react-msaview 4.3.0 → 4.4.1

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 (69) hide show
  1. package/bundle/index.js +15 -15
  2. package/bundle/index.js.LICENSE.txt +1 -9
  3. package/bundle/index.js.map +1 -1
  4. package/dist/colorSchemes.js +2 -2
  5. package/dist/colorSchemes.js.map +1 -1
  6. package/dist/components/VerticalScrollbar.js +2 -2
  7. package/dist/components/VerticalScrollbar.js.map +1 -1
  8. package/dist/components/dialogs/SettingsDialog.js +1 -1
  9. package/dist/components/dialogs/SettingsDialog.js.map +1 -1
  10. package/dist/components/header/{SettingsMenu.d.ts → ColorMenu.d.ts} +2 -2
  11. package/dist/components/header/ColorMenu.js +19 -0
  12. package/dist/components/header/ColorMenu.js.map +1 -0
  13. package/dist/components/header/Header.js +6 -2
  14. package/dist/components/header/Header.js.map +1 -1
  15. package/dist/components/header/HeaderInfoArea.js +3 -2
  16. package/dist/components/header/HeaderInfoArea.js.map +1 -1
  17. package/dist/components/header/HeaderMenu.js +15 -97
  18. package/dist/components/header/HeaderMenu.js.map +1 -1
  19. package/dist/components/header/MSAMenu.d.ts +6 -0
  20. package/dist/components/header/MSAMenu.js +44 -0
  21. package/dist/components/header/MSAMenu.js.map +1 -0
  22. package/dist/components/header/TreeMenu.d.ts +6 -0
  23. package/dist/components/header/TreeMenu.js +64 -0
  24. package/dist/components/header/TreeMenu.js.map +1 -0
  25. package/dist/components/msa/renderBoxFeatureCanvasBlock.js +4 -4
  26. package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map +1 -1
  27. package/dist/components/msa/renderMSABlock.js +13 -9
  28. package/dist/components/msa/renderMSABlock.js.map +1 -1
  29. package/dist/model.d.ts +7 -1
  30. package/dist/model.js +54 -53
  31. package/dist/model.js.map +1 -1
  32. package/dist/rowCoordinateCalculations.d.ts +13 -2
  33. package/dist/rowCoordinateCalculations.js +60 -17
  34. package/dist/rowCoordinateCalculations.js.map +1 -1
  35. package/dist/rowCoordinateCalculations.test.js +96 -2
  36. package/dist/rowCoordinateCalculations.test.js.map +1 -1
  37. package/dist/seqCoordToRowSpecificGlobalCoord.d.ts +4 -0
  38. package/dist/seqCoordToRowSpecificGlobalCoord.js +15 -0
  39. package/dist/seqCoordToRowSpecificGlobalCoord.js.map +1 -0
  40. package/dist/seqCoordToRowSpecificGlobalCoord.test.d.ts +1 -0
  41. package/dist/seqCoordToRowSpecificGlobalCoord.test.js +42 -0
  42. package/dist/seqCoordToRowSpecificGlobalCoord.test.js.map +1 -0
  43. package/dist/util.d.ts +1 -6
  44. package/dist/util.js +5 -22
  45. package/dist/util.js.map +1 -1
  46. package/dist/version.d.ts +1 -1
  47. package/dist/version.js +1 -1
  48. package/package.json +1 -1
  49. package/src/colorSchemes.ts +2 -2
  50. package/src/components/VerticalScrollbar.tsx +2 -3
  51. package/src/components/dialogs/SettingsDialog.tsx +1 -1
  52. package/src/components/header/ColorMenu.tsx +33 -0
  53. package/src/components/header/Header.tsx +6 -2
  54. package/src/components/header/HeaderInfoArea.tsx +5 -2
  55. package/src/components/header/HeaderMenu.tsx +15 -110
  56. package/src/components/header/MSAMenu.tsx +55 -0
  57. package/src/components/header/TreeMenu.tsx +82 -0
  58. package/src/components/msa/renderBoxFeatureCanvasBlock.ts +4 -4
  59. package/src/components/msa/renderMSABlock.ts +26 -22
  60. package/src/model.ts +73 -61
  61. package/src/rowCoordinateCalculations.test.ts +138 -2
  62. package/src/rowCoordinateCalculations.ts +95 -18
  63. package/src/seqCoordToRowSpecificGlobalCoord.test.ts +53 -0
  64. package/src/seqCoordToRowSpecificGlobalCoord.ts +20 -0
  65. package/src/util.ts +5 -28
  66. package/src/version.ts +1 -1
  67. package/dist/components/header/SettingsMenu.js +0 -141
  68. package/dist/components/header/SettingsMenu.js.map +0 -1
  69. package/src/components/header/SettingsMenu.tsx +0 -169
package/dist/components/msa/renderMSABlock.js CHANGED
@@ -1,6 +1,6 @@
1
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  import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
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  export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
