@jbrowse/plugin-linear-comparative-view 3.2.0 → 3.4.0

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Files changed (25) hide show
  1. package/dist/LGVSyntenyDisplay/model.d.ts +1 -1
  2. package/dist/LinearComparativeView/model.d.ts +8 -6
  3. package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.js +2 -2
  4. package/dist/LinearSyntenyView/model.d.ts +8 -6
  5. package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js +1 -1
  6. package/dist/SyntenyFeatureDetail/Formatter.d.ts +3 -0
  7. package/dist/SyntenyFeatureDetail/Formatter.js +23 -0
  8. package/dist/SyntenyFeatureDetail/LinkToSyntenyView.d.ts +3 -1
  9. package/dist/SyntenyFeatureDetail/LinkToSyntenyView.js +7 -7
  10. package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts +1 -1
  11. package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js +7 -3
  12. package/dist/SyntenyFeatureDetail/types.d.ts +1 -1
  13. package/esm/LGVSyntenyDisplay/model.d.ts +1 -1
  14. package/esm/LinearComparativeView/model.d.ts +8 -6
  15. package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.js +3 -3
  16. package/esm/LinearSyntenyView/model.d.ts +8 -6
  17. package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js +1 -1
  18. package/esm/SyntenyFeatureDetail/Formatter.d.ts +3 -0
  19. package/esm/SyntenyFeatureDetail/Formatter.js +17 -0
  20. package/esm/SyntenyFeatureDetail/LinkToSyntenyView.d.ts +3 -1
  21. package/esm/SyntenyFeatureDetail/LinkToSyntenyView.js +7 -7
  22. package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts +1 -1
  23. package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js +7 -3
  24. package/esm/SyntenyFeatureDetail/types.d.ts +1 -1
  25. package/package.json +7 -7
package/dist/LGVSyntenyDisplay/model.d.ts CHANGED
@@ -201,7 +201,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
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  } & {
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  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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  deleteBlock(key: string): void;
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- selectFeature(feature: Feature): void;
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+ selectFeature(feature: Feature): Promise<void>;
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  navToFeature(feature: Feature): void;
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  clearFeatureSelection(): void;
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  setFeatureIdUnderMouse(feature?: string): void;
package/dist/LinearComparativeView/model.d.ts CHANGED
@@ -188,12 +188,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
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  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
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  } & {
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  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
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- navToLocString(input: string, optAssemblyName?: string): Promise<void>;
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+ navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
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  navToSearchString({ input, assembly, }: {
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  input: string;
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  assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
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  }): Promise<void>;
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- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
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+ navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
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+ navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
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  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
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  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
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  } & {
@@ -261,9 +262,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
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  displayName: string | undefined;
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  tracks: any[];
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  minimized: boolean;
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- displayedRegions: import("@jbrowse/core/util").Region[];
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  offsetPx: number;
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  bpPerPx: number;
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+ displayedRegions: import("@jbrowse/core/util").Region[];
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  hideHeader: boolean;
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  hideHeaderOverview: boolean;
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  hideNoTracksActive: boolean;
@@ -502,12 +503,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
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  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
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  } & {
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  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
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- navToLocString(input: string, optAssemblyName?: string): Promise<void>;
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+ navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
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  navToSearchString({ input, assembly, }: {
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  input: string;
