@jbrowse/plugin-linear-genome-view 2.0.0 → 2.0.1

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 (38) hide show
  1. package/dist/LinearGenomeView/components/{VerticalGuides.d.ts → Gridlines.d.ts} +0 -0
  2. package/dist/LinearGenomeView/components/{VerticalGuides.js → Gridlines.js} +1 -1
  3. package/dist/LinearGenomeView/components/Gridlines.js.map +1 -0
  4. package/dist/LinearGenomeView/components/OverviewRubberBand.js +13 -10
  5. package/dist/LinearGenomeView/components/OverviewRubberBand.js.map +1 -1
  6. package/dist/LinearGenomeView/components/RubberBand.js +0 -1
  7. package/dist/LinearGenomeView/components/RubberBand.js.map +1 -1
  8. package/dist/LinearGenomeView/components/SequenceDialog.js +1 -1
  9. package/dist/LinearGenomeView/components/SequenceDialog.js.map +1 -1
  10. package/dist/LinearGenomeView/components/TracksContainer.js +2 -2
  11. package/dist/LinearGenomeView/components/TracksContainer.js.map +1 -1
  12. package/dist/LinearGenomeView/index.d.ts +63 -76
  13. package/dist/LinearGenomeView/index.js +239 -365
  14. package/dist/LinearGenomeView/index.js.map +1 -1
  15. package/esm/LinearGenomeView/components/{VerticalGuides.d.ts → Gridlines.d.ts} +0 -0
  16. package/esm/LinearGenomeView/components/{VerticalGuides.js → Gridlines.js} +1 -1
  17. package/esm/LinearGenomeView/components/Gridlines.js.map +1 -0
  18. package/esm/LinearGenomeView/components/OverviewRubberBand.js +13 -10
  19. package/esm/LinearGenomeView/components/OverviewRubberBand.js.map +1 -1
  20. package/esm/LinearGenomeView/components/RubberBand.js +0 -1
  21. package/esm/LinearGenomeView/components/RubberBand.js.map +1 -1
  22. package/esm/LinearGenomeView/components/SequenceDialog.js +1 -1
  23. package/esm/LinearGenomeView/components/SequenceDialog.js.map +1 -1
  24. package/esm/LinearGenomeView/components/TracksContainer.js +2 -2
  25. package/esm/LinearGenomeView/components/TracksContainer.js.map +1 -1
  26. package/esm/LinearGenomeView/index.d.ts +63 -76
  27. package/esm/LinearGenomeView/index.js +243 -389
  28. package/esm/LinearGenomeView/index.js.map +1 -1
  29. package/package.json +3 -3
  30. package/src/LinearGenomeView/components/{VerticalGuides.tsx → Gridlines.tsx} +0 -0
  31. package/src/LinearGenomeView/components/OverviewRubberBand.tsx +14 -19
  32. package/src/LinearGenomeView/components/RubberBand.tsx +0 -1
  33. package/src/LinearGenomeView/components/SequenceDialog.tsx +1 -1
  34. package/src/LinearGenomeView/components/TracksContainer.tsx +2 -2
  35. package/src/LinearGenomeView/index.test.ts +13 -36
  36. package/src/LinearGenomeView/index.tsx +360 -519
  37. package/dist/LinearGenomeView/components/VerticalGuides.js.map +0 -1
  38. package/esm/LinearGenomeView/components/VerticalGuides.js.map +0 -1
package/dist/LinearGenomeView/index.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/LinearGenomeView/components/{VerticalGuides.js → Gridlines.js} RENAMED
@@ -68,4 +68,4 @@ function VerticalGuides({ model }) {
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68
  React.createElement(RenderedVerticalGuides, { model: model }))));
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  }
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  export default observer(VerticalGuides);
