@jbrowse/bandage-core 11.7.1 → 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.
Files changed (101) hide show
  1. package/README.md +106 -48
  2. package/dist/bubbles/bubbleHalos.js +6 -6
  3. package/dist/bubbles/classifyBubble.js +5 -5
  4. package/dist/bubbles/superbubbles.js +7 -7
  5. package/dist/chunks/{chunk-3PZSBNLI.js → chunk-22ZMVREZ.js} +19 -14
  6. package/dist/chunks/{chunk-VB4IXIPM.js → chunk-2H3ALI6L.js} +223 -45
  7. package/dist/chunks/{chunk-FBPAX5K6.js → chunk-2RCKHCF7.js} +1 -1
  8. package/dist/chunks/{chunk-5NZRT7GL.js → chunk-3CXZUC2Y.js} +2 -2
  9. package/dist/chunks/{chunk-WUZH2OJ6.js → chunk-3XYLEK4H.js} +2 -2
  10. package/dist/chunks/{chunk-F7O56DVR.js → chunk-4OVIUCSB.js} +2 -2
  11. package/dist/chunks/{chunk-JGH2V54E.js → chunk-4YPCUVMC.js} +2 -2
  12. package/dist/chunks/{chunk-FU57ZNRQ.js → chunk-6CXLLJ2C.js} +3 -3
  13. package/dist/chunks/{chunk-SACSQ45G.js → chunk-6MD4VS2F.js} +1 -1
  14. package/dist/chunks/{chunk-VACK24HF.js → chunk-735MPLUL.js} +35 -9
  15. package/dist/chunks/chunk-7GDNDQD7.js +504 -0
  16. package/dist/chunks/{chunk-IN4IYSA2.js → chunk-7PEYA3NA.js} +2 -2
  17. package/dist/chunks/{chunk-CWCVQJYY.js → chunk-AXE3RR7J.js} +1 -1
  18. package/dist/chunks/{chunk-BXE3SBBN.js → chunk-C3KAPREU.js} +1 -1
  19. package/dist/chunks/{chunk-ATDVS2CW.js → chunk-G3GLGDKV.js} +2 -2
  20. package/dist/chunks/{chunk-RB2MDFQU.js → chunk-G4WQBRDS.js} +4 -4
  21. package/dist/chunks/{chunk-SDI6BVG7.js → chunk-J4PDHWP2.js} +1 -1
  22. package/dist/chunks/{chunk-3UGWYQNY.js → chunk-JKIAHYAW.js} +14 -8
  23. package/dist/chunks/{chunk-TCSV3II7.js → chunk-L2RQV23D.js} +1 -1
  24. package/dist/chunks/{chunk-6XDTAKO7.js → chunk-LA6JHEVV.js} +1 -1
  25. package/dist/chunks/{chunk-G7SG4XMK.js → chunk-LODKC7PJ.js} +7 -0
  26. package/dist/chunks/{chunk-RK7ZOFPR.js → chunk-MO4DIRHD.js} +80 -38
  27. package/dist/chunks/{chunk-PCHEUVHB.js → chunk-N2GAA7RB.js} +1 -1
  28. package/dist/chunks/{chunk-I5SGYTRM.js → chunk-N4AJV4GH.js} +25 -14
  29. package/dist/chunks/{chunk-Q7I563MH.js → chunk-NHOXLUIL.js} +2 -2
  30. package/dist/chunks/{chunk-RT4K2JMZ.js → chunk-NQWEYJDD.js} +1 -1
  31. package/dist/chunks/{chunk-3Y2EFDID.js → chunk-OIOAK7BS.js} +1 -1
  32. package/dist/chunks/{chunk-EZGNBDHD.js → chunk-R3NPBUKT.js} +8 -8
  33. package/dist/chunks/{chunk-KJDERUQF.js → chunk-R4XCTRIU.js} +45 -10
  34. package/dist/chunks/{chunk-HTF32WSW.js → chunk-S3ICPPXC.js} +3 -3
  35. package/dist/chunks/{chunk-OXW5OHYQ.js → chunk-S4CH434Z.js} +1 -1
  36. package/dist/chunks/{chunk-HMEAGAGC.js → chunk-S7BCZVRK.js} +2 -2
  37. package/dist/chunks/{chunk-UV2IJMIG.js → chunk-SDDMV2MM.js} +1 -1
  38. package/dist/chunks/{chunk-J6XHW4KI.js → chunk-SIXFXXRI.js} +3 -3
  39. package/dist/chunks/{chunk-LKQOIPGE.js → chunk-U6JPSXJ3.js} +90 -21
  40. package/dist/chunks/{chunk-SENPGW4O.js → chunk-VCUOYVLC.js} +1 -1
  41. package/dist/chunks/{chunk-XTF2VWJN.js → chunk-VSRRIFRF.js} +1 -1
  42. package/dist/chunks/{chunk-BFUS3ENH.js → chunk-X5ULFAMM.js} +2 -2
  43. package/dist/chunks/{chunk-PJWLYGRL.js → chunk-XOIYBEU7.js} +1 -1
  44. package/dist/chunks/{chunk-JLIVX2SF.js → chunk-YEDZ37PH.js} +1 -1
  45. package/dist/chunks/{chunk-APLWFV4I.js → chunk-YF6T33PU.js} +10 -2
  46. package/dist/chunks/{chunk-2VMKQKVO.js → chunk-YIWN32ZX.js} +1 -1
  47. package/dist/chunks/{chunk-3WSA4NNP.js → chunk-ZKIH2USC.js} +1 -1
  48. package/dist/cli/figure.js +31 -30
  49. package/dist/cli/fold.js +6 -6
  50. package/dist/deletionEdges.js +2 -2
  51. package/dist/figure.js +27 -26
  52. package/dist/figureData.js +25 -24
  53. package/dist/figureScene.js +18 -17
  54. package/dist/figureSettings.js +6 -6
  55. package/dist/foldVariants.js +2 -2
  56. package/dist/genes/genePins.js +3 -3
  57. package/dist/graphLabels.js +4 -4
  58. package/dist/index.js +45 -44
  59. package/dist/labelLayout.js +8 -8
  60. package/dist/layout/forceCache.js +6 -6
  61. package/dist/layout/mergeRuns.js +2 -2
  62. package/dist/layout/orientToReference.js +3 -1
  63. package/dist/layout/tubeMapLayout.js +9 -9
  64. package/dist/layout/walkRowDraw.js +9 -8
  65. package/dist/layout/walkRowLayout.js +3 -3
  66. package/dist/layout/walkRowRuns.js +1 -1
  67. package/dist/layout/walkRows.js +2 -2
