@jbrowse/bandage-core 10.3.0 → 11.0.0
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 +5 -0
- package/dist/bubbles/popBubble.js +2 -2
- package/dist/bubbles/superbubbles.js +3 -3
- package/dist/chunks/{chunk-EHXBZ5JZ.js → chunk-2Q22S52W.js} +1 -1
- package/dist/chunks/{chunk-IYALCKNB.js → chunk-3GP3KT5L.js} +1 -1
- package/dist/chunks/{chunk-A54O52XZ.js → chunk-3UST3ZQE.js} +1 -1
- package/dist/chunks/{chunk-DBLV7PGG.js → chunk-3XSRT7RQ.js} +16 -2
- package/dist/chunks/{chunk-7JGLJK44.js → chunk-5LTZVKZQ.js} +10 -10
- package/dist/chunks/{chunk-PTQPTDZH.js → chunk-6OP4HPXG.js} +1 -1
- package/dist/chunks/{chunk-WONB6LMC.js → chunk-AI5PTOSV.js} +1 -1
- package/dist/chunks/{chunk-LGJBB5BP.js → chunk-B5X2RLJG.js} +9 -1
- package/dist/chunks/{chunk-TCOLHD7N.js → chunk-BIOKXS3M.js} +2 -2
- package/dist/chunks/{chunk-BVYR7IFN.js → chunk-C3NT37C3.js} +24 -3
- package/dist/chunks/{chunk-5YILQTHE.js → chunk-CIDSF47D.js} +29 -9
- package/dist/chunks/{chunk-AMX4OQAW.js → chunk-CTZRIDMY.js} +7 -7
- package/dist/chunks/{chunk-XUT4HXVE.js → chunk-CZT33FZG.js} +8 -8
- package/dist/chunks/{chunk-CGFPFBT2.js → chunk-D4ZFRBB4.js} +11 -2
- package/dist/chunks/{chunk-V7J6U4XC.js → chunk-DO62DG26.js} +1 -1
- package/dist/chunks/{chunk-Z6XZWPXK.js → chunk-DZR37KXT.js} +51 -2
- package/dist/chunks/{chunk-MD5VPXXT.js → chunk-EDWU7OM4.js} +5 -5
- package/dist/chunks/chunk-EIY2SKD3.js +164 -0
- package/dist/chunks/{chunk-A55OZVYX.js → chunk-EY2ZGSCP.js} +2 -2
- package/dist/chunks/{chunk-RWKP7UO4.js → chunk-FFHJGWDK.js} +6 -2
- package/dist/chunks/{chunk-KWHWNOTY.js → chunk-KDU4EF66.js} +4 -4
- package/dist/chunks/{chunk-65ILXEIN.js → chunk-L5IETLWP.js} +5 -5
- package/dist/chunks/{chunk-GIHTHYXY.js → chunk-NMWQUFPF.js} +1 -1
- package/dist/chunks/{chunk-QQCOVMMT.js → chunk-OLKXMZ6J.js} +1 -1
- package/dist/chunks/{chunk-ZNJ4JAPT.js → chunk-PK5QQOMN.js} +3 -3
- package/dist/chunks/{chunk-PPDE4IVT.js → chunk-PNMJFFNB.js} +1 -1
- package/dist/chunks/{chunk-WJ4TIAVA.js → chunk-RNYPCQZ3.js} +1 -1
- package/dist/chunks/{chunk-2XEQR54X.js → chunk-SWCULW6S.js} +1 -1
- package/dist/chunks/{chunk-SHKGYGM4.js → chunk-TEF3NBG3.js} +3 -3
- package/dist/chunks/{chunk-M5NPD55W.js → chunk-TUQKGAK3.js} +1 -1
- package/dist/chunks/{chunk-ZPBEUOBM.js → chunk-W6EXQDV5.js} +1 -1
- package/dist/chunks/{chunk-7XR26JST.js → chunk-XVS52NMZ.js} +1 -1
- package/dist/chunks/{chunk-SZHQK6GL.js → chunk-XZ6PQBU6.js} +59 -13
- package/dist/cli/figure.js +26 -25
- package/dist/cli/fold.js +6 -5
- package/dist/figure.js +20 -19
- package/dist/figureData.js +23 -22
- package/dist/figureScene.js +15 -14
- package/dist/figureSettings.js +7 -6
- package/dist/gbzCut.js +4 -3
- package/dist/gbzWindow.js +3 -2
- package/dist/gfa/gfaConverter.js +3 -2
- package/dist/gfa/gfaTables.js +2 -1
- package/dist/gfa/graphTables.js +2 -1
- package/dist/gfa/walkStops.js +28 -0
- package/dist/index.js +60 -42
- package/dist/layout/forceCache.js +7 -6
- package/dist/layout/trimToWindow.js +1 -1
- package/dist/layout/tubeMapLayout.js +5 -4
- package/dist/layout/walkRowDraw.js +13 -4
- package/dist/layout/walkRowLayout.js +4 -3
- package/dist/layout/walkRows.js +3 -2
- package/dist/layout/walkStrip.js +8 -7
- package/dist/layoutModes.js +8 -7
- package/dist/pathAnchoring.js +1 -1
- package/dist/pathColors.js +2 -2
- package/dist/pipeline.js +6 -5
- package/dist/referenceStrip.js +4 -4
- package/dist/renderer/GeometryBuilder.js +3 -3
- package/dist/tubeMap/bundle.js +6 -5
- package/dist/tubeMap/coarsen.js +6 -5
- package/dist/tubeMap/deviations.js +6 -5
- package/dist/tubeMap/draw.js +5 -4
- package/dist/tubeMap/nodeColors.js +4 -4
- package/dist/types/gfa/graphTables.d.ts +3 -0
- package/dist/types/gfa/walkStops.d.ts +59 -0
- package/dist/types/index.d.ts +4 -2
- package/dist/types/layout/walkRowDraw.d.ts +14 -1
- package/dist/types/layout/walkRows.d.ts +4 -1
- package/dist/types/types.d.ts +19 -0
- package/dist/types/version.d.ts +1 -1
- package/dist/types/walkHighlight.d.ts +2 -0
- package/dist/types/walkKey.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/viewport.js +7 -6
- package/dist/walkEncoding.js +4 -4
- package/dist/walkHighlight.js +6 -5
- package/dist/walkKey.js +2 -1
- package/package.json +1 -1
package/dist/figure.js
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import "./chunks/chunk-3XSRT7RQ.js";
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import "./chunks/chunk-B5X2RLJG.js";
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import "./chunks/chunk-VX656OAZ.js";
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import "./chunks/chunk-
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import "./chunks/chunk-DZR37KXT.js";