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  assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
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  }): Promise<void>;
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- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
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+ navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
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+ navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
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  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
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  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
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  } & {
@@ -575,9 +577,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
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  displayName: string | undefined;
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  tracks: any[];
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  minimized: boolean;
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- displayedRegions: import("@jbrowse/core/util").Region[];
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  offsetPx: number;
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  bpPerPx: number;
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+ displayedRegions: import("@jbrowse/core/util").Region[];
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  hideHeader: boolean;
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  hideHeaderOverview: boolean;
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  hideNoTracksActive: boolean;
package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.js CHANGED
@@ -73,7 +73,7 @@ const ImportSyntenyOpenCustomTrack = (0, mobx_react_1.observer)(function ({ mode
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  };
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  return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 12 }, children: [error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)(material_1.Typography, { style: { textAlign: 'center' }, children: "Add a .paf (minimap2), .delta (Mummer), .chain (UCSC liftover), .anchors or .anchors.simple (MCScan), or .pif.gz (jbrowse CLI make-pif) file to view. These file types can also be gzipped." }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { value: radioOption, onChange: event => {
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  setValue(event.target.value);
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- }, children: (0, jsx_runtime_1.jsx)(material_1.Grid2, { container: true, justifyContent: "center", children: [
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+ }, children: (0, jsx_runtime_1.jsx)(material_1.Grid, { container: true, justifyContent: "center", children: [
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  '.paf',
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  '.delta',
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  '.out',
@@ -81,7 +81,7 @@ const ImportSyntenyOpenCustomTrack = (0, mobx_react_1.observer)(function ({ mode
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  '.anchors',
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  '.anchors.simple',
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  '.pif.gz',
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- ].map(extension => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: extension, control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: extension }, extension))) }) }), (0, jsx_runtime_1.jsx)(material_1.Grid2, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
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+ ].map(extension => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: extension, control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: extension }, extension))) }) }), (0, jsx_runtime_1.jsx)(material_1.Grid, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
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  radioOption === '.out' ||
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  radioOption === '.delta' ||
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  radioOption === '.chain' ||
package/dist/LinearSyntenyView/model.d.ts CHANGED
@@ -205,12 +205,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
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  } & {
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  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
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- navToLocString(input: string, optAssemblyName?: string): Promise<void>;
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+ navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
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  navToSearchString({ input, assembly, }: {
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  input: string;
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  assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
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  }): Promise<void>;
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- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
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+ navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
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+ navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
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  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
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  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
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  } & {