  68. package/dist/layout/walkStrip.js +13 -12
  69. package/dist/layoutModes.js +11 -11
  70. package/dist/pathColors.js +5 -5
  71. package/dist/pipeline.js +5 -5
  72. package/dist/referenceStrip.js +9 -8
  73. package/dist/renderer/GeometryBuilder.js +8 -7
  74. package/dist/renderer/walkLanes.js +44 -0
  75. package/dist/tubeMap/axis.js +5 -5
  76. package/dist/tubeMap/bundle.js +10 -10
  77. package/dist/tubeMap/coarsen.js +10 -10
  78. package/dist/tubeMap/deviations.js +11 -11
  79. package/dist/tubeMap/draw.js +5 -5
  80. package/dist/tubeMap/genes.js +6 -6
  81. package/dist/tubeMap/nodeColors.js +9 -8
  82. package/dist/tubeMap/reads.js +2 -2
  83. package/dist/types/figureData.d.ts +22 -0
  84. package/dist/types/foldVariants.d.ts +3 -1
  85. package/dist/types/renderer/types.d.ts +20 -0
  86. package/dist/types/renderer/walkLanes.d.ts +60 -0
  87. package/dist/types/types.d.ts +1 -0
  88. package/dist/types/util/geometry.d.ts +13 -1
  89. package/dist/types/version.d.ts +1 -1
  90. package/dist/types/walkEncoding.d.ts +7 -5
  91. package/dist/types/walkHighlight.d.ts +3 -0
  92. package/dist/util/SpatialIndex.js +4 -4
  93. package/dist/util/edgeCurves.js +3 -3
  94. package/dist/util/geometry.js +7 -1
  95. package/dist/util/hitDetection.js +5 -5
  96. package/dist/version.js +1 -1
  97. package/dist/viewport.js +6 -6
  98. package/dist/walkEncoding.js +9 -8
  99. package/dist/walkHighlight.js +10 -9
  100. package/dist/walkKey.js +5 -5
  101. package/package.json +1 -1
@@ -4,30 +4,30 @@ import {
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  LAYOUT_MODE_VALUES,
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  layoutModeByValue,
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  modeUsesLayoutEngine
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- } from "./chunks/chunk-WUZH2OJ6.js";
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- import "./chunks/chunk-RB2MDFQU.js";
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- import "./chunks/chunk-SDI6BVG7.js";
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+ } from "./chunks/chunk-3XYLEK4H.js";
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+ import "./chunks/chunk-G4WQBRDS.js";
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+ import "./chunks/chunk-J4PDHWP2.js";
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  import "./chunks/chunk-XR2HMGAS.js";
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  import "./chunks/chunk-GJLZ2MKE.js";
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  import "./chunks/chunk-MYLAJDKB.js";
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  import "./chunks/chunk-5OJZV6YT.js";
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  import "./chunks/chunk-UAFATXYA.js";
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  import "./chunks/chunk-3GLG3ZLE.js";
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- import "./chunks/chunk-SENPGW4O.js";
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- import "./chunks/chunk-BXE3SBBN.js";
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- import "./chunks/chunk-G7SG4XMK.js";
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- import "./chunks/chunk-3UGWYQNY.js";
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+ import "./chunks/chunk-VCUOYVLC.js";
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+ import "./chunks/chunk-C3KAPREU.js";
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+ import "./chunks/chunk-LODKC7PJ.js";
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+ import "./chunks/chunk-JKIAHYAW.js";
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  import "./chunks/chunk-7L7MN2OM.js";
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  import "./chunks/chunk-VX656OAZ.js";
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  import "./chunks/chunk-LG2UK4MB.js";
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- import "./chunks/chunk-FU57ZNRQ.js";
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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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- import "./chunks/chunk-2VMKQKVO.js";