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- const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, actuallyShowDomains, leaves, } = model;
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+ const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, actuallyShowDomains, leaves, bgColor, } = model;
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  const k = highResScaleFactorOverride || highResScaleFactor;
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  const bx = blockSizeXOverride || blockSize;
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  const by = blockSizeYOverride || blockSize;
@@ -8,7 +8,7 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
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  ctx.scale(k, k);
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  ctx.translate(-offsetX, rowHeight / 2 - offsetY);
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  ctx.textAlign = 'center';
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- ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
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+ ctx.font = ctx.font.replace(/\d+px/, `${bgColor ? '' : 'bold '}${fontSize}px`);
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  const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
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  const yEnd = Math.max(0, Math.ceil((offsetY + by + rowHeight) / rowHeight));
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  const xStart = Math.max(0, Math.floor(offsetX / colWidth));
@@ -40,25 +40,28 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
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  }
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  function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, }) {
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  const { bgColor, colorSchemeName, colorScheme, columns, colWidth, rowHeight, } = model;
43
- for (const node of visibleLeaves) {
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+ for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
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+ const node = visibleLeaves[i];
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  const { data: { name }, } = node;
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  const y = node.x;
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  const str = columns[name]?.slice(xStart, xEnd);
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  if (str) {
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- for (let i = 0; i < str.length; i++) {
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+ for (let i = 0, l2 = str.length; i < l2; i++) {
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  const letter = str[i];
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- const color = colorSchemeName === 'clustalx_protein_dynamic'
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+ const r1 = colorSchemeName === 'clustalx_protein_dynamic';
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+ const r2 = colorSchemeName === 'percent_identity_dynamic';
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+ const color = r1
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  ? getClustalXColor(
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  // use model.colStats dot notation here: delay use of colStats
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  // until absolutely needed
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  model.colStats[xStart + i], model.colStatsSums[xStart + i], model, name, xStart + i)
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- : colorSchemeName === 'percent_identity_dynamic'
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+ : r2
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  ? getPercentIdentityColor(
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  // use model.colStats dot notation here: delay use of
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  // colStats until absolutely needed
