@jbrowse/bandage-core 9.9.2 → 9.10.0

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.
Files changed (52) hide show
  1. package/README.md +3 -0
  2. package/dist/bubbles/superbubbles.js +2 -2
  3. package/dist/chunks/{chunk-IZ3W5IU2.js → chunk-2FLBFVMO.js} +33 -33
  4. package/dist/chunks/{chunk-BQ33OOLC.js → chunk-2VTM3DHG.js} +1 -1
  5. package/dist/chunks/{chunk-F4BKWWLS.js → chunk-4IYP43W6.js} +4 -4
  6. package/dist/chunks/{chunk-RK3MF4FD.js → chunk-BDWQQK33.js} +1 -1
  7. package/dist/chunks/{chunk-HOZI3FBG.js → chunk-CXKZYLYS.js} +1 -1
  8. package/dist/chunks/{chunk-MECWJY2R.js → chunk-DMH4NL2M.js} +4 -4
  9. package/dist/chunks/{chunk-P6O4RSOQ.js → chunk-FJZ2TB46.js} +5 -5
  10. package/dist/chunks/{chunk-IJRNMO4D.js → chunk-FUUJ76KD.js} +1 -1
  11. package/dist/chunks/{chunk-FPTI3WAV.js → chunk-HRAU4VTB.js} +12 -7
  12. package/dist/chunks/{chunk-YGN4KL7W.js → chunk-IZI7KIVX.js} +1 -1
  13. package/dist/chunks/{chunk-YS7VA5SI.js → chunk-K5NYTPLC.js} +1 -1
  14. package/dist/chunks/{chunk-F5BYHLIN.js → chunk-KYY5363X.js} +1 -1
  15. package/dist/chunks/{chunk-WVBYR6Y7.js → chunk-LZWSZRUY.js} +1 -1
  16. package/dist/chunks/{chunk-EE37PVQY.js → chunk-MVMP6AGI.js} +1 -1
  17. package/dist/chunks/chunk-NGODVSCA.js +292 -0
  18. package/dist/chunks/chunk-OPPVSPEF.js +57 -0
  19. package/dist/chunks/{chunk-ZBLKAWSD.js → chunk-PT37VS5B.js} +1 -1
  20. package/dist/chunks/{chunk-YAN2ZPNV.js → chunk-Q6UIUY6X.js} +1 -1
  21. package/dist/chunks/{chunk-KJEMKHVB.js → chunk-TFAFIRZB.js} +1 -1
  22. package/dist/cli/figure.js +41 -40
  23. package/dist/cli/fold.js +4 -3
  24. package/dist/figure.js +25 -24
  25. package/dist/figureData.js +62 -0
  26. package/dist/figureSettings.js +5 -4
  27. package/dist/index.js +150 -143
  28. package/dist/layout/forceCache.js +5 -4
  29. package/dist/layout/smoothChains.js +6 -0
  30. package/dist/layout/tubeMapLayout.js +4 -4
  31. package/dist/layout/walkRowDraw.js +9 -9
  32. package/dist/layout/walkStrip.js +10 -10
  33. package/dist/layoutModes.js +7 -7
  34. package/dist/pathColors.js +3 -3
  35. package/dist/pipeline.js +4 -3
  36. package/dist/referenceRampCss.js +7 -7
  37. package/dist/referenceStrip.js +7 -7
  38. package/dist/renderer/GeometryBuilder.js +6 -6
  39. package/dist/tubeMap/bundle.js +5 -5
  40. package/dist/tubeMap/coarsen.js +4 -4
  41. package/dist/tubeMap/nodeColors.js +7 -7
  42. package/dist/types/figureData.d.ts +146 -0
  43. package/dist/types/index.d.ts +2 -0
  44. package/dist/types/layout/smoothChains.d.ts +2 -0
  45. package/dist/types/version.d.ts +1 -1
  46. package/dist/version.js +1 -1
  47. package/dist/viewport.js +5 -4
  48. package/dist/walkEncoding.js +7 -7
  49. package/dist/walkHighlight.js +8 -8
  50. package/package.json +1 -1
  51. package/dist/chunks/{chunk-ROQGMTFB.js → chunk-5GZEPPEW.js} +5 -5
  52. package/dist/chunks/{chunk-EDASNMLY.js → chunk-XZ2BLAA6.js} +3 -3
package/dist/chunks/{chunk-YAN2ZPNV.js → chunk-Q6UIUY6X.js} RENAMED
@@ -1,7 +1,7 @@
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  import {
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  engineKey,
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  forceLayout
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- } from "./chunk-FPTI3WAV.js";
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+ } from "./chunk-HRAU4VTB.js";
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  // src/layout/forceCache.ts
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  var DEFAULT_SIZE = 4;
package/dist/chunks/{chunk-KJEMKHVB.js → chunk-TFAFIRZB.js} RENAMED
@@ -1,7 +1,7 @@
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  import {
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  computeColorSchemeRange,
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  getNodeColor
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- } from "./chunk-F4BKWWLS.js";
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+ } from "./chunk-4IYP43W6.js";
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  import {
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  abgrToCssRgba
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  } from "./chunk-G2FD7S3C.js";
package/dist/cli/figure.js CHANGED
@@ -4,6 +4,24 @@ import {
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  genesFromGff3Lines,
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  genesFromText
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  } from "../chunks/chunk-BXEPA4KS.js";
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+ import {
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+ figureSvg
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+ } from "../chunks/chunk-2FLBFVMO.js";
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+ import "../chunks/chunk-47DYCZOK.js";
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+ import "../chunks/chunk-DMH4NL2M.js";
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+ import {
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+ genesOnRow,
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+ placeRowGenes
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+ } from "../chunks/chunk-FJZ2TB46.js";
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+ import "../chunks/chunk-WBCOREDZ.js";
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+ import "../chunks/chunk-4BYTEJGW.js";
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+ import "../chunks/chunk-BUBZ32IC.js";
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+ import "../chunks/chunk-3S3YVOJ7.js";
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+ import "../chunks/chunk-K5NYTPLC.js";