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- import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-YIWN32ZX.js";
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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-VACK24HF.js";
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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";
@@ -9,15 +9,15 @@ import {
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  pathHueAt,
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  pathLegend,
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  walkLabelsOf
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- } from "./chunks/chunk-3UGWYQNY.js";
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- import "./chunks/chunk-FU57ZNRQ.js";
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+ } from "./chunks/chunk-JKIAHYAW.js";
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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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- import "./chunks/chunk-2VMKQKVO.js";
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- import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-YIWN32ZX.js";
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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-VACK24HF.js";
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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/pipeline.js CHANGED
@@ -11,9 +11,9 @@ import {
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  forceLayout,
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  layoutExtent,
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  loadGraph
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- } from "./chunks/chunk-HTF32WSW.js";
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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-3PZSBNLI.js";
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+ import "./chunks/chunk-22ZMVREZ.js";
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  import "./chunks/chunk-CKUVEHSS.js";
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  import "./chunks/chunk-VPE4AYP7.js";
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  import "./chunks/chunk-TUMJNAOL.js";
@@ -23,13 +23,13 @@ import "./chunks/chunk-7L7MN2OM.js";
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  import "./chunks/chunk-VX656OAZ.js";
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  import "./chunks/chunk-VSSIYQYF.js";
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  import "./chunks/chunk-LG2UK4MB.js";
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- import "./chunks/chunk-2VMKQKVO.js";
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+ import "./chunks/chunk-YIWN32ZX.js";
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  import "./chunks/chunk-HKYXWZQS.js";
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  import "./chunks/chunk-34BOZKIE.js";
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- import "./chunks/chunk-5NZRT7GL.js";
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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-VACK24HF.js";
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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";
@@ -7,22 +7,23 @@ import {
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  stripBlockAt,
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  stripOverhang,
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  stripPixels
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- } from "./chunks/chunk-RT4K2JMZ.js";
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- import "./chunks/chunk-VB4IXIPM.js";
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+ } from "./chunks/chunk-NQWEYJDD.js";
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+ import "./chunks/chunk-2H3ALI6L.js";
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+ import "./chunks/chunk-7GDNDQD7.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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  import "./chunks/chunk-GQZVR5DW.js";
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- import "./chunks/chunk-XTF2VWJN.js";
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- import "./chunks/chunk-3UGWYQNY.js";