@@ -278,9 +279,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  displayName: string | undefined;
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  tracks: any[];
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  minimized: boolean;
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- displayedRegions: import("@jbrowse/core/util").Region[];
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  offsetPx: number;
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  bpPerPx: number;
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+ displayedRegions: import("@jbrowse/core/util").Region[];
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  hideHeader: boolean;
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  hideHeaderOverview: boolean;
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  hideNoTracksActive: boolean;
@@ -586,12 +587,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
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  } & {
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  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
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- navToLocString(input: string, optAssemblyName?: string): Promise<void>;
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+ navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
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  navToSearchString({ input, assembly, }: {
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  input: string;
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  assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
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  }): Promise<void>;
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- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
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+ navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
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+ navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
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  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
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  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
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  } & {
@@ -659,9 +661,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  displayName: string | undefined;
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  tracks: any[];
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  minimized: boolean;
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- displayedRegions: import("@jbrowse/core/util").Region[];
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  offsetPx: number;
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  bpPerPx: number;
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+ displayedRegions: import("@jbrowse/core/util").Region[];
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  hideHeader: boolean;
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  hideHeaderOverview: boolean;
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  hideNoTracksActive: boolean;
package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js CHANGED
@@ -73,7 +73,7 @@ async function renderToSvg(model, opts) {
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  const rendering = renderings[i - 1];
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  const height = heights[i];
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  const levelHeight = level.height || 0;
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- RenderList.push((0, jsx_runtime_1.jsxs)("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? ((0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: `synclip-${i}`, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, (0, jsx_runtime_1.jsx)("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => ((0, jsx_runtime_1.jsx)(util_1.ReactRendering, { rendering: r }, i))) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${levelHeight})`, children: (0, jsx_runtime_1.jsx)(SVGLinearGenomeView_1.default, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
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+ RenderList.push((0, jsx_runtime_1.jsxs)("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? ((0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: `synclip-${i}`, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, (0, jsx_runtime_1.jsx)("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (0, jsx_runtime_1.jsx)(util_1.ReactRendering, { rendering: r }, i)) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${levelHeight})`, children: (0, jsx_runtime_1.jsx)(SVGLinearGenomeView_1.default, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
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  currOffset += height + fontSize + rulerHeight + levelHeight;
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  }
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  return (0, util_1.renderToStaticMarkup)((0, jsx_runtime_1.jsx)(material_1.ThemeProvider, { theme: theme, children: (0, jsx_runtime_1.jsx)(Wrapper, { children: (0, jsx_runtime_1.jsxs)("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString(), children: [(0, jsx_runtime_1.jsx)(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }), RenderList] }) }) }));
package/dist/SyntenyFeatureDetail/Formatter.d.ts ADDED
@@ -0,0 +1,3 @@
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+ export default function Formatter({ value }: {
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+ value: unknown;
3
+ }): import("react/jsx-runtime").JSX.Element;
package/dist/SyntenyFeatureDetail/Formatter.js ADDED
@@ -0,0 +1,23 @@
1
+ "use strict";
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+ var __importDefault = (this && this.__importDefault) || function (mod) {