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package/dist/gbzCut.js
CHANGED
|
@@ -5,11 +5,12 @@ import {
|
|
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5
5
|
haplotypeIndexBeside,
|
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6
6
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openGbz,
|
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7
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parseRegion
|
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-
} from "./chunks/chunk-
|
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-
import "./chunks/chunk-
|
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|
+
} from "./chunks/chunk-TUQKGAK3.js";
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import "./chunks/chunk-NMWQUFPF.js";
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import "./chunks/chunk-234NFZS4.js";
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import "./chunks/chunk-
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import "./chunks/chunk-DZR37KXT.js";
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import "./chunks/chunk-EIY2SKD3.js";
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|
package/dist/gbzWindow.js
CHANGED
|
@@ -12,10 +12,11 @@ import {
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|
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|
referencePathQuery,
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referenceSamplesOf,
|
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|
resolveReferenceSample
|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-NMWQUFPF.js";
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import "./chunks/chunk-HNWJ4B7S.js";
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import "./chunks/chunk-
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import "./chunks/chunk-EIY2SKD3.js";
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|
package/dist/gfa/gfaConverter.js
CHANGED
|
@@ -1,9 +1,10 @@
|
|
|
1
1
|
import {
|
|
2
2
|
convertGFAToGraph
|
|
3
|
-
} from "../chunks/chunk-
|
|
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|
+
} from "../chunks/chunk-FFHJGWDK.js";
|
|
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|
import "../chunks/chunk-QYBZZI5H.js";
|
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5
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import "../chunks/chunk-5I3K4R2G.js";
|
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import "../chunks/chunk-
|
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|
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import "../chunks/chunk-B5X2RLJG.js";
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|
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import "../chunks/chunk-EIY2SKD3.js";
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|
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|
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|
|
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10
|
import "../chunks/chunk-RJWPJCIB.js";
|
package/dist/gfa/gfaTables.js
CHANGED
package/dist/gfa/graphTables.js
CHANGED
|
@@ -0,0 +1,28 @@
|
|
|
1
|
+
import {
|
|
2
|
+
END_STOP_TAG,
|
|
3
|
+
GAP_CAUSE_TEXT,
|
|
4
|
+
OUTSIDE_TEXT,
|
|
5
|
+
START_STOP_TAG,
|
|
6
|
+
StopColumns,
|
|
7
|
+
gapParts,
|
|
8
|
+
parseStopTag,
|
|
9
|
+
stopAt,
|
|
10
|
+
stopFields,
|
|
11
|
+
stopTag,
|
|
12
|
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walkStopFields,
|
|
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+
walkStopTags
|
|
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|
+
} from "../chunks/chunk-EIY2SKD3.js";
|
|
15
|
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export {
|
|
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|
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END_STOP_TAG,
|
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|
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GAP_CAUSE_TEXT,
|
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|
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OUTSIDE_TEXT,
|
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|
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START_STOP_TAG,
|
|
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StopColumns,
|
|
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|
+
gapParts,
|
|
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|
+
parseStopTag,
|
|
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|
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stopAt,
|
|
24
|
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stopFields,
|
|
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|
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stopTag,
|
