@jbrowse/plugin-breakpoint-split-view 2.10.3 → 2.11.0

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Files changed (19) hide show
  1. package/dist/BreakpointSplitView/components/AlignmentConnections.d.ts +1 -1
  2. package/dist/BreakpointSplitView/components/AlignmentConnections.js +4 -5
  3. package/dist/BreakpointSplitView/components/Breakends.d.ts +1 -1
  4. package/dist/BreakpointSplitView/components/ExportSvgDialog.js +9 -4
  5. package/dist/BreakpointSplitView/components/Overlay.d.ts +1 -1
  6. package/dist/BreakpointSplitView/components/Translocations.d.ts +1 -1
  7. package/dist/BreakpointSplitView/model.d.ts +44 -13
  8. package/dist/BreakpointSplitView/model.js +1 -1
  9. package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js +1 -1
  10. package/esm/BreakpointSplitView/components/AlignmentConnections.d.ts +1 -1
  11. package/esm/BreakpointSplitView/components/AlignmentConnections.js +4 -5
  12. package/esm/BreakpointSplitView/components/Breakends.d.ts +1 -1
  13. package/esm/BreakpointSplitView/components/ExportSvgDialog.js +9 -4
  14. package/esm/BreakpointSplitView/components/Overlay.d.ts +1 -1
  15. package/esm/BreakpointSplitView/components/Translocations.d.ts +1 -1
  16. package/esm/BreakpointSplitView/model.d.ts +44 -13
  17. package/esm/BreakpointSplitView/model.js +1 -1
  18. package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js +1 -1
  19. package/package.json +2 -2
package/dist/BreakpointSplitView/components/AlignmentConnections.d.ts CHANGED
@@ -4,6 +4,6 @@ declare const AlignmentConnections: ({ model, trackId, parentRef, getTrackYPosOv
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  model: BreakpointViewModel;
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  trackId: string;
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  parentRef: React.RefObject<SVGSVGElement>;
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- getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
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+ getTrackYPosOverride?: (trackId: string, level: number) => number;
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  }) => React.JSX.Element | null;
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  export default AlignmentConnections;
package/dist/BreakpointSplitView/components/AlignmentConnections.js CHANGED
@@ -28,6 +28,7 @@ const mobx_react_1 = require("mobx-react");
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  const mobx_state_tree_1 = require("mobx-state-tree");
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  const material_1 = require("@mui/material");
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  const util_1 = require("@jbrowse/core/util");
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+ const colord_1 = require("@jbrowse/core/util/colord");
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  // locals
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  const util_2 = require("./util");
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  const util_3 = require("../util");
@@ -42,6 +43,7 @@ const AlignmentConnections = (0, mobx_react_1.observer)(function ({ model, track
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  (0, util_3.useNextFrame)(snap);
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  const allFeatures = model.getTrackFeatures(trackId);
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  const hasPaired = (0, react_1.useMemo)(() => (0, util_2.hasPairedReads)(allFeatures), [allFeatures]);
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+ const { r, g, b, a } = (0, colord_1.colord)(theme.palette.text.disabled).rgba;
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  const layoutMatches = (0, react_1.useMemo)(() => {
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  const layoutMatches = model.getMatchedFeaturesInLayout(trackId, hasPaired
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  ? (0, util_2.getBadlyPairedAlignments)(allFeatures)
@@ -59,10 +61,7 @@ const AlignmentConnections = (0, mobx_react_1.observer)(function ({ model, track
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  const rect = parentRef.current.getBoundingClientRect();
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  yOffset = rect.top;
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  }
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- if (!assembly) {
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- return null;
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- }
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- return (react_1.default.createElement("g", { stroke: theme.palette.text.disabled, fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
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+ return assembly ? (react_1.default.createElement("g", { fill: "none", stroke: `rgb(${r},${g},${b})`, strokeOpacity: a, "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
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  const ret = [];
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  // we follow a path in the list of chunks, not from top to bottom, just in series
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  // following x1,y1 -> x2,y2
@@ -127,6 +126,6 @@ const AlignmentConnections = (0, mobx_react_1.observer)(function ({ model, track
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  }, onMouseOver: () => setMouseoverElt(id), onMouseOut: () => setMouseoverElt(undefined) }));
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  }
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  return ret;
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- })));
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+ }))) : null;
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  });
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  exports.default = AlignmentConnections;
package/dist/BreakpointSplitView/components/Breakends.d.ts CHANGED
@@ -4,6 +4,6 @@ declare const Breakends: ({ model, trackId, parentRef: ref, getTrackYPosOverride
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  model: BreakpointViewModel;
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  trackId: string;
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  parentRef: React.RefObject<SVGSVGElement>;
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- getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
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+ getTrackYPosOverride?: (trackId: string, level: number) => number;