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+ import "../chunks/chunk-DRG4236Y.js";
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+ import "../chunks/chunk-FP4H7SFT.js";
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+ import "../chunks/chunk-MLSWIMZO.js";
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+ import "../chunks/chunk-NNODIW4U.js";
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  import {
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  LAYOUT_ENGINE_VALUES,
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  isLayoutEngineKind,
@@ -14,15 +32,15 @@ import "../chunks/chunk-LYJ4US66.js";
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  import {
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  LAYOUT_MODES,
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  layoutModeByValue
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- } from "../chunks/chunk-IJRNMO4D.js";
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+ } from "../chunks/chunk-FUUJ76KD.js";
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  import "../chunks/chunk-LOEA5IHZ.js";
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- import "../chunks/chunk-HOZI3FBG.js";
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+ import "../chunks/chunk-CXKZYLYS.js";
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  import "../chunks/chunk-CWFNEKST.js";
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  import "../chunks/chunk-L3O7AWLI.js";
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  import "../chunks/chunk-TZFWUT2C.js";
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+ import "../chunks/chunk-HNQPEMYE.js";
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  import "../chunks/chunk-C44YRP5F.js";
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  import "../chunks/chunk-RVS2QCOX.js";
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- import "../chunks/chunk-HNQPEMYE.js";
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  import "../chunks/chunk-7XHHVYG7.js";
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  import {
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  HPRC_GBZ,
@@ -33,72 +51,55 @@ import {
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  } from "../chunks/chunk-73RSLGZT.js";
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  import "../chunks/chunk-LTUWJKHD.js";
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  import "../chunks/chunk-WSIFAZU7.js";
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- import {
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- figureSvg
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- } from "../chunks/chunk-IZ3W5IU2.js";
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- import "../chunks/chunk-47DYCZOK.js";
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- import "../chunks/chunk-MECWJY2R.js";
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- import "../chunks/chunk-WBCOREDZ.js";
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- import "../chunks/chunk-4BYTEJGW.js";
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  import "../chunks/chunk-LOCJN3BZ.js";
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- import {
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- genesOnRow,
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- placeRowGenes
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- } from "../chunks/chunk-P6O4RSOQ.js";
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- import "../chunks/chunk-BUBZ32IC.js";
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- import "../chunks/chunk-3S3YVOJ7.js";
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- import "../chunks/chunk-ZBLKAWSD.js";
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- import "../chunks/chunk-EE37PVQY.js";
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- import "../chunks/chunk-F5BYHLIN.js";
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+ import "../chunks/chunk-2VTM3DHG.js";
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+ import "../chunks/chunk-PT37VS5B.js";
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+ import "../chunks/chunk-MVMP6AGI.js";
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+ import "../chunks/chunk-KYY5363X.js";
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  import "../chunks/chunk-2LQ5BWT7.js";
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- import "../chunks/chunk-YS7VA5SI.js";
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- import "../chunks/chunk-F4BKWWLS.js";
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+ import "../chunks/chunk-4IYP43W6.js";
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  import "../chunks/chunk-G2FD7S3C.js";
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- import "../chunks/chunk-BQ33OOLC.js";
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+ import "../chunks/chunk-WFB5TXRA.js";
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  import "../chunks/chunk-TOVOJNT7.js";
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  import {
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  filterSamples,
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  walkRows
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  } from "../chunks/chunk-6PYZYBBF.js";
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- import "../chunks/chunk-EDASNMLY.js";
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+ import "../chunks/chunk-XZ2BLAA6.js";
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  import "../chunks/chunk-PBENCR5L.js";
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- import {
