@jbrowse/plugin-breakpoint-split-view 2.12.0 → 2.12.2

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 (12) hide show
  1. package/dist/BreakpointAlignmentsFeatureDetail/index.js +1 -1
  2. package/dist/BreakpointSplitView/components/ExportSvgDialog.js +1 -1
  3. package/dist/BreakpointSplitView/components/util.js +6 -7
  4. package/dist/BreakpointSplitView/index.js +1 -1
  5. package/dist/BreakpointSplitView/model.d.ts +22 -152
  6. package/dist/BreakpointSplitView/model.js +1 -1
  7. package/dist/BreakpointSplitView/svgcomponents/SVGBackground.js +1 -1
  8. package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js +1 -2
  9. package/dist/BreakpointSplitView/svgcomponents/util.js +2 -3
  10. package/dist/BreakpointSplitView/util.js +4 -4
  11. package/esm/BreakpointSplitView/model.d.ts +22 -152
  12. package/package.json +2 -2
package/dist/BreakpointAlignmentsFeatureDetail/index.js CHANGED
@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
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  return result;
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.default = BreakpointAlignmentsFeatureDetailF;
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  const react_1 = require("react");
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  const configuration_1 = require("@jbrowse/core/configuration");
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  const mst_1 = require("@jbrowse/core/util/types/mst");
@@ -54,4 +55,3 @@ function BreakpointAlignmentsFeatureDetailF(pluginManager) {
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  });
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  });
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  }
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- exports.default = BreakpointAlignmentsFeatureDetailF;
package/dist/BreakpointSplitView/components/ExportSvgDialog.js CHANGED
@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
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  return result;
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.default = ExportSvgDialog;
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  const react_1 = __importStar(require("react"));
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  const material_1 = require("@mui/material");
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  const ui_1 = require("@jbrowse/core/ui");
@@ -85,4 +86,3 @@ function ExportSvgDialog({ model, handleClose, }) {
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  }
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  } }, "Submit"))));
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  }
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- exports.default = ExportSvgDialog;
package/dist/BreakpointSplitView/components/util.js CHANGED
@@ -1,6 +1,11 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.getMatchedTranslocationFeatures = exports.getMatchedBreakendFeatures = exports.findMatchingAlt = exports.hasPairedReads = exports.getMatchedAlignmentFeatures = exports.getBadlyPairedAlignments = void 0;
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+ exports.getBadlyPairedAlignments = getBadlyPairedAlignments;
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+ exports.getMatchedAlignmentFeatures = getMatchedAlignmentFeatures;
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+ exports.hasPairedReads = hasPairedReads;
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+ exports.findMatchingAlt = findMatchingAlt;
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+ exports.getMatchedBreakendFeatures = getMatchedBreakendFeatures;
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+ exports.getMatchedTranslocationFeatures = getMatchedTranslocationFeatures;
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  const util_1 = require("@jbrowse/core/util");
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  const vcf_1 = require("@gmod/vcf");
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  // this finds candidate alignment features, aimed at plotting split reads from
@@ -27,7 +32,6 @@ function getBadlyPairedAlignments(features) {
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  }
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  return [...candidates.values()].filter(v => v.length > 1);
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  }
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- exports.getBadlyPairedAlignments = getBadlyPairedAlignments;
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  function getTag(f, tag) {
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  const tags = f.get('tags');
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  return tags ? tags[tag] : f.get(tag);
@@ -55,7 +59,6 @@ function getMatchedAlignmentFeatures(features) {
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  }
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  return [...candidates.values()].filter(v => v.length > 1);
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  }
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- exports.getMatchedAlignmentFeatures = getMatchedAlignmentFeatures;
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  function hasPairedReads(features) {
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  for (const f of features.values()) {
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  if (f.get('flags') & 1) {
@@ -64,7 +67,6 @@ function hasPairedReads(features) {
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  }
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  return false;
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  }
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- exports.hasPairedReads = hasPairedReads;
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  function findMatchingAlt(feat1, feat2) {
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  const alts = feat1.get('ALT');
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  if (alts) {
@@ -72,7 +74,6 @@ function findMatchingAlt(feat1, feat2) {
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  }
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  return undefined;
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  }
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- exports.findMatchingAlt = findMatchingAlt;
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  // Returns paired BND features across multiple views by inspecting the ALT
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  // field to get exact coordinate matches
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  function getMatchedBreakendFeatures(feats) {
@@ -99,7 +100,6 @@ function getMatchedBreakendFeatures(feats) {
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  }
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  return [...candidates.values()].filter(v => v.length > 1);
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  }
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- exports.getMatchedBreakendFeatures = getMatchedBreakendFeatures;
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  // Getting "matched" TRA means just return all TRA
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  function getMatchedTranslocationFeatures(feats) {
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  const ret = [];
@@ -112,4 +112,3 @@ function getMatchedTranslocationFeatures(feats) {
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  }
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  return ret;
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  }
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- exports.getMatchedTranslocationFeatures = getMatchedTranslocationFeatures;
package/dist/BreakpointSplitView/index.js CHANGED
@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  return (mod && mod.__esModule) ? mod : { "default": mod };
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.default = BreakpointSplitViewF;
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  const react_1 = require("react");
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  // locals
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  const BreakpointSplitView_1 = __importDefault(require("./BreakpointSplitView"));
@@ -40,4 +41,3 @@ function BreakpointSplitViewF(pluginManager) {
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  });
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  });
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  }
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- exports.default = BreakpointSplitViewF;
package/dist/BreakpointSplitView/model.d.ts CHANGED
@@ -74,17 +74,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  } & {
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  volatileWidth: number | undefined;
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  minimumBlockWidth: number;
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- draggingTrackId: string | undefined;