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  }) => React.JSX.Element | null;
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  export default Breakends;
package/dist/BreakpointSplitView/components/ExportSvgDialog.js CHANGED
@@ -32,6 +32,10 @@ function LoadingMessage() {
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  react_1.default.createElement(material_1.CircularProgress, { size: 20, style: { marginRight: 20 } }),
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  react_1.default.createElement(material_1.Typography, { display: "inline" }, "Creating SVG")));
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  }
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+ function TextField2({ children, ...rest }) {
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+ return (react_1.default.createElement("div", null,
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+ react_1.default.createElement(material_1.TextField, { ...rest }, children)));
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+ }
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  function useSvgLocal(key, val) {
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  return (0, util_1.useLocalStorage)('svg-' + key, val);
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  }
@@ -47,15 +51,14 @@ function ExportSvgDialog({ model, handleClose, }) {
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  return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
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  react_1.default.createElement(material_1.DialogContent, null,
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  error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
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- react_1.default.createElement(material_1.TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
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- react_1.default.createElement("br", null),
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- react_1.default.createElement(material_1.TextField, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
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+ react_1.default.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
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+ react_1.default.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
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  react_1.default.createElement(material_1.MenuItem, { value: "offset" }, "Offset"),
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  react_1.default.createElement(material_1.MenuItem, { value: "overlay" }, "Overlay"),
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  react_1.default.createElement(material_1.MenuItem, { value: "left" }, "Left"),
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  react_1.default.createElement(material_1.MenuItem, { value: "none" }, "None")),
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  react_1.default.createElement("br", null),
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- session.allThemes ? (react_1.default.createElement(material_1.TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key },
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+ session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key },
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  // @ts-expect-error
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  val.name || '(Unknown name)'))))) : null,
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  offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
@@ -76,6 +79,8 @@ function ExportSvgDialog({ model, handleClose, }) {
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  catch (e) {
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  console.error(e);
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  setError(e);
82
+ }
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+ finally {
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  setLoading(false);
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  }
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  } }, "Submit"))));
package/dist/BreakpointSplitView/components/Overlay.d.ts CHANGED
@@ -4,6 +4,6 @@ declare const Overlay: (props: {
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  parentRef: React.RefObject<SVGSVGElement>;
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  model: BreakpointViewModel;
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  trackId: string;
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- getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
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+ getTrackYPosOverride?: (trackId: string, level: number) => number;
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  }) => React.JSX.Element | null;
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  export default Overlay;
package/dist/BreakpointSplitView/components/Translocations.d.ts CHANGED
@@ -4,6 +4,6 @@ declare const Translocations: ({ model, trackId, parentRef: ref, getTrackYPosOve
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  model: BreakpointViewModel;
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  trackId: string;
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  parentRef: React.RefObject<SVGSVGElement>;
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- getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
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+ getTrackYPosOverride?: (trackId: string, level: number) => number;
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  }) => React.JSX.Element | null;
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  export default Translocations;
package/dist/BreakpointSplitView/model.d.ts CHANGED
@@ -70,7 +70,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- highlight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
73
+ highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
74
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
74
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  }, {
75
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  width: number;
76
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  } & {
@@ -82,20 +83,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
82
83
  } & {
83
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  volatileWidth: number | undefined;
84
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  minimumBlockWidth: number;
85
- /**
86
- * #action
87
- */
88