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- featuresOnBackbone,
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- graphBackbone,
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- refNameBinding
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- } from "../chunks/chunk-RAKOB6IV.js";
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- import "../chunks/chunk-DRG4236Y.js";
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- import "../chunks/chunk-FP4H7SFT.js";
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- import "../chunks/chunk-MLSWIMZO.js";
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- import "../chunks/chunk-WFB5TXRA.js";
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- import "../chunks/chunk-3ZZSX5HN.js";
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- import "../chunks/chunk-AB35TJST.js";
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- import "../chunks/chunk-JKJWSY4V.js";
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- import "../chunks/chunk-NNODIW4U.js";
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- import "../chunks/chunk-XV4P5KEQ.js";
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  import {
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  engineSettingsOf,
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  forceLayout,
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  loadGraph
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- } from "../chunks/chunk-FPTI3WAV.js";
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- import "../chunks/chunk-PUG7LXDF.js";
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+ } from "../chunks/chunk-HRAU4VTB.js";
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  import "../chunks/chunk-IGVV37VI.js";
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+ import "../chunks/chunk-OPPVSPEF.js";
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+ import "../chunks/chunk-PUG7LXDF.js";
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  import "../chunks/chunk-J7YKQ5YW.js";
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  import "../chunks/chunk-G45YY72K.js";
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  import "../chunks/chunk-OA7RIMZ2.js";
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  import "../chunks/chunk-QYBZZI5H.js";
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  import "../chunks/chunk-CDLPYR5O.js";
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  import "../chunks/chunk-JVLURPFW.js";
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- import "../chunks/chunk-ES2N6V56.js";
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  import "../chunks/chunk-IGJCTPFB.js";
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+ import "../chunks/chunk-ES2N6V56.js";
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+ import {
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+ featuresOnBackbone,
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+ graphBackbone,
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+ refNameBinding
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+ } from "../chunks/chunk-RAKOB6IV.js";
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  import "../chunks/chunk-BPLIXMH7.js";
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+ import "../chunks/chunk-3ZZSX5HN.js";
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+ import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-TAMCZHLW.js";
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  import "../chunks/chunk-UVBGRJQX.js";
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  import "../chunks/chunk-6JEWNXCQ.js";
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+ import "../chunks/chunk-JKJWSY4V.js";
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  import "../chunks/chunk-N6FECAXP.js";
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  import "../chunks/chunk-2CVHXFK7.js";
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  import "../chunks/chunk-CPMHA4W5.js";
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  import "../chunks/chunk-FYQWPEEY.js";
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+ import "../chunks/chunk-XV4P5KEQ.js";
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  // src/cli/figure.ts
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  import { access, open, readFile, writeFile } from "node:fs/promises";
package/dist/cli/fold.js CHANGED
@@ -7,17 +7,18 @@ import {
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  } from "../chunks/chunk-B4645SM2.js";
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  import {
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  loadGraph
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- } from "../chunks/chunk-FPTI3WAV.js";
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- import "../chunks/chunk-PUG7LXDF.js";
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+ } from "../chunks/chunk-HRAU4VTB.js";
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  import "../chunks/chunk-IGVV37VI.js";
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+ import "../chunks/chunk-OPPVSPEF.js";
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+ import "../chunks/chunk-PUG7LXDF.js";
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  import "../chunks/chunk-J7YKQ5YW.js";
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  import "../chunks/chunk-G45YY72K.js";
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  import "../chunks/chunk-OA7RIMZ2.js";
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  import "../chunks/chunk-QYBZZI5H.js";
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- import "../chunks/chunk-ES2N6V56.js";