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  model.colStats[xStart + i], model.colStatsSums[xStart + i], model, name, xStart + i)
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  : colorScheme[letter.toUpperCase()];
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- if (bgColor) {
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+ if (bgColor || r1 || r2) {
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  ctx.fillStyle = color || theme.palette.background.default;
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  ctx.fillRect(i * colWidth + offsetX - (offsetX % colWidth), y - rowHeight, colWidth, rowHeight);
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  }
@@ -69,12 +72,13 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
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  function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart, xEnd, }) {
70
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  const { bgColor, actuallyShowDomains, showMsaLetters, colorScheme, columns, colWidth, contrastLettering, rowHeight, } = model;
71
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  if (showMsaLetters) {
72
- for (const node of visibleLeaves) {
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+ for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
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+ const node = visibleLeaves[i];
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  const { data: { name }, } = node;
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  const y = node.x;
75
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  const str = columns[name]?.slice(xStart, xEnd);
76
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  if (str) {
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- for (let i = 0; i < str.length; i++) {
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+ for (let i = 0, l2 = str.length; i < l2; i++) {
78
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  const letter = str[i];
79
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  const color = colorScheme[letter.toUpperCase()];
80
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  const contrast = contrastLettering
package/dist/components/msa/renderMSABlock.js.map CHANGED
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1
+ {"version":3,"file":"renderMSABlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderMSABlock.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,uBAAuB,EAAE,MAAM,oBAAoB,CAAA;AAO9E,MAAM,UAAU,cAAc,CAAC,EAC7B,KAAK,EACL,OAAO,EACP,OAAO,EACP,cAAc,EACd,GAAG,EACH,KAAK,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,kBAAkB,GAWnB;IACC,MAAM,EACJ,QAAQ,EACR,SAAS,EACT,SAAS,EACT,QAAQ,EACR,kBAAkB,EAClB,mBAAmB,EACnB,MAAM,EACN,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;IAChD,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;IACxB,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,GAAG,QAAQ,IAAI,CAAC,CAAA;IAE9E,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IAC3E,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC1D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC9D,MAAM,aAAa,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAEhD,IAAI,CAAC,mBAAmB,EAAE,CAAC;QACzB,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,KAAK;YACL,OAAO;YACP,OAAO;YACP,MAAM;YACN,IAAI;YACJ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;IACD,QAAQ,CAAC;QACP,KAAK;QACL,GAAG;QACH,OAAO;QACP,cAAc;QACd,KAAK;QACL,MAAM;QACN,IAAI;QACJ,aAAa;KACd,CAAC,CAAA;IACF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,OAAO,EACP,GAAG,EACH,aAAa,EACb,KAAK,EACL,MAAM,EACN,IAAI,GAUL;IACC,MAAM,EACJ,OAAO,EACP,eAAe,EACf,WAAW,EACX,OAAO,EACP,QAAQ,EACR,SAAS,GACV,GAAG,KAAK,CAAA;IAET,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;QACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;QACjB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAC9C,IAAI,GAAG,EAAE,CAAC;YACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;gBACtB,MAAM,EAAE,GAAG,eAAe,KAAK,0BAA0B,CAAA;gBACzD,MAAM,EAAE,GAAG,eAAe,KAAK,0BAA0B,CAAA;gBACzD,MAAM,KAAK,GAAG,EAAE;oBACd,CAAC,CAAC,gBAAgB;oBACd,8DAA8D;oBAC9D,0BAA0B;oBAC1B,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAE,EAC3B,KAAK,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,EAC/B,KAAK,EACL,IAAI,EACJ,MAAM,GAAG,CAAC,CACX;oBACH,CAAC,CAAC,EAAE;wBACF,CAAC,CAAC,uBAAuB;wBACrB,qDAAqD;wBACrD,mCAAmC;wBACnC,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAE,EAC3B,KAAK,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,EAC/B,KAAK,EACL,IAAI,EACJ,MAAM,GAAG,CAAC,CACX;wBACH,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;gBACvC,IAAI,OAAO,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;oBACxB,GAAG,CAAC,SAAS,GAAG,KAAK,IAAI,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAA;oBACzD,GAAG,CAAC,QAAQ,CACV,CAAC,GAAG,QAAQ,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,EAC7C,CAAC,GAAG,SAAS,EACb,QAAQ,EACR,SAAS,CACV,CAAA;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,EAChB,KAAK,EACL,OAAO,EACP,cAAc,EACd,GAAG,EACH,aAAa,EACb,MAAM,EACN,IAAI,GAUL;IACC,MAAM,EACJ,OAAO,EACP,mBAAmB,EACnB,cAAc,EACd,WAAW,EACX,OAAO,EACP,QAAQ,EACR,iBAAiB,EACjB,SAAS,GACV,GAAG,KAAK,CAAA;IACT,IAAI,cAAc,EAAE,CAAC;QACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;YAC9B,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;YACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;YACjB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,GAAG,EAAE,CAAC;gBACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;oBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;oBACtB,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;oBAC/C,MAAM,QAAQ,GAAG,iBAAiB;wBAChC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,OAAO;wBACjD,CAAC,CAAC,OAAO,CAAA;oBACX,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;oBAEvD,kDAAkD;oBAClD,GAAG,CAAC,SAAS,GAAG,mBAAmB;wBACjC,CAAC,CAAC,OAAO;wBACT,CAAC,CAAC,OAAO;4BACP,CAAC,CAAC,QAAQ;4BACV,CAAC,CAAC,KAAK,IAAI,OAAO,CAAA;oBACtB,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,GAAG,CAAC,CAAC,CAAA;gBAC3D,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}
package/dist/model.d.ts CHANGED
@@ -734,13 +734,19 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
734
734
  * #method
735
735
  * return a row-specific letter, or undefined if gap
736
736
  */
737
- mouseOverCoordToRowLetter(rowName: string, position: number): string | undefined;
737
+ mouseOverCoordToRowLetter(rowName: string, pos: number): string | undefined;
738
738
  /**
739
739
  * #method
740
740
  * return a row-specific sequence coordinate, skipping gaps, given a
741
741
  * global coordinate
742
742
  */
743
743
  mouseOverCoordToGapRemovedRowCoord(rowName: string, position: number): number | undefined;
744
+ /**
745
+ * #method
746
+ * return a row-specific sequence coordinate, skipping gaps, given a
747
+ * global coordinate
748
+ */
749
+ mouseOverCoordToGapRemovedRowCoordOneBased(rowName: string, position: number): number | undefined;
744
750
  /**
745
751
  * #method
746
752
  * return a global coordinate given a row-specific sequence coordinate
package/dist/model.js CHANGED
@@ -1,4 +1,4 @@
1
- import { groupBy, notEmpty, sum } from '@jbrowse/core/util';
1
+ import { clamp, fetchAndMaybeUnzipText, groupBy, localStorageGetBoolean, localStorageSetBoolean, notEmpty, sum, } from '@jbrowse/core/util';
2
2
  import { openLocation } from '@jbrowse/core/util/io';
3
3
  import { ElementId, FileLocation } from '@jbrowse/core/util/types/mst';
4
4
  import { colord } from 'colord';
@@ -8,7 +8,6 @@ import { parseEmfTree } from 'emf-js';
8
8
  import { saveAs } from 'file-saver';
9
9
  import { autorun, transaction } from 'mobx';
10
10
  import { addDisposer, cast, types } from 'mobx-state-tree';
11
- import { ungzip } from 'pako';
12
11
  import Stockholm from 'stockholm-js';
13
12
  import { blocksX, blocksY } from './calculateBlocks';
14
13
  import colorSchemes from './colorSchemes';
@@ -27,8 +26,9 @@ import EmfMSA from './parsers/EmfMSA';
27
26
  import FastaMSA from './parsers/FastaMSA';
28
27
  import StockholmMSA from './parsers/StockholmMSA';
29
28
  import { reparseTree } from './reparseTree';
30
- import { globalCoordToRowSpecificCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
31
- import { clamp, collapse, generateNodeIds, isGzip, len, localStorageGetBoolean, localStorageSetBoolean, maxLength, setBrLength, skipBlanks, } from './util';