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- //# sourceMappingURL=VerticalGuides.js.map
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+ //# sourceMappingURL=Gridlines.js.map
package/esm/LinearGenomeView/components/Gridlines.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"Gridlines.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/Gridlines.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EACL,YAAY,EACZ,WAAW,EACX,uBAAuB,GACxB,MAAM,+BAA+B,CAAA;AACtC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,YAAY,IAAI,qBAAqB,EACrC,WAAW,IAAI,oBAAoB,EACnC,uBAAuB,IAAI,gCAAgC,GAC5D,MAAM,0CAA0C,CAAA;AAEjD,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAInC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,2BAA2B,EAAE;QAC3B,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,MAAM;QACd,KAAK,EAAE,MAAM;QACb,MAAM,EAAE,CAAC;QACT,aAAa,EAAE,MAAM;KACtB;IACD,uBAAuB,EAAE;QACvB,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,MAAM;QACd,MAAM,EAAE,CAAC;QACT,aAAa,EAAE,MAAM;QACrB,OAAO,EAAE,MAAM;KAChB;IACD,IAAI,EAAE;QACJ,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,MAAM;QACd,KAAK,EAAE,CAAC;KACT;IACD,SAAS,EAAE;QACT,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS;KACzC;IACD,SAAS,EAAE;QACT,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,OAAO;KAClC;CACF,CAAC,CAAC,CAAA;AACH,MAAM,sBAAsB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAAkB,EAAE,EAAE;IACpE,MAAM,EAAE,OAAO,EAAE,EAAE,EAAE,GAAG,SAAS,EAAE,CAAA;IACnC,OAAO,CACL,0CACG,KAAK,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE;QACvC,IAAI,KAAK,YAAY,YAAY,EAAE;YACjC,MAAM,KAAK,GAAG,SAAS,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAA;YAC9D,OAAO,CACL,oBAAC,qBAAqB,IAAC,GAAG,EAAE,GAAG,KAAK,CAAC,GAAG,IAAI,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,IAC9D,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;gBAChB,MAAM,CAAC,GACL,CAAC,KAAK,CAAC,QAAQ;oBACb,CAAC,CAAC,KAAK,CAAC,GAAG,GAAG,IAAI,CAAC,IAAI;oBACvB,CAAC,CAAC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,GAAG,KAAK,CAAC,OAAO,CAAA;gBAC9C,OAAO,CACL,6BACE,GAAG,EAAE,IAAI,CAAC,IAAI,EACd,SAAS,EAAE,EAAE,CACX,OAAO,CAAC,IAAI,EACZ,IAAI,CAAC,IAAI,KAAK,OAAO,IAAI,IAAI,CAAC,IAAI,KAAK,cAAc;wBACnD,CAAC,CAAC,OAAO,CAAC,SAAS;wBACnB,CAAC,CAAC,OAAO,CAAC,SAAS,CACtB,EACD,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,GAClB,CACH,CAAA;YACH,CAAC,CAAC,CACoB,CACzB,CAAA;SACF;QACD,IAAI,KAAK,YAAY,WAAW,EAAE;YAChC,OAAO,oBAAC,oBAAoB,IAAC,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,KAAK,EAAE,KAAK,CAAC,OAAO,GAAI,CAAA;SACtE;QACD,IAAI,KAAK,YAAY,uBAAuB,EAAE;YAC5C,OAAO,CACL,oBAAC,gCAAgC,IAC/B,GAAG,EAAE,KAAK,CAAC,GAAG,EACd,KAAK,EAAE,KAAK,CAAC,OAAO,EACpB,QAAQ,EAAE,KAAK,CAAC,OAAO,KAAK,UAAU,GACtC,CACH,CAAA;SACF;QACD,OAAO,IAAI,CAAA;IACb,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AACF,SAAS,cAAc,CAAC,EAAE,KAAK,EAAkB;IAC/C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,iEAAiE;IACjE,MAAM,UAAU,GAAG,KAAK,CAAC,YAAY,CAAC,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAA;IAC/D,OAAO,CACL,6BACE,SAAS,EAAE,OAAO,CAAC,2BAA2B,EAC9C,KAAK,EAAE;YACL,SAAS,EACP,KAAK,CAAC,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC,CAAC,SAAS;SACvE;QAED,6BACE,SAAS,EAAE,OAAO,CAAC,uBAAuB,EAC1C,KAAK,EAAE;gBACL,IAAI,EAAE,UAAU;gBAChB,KAAK,EAAE,KAAK,CAAC,YAAY,CAAC,YAAY;aACvC;YAED,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI,CACpC,CACF,CACP,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,cAAc,CAAC,CAAA"}