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+ import "../chunks/chunk-ES2N6V56.js";
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package/dist/figure.js CHANGED
@@ -1,55 +1,56 @@
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  import {
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  figureSvg
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- } from "./chunks/chunk-IZ3W5IU2.js";
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+ } from "./chunks/chunk-2FLBFVMO.js";
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  import "./chunks/chunk-47DYCZOK.js";
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- import "./chunks/chunk-MECWJY2R.js";
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+ import "./chunks/chunk-DMH4NL2M.js";
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+ import "./chunks/chunk-FJZ2TB46.js";
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  import "./chunks/chunk-WBCOREDZ.js";
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- import "./chunks/chunk-LOCJN3BZ.js";
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- import "./chunks/chunk-P6O4RSOQ.js";
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- import "./chunks/chunk-ZBLKAWSD.js";
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- import "./chunks/chunk-EE37PVQY.js";
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- import "./chunks/chunk-F5BYHLIN.js";
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+ import "./chunks/chunk-K5NYTPLC.js";
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+ import "./chunks/chunk-DRG4236Y.js";
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+ import "./chunks/chunk-FP4H7SFT.js";
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+ import "./chunks/chunk-MLSWIMZO.js";
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+ import "./chunks/chunk-NNODIW4U.js";
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+ import "./chunks/chunk-LOCJN3BZ.js";
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+ import "./chunks/chunk-2VTM3DHG.js";
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+ import "./chunks/chunk-PT37VS5B.js";
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+ import "./chunks/chunk-MVMP6AGI.js";
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+ import "./chunks/chunk-KYY5363X.js";
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- import "./chunks/chunk-YS7VA5SI.js";
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- import "./chunks/chunk-RAKOB6IV.js";
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- import "./chunks/chunk-DRG4236Y.js";
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- import "./chunks/chunk-FP4H7SFT.js";
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- import "./chunks/chunk-MLSWIMZO.js";
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- import "./chunks/chunk-WFB5TXRA.js";
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- import "./chunks/chunk-3ZZSX5HN.js";
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- import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-JKJWSY4V.js";
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- import "./chunks/chunk-NNODIW4U.js";
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- import "./chunks/chunk-XV4P5KEQ.js";
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- import "./chunks/chunk-FPTI3WAV.js";
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- import "./chunks/chunk-PUG7LXDF.js";
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+ import "./chunks/chunk-HRAU4VTB.js";
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  import "./chunks/chunk-IGVV37VI.js";
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+ import "./chunks/chunk-OPPVSPEF.js";
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+ import "./chunks/chunk-PUG7LXDF.js";
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- import "./chunks/chunk-ES2N6V56.js";
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+ import "./chunks/chunk-ES2N6V56.js";
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+ import "./chunks/chunk-RAKOB6IV.js";
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+ import "./chunks/chunk-3ZZSX5HN.js";
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+ import "./chunks/chunk-AB35TJST.js";
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package/dist/figureData.js ADDED
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+ gfaFigureData
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+ } from "./chunks/chunk-NGODVSCA.js";
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+ import "./chunks/chunk-VK6XMP6B.js";
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+ import "./chunks/chunk-Q6FRNVDU.js";
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+ import "./chunks/chunk-LYJ4US66.js";
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+ import "./chunks/chunk-FUUJ76KD.js";
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+ import "./chunks/chunk-LOEA5IHZ.js";
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+ import "./chunks/chunk-CXKZYLYS.js";
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+ import "./chunks/chunk-CWFNEKST.js";
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+ import "./chunks/chunk-L3O7AWLI.js";
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+ import "./chunks/chunk-TZFWUT2C.js";
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+ import "./chunks/chunk-HNQPEMYE.js";
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+ import "./chunks/chunk-C44YRP5F.js";
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+ import "./chunks/chunk-RVS2QCOX.js";