29
+ import { mouseOverCoordToGapRemovedRowCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
30
+ import { seqCoordToRowSpecificGlobalCoord } from './seqCoordToRowSpecificGlobalCoord';
31
+ import { collapse, generateNodeIds, isBlank, len, maxLength, setBrLength, skipBlanks, } from './util';
32
32
  const defaultRowHeight = 16;
33
33
  const defaultColWidth = 12;
34
34
  const showZoomStarKey = 'msa-showZoomStar';
@@ -547,11 +547,11 @@ function stateModelFactory() {
547
547
  */
548
548
  get tree() {
549
549
  const text = self.data.tree;
550
- return text
551
- ? reparseTree(generateNodeIds(text.startsWith('BioTreeContainer')
550
+ return reparseTree(text
551
+ ? generateNodeIds(text.startsWith('BioTreeContainer')
552
552
  ? flatToTree(parseAsn1(text))
553
- : parseNewick(text.startsWith('SEQ') ? parseEmfTree(text).tree : text)))
554
- : reparseTree(this.MSA?.getTree() || {
553
+ : parseNewick(text.startsWith('SEQ') ? parseEmfTree(text).tree : text))
554
+ : this.MSA?.getTree() || {
555
555
  noTree: true,
556
556
  children: [],
557
557
  id: 'empty',
@@ -617,16 +617,18 @@ function stateModelFactory() {
617
617
  if (hideGaps) {
618
618
  const strs = this.leaves
619
619
  .map(leaf => this.MSA?.getRow(leaf.data.name))
620
- .filter((item) => !!item);
620
+ .filter(notEmpty);
621
621
  if (strs.length) {
622
- for (let i = 0; i < strs[0].length; i++) {
622
+ const s0len = strs[0].length;
623
+ for (let i = 0; i < s0len; i++) {
623
624
  let counter = 0;
624
- for (const str of strs) {
625
- if (str[i] === '-') {
625
+ const l = strs.length;
626
+ for (let j = 0; j < l; j++) {
627
+ if (isBlank(strs[j][i])) {
626
628
  counter++;
627
629
  }
628
630
  }
629
- if (counter / strs.length >= realAllowedGappyness / 100) {
631
+ if (counter / l >= realAllowedGappyness / 100) {
630
632
  blanks.push(i);
631
633
  }
632
634
  }
@@ -838,14 +840,14 @@ function stateModelFactory() {
838
840
  */
839
841
  zoomOutHorizontal() {
840
842
  self.colWidth = Math.max(1, Math.floor(self.colWidth * 0.75));
841
- self.scrollX = clamp(self.maxScrollX, self.scrollX, 0);
843
+ self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
842
844
  },
843
845
  /**
844
846
  * #action
845
847
  */
846
848
  zoomInHorizontal() {
847
849
  self.colWidth = Math.ceil(self.colWidth * 1.5);
848
- self.scrollX = clamp(self.maxScrollX, self.scrollX, 0);
850
+ self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
849
851
  },
850
852
  /**
851
853
  * #action
@@ -866,7 +868,7 @@ function stateModelFactory() {
866
868
  transaction(() => {
867
869
  self.colWidth = Math.ceil(self.colWidth * 1.5);
868
870
  self.rowHeight = Math.ceil(self.rowHeight * 1.5);
869
- self.scrollX = clamp(self.maxScrollX, self.scrollX, 0);
871
+ self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
870
872
  });
871
873
  },
872
874
  /**
@@ -876,7 +878,7 @@ function stateModelFactory() {
876
878
  transaction(() => {
877
879
  self.colWidth = Math.max(1, Math.floor(self.colWidth * 0.75));
878
880
  self.rowHeight = Math.max(1.5, Math.floor(self.rowHeight * 0.75));
879
- self.scrollX = clamp(self.maxScrollX, self.scrollX, 0);
881
+ self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
880
882
  });
881
883
  },
882
884
  /**
@@ -889,19 +891,19 @@ function stateModelFactory() {
889
891
  * #action
890
892
  */
891
893
  doScrollY(deltaY) {
892
- self.scrollY = clamp(-self.totalHeight + 10, self.scrollY + deltaY, 0);
894
+ self.scrollY = clamp(self.scrollY + deltaY, -self.totalHeight + 10, 0);
893
895
  },
894
896
  /**
895
897
  * #action
896
898
  */
897
899
  doScrollX(deltaX) {
898
- self.scrollX = clamp(self.maxScrollX, self.scrollX + deltaX, 0);
900
+ self.scrollX = clamp(self.scrollX + deltaX, self.maxScrollX, 0);
899
901
  },
900
902
  /**
901
903
  * #action
902
904
  */
903
905
  setScrollX(n) {
904
- self.scrollX = clamp(self.maxScrollX, n, 0);
906
+ self.scrollX = clamp(n, self.maxScrollX, 0);
905
907
  },
906
908
  /**
907
909
  * #action
@@ -1007,9 +1009,9 @@ function stateModelFactory() {
1007
1009
  * #method
1008
1010
  * return a row-specific letter, or undefined if gap