package/esm/LinearGenomeView/components/OverviewRubberBand.js CHANGED
@@ -78,19 +78,22 @@ function OverviewRubberBand({ model, overview, ControlComponent = React.createEl
78
78
  }
79
79
  }
80
80
  function globalMouseUp() {
81
- if (controlsRef.current &&
82
- startX !== undefined &&
83
- currentX !== undefined) {
81
+ // click and drag
82
+ if (startX !== undefined && currentX !== undefined) {
84
83
  if (Math.abs(currentX - startX) > 3) {
85
- model.zoomToDisplayedRegions(overview.pxToBp(startX - cytobandOffset), overview.pxToBp(currentX - cytobandOffset));
84
+ model.moveTo(overview.pxToBp(startX - cytobandOffset), overview.pxToBp(currentX - cytobandOffset));
86
85
  }
87
86
  }
88
- /* handling clicking and centering at a specific Bp */
89
- if (controlsRef.current &&
90
- startX !== undefined &&
91
- currentX === undefined) {
92
- const clickedAt = overview.pxToBp(startX - cytobandOffset);
93
- model.centerAt(Math.round(clickedAt.coord), clickedAt.refName, clickedAt.index);
87
+ // just a click
88
+ if (startX !== undefined && currentX === undefined) {
89
+ const click = overview.pxToBp(startX - cytobandOffset);
90
+ if (!click.refName) {
91
+ getSession(model).notify('unknown position clicked');
92
+ console.error('unknown position clicked', click);
93
+ }
94
+ else {
95
+ model.centerAt(Math.round(click.coord), click.refName, click.index);
96
+ }
94
97
  }
95
98
  setStartX(undefined);
96
99
  setCurrentX(undefined);
package/esm/LinearGenomeView/components/OverviewRubberBand.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/esm/LinearGenomeView/components/RubberBand.js CHANGED
@@ -71,7 +71,6 @@ function RubberBand({ model, ControlComponent = React.createElement("div", null)
71
71
  }
72
72
  let leftPx = startX;
73
73
  let rightPx = offsetX;
74
- // handles clicking and draging to the left
75
74
  if (rightPx < leftPx) {
76
75
  ;
77
76
  [leftPx, rightPx] = [rightPx, leftPx];
package/esm/LinearGenomeView/components/RubberBand.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/LinearGenomeView/components/SequenceDialog.js CHANGED
@@ -141,7 +141,7 @@ function SequenceDialog({ model, handleClose, }) {
141
141
  });
142
142
  saveAs(seqFastaFile, 'jbrowse_ref_seq.fa');
143
143
  }, disabled: loading || !!error, color: "primary", startIcon: React.createElement(GetAppIcon, null) }, "Download FASTA"),
144
- React.createElement(Button, { onClick: handleClose, color: "primary", autoFocus: true }, "Close"))));
144
+ React.createElement(Button, { onClick: handleClose, variant: "contained" }, "Close"))));
145
145
  }
146
146
  export default observer(SequenceDialog);
147
147
  //# sourceMappingURL=SequenceDialog.js.map
package/esm/LinearGenomeView/components/SequenceDialog.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/LinearGenomeView/components/TracksContainer.js CHANGED
@@ -5,7 +5,7 @@ import normalizeWheel from 'normalize-wheel';
5
5
  import { SCALE_BAR_HEIGHT } from '..';
6
6
  import RubberBand from './RubberBand';
7
7
  import ScaleBar from './ScaleBar';
8
- import VerticalGuides from './VerticalGuides';
8
+ import Gridlines from './Gridlines';
9
9
  import CenterLine from './CenterLine';
10
10
  const useStyles = makeStyles()({