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+ import "./chunks/chunk-VSRRIFRF.js";
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+ import "./chunks/chunk-JKIAHYAW.js";
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  import "./chunks/chunk-ZANALBSX.js";
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  import "./chunks/chunk-VX656OAZ.js";
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- import "./chunks/chunk-FU57ZNRQ.js";
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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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- import "./chunks/chunk-2VMKQKVO.js";
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- import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-YIWN32ZX.js";
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+ import "./chunks/chunk-3CXZUC2Y.js";
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- import "./chunks/chunk-VACK24HF.js";
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+ import "./chunks/chunk-735MPLUL.js";
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@@ -11,23 +11,24 @@ import {
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  getNodeColor,
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  rampFraction
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- } from "../chunks/chunk-VB4IXIPM.js";
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+ } from "../chunks/chunk-2H3ALI6L.js";
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+ import "../chunks/chunk-7GDNDQD7.js";
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- import "../chunks/chunk-XTF2VWJN.js";
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- import "../chunks/chunk-3UGWYQNY.js";
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+ import "../chunks/chunk-VSRRIFRF.js";
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+ import "../chunks/chunk-JKIAHYAW.js";
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- import "../chunks/chunk-FU57ZNRQ.js";
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+ import "../chunks/chunk-6CXLLJ2C.js";
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- import "../chunks/chunk-5NZRT7GL.js";
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+ import "../chunks/chunk-YIWN32ZX.js";
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+ import "../chunks/chunk-3CXZUC2Y.js";
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+ import "../chunks/chunk-735MPLUL.js";
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@@ -0,0 +1,44 @@
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+ import {
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+ THREAD_PITCH_PX,
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+ THREAD_PX,
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+ THREAD_REACH_PX,
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+ THREAD_TAPER_PX,
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+ bandScale,
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+ bandSpans,
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+ bandWidthPx,
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+ laneLines,
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+ laneRuns,
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+ laneSlideAt,
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+ passesKey,
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+ slotCentres,
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+ threadsPasses,
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+ } from "../chunks/chunk-7GDNDQD7.js";
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+ import "../chunks/chunk-735MPLUL.js";
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+ import "../chunks/chunk-CPMHA4W5.js";
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+ export {
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+ LANE_SMOOTHING_PX,
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+ MAX_BAND_PX,
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+ PASSES_KEY,
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+ SLOT_GAP_PX,
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+ THREAD_GAP_PX,
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+ THREAD_PITCH_PX,