1009
1011
  */
1010
- mouseOverCoordToRowLetter(rowName, position) {
1012
+ mouseOverCoordToRowLetter(rowName, pos) {
1011
1013
  const { rowMap, blanks } = self;
1012
- return rowMap.get(rowName)?.[mouseOverCoordToGlobalCoord(blanks, position)];
1014
+ return rowMap.get(rowName)?.[mouseOverCoordToGlobalCoord(blanks, pos)];
1013
1015
  },
1014
1016
  /**
1015
1017
  * #method
@@ -1017,16 +1019,21 @@ function stateModelFactory() {
1017
1019
  * global coordinate
1018
1020
  */
1019
1021
  mouseOverCoordToGapRemovedRowCoord(rowName, position) {
1020
- const { rowMap, blanks } = self;
1021
- const seq = rowMap.get(rowName);
1022
- if (seq !== undefined) {
1023
- const pos2 = mouseOverCoordToGlobalCoord(blanks, position);
1024
- const pos1 = globalCoordToRowSpecificCoord(seq, pos2);
1025
- return seq[pos1] === '-' || !seq[pos1] ? undefined : pos1;
1026
- }
1027
- else {
1028
- return undefined;
1029
- }
1022
+ return mouseOverCoordToGapRemovedRowCoord({
1023
+ rowName,
1024
+ position,
1025
+ rowMap: self.rowMap,
1026
+ blanks: self.blanks,
1027
+ });
1028
+ },
1029
+ /**
1030
+ * #method
1031
+ * return a row-specific sequence coordinate, skipping gaps, given a
1032
+ * global coordinate
1033
+ */
1034
+ mouseOverCoordToGapRemovedRowCoordOneBased(rowName, position) {
1035
+ const val = this.mouseOverCoordToGapRemovedRowCoord(rowName, position);
1036
+ return val !== undefined ? val + 1 : undefined;
1030
1037
  },
1031
1038
  /**
1032
1039
  * #method
@@ -1036,21 +1043,12 @@ function stateModelFactory() {
1036
1043
  seqCoordToRowSpecificGlobalCoord(rowName, position) {
1037
1044
  const { rowNames, rows } = self;
1038
1045
  const index = rowNames.indexOf(rowName);
1039
- if (index !== -1 && rows[index]) {
1040
- const row = rows[index][1];
1041
- let k = 0;
1042
- let i = 0;
1043
- for (; k < position; i++) {
1044
- if (row[i] !== '-') {
1045
- k++;
1046
- }
1047
- else if (k >= position) {
1048
- break;
1049
- }
1050
- }
1051
- return i;
1052
- }
1053
- return 0;
1046
+ return index !== -1 && rows[index]
1047
+ ? seqCoordToRowSpecificGlobalCoord({
1048
+ row: rows[index][1],
1049
+ position,
1050
+ })
1051
+ : 0;
1054
1052
  },
1055
1053
  }))
1056
1054
  .views(self => ({
@@ -1180,7 +1178,11 @@ function stateModelFactory() {
1180
1178
  * #action
1181
1179
  */
1182
1180
  reset() {
1183
- self.setData({ tree: '', msa: '' });
1181
+ self.setData({
1182
+ tree: '',
1183
+ msa: '',
1184
+ });
1185
+ self.resetZoom();
1184
1186
  self.setError(undefined);
1185
1187
  self.setScrollY(0);
1186
1188
  self.setScrollX(0);
@@ -1244,7 +1246,7 @@ function stateModelFactory() {
1244
1246
  if (treeFilehandle) {
1245
1247
  try {
1246
1248
  self.setLoadingTree(true);
1247
- self.setTree(await openLocation(treeFilehandle).readFile('utf8'));
1249
+ self.setTree(await fetchAndMaybeUnzipText(openLocation(treeFilehandle)));
1248
1250
  if (treeFilehandle.locationType === 'BlobLocation') {
1249
1251
  // clear filehandle after loading if from a local file
1250
1252
  self.setTreeFilehandle(undefined);
@@ -1264,7 +1266,7 @@ function stateModelFactory() {
1264
1266
  const { treeMetadataFilehandle } = self;
1265
1267
  if (treeMetadataFilehandle) {
1266
1268
  try {
1267
- self.setTreeMetadata(await openLocation(treeMetadataFilehandle).readFile('utf8'));
1269
+ self.setTreeMetadata(await fetchAndMaybeUnzipText(openLocation(treeMetadataFilehandle)));
1268
1270
  }
1269
1271
  catch (e) {
1270
1272
  console.error(e);
@@ -1278,9 +1280,8 @@ function stateModelFactory() {
1278
1280
  if (msaFilehandle) {
1279
1281
  try {
1280
1282
  self.setLoadingMSA(true);
1281
- const res = await openLocation(msaFilehandle).readFile();
1282
- const buf = isGzip(res) ? ungzip(res) : res;
1283
- const txt = new TextDecoder('utf8').decode(buf);
1283
+ self.setError(undefined);
1284
+ const txt = await fetchAndMaybeUnzipText(openLocation(msaFilehandle));
1284
1285
  transaction(() => {
1285
1286
  self.setMSA(txt);
1286
1287
  if (msaFilehandle.locationType === 'BlobLocation') {
package/dist/model.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/rowCoordinateCalculations.d.ts CHANGED