|
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|
+
walkStopFields,
|
|
27
|
+
walkStopTags
|
|
28
|
+
};
|
package/dist/index.js
CHANGED
|
@@ -1,17 +1,27 @@
|
|
|
1
1
|
import {
|
|
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2
|
wheelZoomFactor
|
|
3
3
|
} from "./chunks/chunk-TDQLINVI.js";
|
|
4
|
+
import {
|
|
5
|
+
connectorAt,
|
|
6
|
+
drawLitConnector,
|
|
7
|
+
drawTubeMapConnectors,
|
|
8
|
+
tubeMapConnectors
|
|
9
|
+
} from "./chunks/chunk-2ZT7ZF7A.js";
|
|
4
10
|
import {
|
|
5
11
|
drawTubeMap,
|
|
6
12
|
drawTubeMapHighlight,
|
|
7
13
|
tubeMapMismatchAt,
|
|
8
14
|
tubeMapPicture,
|
|
9
15
|
tubeMapTrackAt
|
|
10
|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-L5IETLWP.js";
|
|
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17
|
import {
|
|
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18
|
tubeMapFrame,
|
|
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19
|
tubeMapNodeAt
|
|
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20
|
} from "./chunks/chunk-SI3BB4DO.js";
|
|
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|
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import {
|
|
22
|
+
referenceKnots,
|
|
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|
+
warpX
|
|
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|
+
} from "./chunks/chunk-MYDHU2UV.js";
|
|
15
25
|
import {
|
|
16
26
|
drawTubeMapGenes,
|
|
17
27
|
tubeMapGenes
|
|
@@ -19,11 +29,7 @@ import {
|
|
|
19
29
|
import "./chunks/chunk-BX4AUMZE.js";
|
|
20
30
|
import {
|
|
21
31
|
tubeMapNodeColors
|
|
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|
-
} from "./chunks/chunk-
|
|
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|
-
import {
|
|
24
|
-
referenceKnots,
|
|
25
|
-
warpX
|
|
26
|
-
} from "./chunks/chunk-MYDHU2UV.js";
|
|
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|
+
} from "./chunks/chunk-XVS52NMZ.js";
|
|
27
33
|
import {
|
|
28
34
|
drawTubeMapRuler,
|
|
29
35
|
referenceBoxes,
|
|
@@ -32,26 +38,20 @@ import {
|
|
|
32
38
|
} from "./chunks/chunk-HSVFCA2J.js";
|
|
33
39
|
import {
|
|
34
40
|
bundleRoutes
|
|
35
|
-
} from "./chunks/chunk-
|
|
36
|
-
import {
|
|
37
|
-
connectorAt,
|
|
38
|
-
drawLitConnector,
|
|
39
|
-
drawTubeMapConnectors,
|
|
40
|
-
tubeMapConnectors
|
|
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|
-
} from "./chunks/chunk-2ZT7ZF7A.js";
|
|
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|
+
} from "./chunks/chunk-BIOKXS3M.js";
|
|
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42
|
import {
|
|
43
43
|
createForceLayoutCache
|
|
44
|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-RNYPCQZ3.js";
|
|
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45
|
import {
|
|
46
46
|
graphBubbles,
|
|
47
47
|
superbubblesFromGraph
|
|
48
|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-2Q22S52W.js";
|
|
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49
|
import {
|
|
50
50
|
bubblesFromGraph
|
|
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51
|
} from "./chunks/chunk-RFG42VIO.js";
|
|
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52
|
import {
|
|
53
53
|
bubbleSubgraph
|
|
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|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-PNMJFFNB.js";
|
|
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55
|
import {
|
|
56
56
|
genesFromBed,
|
|
57
57
|
genesFromGff3Lines,
|
|
@@ -73,7 +73,7 @@ import {
|
|
|
73
73
|
drawReferenceStrip,
|
|
74
74
|
referenceStripBlocks,
|
|
75
75
|
stripBlockAt
|
|
76
|
-
} from "./chunks/chunk-
|
|
76
|
+
} from "./chunks/chunk-3UST3ZQE.js";
|
|
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77
|
import {
|
|
78
78
|
LAYOUT_QUALITIES
|
|
79
79
|
} from "./chunks/chunk-K5SIJGAE.js";
|
|
@@ -83,7 +83,7 @@ import {
|
|
|
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83
|
} from "./chunks/chunk-AZFVORTC.js";
|
|
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84
|
import {
|
|
85
85
|
figureSvg
|
|
86
|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-5LTZVKZQ.js";
|
|
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87
|
import {
|
|
88
88
|
svgCanvas
|
|
89
89
|
} from "./chunks/chunk-V4YML3GR.js";
|
|
@@ -98,7 +98,7 @@ import {
|
|
|
98
98
|
walkStripApplies,
|
|
99
99
|
walkStripFrame,
|
|
100
100
|
walkStripLabelsTree
|
|
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|
-
} from "./chunks/chunk-
|
|
101
|
+
} from "./chunks/chunk-TEF3NBG3.js";
|
|
102
102
|
import {
|
|
103
103
|
BAR_PX,
|
|
104
104
|
CALL_TICK,
|
|
@@ -113,6 +113,7 @@ import {
|
|
|
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113
|
alongRow,
|
|
114
114
|
callTickInk,
|
|
115
115
|