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  draggingTrackId: string | undefined;
89
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  volatileError: unknown;
90
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  afterDisplayedRegionsSetCallbacks: Function[];
91
- scaleFactor: number; /**
92
- * #action
93
- */
89
+ scaleFactor: number;
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  trackRefs: Record<string, HTMLDivElement>;
95
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  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
96
- coarseTotalBp: number; /**
97
- * #action
98
- */
92
+ coarseTotalBp: number;
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  leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
100
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  rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
101
95
  } & {
@@ -133,6 +127,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
133
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  rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
134
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  readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
135
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  } & {
130
+ setColorByCDS(flag: boolean): void;
136
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  setShowCytobands(flag: boolean): void;
137
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  setWidth(newWidth: number): void;
138
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  setError(error: unknown): void;
@@ -140,7 +135,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  setHideHeaderOverview(b: boolean): void;
141
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  setHideNoTracksActive(b: boolean): void;
142
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  setShowGridlines(b: boolean): void;
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- setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
138
+ addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
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+ setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
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+ removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
144
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  scrollTo(offsetPx: number): number;
145
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  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
146
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  setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
@@ -150,6 +147,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
151
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  hideTrack(trackId: string): number;
152
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  } & {
150
+ moveTrackDown(id: string): void;
151
+ moveTrackUp(id: string): void;
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+ moveTrackToTop(id: string): void;
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+ moveTrackToBottom(id: string): void;
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  moveTrack(movingId: string, targetId: string): void;
154
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  closeView(): void;
155
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  toggleTrack(trackId: string): boolean;
@@ -347,7 +348,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  index: number;
348
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  offsetPx: number;
349
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  } | undefined;
350
- centerAt(coord: number, refName: string, regionNumber: number): void;
351
+ centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
351
352
  pxToBp(px: number): {
352
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  coord: number;
353
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  index: number;
@@ -372,7 +373,37 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
372
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  } | undefined;
373
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  } & {
374
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  afterCreate(): void;
375
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
376
+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
377
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
378
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
379
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
380
+ } & {
381
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
382
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
383
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
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+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
385
+ displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
386
+ refName: import("mobx-state-tree").ISimpleType<string>;
387
+ start: import("mobx-state-tree").ISimpleType<number>;
388
+ end: import("mobx-state-tree").ISimpleType<number>;
389
+ reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
390
+ } & {
391
+ assemblyName: import("mobx-state-tree").ISimpleType<string>;
392
+ }, {
393
+ setRefName(newRefName: string): void;
394
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
395
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
396
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
397
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
398
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
399
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
400
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
401
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
402
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
403
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
404
+ highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
405
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
406
+ }>>, import("mobx-state-tree")._NotCustomized>>;
376
407
  }, {
377
408
  width: number;
378
409
  } & {
package/dist/BreakpointSplitView/model.js CHANGED
@@ -259,7 +259,7 @@ function stateModelFactory(pluginManager) {
259
259
  }
260
260
  catch (e) {
261
261
  console.error(e);
262
- (0, util_1.getSession)(self).notify(`${e}`, 'error');
262
+ (0, util_1.getSession)(self).notifyError(`${e}`, e);
263
263
  }
264
264
  }));
265
265
  },
package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js CHANGED
@@ -18,7 +18,7 @@ const util_2 = require("./util");
18
18
  // render LGV to SVG
19
19
  async function renderToSvg(model, opts) {
20
20
  var _a;
21