@@ -1,2 +1,13 @@
1
- export declare function mouseOverCoordToGlobalCoord(blanks: number[], pos: number): number;
2
- export declare function globalCoordToRowSpecificCoord(seq: string, pos: number): number;
1
+ export declare function mouseOverCoordToGlobalCoord(blanks: number[], position: number): number;
2
+ export declare function globalCoordToRowSpecificCoord(seq: string, position: number): number;
3
+ export declare function mouseOverCoordToGapRemovedRowCoord({ rowName, position, rowMap, blanks, }: {
4
+ rowName: string;
5
+ position: number;
6
+ rowMap: Map<string, string>;
7
+ blanks: number[];
8
+ }): number | undefined;
9
+ export declare function mouseOverCoordToGapRemovedCoord({ seq, blanks, position, }: {
10
+ seq: string;
11
+ blanks: number[];
12
+ position: number;
13
+ }): number | undefined;
package/dist/rowCoordinateCalculations.js CHANGED
@@ -1,26 +1,69 @@
1
- export function mouseOverCoordToGlobalCoord(blanks, pos) {
2
- let i = 0; // 'mouse over coord'
3
- let j = 0; // 'position in blanks array'
4
- let k = 0; // 'global coord'/return value
5
- for (; i < pos; i++, k++) {
6
- // skip multiple gaps in a row
7
- while (j < blanks.length && blanks[j] - 1 === k) {
8
- j++;
9
- k++;
1
+ import { isBlank } from './util';
2
+ export function mouseOverCoordToGlobalCoord(blanks, position) {
3
+ let mousePosition = 0; // Current position in mouse coordinates
4
+ let blankArrayIndex = 0; // Current index in the blanks array
5
+ let globalPosition = 0; // Position in global coordinates (return value)
6
+ const blanksLen = blanks.length;
7
+ // Iterate until we reach the target mouse position
8
+ while (mousePosition < position) {
9
+ // Skip any blank positions in the sequence
10
+ while (blankArrayIndex < blanksLen &&
11
+ blanks[blankArrayIndex] - 1 === globalPosition) {
12
+ blankArrayIndex++;
13
+ globalPosition++;
10
14
  }
15
+ // Move to next position
16
+ mousePosition++;
17
+ globalPosition++;
11
18
  }
12
- return k;
19
+ return globalPosition;
13
20
  }
14
- export function globalCoordToRowSpecificCoord(seq, pos) {
15
- let k = 0;
16
- for (let i = 0; i < pos; i++) {
17
- if (seq[i] !== '-') {
18
- k++;
21
+ export function globalCoordToRowSpecificCoord(seq, position) {
22
+ // Initialize counter for non-gap characters
23
+ let nonGapCount = 0;
24
+ // Initialize position counter
25
+ let currentPosition = 0;
26
+ const sequenceLength = seq.length;
27
+ // Iterate until we reach the target position or end of sequence
28
+ while (currentPosition < position && currentPosition < sequenceLength) {
29
+ // If current character is not a gap, increment the non-gap counter
30
+ if (seq[currentPosition] !== '-') {
31
+ nonGapCount++;
19
32
  }
20
- else if (k >= pos) {
33
+ // If we've reached the target position in non-gap coordinates, break
34
+ else if (nonGapCount >= position) {
21
35
  break;
22
36
  }
37
+ currentPosition++;
23
38
  }
24
- return k;
39
+ return nonGapCount;
40
+ }
41
+ export function mouseOverCoordToGapRemovedRowCoord({ rowName, position, rowMap, blanks, }) {
42
+ const seq = rowMap.get(rowName);
43
+ return seq !== undefined
44
+ ? mouseOverCoordToGapRemovedCoord({
45
+ seq,
46
+ position,
47
+ blanks,
48
+ })
49
+ : undefined;
50
+ }
51
+ export function mouseOverCoordToGapRemovedCoord({ seq, blanks, position, }) {
52
+ // First convert the mouse position to global coordinates
53
+ const globalPos = mouseOverCoordToGlobalCoord(blanks, position);
54
+ const seqLen = seq.length;
55
+ // Check if the position in the sequence is a gap
56
+ if (globalPos < seqLen && isBlank(seq[globalPos])) {
57
+ return undefined;
58
+ }
59
+ // Count non-gap characters up to the global position
60
+ let nonGapCount = 0;
61
+ for (let i = 0; i < globalPos && i < seqLen; i++) {
62
+ if (!isBlank(seq[i])) {
63
+ nonGapCount++;
64
+ }
65
+ }
66
+ // If we're at a valid position, return the count of non-gap characters
67
+ return globalPos < seqLen ? nonGapCount : undefined;
25
68
  }
26
69
  //# sourceMappingURL=rowCoordinateCalculations.js.map
package/dist/rowCoordinateCalculations.js.map CHANGED
@@ -1 +1 @@
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