11
11
  tracksContainer: {
@@ -133,7 +133,7 @@ function TracksContainer({ children, model, }) {
133
133
  return () => { };
134
134
  }, [model]);
135
135
  return (React.createElement("div", { ref: ref, "data-testid": "trackContainer", className: classes.tracksContainer, onMouseDown: mouseDown, onMouseUp: mouseUp, onMouseLeave: mouseLeave },
136
- React.createElement(VerticalGuides, { model: model }),
136
+ model.showGridlines ? React.createElement(Gridlines, { model: model }) : null,
137
137
  model.showCenterLine ? React.createElement(CenterLine, { model: model }) : null,
138
138
  React.createElement(RubberBand, { model: model, ControlComponent: React.createElement(ScaleBar, { model: model, style: { height: SCALE_BAR_HEIGHT, boxSizing: 'border-box' } }) }),
139
139
  children));
package/esm/LinearGenomeView/components/TracksContainer.js.map CHANGED
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+ {"version":3,"file":"TracksContainer.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/TracksContainer.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC1D,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAE5C,OAAO,EAA8B,gBAAgB,EAAE,MAAM,IAAI,CAAA;AACjE,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,UAAU,MAAM,cAAc,CAAA;AAErC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,eAAe,EAAE;QACf,QAAQ,EAAE,UAAU;QACpB,QAAQ,EAAE,QAAQ;KACnB;IACD,MAAM,EAAE;QACN,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAA;AAKF,SAAS,eAAe,CAAC,EACvB,QAAQ,EACR,KAAK,GAIN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,2EAA2E;IAC3E,yBAAyB;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IACvB,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC/B,MAAM,OAAO,GAAG,MAAM,EAAS,CAAA;IAC/B,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,KAAK,GAAG,MAAM,CAAS,CAAC,CAAC,CAAA;IAE/B,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEzD,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,OAAO,GAAG,GAAG,EAAE,GAAE,CAAC,CAAA;QAEtB,SAAS,eAAe,CAAC,KAAiB;YACxC,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YAC3B,MAAM,QAAQ,GAAG,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YACtC,IAAI,QAAQ,EAAE;gBACZ,uEAAuE;gBACvE,8EAA8E;gBAC9E,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE;oBACtB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;oBACxB,MAAM,CAAC,qBAAqB,CAAC,GAAG,EAAE;wBAChC,KAAK,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAAC,CAAA;wBACjC,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;wBACzB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;oBAC/B,CAAC,CAAC,CAAA;iBACH;aACF;QACH,CAAC;QAED,SAAS,aAAa;YACpB,KAAK,CAAC,OAAO,GAAG,CAAC,CAAA;YACjB,IAAI,aAAa,EAAE;gBACjB,gBAAgB,CAAC,KAAK,CAAC,CAAA;aACxB;QACH,CAAC;QAED,IAAI,aAAa,EAAE;YACjB,MAAM,CAAC,gBAAgB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;YAC3D,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,OAAO,GAAG,GAAG,EAAE;gBACb,MAAM,CAAC,mBAAmB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;gBAC9D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YAC5D,CAAC,CAAA;SACF;QACD,OAAO,OAAO,CAAA;IAChB,CAAC,EAAE,CAAC,KAAK,EAAE,aAAa,EAAE,KAAK,CAAC,CAAC,CAAA;IAEjC,SAAS,SAAS,CAAC,KAAuB;QACxC,2DAA2D;QAC3D,MAAM,MAAM,GAAG,KAAK,CAAC,MAAqB,CAAA;QAC1C,IAAI,MAAM,CAAC,SAAS,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE;YAC