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+ import "./chunks/chunk-7XHHVYG7.js";
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+ import "./chunks/chunk-73RSLGZT.js";
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+ import "./chunks/chunk-LTUWJKHD.js";
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+ import "./chunks/chunk-WSIFAZU7.js";
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+ import "./chunks/chunk-LOCJN3BZ.js";
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+ import "./chunks/chunk-2VTM3DHG.js";
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+ import "./chunks/chunk-PT37VS5B.js";
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+ import "./chunks/chunk-MVMP6AGI.js";
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+ import "./chunks/chunk-KYY5363X.js";
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+ import "./chunks/chunk-2LQ5BWT7.js";
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+ import "./chunks/chunk-4IYP43W6.js";
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+ import "./chunks/chunk-G2FD7S3C.js";
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+ import "./chunks/chunk-WFB5TXRA.js";
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+ import "./chunks/chunk-TOVOJNT7.js";
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+ import "./chunks/chunk-6PYZYBBF.js";
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+ import "./chunks/chunk-XZ2BLAA6.js";
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+ import "./chunks/chunk-PBENCR5L.js";
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+ import "./chunks/chunk-HRAU4VTB.js";
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+ import "./chunks/chunk-IGVV37VI.js";
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+ import "./chunks/chunk-OPPVSPEF.js";
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+ import "./chunks/chunk-PUG7LXDF.js";
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+ import "./chunks/chunk-J7YKQ5YW.js";
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+ import "./chunks/chunk-G45YY72K.js";
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+ import "./chunks/chunk-OA7RIMZ2.js";
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+ import "./chunks/chunk-QYBZZI5H.js";
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+ import "./chunks/chunk-CDLPYR5O.js";
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+ import "./chunks/chunk-JVLURPFW.js";
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+ import "./chunks/chunk-IGJCTPFB.js";
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+ import "./chunks/chunk-ES2N6V56.js";
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+ import "./chunks/chunk-RAKOB6IV.js";
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+ import "./chunks/chunk-BPLIXMH7.js";
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+ import "./chunks/chunk-3ZZSX5HN.js";
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+ import "./chunks/chunk-AB35TJST.js";
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+ import "./chunks/chunk-TAMCZHLW.js";
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+ import "./chunks/chunk-UVBGRJQX.js";
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+ import "./chunks/chunk-6JEWNXCQ.js";
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+ import "./chunks/chunk-JKJWSY4V.js";
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+ import "./chunks/chunk-N6FECAXP.js";
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+ import "./chunks/chunk-2CVHXFK7.js";
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+ import "./chunks/chunk-CPMHA4W5.js";
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+ import "./chunks/chunk-FYQWPEEY.js";
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+ import "./chunks/chunk-XV4P5KEQ.js";
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+ export {
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+ gfaFigureData
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+ };
package/dist/figureSettings.js CHANGED
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- import "./chunks/chunk-FPTI3WAV.js";
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- import "./chunks/chunk-PUG7LXDF.js";
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+ } from "./chunks/chunk-IZI7KIVX.js";
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+ import "./chunks/chunk-HRAU4VTB.js";
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  import "./chunks/chunk-IGVV37VI.js";
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+ import "./chunks/chunk-OPPVSPEF.js";
8
+ import "./chunks/chunk-PUG7LXDF.js";
8
9
  import "./chunks/chunk-J7YKQ5YW.js";
9
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  import "./chunks/chunk-G45YY72K.js";
10
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  import "./chunks/chunk-OA7RIMZ2.js";
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  import "./chunks/chunk-QYBZZI5H.js";
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  import "./chunks/chunk-CDLPYR5O.js";
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  import "./chunks/chunk-JVLURPFW.js";
14
- import "./chunks/chunk-ES2N6V56.js";
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  import "./chunks/chunk-IGJCTPFB.js";
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+ import "./chunks/chunk-ES2N6V56.js";
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  import "./chunks/chunk-BPLIXMH7.js";
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  import "./chunks/chunk-TAMCZHLW.js";
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  import "./chunks/chunk-UVBGRJQX.js";