coalesceRuns,
|
|
116
|
+
gapStyle,
|
|
116
117
|
genesOnRow,
|
|
117
118
|
placeRowGenes,
|
|
118
119
|
readoutPlacement,
|
|
@@ -125,7 +126,7 @@ import {
|
|
|
125
126
|
walkRowsKey,
|
|
126
127
|
walkRowsKeyTree,
|
|
127
128
|
walkRowsTree
|
|
128
|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-XZ6PQBU6.js";
|
|
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130
|
import {
|
|
130
131
|
Canvas2DRenderer
|
|
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132
|
} from "./chunks/chunk-EJRJAAN7.js";
|
|
@@ -158,7 +159,7 @@ import {
|
|
|
158
159
|
import {
|
|
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160
|
figureData,
|
|
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161
|
gfaFigureData
|
|
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|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-CTZRIDMY.js";
|
|
162
163
|
import {
|
|
163
164
|
LAYOUT_ENGINES,
|
|
164
165
|
layoutEngine
|
|
@@ -168,10 +169,10 @@ import {
|
|
|
168
169
|
LAYOUT_MODES,
|
|
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170
|
layoutModeByValue,
|
|
170
171
|
modeUsesLayoutEngine
|
|
171
|
-
} from "./chunks/chunk-
|
|
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|
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import "./chunks/chunk-
|
|
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|
-
import "./chunks/chunk-ZNJ4JAPT.js";
|
|
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|
+
} from "./chunks/chunk-EDWU7OM4.js";
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|
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import "./chunks/chunk-PK5QQOMN.js";
|
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|
import "./chunks/chunk-A7H753BA.js";
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|
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import "./chunks/chunk-GJU6BJJA.js";
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|
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|
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|
import "./chunks/chunk-MYLAJDKB.js";
|
|
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|
import "./chunks/chunk-C44YRP5F.js";
|
|
@@ -182,7 +183,7 @@ import {
|
|
|
182
183
|
cutGbzRegion,
|
|
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184
|
openGbz,
|
|
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185
|
parseRegion
|
|
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|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-TUQKGAK3.js";
|
|
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187
|
import {
|
|
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|
compactTables,
|
|
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189
|
cutWindowGFA,
|
|
@@ -191,11 +192,11 @@ import {
|
|
|
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192
|
referencePathQuery,
|
|
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193
|
referenceSamplesOf,
|
|
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194
|
resolveReferenceSample
|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-NMWQUFPF.js";
|
|
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196
|
import "./chunks/chunk-HNWJ4B7S.js";
|
|
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|
import {
|
|
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198
|
version
|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-6OP4HPXG.js";
|
|
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200
|
import {
|
|
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|
axisScaleOf,
|
|
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202
|
contains,
|
|
@@ -203,8 +204,8 @@ import {
|
|
|
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|
screenToLayout,
|
|
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|
viewportOf,
|
|
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206
|
zoomAbout
|
|
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|
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} from "./chunks/chunk-
|
|
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|
-
import "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-AI5PTOSV.js";
|
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|
+
import "./chunks/chunk-CZT33FZG.js";
|
|
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209
|
import {
|
|
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210
|
layoutGeometryInputs
|
|
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211
|
} from "./chunks/chunk-LOCJN3BZ.js";
|
|
@@ -212,7 +213,7 @@ import {
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|
|
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|
facetLifts,
|
|
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214
|