9C,OAAM;SACP;QAED,qCAAqC;QACrC,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE;YACtB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;YAC7B,gBAAgB,CAAC,IAAI,CAAC,CAAA;SACvB;IACH,CAAC;IAED,yEAAyE;IACzE,wEAAwE;IACxE,SAAS,OAAO,CAAC,KAAuB;QACtC,KAAK,CAAC,cAAc,EAAE,CAAA;QACtB,gBAAgB,CAAC,KAAK,CAAC,CAAA;IACzB,CAAC;IAED,SAAS,UAAU,CAAC,KAAuB;QACzC,KAAK,CAAC,cAAc,EAAE,CAAA;IACxB,CAAC;IAED,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,CAAA;QACxB,8CAA8C;QAC9C,yCAAyC;QACzC,SAAS,OAAO,CAAC,SAAqB;YACpC,MAAM,KAAK,GAAG,cAAc,CAAC,SAAS,CAAC,CAAA;YACvC,IAAI,SAAS,CAAC,OAAO,KAAK,IAAI,EAAE;gBAC9B,SAAS,CAAC,cAAc,EAAE,CAAA;gBAC1B,KAAK,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,GAAG,GAAG,CAAA;gBACnC,KAAK,CAAC,cAAc,CAClB,KAAK,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,OAAO,CAAC,CAChE,CAAA;gBACD,IAAI,OAAO,CAAC,OAAO,EAAE;oBACnB,YAAY,CAAC,OAAO,CAAC,OAAO,CAAC,CAAA;iBAC9B;gBACD,OAAO,CAAC,OAAO,GAAG,UAAU,CAAC,GAAG,EAAE;oBAChC,KAAK,CAAC,cAAc,CAAC,CAAC,CAAC,CAAA;oBACvB,KAAK,CAAC,MAAM,CACV,KAAK,CAAC,OAAO,GAAG,CAAC;wBACf,CAAC,CAAC,KAAK,CAAC,OAAO,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,OAAO,CAAC;wBACrC,CAAC,CAAC,KAAK,CAAC,OAAO,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,OAAO,CAAC,CACxC,CAAA;oBACD,KAAK,CAAC,OAAO,GAAG,CAAC,CAAA;gBACnB,CAAC,EAAE,GAAG,CAAC,CAAA;aACR;iBAAM;gBACL,gEAAgE;gBAChE,qEAAqE;gBACrE,8BAA8B;gBAC9B,IAAI,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE;oBACvD,SAAS,CAAC,cAAc,EAAE,CAAA;iBAC3B;gBACD,KAAK,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,CAAA;gBAC7B,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE;oBACtB,uEAAuE;oBACvE,8EAA8E;oBAC9E,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;oBACxB,MAAM,CAAC,qBAAqB,CAAC,GAAG,EAAE;wBAChC,KAAK,CAAC,gBAAgB,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;wBACrC,KAAK,CAAC,OAAO,GAAG,CAAC,CAAA;wBACjB,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;oBAC3B,CAAC,CAAC,CAAA;iBACH;aACF;QACH,CAAC;QACD,IAAI,IAAI,EAAE;YACR,IAAI,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;YACvC,OAAO,GAAG,EAAE;gBACV,IAAI,CAAC,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;YAC5C,CAAC,CAAA;SACF;QACD,OAAO,GAAG,EAAE,GAAE,CAAC,CAAA;IACjB,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAEX,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,iBACI,gBAAgB,EAC5B,SAAS,EAAE,OAAO,CAAC,eAAe,EAClC,WAAW,EAAE,SAAS,EACtB,SAAS,EAAE,OAAO,EAClB,YAAY,EAAE,UAAU;QAEvB,KAAK,CAAC,aAAa,CAAC,CAAC,CAAC,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QACxD,KAAK,CAAC,cAAc,CAAC,CAAC,CAAC,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAE3D,oBAAC,UAAU,IACT,KAAK,EAAE,KAAK,EACZ,gBAAgB,EACd,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,EAAE,MAAM,EAAE,gBAAgB,EAAE,SAAS,EAAE,YAAY,EAAE,GAC5D,GAEJ;QACD,QAAQ,CACL,CACP,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,eAAe,CAAC,CAAA"}
package/esm/LinearGenomeView/index.d.ts CHANGED
@@ -61,6 +61,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
61
61
  trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
62
62
  showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
63
63
  showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
64
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
64
65
  }, {
65
66
  width: number;
66
67
  } & {
@@ -113,45 +114,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
