@jbrowse/plugin-breakpoint-split-view 2.8.0 → 2.9.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (7) hide show
  1. package/dist/BreakpointSplitView/components/Breakends.js +5 -5
  2. package/dist/BreakpointSplitView/components/Translocations.js +4 -4
  3. package/dist/BreakpointSplitView/model.d.ts +124 -2
  4. package/esm/BreakpointSplitView/components/Breakends.js +5 -5
  5. package/esm/BreakpointSplitView/components/Translocations.js +4 -4
  6. package/esm/BreakpointSplitView/model.d.ts +124 -2
  7. package/package.json +2 -2
package/dist/BreakpointSplitView/components/Breakends.js CHANGED
@@ -82,26 +82,26 @@ const Breakends = (0, mobx_react_1.observer)(function ({ model, trackId, parentR
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  }
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  else {
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  const path = [
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- 'M',
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+ 'M', // move to
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  x1 -
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  20 *
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  (relevantAlt.Join === 'left' ? -1 : 1) *
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  (reversed1 ? -1 : 1),
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  y1,
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- 'L',
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+ 'L', // line to
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  x1,
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  y1,
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- 'L',
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+ 'L', // line to
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  x2,
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  y2,
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- 'L',
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+ 'L', // line to
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  x2 -
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  20 *
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  (relevantAlt.MateDirection === 'left' ? 1 : -1) *
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  (reversed2 ? -1 : 1),
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  y2,
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  ].join(' ');
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- ret.push(react_1.default.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
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+ ret.push(react_1.default.createElement("path", { d: path, "data-testid": "r2", key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
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  var _a, _b, _c;
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  const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
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  featureData: (_b = totalFeatures.get(id)) === null || _b === void 0 ? void 0 : _b.toJSON(),
package/dist/BreakpointSplitView/components/Translocations.js CHANGED
@@ -83,16 +83,16 @@ const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, pa
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  const y2 = (0, util_3.yPos)(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
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  yOffset;
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  const path = [
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- 'M',
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+ 'M', // move to
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  x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1),
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  y1,
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- 'L',
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+ 'L', // line to
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  x1,
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  y1,
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- 'L',
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+ 'L', // line to
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  x2,
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  y2,
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- 'L',
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+ 'L', // line to
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  x2 - 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1),
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  y2,
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  ].join(' ');
package/dist/BreakpointSplitView/model.d.ts CHANGED
@@ -84,7 +84,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  trackRefs: Record<string, HTMLDivElement>;
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  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
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  coarseTotalBp: number;
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- leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
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+ leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined; /**
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+ * #action
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+ */
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  rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
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  } & {
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  readonly trackLabelsSetting: any;
@@ -139,7 +141,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  } & {
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  moveTrack(movingId: string, targetId: string): void;
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  closeView(): void;
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- toggleTrack(trackId: string): void;
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+ toggleTrack(trackId: string): boolean;
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  setTrackLabels(setting: "hidden" | "offset" | "overlapping"): void;
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  toggleCenterLine(): void;
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  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -189,6 +191,126 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  } & {
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  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
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  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
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+ navToSearchString({ input, assembly, }: {
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+ input: string;
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+ assembly: {
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+ configuration: any;
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+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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+ error: unknown;
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+ loaded: boolean;
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+ loadingP: Promise<void> | undefined;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ refNameAliases: {
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+ [x: string]: string | undefined;
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+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string | undefined;