walkHighlight,
|
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|
walkLift
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-C3NT37C3.js";
|
|
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217
|
import {
|
|
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218
|
WALK_FIELDS,
|
|
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219
|
WALK_SCHEMES,
|
|
@@ -220,16 +221,16 @@ import {
|
|
|
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221
|
encodingSwatchCss,
|
|
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222
|
resolveEncoding,
|
|
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|
schemeCss
|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-DO62DG26.js";
|
|
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|
import {
|
|
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|
rangeText,
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|
walkKey,
|
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|
walkPosition
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-D4ZFRBB4.js";
|
|
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|
import {
|
|
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|
buildGeometry,
|
|
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|
computeReferenceRamp
|
|
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|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-SWCULW6S.js";
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|
import "./chunks/chunk-G2FD7S3C.js";
|
|
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|
import {
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|
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236
|
RAMP_GRADIENT_CSS,
|
|
@@ -242,16 +243,16 @@ import "./chunks/chunk-WA5WNP6V.js";
|
|
|
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|
import {
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|
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244
|
walkRowLabels,
|
|
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|
walkRowsExtent
|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-OLKXMZ6J.js";
|
|
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|
import {
|
|
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248
|
filterSamples,
|
|
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|
walkRows
|
|
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|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-CIDSF47D.js";
|
|
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|
import {
|
|
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|
pathColorsLegible,
|
|
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253
|
pathLegend,
|
|
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254
|
walkLabelsOf
|
|
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|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-3GP3KT5L.js";
|
|
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256
|
import {
|
|
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257
|
NODE_WIDTHS,
|
|
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|
maxNodeWidthPx,
|
|
@@ -262,7 +263,7 @@ import {
|
|
|
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|
import {
|
|
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264
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FIGURE_DEFAULTS,
|
|
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265
|
figureSpecSettings
|
|
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|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-W6EXQDV5.js";
|
|
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|
import {
|
|
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268
|
ENGINE_DEFAULTS,
|
|
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269
|
FIT_PADDING,
|
|
@@ -275,19 +276,19 @@ import {
|
|
|
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276
|
forceLayout,
|
|
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277
|
layoutExtent,
|
|
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278
|
loadGraph
|
|
278
|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-KDU4EF66.js";
|
|
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280
|
import "./chunks/chunk-3PZSBNLI.js";
|
|
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|
import "./chunks/chunk-CKUVEHSS.js";
|
|
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|
import "./chunks/chunk-OPPVSPEF.js";
|
|
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|
import "./chunks/chunk-VPE4AYP7.js";
|
|
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|
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import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-FFHJGWDK.js";
|
|
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