113
114
  includeAggregateIndexes: boolean;
114
115
  tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
115
116
  };
116
- bpToPx({ refName, coord, regionNumber, }: {
117
- refName: string;
118
- coord: number;
119
- regionNumber?: number | undefined;
120
- }): {
121
- index: number;
122
- offsetPx: number;
123
- } | undefined;
124
- /**
125
- *
126
- * @param px - px in the view area, return value is the displayed regions
127
- * @returns BpOffset of the displayed region that it lands in
128
- */
129
- pxToBp(px: number): {
130
- oob: boolean;
131
- coord: number;
132
- offset: number;
133
- index: number;
134
- start: number;
135
- end: number;
136
- reversed: boolean;
137
- refName: string;
138
- assemblyName: string;
139
- };
140
117
  getTrack(id: string): any;
141
118
  rankSearchResults(results: BaseResult[]): BaseResult[];
142
119
  rewriteOnClicks(trackType: string, viewMenuActions: MenuItem[]): void;
143
120
  readonly trackTypeActions: Map<string, MenuItem[]>;
144
- readonly centerLineInfo: {
145
- oob: boolean;
146
- coord: number;
147
- offset: number;
148
- index: number;
149
- start: number;
150
- end: number;
151
- reversed: boolean;
152
- refName: string;
153
- assemblyName: string;
154
- } | undefined;
155
121
  } & {
156
122
  setShowCytobands(flag: boolean): void;
157
123
  setWidth(newWidth: number): void;
@@ -159,6 +125,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
159
125
  toggleHeader(): void;
160
126
  toggleHeaderOverview(): void;
161
127
  toggleNoTracksActive(): void;
128
+ toggleShowGridlines(): void;
162
129
  scrollTo(offsetPx: number): number;
163
130
  zoomTo(bpPerPx: number): number;
164
131
  setOffsets(left: undefined | BpOffset, right: undefined | BpOffset): void;
@@ -176,30 +143,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
176
143
  toggleCenterLine(): void;
177
144
  setDisplayedRegions(regions: Region[]): void;
178
145
  activateTrackSelector(): import("@jbrowse/core/util").Widget;
179
- navToLocString(locString: string, optAssemblyName?: string): void;
180
- /**
181
- * Navigate to a location based on its refName and optionally start, end,
182
- * and assemblyName. Can handle if there are multiple displayedRegions
183
- * from same refName. Only navigates to a location if it is entirely
184
- * within a displayedRegion. Navigates to the first matching location
185
- * encountered.
186
- *
187
- * Throws an error if navigation was unsuccessful
188
- *
189
- * @param location - a proposed location to navigate to
190
- */
191
- navTo(query: NavLocation): void;
192
- navToMultiple(locations: NavLocation[]): void;
193
- /**
194
- * Navigate to a location based on user clicking and dragging on the
195
- * overview scale bar to select a region to zoom into.
196
- * Can handle if there are multiple displayedRegions from same refName.
197
- * Only navigates to a location if it is entirely within a displayedRegion.
198
- *
199
- * @param leftPx- `object as {start, end, index, offset}`, offset = start of user drag
200
- * @param rightPx- `object as {start, end, index, offset}`, offset = end of user drag
201
- */
202
- zoomToDisplayedRegions(leftPx: BpOffset, rightPx: BpOffset): void;
203
146
  /**
204
147
  * Helper method for the fetchSequence.