- const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => react_1.default.createElement(react_1.default.Fragment, null, children), themeName = 'default', } = opts;
21
+ const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = opts;
22
22
  // eslint-disable-next-line @typescript-eslint/no-explicit-any
23
23
  const { createRootFn } = (0, mobx_state_tree_1.getRoot)(model);
24
24
  const session = (0, util_1.getSession)(model);
package/esm/BreakpointSplitView/components/AlignmentConnections.d.ts CHANGED
@@ -4,6 +4,6 @@ declare const AlignmentConnections: ({ model, trackId, parentRef, getTrackYPosOv
4
4
  model: BreakpointViewModel;
5
5
  trackId: string;
6
6
  parentRef: React.RefObject<SVGSVGElement>;
7
- getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
7
+ getTrackYPosOverride?: (trackId: string, level: number) => number;
8
8
  }) => React.JSX.Element | null;
9
9
  export default AlignmentConnections;
package/esm/BreakpointSplitView/components/AlignmentConnections.js CHANGED
@@ -3,6 +3,7 @@ import { observer } from 'mobx-react';
3
3
  import { getSnapshot } from 'mobx-state-tree';
4
4
  import { useTheme } from '@mui/material';
5
5
  import { getSession } from '@jbrowse/core/util';
6
+ import { colord } from '@jbrowse/core/util/colord';
6
7
  // locals
7
8
  import { getBadlyPairedAlignments, getMatchedAlignmentFeatures, hasPairedReads, } from './util';
8
9
  import { yPos, useNextFrame, getPxFromCoordinate } from '../util';
@@ -17,6 +18,7 @@ const AlignmentConnections = observer(function ({ model, trackId, parentRef, get
17
18
  useNextFrame(snap);
18
19
  const allFeatures = model.getTrackFeatures(trackId);
19
20
  const hasPaired = useMemo(() => hasPairedReads(allFeatures), [allFeatures]);
21
+ const { r, g, b, a } = colord(theme.palette.text.disabled).rgba;
20
22
  const layoutMatches = useMemo(() => {
21
23
  const layoutMatches = model.getMatchedFeaturesInLayout(trackId, hasPaired
22
24
  ? getBadlyPairedAlignments(allFeatures)
@@ -34,10 +36,7 @@ const AlignmentConnections = observer(function ({ model, trackId, parentRef, get
34
36
  const rect = parentRef.current.getBoundingClientRect();
35
37
  yOffset = rect.top;
36
38
  }
37
- if (!assembly) {
38
- return null;
39
- }
40
- return (React.createElement("g", { stroke: theme.palette.text.disabled, fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
39
+ return assembly ? (React.createElement("g", { fill: "none", stroke: `rgb(${r},${g},${b})`, strokeOpacity: a, "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
41
40
  const ret = [];
42
41
  // we follow a path in the list of chunks, not from top to bottom, just in series
43
42
  // following x1,y1 -> x2,y2
@@ -102,6 +101,6 @@ const AlignmentConnections = observer(function ({ model, trackId, parentRef, get
102
101
  }, onMouseOver: () => setMouseoverElt(id), onMouseOut: () => setMouseoverElt(undefined) }));
103
102
  }
104
103
  return ret;
105
- })));
104
+ }))) : null;
106
105
  });
107
106
  export default AlignmentConnections;
package/esm/BreakpointSplitView/components/Breakends.d.ts CHANGED
@@ -4,6 +4,6 @@ declare const Breakends: ({ model, trackId, parentRef: ref, getTrackYPosOverride
4
4
  model: BreakpointViewModel;
5
5
  trackId: string;
6
6
  parentRef: React.RefObject<SVGSVGElement>;
7
- getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
7
+ getTrackYPosOverride?: (trackId: string, level: number) => number;
8
8
  }) => React.JSX.Element | null;
9
9
  export default Breakends;
package/esm/BreakpointSplitView/components/ExportSvgDialog.js CHANGED
@@ -7,6 +7,10 @@ function LoadingMessage() {
7
7
  React.createElement(CircularProgress, { size: 20, style: { marginRight: 20 } }),
8
8
  React.createElement(Typography, { display: "inline" }, "Creating SVG")));
9
9
  }
10
+ function TextField2({ children, ...rest }) {
11
+ return (React.createElement("div", null,
12
+ React.createElement(TextField, { ...rest }, children)));
13
+ }
10
14
  function useSvgLocal(key, val) {
11
15
  return useLocalStorage('svg-' + key, val);
12
16
  }
@@ -22,15 +26,14 @@ export default function ExportSvgDialog({ model, handleClose, }) {
22
26
  return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
23
27
  React.createElement(DialogContent, null,
24
28
  error ? (React.createElement(ErrorMessage, { error: error })) : loading ? (React.createElement(LoadingMessage, null)) : null,
25
- React.createElement(TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
26
- React.createElement("br", null),
27
- React.createElement(TextField, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
29
+ React.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
30
+ React.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
28
31
  React.createElement(MenuItem, { value: "offset" }, "Offset"),
29
32
  React.createElement(MenuItem, { value: "overlay" }, "Overlay"),
30
33
  React.createElement(MenuItem, { value: "left" }, "Left"),
31
34
  React.createElement(MenuItem, { value: "none" }, "None")),
32
35
  React.createElement("br", null),
33
- session.allThemes ? (React.createElement(TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key },
36
+ session.allThemes ? (React.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key },
34
37
  // @ts-expect-error
35
38
  val.name || '(Unknown name)'))))) : null,
36
39
  offscreenCanvas ? (React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (React.createElement(Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
@@ -51,6 +54,8 @@ export default function ExportSvgDialog({ model, handleClose, }) {
51
54
  catch (e) {
52
55
  console.error(e);
53
56
  setError(e);
57
+ }
58
+ finally {
54
59
  setLoading(false);
55
60
  }
56
61
  } }, "Submit"))));
package/esm/BreakpointSplitView/components/Overlay.d.ts CHANGED
@@ -4,6 +4,6 @@ declare const Overlay: (props: {
4
4
  parentRef: React.RefObject<SVGSVGElement>;
5
5
  model: BreakpointViewModel;
6
6
  trackId: string;
7
- getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
7
+ getTrackYPosOverride?: (trackId: string, level: number) => number;
8
8
  }) => React.JSX.Element | null;
9
9
  export default Overlay;
package/esm/BreakpointSplitView/components/Translocations.d.ts CHANGED
@@ -4,6 +4,6 @@ declare const Translocations: ({ model, trackId, parentRef: ref, getTrackYPosOve
4
4
  model: BreakpointViewModel;
5
5
  trackId: string;
6
6
  parentRef: React.RefObject<SVGSVGElement>;
7
- getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
7
+ getTrackYPosOverride?: (trackId: string, level: number) => number;
8
8
  }) => React.JSX.Element | null;
9
9
