf,
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fitTransform,
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forceLayout,
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loadGraph
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referenceVisitStarts
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}
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const axis = axisScaleOf(fit.scale, pixelRows);
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const panels = [];
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const keys = columns([
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const keys = columns([
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"panel",
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"walk",
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"name",
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"color",
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"note",
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"scale",
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"stops",
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"field"
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]);
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const threadKeys = columns(["panel", "note"]);
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const pushKey = (walk, panel) => {
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const key = keyText(walk);
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const stops = encodingStops(walk.encoding).map((s) => cssHex(s.abgr));
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keys.push({
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panel,
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walk: labelOf(walk.name),
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name: walk.name,
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color: walk.encoding.field === "walk" ? stops[0] : "",
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note: key.note,
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scale: key.scale ?? "",
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stops: stops.join(","),
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field: walk.encoding.field
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return key;
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const walk = panel.walks[0];
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panels.push({
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name,
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key: key.note,
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for (const walk of lift?.walks ?? []) {
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threadKeys.push({ panel: "", note: passesKey(lift?.walks ?? []) });
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panels.push({
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name: "",
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key: "",
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range: "",
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firstKeyRow: 0
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});
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const pins = columns(["gene", "x", "y", "covered", "bp"]);
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threadKeys: threadKeys.out,
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pins: pins.out,
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exons: exons.out,
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walkNames: [...new Set((graph.paths ?? []).map((p) => p.name))],
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|
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|
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|
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|
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|
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|
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|
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|
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|
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import "../chunks/chunk-YIWN32ZX.js";
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|
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package/dist/cli/fold.js
CHANGED
|
@@ -7,12 +7,12 @@ import {
|
|
|
7
7
|
} from "../chunks/chunk-O4EGE27I.js";
|
|
8
8
|
import {
|
|
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9
|
foldVariants
|
|
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|
-
} from "../chunks/chunk-
|
|
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|
+
} from "../chunks/chunk-R4XCTRIU.js";
|
|
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|
import {
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|
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|
loadGraph
|
|
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|
-
} from "../chunks/chunk-
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|
+
} from "../chunks/chunk-S3ICPPXC.js";
|
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|
import "../chunks/chunk-OPPVSPEF.js";
|
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import "../chunks/chunk-
|
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|
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import "../chunks/chunk-22ZMVREZ.js";
|
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|
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|
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|
import "../chunks/chunk-TUMJNAOL.js";
|
|
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|
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|
import "../chunks/chunk-VX656OAZ.js";
|
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|
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|
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import "../chunks/chunk-
|
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|
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|
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import "../chunks/chunk-
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|
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|
package/dist/deletionEdges.js
CHANGED
|
@@ -3,10 +3,10 @@ import {
|
|
|
3
3
|
deletionDrawing,
|
|
4
4
|
deletionEdges,
|
|
5
5
|
edgeCurvesOf
|
|
6
|
-
} from "./chunks/chunk-
|
|
6
|
+
} from "./chunks/chunk-3CXZUC2Y.js";
|
|
7
7
|
import "./chunks/chunk-TLWXLNLY.js";
|
|
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8
|
import "./chunks/chunk-3YBP46PB.js";
|
|
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|
-
import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-735MPLUL.js";
|
|
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|
import "./chunks/chunk-CPMHA4W5.js";
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|
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|
import "./chunks/chunk-ZPZ7GNBT.js";
|
|
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12
|
import "./chunks/chunk-BSOZW3FC.js";
|
package/dist/figure.js
CHANGED
|
@@ -1,37 +1,38 @@
|
|
|
1
1
|
import {
|
|
2
2
|
figureSvg
|
|
3
|
-
} from "./chunks/chunk-
|
|
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|
-
import "./chunks/chunk-
|
|
3
|
+
} from "./chunks/chunk-MO4DIRHD.js";
|
|
4
|
+
import "./chunks/chunk-4OVIUCSB.js";
|
|
5
5
|
import "./chunks/chunk-4DMSPNYV.js";
|
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|
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|
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|
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import "./chunks/chunk-
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|
+
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|
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|
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import "./chunks/chunk-
|
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import "./chunks/chunk-
|
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|
+
import "./chunks/chunk-G3GLGDKV.js";
|
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|
+
import "./chunks/chunk-NHOXLUIL.js";
|
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|
+
import "./chunks/chunk-7PEYA3NA.js";
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|
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|
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|
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import "./chunks/chunk-
|
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|
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|
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|
+
import "./chunks/chunk-X5ULFAMM.js";
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|
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|
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|
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import "./chunks/chunk-R3NPBUKT.js";
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|
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|
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import "./chunks/chunk-
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|
+
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|
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|
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|
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|
+
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|
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|
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|
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|
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|
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|
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|
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|
+
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|
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|
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|
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|
+
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|
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|
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|
|
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|
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import "./chunks/chunk-
|
|
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|
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import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-6MD4VS2F.js";
|
|
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|
+
import "./chunks/chunk-S3ICPPXC.js";
|
|
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|
import "./chunks/chunk-OPPVSPEF.js";
|
|
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|
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import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-22ZMVREZ.js";
|
|
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|
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|
import "./chunks/chunk-VPE4AYP7.js";
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|
import "./chunks/chunk-TUMJNAOL.js";
|
|
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|
|
|
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|
import "./chunks/chunk-5ORP7EFJ.js";
|
|
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|
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|
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|
import "./chunks/chunk-LG2UK4MB.js";
|
|
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|
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import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-6CXLLJ2C.js";
|
|
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|
import "./chunks/chunk-HMXCN6PG.js";
|
|
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|
import "./chunks/chunk-AB35TJST.js";
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|
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|
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|
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|
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import "./chunks/chunk-YIWN32ZX.js";
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|
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|
import "./chunks/chunk-HKYXWZQS.js";
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|
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|
import "./chunks/chunk-34BOZKIE.js";
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|
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|
import "./chunks/chunk-JKJWSY4V.js";
|
|
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|
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import "./chunks/chunk-
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|
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|
+
import "./chunks/chunk-3CXZUC2Y.js";
|
|
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|
import "./chunks/chunk-TLWXLNLY.js";
|
|
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|
import "./chunks/chunk-3YBP46PB.js";
|
|
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|
-
import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-735MPLUL.js";
|
|
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|
import "./chunks/chunk-CPMHA4W5.js";
|
|
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|
import "./chunks/chunk-ZPZ7GNBT.js";
|
|
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|
import "./chunks/chunk-BSOZW3FC.js";
|
package/dist/figureData.js
CHANGED
|
@@ -3,11 +3,11 @@ import {
|
|
|
3
3
|
gfaFigureData,
|
|
4
4
|
laidOutGraph,
|
|
5
5
|
walkLayers
|
|
6
|
-
} from "./chunks/chunk-
|
|
6
|
+
} from "./chunks/chunk-U6JPSXJ3.js";
|
|
7
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