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+ return (mod && mod.__esModule) ? mod : { "default": mod };
4
+ };
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+ Object.defineProperty(exports, "__esModule", { value: true });
6
+ exports.default = Formatter;
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+ const jsx_runtime_1 = require("react/jsx-runtime");
8
+ const react_1 = require("react");
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+ const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
10
+ function Formatter({ value }) {
11
+ const [show, setShow] = (0, react_1.useState)(false);
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+ const [copied, setCopied] = (0, react_1.useState)(false);
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+ const display = String(value);
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+ return display.length > 100 ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
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+ (0, copy_to_clipboard_1.default)(display);
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+ setCopied(true);
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+ setTimeout(() => {
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+ setCopied(false);
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+ }, 700);
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+ }, children: copied ? 'Copied to clipboard' : 'Copy' }), (0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
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+ setShow(val => !val);
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+ }, children: show ? 'Show less' : 'Show more' }), (0, jsx_runtime_1.jsx)("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : ((0, jsx_runtime_1.jsx)("div", { children: display }));
23
+ }
package/dist/SyntenyFeatureDetail/LinkToSyntenyView.d.ts CHANGED
@@ -1,5 +1,7 @@
1
1
  import type { SyntenyFeatureDetailModel } from './types';
2
- declare const LinkToSyntenyView: ({ model, }: {
2
+ import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
3
+ declare const LinkToSyntenyView: ({ model, feat, }: {
3
4
  model: SyntenyFeatureDetailModel;
5
+ feat: SimpleFeatureSerialized;
4
6
  }) => import("react/jsx-runtime").JSX.Element;
5
7
  export default LinkToSyntenyView;
package/dist/SyntenyFeatureDetail/LinkToSyntenyView.js CHANGED
@@ -39,19 +39,19 @@ const util_1 = require("@jbrowse/core/util");
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  const material_1 = require("@mui/material");
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  const mobx_react_1 = require("mobx-react");
41
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  const LaunchSyntenyViewDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'))));
42
- const LinkToSyntenyView = (0, mobx_react_1.observer)(function ({ model, }) {
43
- const { featureData, view, level, trackId } = model;
42
+ const LinkToSyntenyView = (0, mobx_react_1.observer)(function ({ model, feat, }) {
43
+ const { view, level, trackId } = model;
44
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  return ((0, jsx_runtime_1.jsxs)("ul", { children: [view.type === 'LinearSyntenyView' ? ((0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
45
45
  var _a, _b;
46
46
  event.preventDefault();
47
47
  const { views } = view;
48
48
  if (level !== undefined) {
49
- (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(featureData);
50
- (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(featureData.mate);
49
+ (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(feat);
50
+ (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(feat.mate);
51
51
  }
52
52
  else {
53
- const f1 = featureData;
54
- const f2 = featureData.mate;
53
+ const f1 = feat;
54
+ const f2 = feat.mate;
55
55
  const r1 = f1.assemblyName;
56
56
  const r2 = f2.assemblyName;
57
57
  const v1 = views.find(view => view.assemblyNames[0] === r1);
@@ -71,7 +71,7 @@ const LinkToSyntenyView = (0, mobx_react_1.observer)(function ({ model, }) {
71
71
  }
72
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  }, children: "Center view on this feature" }) })) : null, (0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
73
73
  event.preventDefault();
74
- const feature = new util_1.SimpleFeature(featureData);
74
+ const feature = new util_1.SimpleFeature(feat);
75
75
  const session = (0, util_1.getSession)(model);
76
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  session.queueDialog(handleClose => [
77
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  LaunchSyntenyViewDialog,
package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  import type { SyntenyFeatureDetailModel } from './types';
2
- declare const SyntenyFeatureDetail: ({ model, }: {
2
+ declare const SyntenyFeatureDetail: (props: {
3
3
  model: SyntenyFeatureDetailModel;
4
4
  }) => import("react/jsx-runtime").JSX.Element;
5
5
  export default SyntenyFeatureDetail;
package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js CHANGED
@@ -4,12 +4,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  const jsx_runtime_1 = require("react/jsx-runtime");
7
- const BaseFeatureDetail_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail"));
8
7
  const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
8
+ const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
9
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  const material_1 = require("@mui/material");
10
10
  const mobx_react_1 = require("mobx-react");
11
+ const Formatter_1 = __importDefault(require("./Formatter"));
11
12
  const LinkToSyntenyView_1 = __importDefault(require("./LinkToSyntenyView"));
12
- const SyntenyFeatureDetail = (0, mobx_react_1.observer)(function ({ model, }) {
13