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+ THREAD_PX,
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+ THREAD_REACH_PX,
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+ THREAD_TAPER_PX,
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+ bandScale,
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+ bandSpans,
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+ bandWidthPx,
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+ laneLines,
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+ laneRuns,
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+ laneSlideAt,
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+ passesKey,
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+ slotCentres,
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+ threadsPasses,
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@@ -7,15 +7,15 @@ import {
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- } from "../chunks/chunk-PJWLYGRL.js";
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- import "../chunks/chunk-FU57ZNRQ.js";
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+ } from "../chunks/chunk-XOIYBEU7.js";
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+ import "../chunks/chunk-6CXLLJ2C.js";
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+ import "../chunks/chunk-3CXZUC2Y.js";
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@@ -1,22 +1,22 @@
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- import "../chunks/chunk-RB2MDFQU.js";
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- import "../chunks/chunk-SDI6BVG7.js";
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+ } from "../chunks/chunk-AXE3RR7J.js";
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+ import "../chunks/chunk-G4WQBRDS.js";
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+ import "../chunks/chunk-J4PDHWP2.js";
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+ import "../chunks/chunk-C3KAPREU.js";
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+ import "../chunks/chunk-LODKC7PJ.js";
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+ import "../chunks/chunk-JKIAHYAW.js";
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@@ -1,23 +1,23 @@
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- import "../chunks/chunk-RB2MDFQU.js";
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- import "../chunks/chunk-SDI6BVG7.js";
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+ } from "../chunks/chunk-YEDZ37PH.js";
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+ import "../chunks/chunk-G4WQBRDS.js";
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+ import "../chunks/chunk-C3KAPREU.js";
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+ import "../chunks/chunk-LODKC7PJ.js";
10
+ import "../chunks/chunk-JKIAHYAW.js";
11
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  import "../chunks/chunk-7L7MN2OM.js";
12
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  import "../chunks/chunk-LG2UK4MB.js";
13
- import "../chunks/chunk-FU57ZNRQ.js";
13
+ import "../chunks/chunk-6CXLLJ2C.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
16
- import "../chunks/chunk-2VMKQKVO.js";
17
- import "../chunks/chunk-5NZRT7GL.js";
16
+ import "../chunks/chunk-YIWN32ZX.js";
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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-VACK24HF.js";
20
+ import "../chunks/chunk-735MPLUL.js";
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  import "../chunks/chunk-CPMHA4W5.js";
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  import "../chunks/chunk-ZPZ7GNBT.js";
23
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  import "../chunks/chunk-BSOZW3FC.js";
@@ -1,28 +1,28 @@
1
1
  import {
2
2
  lastAtMost
3
- } from "../chunks/chunk-JLIVX2SF.js";
3
+ } from "../chunks/chunk-YEDZ37PH.js";
4
4
  import {
5
5
  boxX,
6
6
  referenceBoxes
7
- } from "../chunks/chunk-PJWLYGRL.js";
8
- import "../chunks/chunk-RB2MDFQU.js";
9
- import "../chunks/chunk-SDI6BVG7.js";
7
+ } from "../chunks/chunk-XOIYBEU7.js";
8
+ import "../chunks/chunk-G4WQBRDS.js";
9
+ import "../chunks/chunk-J4PDHWP2.js";
10
10
  import "../chunks/chunk-5OJZV6YT.js";