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+ } | undefined;
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+ cytobands: Feature[] | undefined;
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+ } & {
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+ getConf(arg: string): any;
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+ } & {
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+ readonly initialized: boolean;
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+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly aliases: string[];
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+ readonly displayName: string | undefined;
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+ hasName(name: string): boolean;
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+ readonly allAliases: string[];
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+ readonly allRefNames: string[] | undefined;
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+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
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+ } & {
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+ readonly refNames: string[] | undefined;
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+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
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+ isValidRefName(refName: string): boolean;
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+ } & {
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+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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+ setError(e: unknown): void;
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+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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+ setRefNameAliases(aliases: {
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+ [x: string]: string | undefined;
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+ }, lcAliases: {
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+ [x: string]: string | undefined;
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+ }): void;
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+ setCytobands(cytobands: Feature[]): void; /**
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+ * #property
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+ */
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+ setLoadingP(p?: Promise<void> | undefined): void;
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+ load(): Promise<void>;
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+ loadPre(): Promise<void>;
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+ } & {
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+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string | undefined;
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+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string | undefined;
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+ }>;
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+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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+ }, {
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+ error: unknown;
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+ loaded: boolean;
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+ loadingP: Promise<void> | undefined;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ refNameAliases: {
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+ [x: string]: string | undefined;
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+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string | undefined;
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+ } | undefined;
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+ cytobands: Feature[] | undefined;
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+ } & {
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+ getConf(arg: string): any;
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+ } & {
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+ readonly initialized: boolean;
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+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly aliases: string[];
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+ readonly displayName: string | undefined;
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+ hasName(name: string): boolean;
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+ readonly allAliases: string[];
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+ readonly allRefNames: string[] | undefined;
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+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
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+ } & {
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+ readonly refNames: string[] | undefined;
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+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
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+ isValidRefName(refName: string): boolean;
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+ } & {
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+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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+ setError(e: unknown): void;
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+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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+ setRefNameAliases(aliases: {
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+ [x: string]: string | undefined;
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+ }, lcAliases: {
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+ [x: string]: string | undefined;
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+ }): void;
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+ setCytobands(cytobands: Feature[]): void; /**
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+ * #property
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+ */
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+ setLoadingP(p?: Promise<void> | undefined): void;
302
+ load(): Promise<void>;
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+ loadPre(): Promise<void>;
304
+ } & {
305
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
306
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
307
+ [x: string]: string | undefined;
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+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string | undefined;
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+ }>;
312
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
313
+ }): Promise<void>;
192
314
  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
193
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  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
194
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  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
package/esm/BreakpointSplitView/components/Breakends.js CHANGED
@@ -57,26 +57,26 @@ const Breakends = observer(function ({ model, trackId, parentRef: ref, getTrackY
57
57
  }
58
58
  else {
59
59
  const path = [
60
- 'M',
60
+ 'M', // move to
61
61
  x1 -
62
62
  20 *
63
63
  (relevantAlt.Join === 'left' ? -1 : 1) *
64
64
  (reversed1 ? -1 : 1),
65
65
  y1,
66
- 'L',
66
+ 'L', // line to
67
67
  x1,
68
68
  y1,
69
- 'L',
69
+ 'L', // line to
70