- return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { children: [(0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.default, { title: "Feature", model: model }), (0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "Link to view", children: (0, jsx_runtime_1.jsx)(LinkToSyntenyView_1.default, { model: model }) })] }));
13
+ const SyntenyFeatureDetail = (0, mobx_react_1.observer)(function (props) {
14
+ const { model } = props;
15
+ const { featureData } = model;
16
+ const feat = structuredClone(featureData);
17
+ return feat ? ((0, jsx_runtime_1.jsxs)(material_1.Paper, { children: [(0, jsx_runtime_1.jsx)(FeatureDetails_1.default, { ...props, feature: feat, formatter: value => (0, jsx_runtime_1.jsx)(Formatter_1.default, { value: value }) }), (0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "Link to view", children: (0, jsx_runtime_1.jsx)(LinkToSyntenyView_1.default, { model: model, feat: feat }) })] })) : ((0, jsx_runtime_1.jsx)("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
14
18
  });
15
19
  exports.default = SyntenyFeatureDetail;
package/dist/SyntenyFeatureDetail/types.d.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
2
2
  export interface SyntenyFeatureDetailModel {
3
3
  trackId: string;
4
- featureData: SimpleFeatureSerialized;
4
+ featureData?: SimpleFeatureSerialized;
5
5
  level?: number;
6
6
  view: {
7
7
  type: string;
package/esm/LGVSyntenyDisplay/model.d.ts CHANGED
@@ -201,7 +201,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
201
201
  } & {
202
202
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
203
203
  deleteBlock(key: string): void;
204
- selectFeature(feature: Feature): void;
204
+ selectFeature(feature: Feature): Promise<void>;
205
205
  navToFeature(feature: Feature): void;
206
206
  clearFeatureSelection(): void;
207
207
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/LinearComparativeView/model.d.ts CHANGED
@@ -188,12 +188,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
188
188
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
189
189
  } & {
190
190
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
191
- navToLocString(input: string, optAssemblyName?: string): Promise<void>;
191
+ navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
192
192
  navToSearchString({ input, assembly, }: {
193
193
  input: string;
194
194
  assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
195
195
  }): Promise<void>;
196
- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
196
+ navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
197
+ navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
197
198
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
198
199
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
199
200
  } & {
@@ -261,9 +262,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
261
262
  displayName: string | undefined;
262
263
  tracks: any[];
263
264
  minimized: boolean;
264
- displayedRegions: import("@jbrowse/core/util").Region[];
265
265
  offsetPx: number;
266
266
  bpPerPx: number;
267
+ displayedRegions: import("@jbrowse/core/util").Region[];
267
268
  hideHeader: boolean;
268
269
  hideHeaderOverview: boolean;
269
270
  hideNoTracksActive: boolean;
@@ -502,12 +503,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
502
503
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
503
504
  } & {
504
505
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
505
- navToLocString(input: string, optAssemblyName?: string): Promise<void>;
506
+ navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
506
507
  navToSearchString({ input, assembly, }: {
507
508
  input: string;
508
509
  assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
509
510
  }): Promise<void>;
510
- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
511
+ navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
512
+ navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
511
513
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
512
514
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
513
515
  } & {
@@ -575,9 +577,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
575
577
  displayName: string | undefined;
576
578
  tracks: any[];
577
579
  minimized: boolean;
578
- displayedRegions: import("@jbrowse/core/util").Region[];
579
580
  offsetPx: number;
580
581
  bpPerPx: number;
582
+ displayedRegions: import("@jbrowse/core/util").Region[];
581
583
  hideHeader: boolean;
582
584
  hideHeaderOverview: boolean;
583
585
  hideNoTracksActive: boolean;
package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.js CHANGED
@@ -2,7 +2,7 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
2
  import { useEffect, useState } from 'react';
3
3
  import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
4
4
  import HelpIcon from '@mui/icons-material/Help';
5
- import { Button, FormControlLabel, Grid2, Paper, Radio, RadioGroup, Tooltip, Typography, } from '@mui/material';
5
+ import { Button, FormControlLabel, Grid, Paper, Radio, RadioGroup, Tooltip, Typography, } from '@mui/material';
6
6
  import { observer } from 'mobx-react';
7
7
  import { getAdapter } from './getAdapter';
8
8
  import { basename, extName, getName, stripGz } from './util';
@@ -68,7 +68,7 @@ const ImportSyntenyOpenCustomTrack = observer(function ({ model, assembly1, asse
68
68
  };
69
69
  return (_jsxs(Paper, { style: { padding: 12 }, children: [error ? _jsx(ErrorMessage, { error: error }) : null, _jsx(Typography, { style: { textAlign: 'center' }, children: "Add a .paf (minimap2), .delta (Mummer), .chain (UCSC liftover), .anchors or .anchors.simple (MCScan), or .pif.gz (jbrowse CLI make-pif) file to view. These file types can also be gzipped." }), _jsx(RadioGroup, { value: radioOption, onChange: event => {
70
70
  setValue(event.target.value);
71