11
- import "../chunks/chunk-BXE3SBBN.js";
12
- import "../chunks/chunk-G7SG4XMK.js";
13
- import "../chunks/chunk-3UGWYQNY.js";
11
+ import "../chunks/chunk-C3KAPREU.js";
12
+ import "../chunks/chunk-LODKC7PJ.js";
13
+ import "../chunks/chunk-JKIAHYAW.js";
14
14
  import "../chunks/chunk-7L7MN2OM.js";
15
15
  import "../chunks/chunk-LG2UK4MB.js";
16
- import "../chunks/chunk-FU57ZNRQ.js";
16
+ import "../chunks/chunk-6CXLLJ2C.js";
17
17
  import "../chunks/chunk-HMXCN6PG.js";
18
18
  import "../chunks/chunk-AB35TJST.js";
19
- import "../chunks/chunk-2VMKQKVO.js";
20
- import "../chunks/chunk-5NZRT7GL.js";
19
+ import "../chunks/chunk-YIWN32ZX.js";
20
+ import "../chunks/chunk-3CXZUC2Y.js";
21
21
  import "../chunks/chunk-TLWXLNLY.js";
22
22
  import {
23
23
  pathOrigin
24
24
  } from "../chunks/chunk-3YBP46PB.js";
25
- import "../chunks/chunk-VACK24HF.js";
25
+ import "../chunks/chunk-735MPLUL.js";
26
26
  import "../chunks/chunk-CPMHA4W5.js";
27
27
  import "../chunks/chunk-ZPZ7GNBT.js";
28
28
  import {
@@ -8,17 +8,17 @@ import {
8
8
  tubeMapMismatchAt,
9
9
  tubeMapPicture,
10
10
  tubeMapTrackAt
11
- } from "../chunks/chunk-HMEAGAGC.js";
11
+ } from "../chunks/chunk-S7BCZVRK.js";
12
12
  import "../chunks/chunk-BX4AUMZE.js";
13
13
  import "../chunks/chunk-MYDHU2UV.js";
14
- import "../chunks/chunk-SDI6BVG7.js";
14
+ import "../chunks/chunk-J4PDHWP2.js";
15
15
  import "../chunks/chunk-5OJZV6YT.js";
16
- import "../chunks/chunk-BXE3SBBN.js";
17
- import "../chunks/chunk-G7SG4XMK.js";
16
+ import "../chunks/chunk-C3KAPREU.js";
17
+ import "../chunks/chunk-LODKC7PJ.js";
18
18
  import "../chunks/chunk-7L7MN2OM.js";
19
19
  import "../chunks/chunk-LG2UK4MB.js";
20
20
  import "../chunks/chunk-3YBP46PB.js";
21
- import "../chunks/chunk-VACK24HF.js";
21
+ import "../chunks/chunk-735MPLUL.js";
22
22
  import "../chunks/chunk-CPMHA4W5.js";
23
23
  import "../chunks/chunk-ZPZ7GNBT.js";
24
24
  import "../chunks/chunk-BSOZW3FC.js";
@@ -3,16 +3,16 @@ import {
3
3
  drawTubeMapGenes,
4
4
  tubeMapGeneRows,
5
5
  tubeMapGenes
6
- } from "../chunks/chunk-PCHEUVHB.js";
7
- import "../chunks/chunk-PJWLYGRL.js";
8
- import "../chunks/chunk-FU57ZNRQ.js";
6
+ } from "../chunks/chunk-N2GAA7RB.js";
7
+ import "../chunks/chunk-XOIYBEU7.js";
8
+ import "../chunks/chunk-6CXLLJ2C.js";
9
9
  import "../chunks/chunk-HMXCN6PG.js";
10
10
  import "../chunks/chunk-AB35TJST.js";
11
- import "../chunks/chunk-2VMKQKVO.js";
12
- import "../chunks/chunk-5NZRT7GL.js";
11
+ import "../chunks/chunk-YIWN32ZX.js";
12
+ import "../chunks/chunk-3CXZUC2Y.js";
13
13
  import "../chunks/chunk-TLWXLNLY.js";
14
14
  import "../chunks/chunk-3YBP46PB.js";
15
- import "../chunks/chunk-VACK24HF.js";
15
+ import "../chunks/chunk-735MPLUL.js";
16
16
  import "../chunks/chunk-CPMHA4W5.js";
17
17
  import "../chunks/chunk-ZPZ7GNBT.js";
18
18
  import "../chunks/chunk-BSOZW3FC.js";
@@ -1,21 +1,22 @@
1
1
  import {
2
2
  tubeMapNodeColors
3
- } from "../chunks/chunk-3WSA4NNP.js";
4
- import "../chunks/chunk-VB4IXIPM.js";
3
+ } from "../chunks/chunk-ZKIH2USC.js";
4
+ import "../chunks/chunk-2H3ALI6L.js";
5
+ import "../chunks/chunk-7GDNDQD7.js";
5
6
  import "../chunks/chunk-G2FD7S3C.js";
6
7
  import "../chunks/chunk-GQZVR5DW.js";
7
- import "../chunks/chunk-XTF2VWJN.js";
8
- import "../chunks/chunk-3UGWYQNY.js";
8
+ import "../chunks/chunk-VSRRIFRF.js";
9
+ import "../chunks/chunk-JKIAHYAW.js";
9
10
  import "../chunks/chunk-ZANALBSX.js";
10
11
  import "../chunks/chunk-VX656OAZ.js";
11
- import "../chunks/chunk-FU57ZNRQ.js";
12
+ import "../chunks/chunk-6CXLLJ2C.js";
12
13
  import "../chunks/chunk-HMXCN6PG.js";
13
14
  import "../chunks/chunk-AB35TJST.js";
14
- import "../chunks/chunk-2VMKQKVO.js";
15
- import "../chunks/chunk-5NZRT7GL.js";
15
+ import "../chunks/chunk-YIWN32ZX.js";
16
+ import "../chunks/chunk-3CXZUC2Y.js";
16
17
  import "../chunks/chunk-TLWXLNLY.js";
17
18
  import "../chunks/chunk-3YBP46PB.js";
18
- import "../chunks/chunk-VACK24HF.js";
19
+ import "../chunks/chunk-735MPLUL.js";
19
20
  import "../chunks/chunk-CPMHA4W5.js";
20
21
  import "../chunks/chunk-ZPZ7GNBT.js";
21
22
  import "../chunks/chunk-BSOZW3FC.js";
@@ -4,9 +4,9 @@ import {
4
4
  readColor,
5
5