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  x2,
71
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  y2,
72
- 'L',
72
+ 'L', // line to
73
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  x2 -
74
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  20 *
75
75
  (relevantAlt.MateDirection === 'left' ? 1 : -1) *
76
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  (reversed2 ? -1 : 1),
77
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  y2,
78
78
  ].join(' ');
79
- ret.push(React.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
79
+ ret.push(React.createElement("path", { d: path, "data-testid": "r2", key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
80
80
  var _a, _b, _c;
81
81
  const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
82
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  featureData: (_b = totalFeatures.get(id)) === null || _b === void 0 ? void 0 : _b.toJSON(),
package/esm/BreakpointSplitView/components/Translocations.js CHANGED
@@ -58,16 +58,16 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
58
58
  const y2 = yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
59
59
  yOffset;
60
60
  const path = [
61
- 'M',
61
+ 'M', // move to
62
62
  x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1),
63
63
  y1,
64
- 'L',
64
+ 'L', // line to
65
65
  x1,
66
66
  y1,
67
- 'L',
67
+ 'L', // line to
68
68
  x2,
69
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  y2,
70
- 'L',
70
+ 'L', // line to
71
71
  x2 - 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1),
72
72
  y2,
73
73
  ].join(' ');
package/esm/BreakpointSplitView/model.d.ts CHANGED
@@ -84,7 +84,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
84
84
  trackRefs: Record<string, HTMLDivElement>;
85
85
  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
86
86
  coarseTotalBp: number;
87
- leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
87
+ leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined; /**
88
+ * #action
89
+ */
88
90
  rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
89
91
  } & {
90
92
  readonly trackLabelsSetting: any;
@@ -139,7 +141,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
139
141
  } & {
140
142
  moveTrack(movingId: string, targetId: string): void;
141
143
  closeView(): void;
142
- toggleTrack(trackId: string): void;
144
+ toggleTrack(trackId: string): boolean;
143
145
  setTrackLabels(setting: "hidden" | "offset" | "overlapping"): void;
144
146
  toggleCenterLine(): void;
145
147
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -189,6 +191,126 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
189
191
  } & {
190
192
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
191
193
  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
194
+ navToSearchString({ input, assembly, }: {
195
+ input: string;
196
+ assembly: {
197
+ configuration: any;
198
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
199
+ error: unknown;
200
+ loaded: boolean;
201
+ loadingP: Promise<void> | undefined;
202
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
203
+ refNameAliases: {
204
+ [x: string]: string | undefined;
205
+ } | undefined;
206
+ lowerCaseRefNameAliases: {
207
+ [x: string]: string | undefined;
208
+ } | undefined;
209
+ cytobands: Feature[] | undefined;
210
+ } & {
211
+ getConf(arg: string): any;
212
+ } & {
213
+ readonly initialized: boolean;
214
+ readonly name: string;
215
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
216
+ readonly aliases: string[];
217
+ readonly displayName: string | undefined;
218
+ hasName(name: string): boolean;
219
+ readonly allAliases: string[];
220
+ readonly allRefNames: string[] | undefined;
221
+ readonly lowerCaseRefNames: string[] | undefined;
222
+ readonly allRefNamesWithLowerCase: string[] | undefined;
223
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
224
+ readonly refNameColors: string[];
225
+ } & {
226
+ readonly refNames: string[] | undefined;
227
+ } & {
228
+ getCanonicalRefName(refName: string): string | undefined;
229
+ getRefNameColor(refName: string): string | undefined;
230
+ isValidRefName(refName: string): boolean;
231
+ } & {
232
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
233
+ setError(e: unknown): void;
234
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
235
+ setRefNameAliases(aliases: {
236
+ [x: string]: string | undefined;
237
+ }, lcAliases: {
238
+ [x: string]: string | undefined;
239
+ }): void;
240
+ setCytobands(cytobands: Feature[]): void; /**
241
+ * #property
242
+ */
243
+ setLoadingP(p?: Promise<void> | undefined): void;
244
+ load(): Promise<void>;
245
+ loadPre(): Promise<void>;
246
+ } & {
247
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
248
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
249
+ [x: string]: string | undefined;
250
+ }>;
251
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
252
+ [x: string]: string | undefined;
253
+ }>;
254
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
255
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
256
+ }, {
257
+ error: unknown;
258
+ loaded: boolean;
259
+ loadingP: Promise<void> | undefined;
260
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
261
+ refNameAliases: {
262
+ [x: string]: string | undefined;
263
+ } | undefined;
264
+ lowerCaseRefNameAliases: {
265
+ [x: string]: string | undefined;
266
+ } | undefined;
267
+ cytobands: Feature[] | undefined;
268
+ } & {
269
+ getConf(arg: string): any;
270
+ } & {
271
+ readonly initialized: boolean;
272
+ readonly name: string;
273
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
274
+ readonly aliases: string[];
275
+ readonly displayName: string | undefined;
276
+ hasName(name: string): boolean;
277
+ readonly allAliases: string[];
278
+ readonly allRefNames: string[] | undefined;
279
+ readonly lowerCaseRefNames: string[] | undefined;
280
+ readonly allRefNamesWithLowerCase: string[] | undefined;
281
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
282
+ readonly refNameColors: string[];
283
+ } & {
284
+ readonly refNames: string[] | undefined;
285
+ } & {
286
+ getCanonicalRefName(refName: string): string | undefined;
287
+ getRefNameColor(refName: string): string | undefined;
288
+ isValidRefName(refName: string): boolean;
289
+ } & {
290
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
291
+ setError(e: unknown): void;
292
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
293
+ setRefNameAliases(aliases: {
294
+ [x: string]: string | undefined;
295
+ }, lcAliases: {
296
+ [x: string]: string | undefined;
297
+ }): void;
298
+ setCytobands(cytobands: Feature[]): void; /**
299
+ * #property
300
+ */
301
+ setLoadingP(p?: Promise<void> | undefined): void;
302
+ load(): Promise<void>;
303
+ loadPre(): Promise<void>;
304
+ } & {
305
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
306
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
307
+ [x: string]: string | undefined;
308
+ }>;
309
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
310
+ [x: string]: string | undefined;
311
+ }>;
312
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
313
+ }): Promise<void>;
192
314
  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
193
315
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
194
316
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-breakpoint-split-view",
3
- "version": "2.8.0",
3
+ "version": "2.9.0",
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": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
61
+ "gitHead": "a50b6f67cf8c8f3c65a7b8cd858de2fcca1f2909"
62
62
  }