- }, children: _jsx(Grid2, { container: true, justifyContent: "center", children: [
71
+ }, children: _jsx(Grid, { container: true, justifyContent: "center", children: [
72
72
  '.paf',
73
73
  '.delta',
74
74
  '.out',
@@ -76,7 +76,7 @@ const ImportSyntenyOpenCustomTrack = observer(function ({ model, assembly1, asse
76
76
  '.anchors',
77
77
  '.anchors.simple',
78
78
  '.pif.gz',
79
- ].map(extension => (_jsx(FormControlLabel, { value: extension, control: _jsx(Radio, {}), label: extension }, extension))) }) }), _jsx(Grid2, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
79
+ ].map(extension => (_jsx(FormControlLabel, { value: extension, control: _jsx(Radio, {}), label: extension }, extension))) }) }), _jsx(Grid, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
80
80
  radioOption === '.out' ||
81
81
  radioOption === '.delta' ||
82
82
  radioOption === '.chain' ||
package/esm/LinearSyntenyView/model.d.ts CHANGED
@@ -205,12 +205,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
205
205
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
206
206
  } & {
207
207
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
208
- navToLocString(input: string, optAssemblyName?: string): Promise<void>;
208
+ navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
209
209
  navToSearchString({ input, assembly, }: {
210
210
  input: string;
211
211
  assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
212
212
  }): Promise<void>;
213
- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
213
+ navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
214
+ navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
214
215
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
215
216
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
216
217
  } & {
@@ -278,9 +279,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
278
279
  displayName: string | undefined;
279
280
  tracks: any[];
280
281
  minimized: boolean;
281
- displayedRegions: import("@jbrowse/core/util").Region[];
282
282
  offsetPx: number;
283
283
  bpPerPx: number;
284
+ displayedRegions: import("@jbrowse/core/util").Region[];
284
285
  hideHeader: boolean;
285
286
  hideHeaderOverview: boolean;
286
287
  hideNoTracksActive: boolean;
@@ -586,12 +587,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
586
587
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
587
588
  } & {
588
589
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
589
- navToLocString(input: string, optAssemblyName?: string): Promise<void>;
590
+ navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
590
591
  navToSearchString({ input, assembly, }: {
591
592
  input: string;
592
593
  assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
593
594
  }): Promise<void>;
594
- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
595
+ navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
596
+ navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
595
597
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
596
598
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
597
599
  } & {
@@ -659,9 +661,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
659
661
  displayName: string | undefined;
660
662
  tracks: any[];
661
663
  minimized: boolean;
662
- displayedRegions: import("@jbrowse/core/util").Region[];
663
664
  offsetPx: number;
664
665
  bpPerPx: number;
666
+ displayedRegions: import("@jbrowse/core/util").Region[];
665
667
  hideHeader: boolean;
666
668
  hideHeaderOverview: boolean;
667
669
  hideNoTracksActive: boolean;
package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js CHANGED
@@ -67,7 +67,7 @@ export async function renderToSvg(model, opts) {
67
67
  const rendering = renderings[i - 1];
68
68
  const height = heights[i];
69
69
  const levelHeight = level.height || 0;
70
- RenderList.push(_jsxs("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? (_jsx("defs", { children: _jsx("clipPath", { id: `synclip-${i}`, children: _jsx("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, _jsx("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (_jsx(ReactRendering, { rendering: r }, i))) }), _jsx("g", { transform: `translate(0 ${levelHeight})`, children: _jsx(SVGLinearGenomeView, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
70
+ RenderList.push(_jsxs("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? (_jsx("defs", { children: _jsx("clipPath", { id: `synclip-${i}`, children: _jsx("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, _jsx("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => _jsx(ReactRendering, { rendering: r }, i)) }), _jsx("g", { transform: `translate(0 ${levelHeight})`, children: _jsx(SVGLinearGenomeView, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
71
71
  currOffset += height + fontSize + rulerHeight + levelHeight;
72
72
  }
73
73
  return renderToStaticMarkup(_jsx(ThemeProvider, { theme: theme, children: _jsx(Wrapper, { children: _jsxs("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString(), children: [_jsx(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }), RenderList] }) }) }));
package/esm/SyntenyFeatureDetail/Formatter.d.ts ADDED
@@ -0,0 +1,3 @@
1
+ export default function Formatter({ value }: {
2
+ value: unknown;
3
+ }): import("react/jsx-runtime").JSX.Element;
package/esm/SyntenyFeatureDetail/Formatter.js ADDED
@@ -0,0 +1,17 @@
1
+ import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { useState } from 'react';
3
+ import copy from 'copy-to-clipboard';
4
+ export default function Formatter({ value }) {
5
+ const [show, setShow] = useState(false);
6
+ const [copied, setCopied] = useState(false);
7
+ const display = String(value);
8
+ return display.length > 100 ? (_jsxs(_Fragment, { children: [_jsx("button", { type: "button", onClick: () => {
9
+ copy(display);
10
+ setCopied(true);
11
+ setTimeout(() => {