  stepName,
6
6
  tubeMapReads
7
- } from "../chunks/chunk-SDI6BVG7.js";
7
+ } from "../chunks/chunk-J4PDHWP2.js";
8
8
  import "../chunks/chunk-5OJZV6YT.js";
9
- import "../chunks/chunk-VACK24HF.js";
9
+ import "../chunks/chunk-735MPLUL.js";
10
10
  import "../chunks/chunk-CPMHA4W5.js";
11
11
  export {
12
12
  FORWARD_READ_COLORS,
@@ -17,6 +17,11 @@ interface NodeRow {
17
17
  color: string;
18
18
  alpha: number;
19
19
  width: number;
20
+ walk: number | null;
21
+ pass: number | null;
22
+ nx: number;
23
+ ny: number;
24
+ offset: number;
20
25
  }
21
26
  interface EdgeRow {
22
27
  panel: string;
@@ -34,13 +39,28 @@ interface EdgeRow {
34
39
  alpha: number;
35
40
  width: number;
36
41
  deletion: boolean;
42
+ walk: number | null;
43
+ pass: number | null;
44
+ nx: number;
45
+ ny: number;
46
+ offset: number;
47
+ nx1: number;
48
+ ny1: number;
49
+ offset1: number;
37
50
  }
38
51
  interface KeyRow {
39
52
  panel: string;
40
53
  walk: string;
54
+ name: string;
55
+ color: string;
41
56
  note: string;
42
57
  scale: string;
43
58
  stops: string;
59
+ field: string;
60
+ }
61
+ interface ThreadKeyRow {
62
+ panel: string;
63
+ note: string;
44
64
  }
45
65
  interface PinRow {
46
66
  gene: string;
@@ -89,6 +109,7 @@ export declare function figureData(graph: Graph, layout: LayoutResult, o?: Figur
89
109
  range: string[];
90
110
  };
91
111
  keys: Columns<KeyRow>;
112
+ threadKeys: Columns<ThreadKeyRow>;
92
113
  pins: Columns<PinRow>;
93
114
  exons: Columns<ExonRow>;
94
115
  walkNames: string[];
@@ -146,6 +167,7 @@ export declare function gfaFigureData(text: string, name: string, spec?: GfaFigu
146
167
  range: string[];
147
168
  };
148
169
  keys: Columns<KeyRow>;
170
+ threadKeys: Columns<ThreadKeyRow>;
149
171
  pins: Columns<PinRow>;
150
172
  exons: Columns<ExonRow>;
151
173
  walkNames: string[];
@@ -1,2 +1,4 @@
1
1
  import type { Graph } from './types.js';
2
- export declare function foldVariants(graph: Graph, belowBp: number): Graph;
2
+ export declare function foldVariants(graph: Graph, belowBp: number, { cut }?: {
3
+ cut?: boolean;
4
+ }): Graph;
@@ -3,6 +3,19 @@ export interface EdgeCurveBatch {
3
3
  curves: BezierCurve[];
4
4
  thickness: number;
5
5
  color: number;
6
+ walk?: number;
7
+ pass?: number;
8
+ normal?: LaneSlide['normal'];
9
+ offsetX?: number;
10
+ endNormal?: LaneSlide['normal'];
11
+ endOffsetX?: number;
12
+ }
13
+ export interface LaneSlide {
14
+ normal: {
15
+ nx: number;
16
+ ny: number;
17
+ };
18
+ offsetX: number;
6
19
  }
7
20
  export interface NodeStroke {
8
21
  points: {
@@ -11,6 +24,13 @@ export interface NodeStroke {
11
24
  }[];
12
25
  thickness: number;
13
26
  color: number;
27
+ walk?: number;
28
+ pass?: number;
29
+ normals?: {
30
+ nx: number;
31
+ ny: number;
32
+ }[];
33
+ offsetX?: number;
14
34
  }
15
35
  export interface Arrowhead {
16
36
  x: number;
@@ -0,0 +1,60 @@
1
+ import type { LaneSlide } from './types.js';
2
+ import type { NodeSegment } from '../types.js';
3
+ export declare const THREAD_PX = 2;
4
+ export declare const THREAD_GAP_PX = 1.5;
5
+ export declare const SLOT_GAP_PX = 4;
6
+ export declare const LANE_SMOOTHING_PX = 12;
7
+ export declare const THREAD_REACH_PX = 64;
8
+ export declare const THREAD_TAPER_PX = 24;
9
+ export declare const MAX_BAND_PX = 48;
10
+ export declare const PASSES_KEY = "a thread per pass through a node";
11
+ export declare const threadsPasses: (walks: readonly {
12
+ mostPasses: number;
13
+ }[]) => boolean;
14
+ export interface Normal {
15
+ nx: number;
16
+ ny: number;
17
+ }
18
+ export interface Shift {
19
+ dx: number;
20
+ dy: number;
21
+ }
22
+ export declare const THREAD_PITCH_PX: number;
23
+ export declare function slotCentres(spans: readonly number[], mostPasses: readonly number[], held?: readonly number[]): number[];
24
+ export declare const bandWidthPx: (mostPasses: readonly number[]) => number;
25
+ export declare const bandScale: (mostPasses: readonly number[]) => number;
26
+ export declare const passesKey: (walks: readonly {
27
+ mostPasses: number;
28
+ }[]) => "a thread per pass through a node" | "a thread per pass through a node, thinned to fit";
29
+ export declare function laneSlideAt(start: LaneSlide, end: LaneSlide, along: number): LaneSlide;