205
148
  * Retrieves the corresponding regions that were selected by the rubberband
@@ -208,7 +151,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
208
151
  * @param rightOffset - `object as {start, end, index, offset}`, offset = end of user drag
209
152
  * @returns array of Region[]
210
153
  */
211
- getSelectedRegions(leftOffset: BpOffset | undefined, rightOffset: BpOffset | undefined): {
154
+ getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
212
155
  start: number;
213
156
  end: number;
214
157
  regionNumber?: number | undefined;
@@ -222,23 +165,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
222
165
  isLeftEndOfDisplayedRegion?: boolean | undefined;
223
166
  }[];
224
167
  afterDisplayedRegionsSet(cb: Function): void;
225
- /**
226
- * offset is the base-pair-offset in the displayed region, index is the index of the
227
- * displayed region in the linear genome view
228
- *
229
- * @param start - object as `{start, end, offset, index}`
230
- * @param end - object as `{start, end, offset, index}`
231
- */
232
- moveTo(start: BpOffset, end: BpOffset): void;
233
168
  horizontalScroll(distance: number): number;
234
- /**
235
- * scrolls the view to center on the given bp. if that is not in any
236
- * of the displayed regions, does nothing
237
- * @param bp - basepair at which you want to center the view
238
- * @param refName - refName of the displayedRegion you are centering at
239
- * @param regionIndex - index of the displayedRegion
240
- */
241
- centerAt(bp: number, refName: string, regionIndex: number): void;
242
169
  center(): void;
243
170
  showAllRegions(): void;
244
171
  showAllRegionsInAssembly(assemblyName?: string): void;
@@ -279,8 +206,68 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
279
206
  afterAttach(): void;
280
207
  } & {
281
208
  exportSvg(opts?: ExportSvgOptions): Promise<void>;
209
+ /**
210
+ * offset is the base-pair-offset in the displayed region, index is the index of the
211
+ * displayed region in the linear genome view
212
+ *
213
+ * @param start - object as `{start, end, offset, index}`
214
+ * @param end - object as `{start, end, offset, index}`
215
+ */
216
+ moveTo(start?: BpOffset, end?: BpOffset): void;
217
+ navToLocString(locString: string, optAssemblyName?: string): void;
218
+ /**
219
+ * Navigate to a location based on its refName and optionally start, end,
220
+ * and assemblyName. Can handle if there are multiple displayedRegions
221
+ * from same refName. Only navigates to a location if it is entirely
222
+ * within a displayedRegion. Navigates to the first matching location
223
+ * encountered.
224
+ *
225
+ * Throws an error if navigation was unsuccessful
226
+ *
227
+ * @param location - a proposed location to navigate to
228
+ */
229
+ navTo(query: NavLocation): void;
230
+ navToMultiple(locations: NavLocation[]): void;
282
231
  } & {
283
232
  rubberBandMenuItems(): MenuItem[];
233
+ bpToPx({ refName, coord, regionNumber, }: {
234
+ refName: string;
235
+ coord: number;
236
+ regionNumber?: number | undefined;
237
+ }): {
238
+ index: number;
239
+ offsetPx: number;
240
+ } | undefined;
241
+ /**
242
+ * scrolls the view to center on the given bp. if that is not in any
243
+ * of the displayed regions, does nothing
244
+ * @param coord - basepair at which you want to center the view
245
+ * @param refName - refName of the displayedRegion you are centering at
246
+ * @param regionNumber - index of the displayedRegion
247
+ */
248
+ centerAt(coord: number, refName: string, regionNumber: number): void;
249
+ pxToBp(px: number): {
250
+ coord: number;
251
+ index: number;
252
+ refName: string;
253
+ oob: boolean;
254
+ assemblyName: string;
255
+ offset: number;
256
+ start: number;
257
+ end: number;
258
+ reversed: boolean;
259
+ };
260
+ readonly centerLineInfo: {
261
+ coord: number;
262
+ index: number;
263
+ refName: string;
264
+ oob: boolean;
265
+ assemblyName: string;
266
+ offset: number;
267
+ start: number;
268
+ end: number;
269
+ reversed: boolean;
270
+ } | undefined;
284
271
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
285
272
  export { renderToSvg, RefNameAutocomplete, SearchBox };
286
273
  export declare type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;