12
+ setCopied(false);
13
+ }, 700);
14
+ }, children: copied ? 'Copied to clipboard' : 'Copy' }), _jsx("button", { type: "button", onClick: () => {
15
+ setShow(val => !val);
16
+ }, children: show ? 'Show less' : 'Show more' }), _jsx("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : (_jsx("div", { children: display }));
17
+ }
package/esm/SyntenyFeatureDetail/LinkToSyntenyView.d.ts CHANGED
@@ -1,5 +1,7 @@
1
1
  import type { SyntenyFeatureDetailModel } from './types';
2
- declare const LinkToSyntenyView: ({ model, }: {
2
+ import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
3
+ declare const LinkToSyntenyView: ({ model, feat, }: {
3
4
  model: SyntenyFeatureDetailModel;
5
+ feat: SimpleFeatureSerialized;
4
6
  }) => import("react/jsx-runtime").JSX.Element;
5
7
  export default LinkToSyntenyView;
package/esm/SyntenyFeatureDetail/LinkToSyntenyView.js CHANGED
@@ -4,19 +4,19 @@ import { SimpleFeature, assembleLocString, getSession, } from '@jbrowse/core/uti
4
4
  import { Link } from '@mui/material';
5
5
  import { observer } from 'mobx-react';
6
6
  const LaunchSyntenyViewDialog = lazy(() => import('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'));
7
- const LinkToSyntenyView = observer(function ({ model, }) {
8
- const { featureData, view, level, trackId } = model;
7
+ const LinkToSyntenyView = observer(function ({ model, feat, }) {
8
+ const { view, level, trackId } = model;
9
9
  return (_jsxs("ul", { children: [view.type === 'LinearSyntenyView' ? (_jsx("li", { children: _jsx(Link, { href: "#", onClick: event => {
10
10
  var _a, _b;
11
11
  event.preventDefault();
12
12
  const { views } = view;
13
13
  if (level !== undefined) {
14
- (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(featureData);
15
- (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(featureData.mate);
14
+ (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(feat);
15
+ (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(feat.mate);
16
16
  }
17
17
  else {
18
- const f1 = featureData;
19
- const f2 = featureData.mate;
18
+ const f1 = feat;
19
+ const f2 = feat.mate;
20
20
  const r1 = f1.assemblyName;
21
21
  const r2 = f2.assemblyName;
22
22
  const v1 = views.find(view => view.assemblyNames[0] === r1);
@@ -36,7 +36,7 @@ const LinkToSyntenyView = observer(function ({ model, }) {
36
36
  }
37
37
  }, children: "Center view on this feature" }) })) : null, _jsx("li", { children: _jsx(Link, { href: "#", onClick: event => {
38
38
  event.preventDefault();
39
- const feature = new SimpleFeature(featureData);
39
+ const feature = new SimpleFeature(feat);
40
40
  const session = getSession(model);
41
41
  session.queueDialog(handleClose => [
42
42
  LaunchSyntenyViewDialog,
package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  import type { SyntenyFeatureDetailModel } from './types';
2
- declare const SyntenyFeatureDetail: ({ model, }: {
2
+ declare const SyntenyFeatureDetail: (props: {
3
3
  model: SyntenyFeatureDetailModel;
4
4
  }) => import("react/jsx-runtime").JSX.Element;
5
5
  export default SyntenyFeatureDetail;
package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js CHANGED
@@ -1,10 +1,14 @@
1
1
  import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
- import BaseFeatureDetail from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
3
2
  import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
3
+ import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
4
4
  import { Paper } from '@mui/material';
5
5
  import { observer } from 'mobx-react';
6
+ import Formatter from './Formatter';
6
7
  import LinkToSyntenyView from './LinkToSyntenyView';
7
- const SyntenyFeatureDetail = observer(function ({ model, }) {
8
- return (_jsxs(Paper, { children: [_jsx(BaseFeatureDetail, { title: "Feature", model: model }), _jsx(BaseCard, { title: "Link to view", children: _jsx(LinkToSyntenyView, { model: model }) })] }));
8
+ const SyntenyFeatureDetail = observer(function (props) {
9
+ const { model } = props;
10
+ const { featureData } = model;
11
+ const feat = structuredClone(featureData);
12
+ return feat ? (_jsxs(Paper, { children: [_jsx(FeatureDetails, { ...props, feature: feat, formatter: value => _jsx(Formatter, { value: value }) }), _jsx(BaseCard, { title: "Link to view", children: _jsx(LinkToSyntenyView, { model: model, feat: feat }) })] })) : (_jsx("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
9
13
  });
10
14
  export default SyntenyFeatureDetail;
package/esm/SyntenyFeatureDetail/types.d.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
2
2
  export interface SyntenyFeatureDetailModel {
3
3
  trackId: string;
4
- featureData: SimpleFeatureSerialized;
4
+ featureData?: SimpleFeatureSerialized;
5
5
  level?: number;
6
6
  view: {
7
7
  type: string;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-linear-comparative-view",
3
- "version": "3.2.0",
3
+ "version": "3.4.0",
4
4
  "description": "JBrowse 2 linear comparative view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -36,11 +36,11 @@
36
36
  "clean": "rimraf dist esm *.tsbuildinfo"
37
37
  },
38
38
  "dependencies": {
39
- "@jbrowse/core": "^3.2.0",
40
- "@jbrowse/plugin-alignments": "^3.2.0",
41
- "@jbrowse/plugin-linear-genome-view": "^3.2.0",
42
- "@mui/icons-material": "^6.0.0",
43
- "@mui/material": "^6.0.0",
39
+ "@jbrowse/core": "^3.4.0",
40
+ "@jbrowse/plugin-alignments": "^3.4.0",
41
+ "@jbrowse/plugin-linear-genome-view": "^3.4.0",
42
+ "@mui/icons-material": "^7.0.0",
43
+ "@mui/material": "^7.0.0",
44
44
  "copy-to-clipboard": "^3.3.1",
45
45
  "file-saver": "^2.0.0",
46
46
  "mobx": "^6.0.0",
@@ -59,5 +59,5 @@
59
59
  "publishConfig": {
60
60
  "access": "public"
61
61
  },
62
- "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
62
+ "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
63
63
  }