30
+ interface LinePoint {
31
+ x: number;
32
+ y: number;
33
+ id: string;
34
+ index: number;
35
+ middle: boolean;
36
+ forward: boolean;
37
+ }
38
+ export interface LaneRuns {
39
+ runs: LinePoint[][];
40
+ owned: boolean[][];
41
+ }
42
+ export declare function laneRuns(routes: readonly (readonly string[])[], nodePositions: Record<string, NodeSegment[]>, yToX: number, jump: number): LaneRuns;
43
+ export declare function laneLines(lanes: LaneRuns, nodePositions: Record<string, NodeSegment[]>, yToX: number, reach: number, band: number, smooth?: boolean): {
44
+ normals: Map<string, (Normal | undefined)[]>;
45
+ shifts: Map<string, (Shift | undefined)[]>;
46
+ };
47
+ export interface WalkThreads {
48
+ span: ReadonlyMap<string, number>;
49
+ nodeThreads: Map<string, number[]>;
50
+ linkThreads: Map<string, [number, number][]>;
51
+ }
52
+ export declare function walkThreads(route: readonly (readonly string[])[], passes: ReadonlyMap<string, number>, nodePositions: Record<string, NodeSegment[]>, yToX: number, reach: number): WalkThreads;
53
+ export declare function bandSpans(lanes: LaneRuns, spans: readonly ReadonlyMap<string, number>[], { reach, taper }: {
54
+ reach: number;
55
+ taper: number;
56
+ }): Map<string, {
57
+ slot: number[];
58
+ held: number[];
59
+ }>;
60
+ export {};
@@ -20,6 +20,7 @@ export interface GraphEdge {
20
20
  fromStrand?: '+' | '-';
21
21
  toStrand?: '+' | '-';
22
22
  pathIds?: string[];
23
+ foldBridge?: boolean;
23
24
  }
24
25
  export interface GraphPath {
25
26
  name: string;
@@ -31,7 +31,19 @@ export interface Bounds {
31
31
  maxX: number;
32
32
  maxY: number;
33
33
  }
34
- export declare function dashCurves(curves: BezierCurve[], dashWorld: number, yToX?: number, bounds?: Bounds): BezierCurve[][];
34
+ export declare const dashCurves: (curves: BezierCurve[], dashWorld: number, yToX?: number, bounds?: Bounds) => BezierCurve[][];
35
+ export interface Dash {
36
+ curves: BezierCurve[];
37
+ startAlong: number;
38
+ endAlong: number;
39
+ }
40
+ export declare function dashSpans(curves: BezierCurve[], dashWorld: number, yToX?: number, bounds?: Bounds): Dash[];
41
+ export interface Slide {
42
+ dx: number;
43
+ dy: number;
44
+ }
45
+ export declare const slideAt: (from: Slide, to: Slide, along: number) => Slide;
46
+ export declare function slideCurves(curves: BezierCurve[], from: Slide, to: Slide): BezierCurve[];
35
47
  export declare function translateCurves(curves: BezierCurve[], dx: number, dy: number): BezierCurve[];
36
48
  type Side = 'start' | 'end';
37
49
  export interface EdgeSides {
@@ -1 +1 @@
1
- export declare const version = "11.7.1";
1
+ export declare const version = "11.8.0";
@@ -37,18 +37,20 @@ export type WalkScheme = (typeof WALK_SCHEMES)[number]['value'];
37
37
  export interface WalkEncoding {
38
38
  field: WalkField;
39
39
  scheme: WalkScheme;
40
+ darkest?: number;
41
+ shade?: number;
40
42
  }
41
43
  export interface WalkLayer {
42
44
  walk: string;
43
45
  color?: Partial<WalkEncoding>;
44
46
  }
45
47
  export declare function resolveEncoding(layer: WalkLayer, reference: boolean, picked: number, alone?: boolean): WalkEncoding;
46
- export declare function schemeRgb(scheme: WalkScheme, t: number): number[];
47
- export declare function schemeCss(scheme: WalkScheme, t: number): string;
48
- export declare function schemeColor(scheme: WalkScheme, t: number): number;
49
- export declare function encodedColor({ field, scheme }: WalkEncoding, t?: number): number;
48
+ export declare function schemeRgb(scheme: WalkScheme, t: number, darkest?: number): number[];
49
+ export declare function schemeCss(scheme: WalkScheme, t: number, darkest?: number): string;
50
+ export declare function schemeColor(scheme: WalkScheme, t: number, darkest?: number): number;
51
+ export declare function encodedColor({ field, scheme, darkest, shade }: WalkEncoding, t?: number): number;
50
52
  export declare const NO_VALUE_COLOR: number;
51
- export declare function encodingStops({ field, scheme }: WalkEncoding): {
53
+ export declare function encodingStops({ field, scheme, darkest, shade, }: WalkEncoding): {
52
54
  offset: number;
53
55
  color: string;
54
56
  abgr: number;