  export default Translocations;
package/esm/BreakpointSplitView/model.d.ts CHANGED
@@ -70,7 +70,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
70
70
  showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
71
71
  trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
72
72
  showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
73
- highlight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
73
+ highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
74
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
74
75
  }, {
75
76
  width: number;
76
77
  } & {
@@ -82,20 +83,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
82
83
  } & {
83
84
  volatileWidth: number | undefined;
84
85
  minimumBlockWidth: number;
85
- /**
86
- * #action
87
- */
88
86
  draggingTrackId: string | undefined;
89
87
  volatileError: unknown;
90
88
  afterDisplayedRegionsSetCallbacks: Function[];
91
- scaleFactor: number; /**
92
- * #action
93
- */
89
+ scaleFactor: number;
94
90
  trackRefs: Record<string, HTMLDivElement>;
95
91
  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
96
- coarseTotalBp: number; /**
97
- * #action
98
- */
92
+ coarseTotalBp: number;
99
93
  leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
100
94
  rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
101
95
  } & {
@@ -133,6 +127,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
133
127
  rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
134
128
  readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
135
129
  } & {
130
+ setColorByCDS(flag: boolean): void;
136
131
  setShowCytobands(flag: boolean): void;
137
132
  setWidth(newWidth: number): void;
138
133
  setError(error: unknown): void;
@@ -140,7 +135,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
140
135
  setHideHeaderOverview(b: boolean): void;
141
136
  setHideNoTracksActive(b: boolean): void;
142
137
  setShowGridlines(b: boolean): void;
143
- setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
138
+ addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
139
+ setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
140
+ removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
144
141
  scrollTo(offsetPx: number): number;
145
142
  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
146
143
  setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
@@ -150,6 +147,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
150
147
  showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
151
148
  hideTrack(trackId: string): number;
152
149
  } & {
150
+ moveTrackDown(id: string): void;
151
+ moveTrackUp(id: string): void;
152
+ moveTrackToTop(id: string): void;
153
+ moveTrackToBottom(id: string): void;
153
154
  moveTrack(movingId: string, targetId: string): void;
154
155
  closeView(): void;
155
156
  toggleTrack(trackId: string): boolean;
@@ -347,7 +348,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
347
348
  index: number;
348
349
  offsetPx: number;
349
350
  } | undefined;
350
- centerAt(coord: number, refName: string, regionNumber: number): void;
351
+ centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
351
352
  pxToBp(px: number): {
352
353
  coord: number;
353
354
  index: number;
@@ -372,7 +373,37 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
372
373
  } | undefined;
373
374
  } & {
374
375
  afterCreate(): void;
375
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
376
+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
377
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
378
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
379
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
380
+ } & {
381
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
382
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
383
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
384
+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
385
+ displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
386
+ refName: import("mobx-state-tree").ISimpleType<string>;
387
+ start: import("mobx-state-tree").ISimpleType<number>;
388
+ end: import("mobx-state-tree").ISimpleType<number>;
389
+ reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
390
+ } & {
391
+ assemblyName: import("mobx-state-tree").ISimpleType<string>;
392
+ }, {
393
+ setRefName(newRefName: string): void;
394
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
395
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
396
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
397
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
398
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
399
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
400
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
401
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
402
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
403
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
404
+ highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
405
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
406
+ }>>, import("mobx-state-tree")._NotCustomized>>;
376
407
  }, {
377
408
  width: number;
378
409
  } & {
package/esm/BreakpointSplitView/model.js CHANGED
@@ -231,7 +231,7 @@ export default function stateModelFactory(pluginManager) {
231
231
  }
232
232
  catch (e) {
233
233
  console.error(e);
234
- getSession(self).notify(`${e}`, 'error');
234
+ getSession(self).notifyError(`${e}`, e);
235
235
  }
236
236
  }));
237
237
  },
package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js CHANGED
@@ -12,7 +12,7 @@ import { getTrackNameMaxLen, getTrackOffsets } from './util';
12
12
  // render LGV to SVG
13
13
  export async function renderToSvg(model, opts) {
14
14
  var _a;
15
- const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => React.createElement(React.Fragment, null, children), themeName = 'default', } = opts;
15
+ const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = opts;
16
16
  // eslint-disable-next-line @typescript-eslint/no-explicit-any
17
17
  const { createRootFn } = getRoot(model);
18
18
  const session = getSession(model);
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-breakpoint-split-view",
3
- "version": "2.10.3",
3
+ "version": "2.11.0",
4
4
  "description": "JBrowse 2 breakpoint detail split view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -58,5 +58,5 @@
58
58
  "publishConfig": {
59
59
  "access": "public"
60
60
  },
61
- "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
61
+ "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
62
62
  }