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+ draggingTrackId: undefined | string;
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  volatileError: unknown;
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- afterDisplayedRegionsSetCallbacks: Function[]; /**
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- * #action
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- */
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+ afterDisplayedRegionsSetCallbacks: Function[];
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  scaleFactor: number;
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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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- rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
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+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
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+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
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  } & {
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  readonly trackLabelsSetting: any;
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  readonly width: number;
@@ -133,8 +131,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
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  scrollTo(offsetPx: number): number;
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  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
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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;
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- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
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+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
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+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
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  setNewView(bpPerPx: number, offsetPx: number): void;
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  horizontallyFlip(): void;
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  showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -147,30 +145,30 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  moveTrack(movingId: string, targetId: string): void;
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  closeView(): void;
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  toggleTrack(trackId: string): boolean;
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- setTrackLabels(setting: "hidden" | "offset" | "overlapping"): void;
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+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
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  setShowCenterLine(b: boolean): void;
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  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  activateTrackSelector(): import("@jbrowse/core/util").Widget;
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- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
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+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
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  start: number;
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  end: number;
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  type: string;
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- regionNumber?: number | undefined;
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- reversed?: boolean | undefined;
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+ regionNumber?: number;
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+ reversed?: boolean;
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  refName: string;
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  assemblyName: string;
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  key: string;
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  offsetPx: number;
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  widthPx: number;
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- variant?: string | undefined;
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- isLeftEndOfDisplayedRegion?: boolean | undefined;
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+ variant?: string;
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+ isLeftEndOfDisplayedRegion?: boolean;
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  }[];
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  afterDisplayedRegionsSet(cb: Function): void;
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  horizontalScroll(distance: number): number;
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  center(): void;
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  showAllRegions(): void;
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- showAllRegionsInAssembly(assemblyName?: string | undefined): void;
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- setDraggingTrackId(idx?: string | undefined): void;
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+ showAllRegionsInAssembly(assemblyName?: string): void;
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+ setDraggingTrackId(idx?: string): void;
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  setScaleFactor(factor: number): void;
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  clearView(): void;
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  exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
@@ -195,141 +193,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
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  afterAttach(): void;
197
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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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+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
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+ navToLocString(input: string, optAssemblyName?: string): 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[];
231
- } & {
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- readonly refNames: string[] | undefined;
233
- } & {
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- getCanonicalRefName(refName: string): string | undefined;
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- getRefNameColor(refName: string): string | undefined; /**
236
- * #property
237
- */
238
- isValidRefName(refName: string): boolean;
239
- } & {
240
- 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;
243
- setRefNameAliases(aliases: {
244
- [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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- setLoadingP(p?: Promise<void> | undefined): void;
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- load(): Promise<void>;
251
- loadPre(): Promise<void>;
252
- } & {
253
- getAdapterMapEntry(adapterConf: {
254
- [x: string]: unknown;
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- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
256
- getRefNameMapForAdapter(adapterConf: {
257
- [x: string]: unknown;
258
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
259
- [x: string]: string | undefined;
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- }>;
261
- getReverseRefNameMapForAdapter(adapterConf: {
262
- [x: string]: unknown;
263
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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- [x: string]: string | undefined;
265
- }>;
266
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
267
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
268
- }, {
269
- error: unknown;
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- loaded: boolean;
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- loadingP: Promise<void> | undefined;
272
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
273
- refNameAliases: {
274
- [x: string]: string | undefined;
275
- } | undefined;
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- lowerCaseRefNameAliases: {
277
- [x: string]: string | undefined;
278
- } | undefined;
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- cytobands: Feature[] | undefined;
280
- } & {
281
- getConf(arg: string): any;
282
- } & {
283
- readonly initialized: boolean;
284
- readonly name: string;
285
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
286
- readonly aliases: string[];
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- readonly displayName: string | undefined;
288
- hasName(name: string): boolean;
289
- readonly allAliases: string[];
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- readonly allRefNames: string[] | undefined;
291
- readonly lowerCaseRefNames: string[] | undefined;
292
- readonly allRefNamesWithLowerCase: string[] | undefined;
293
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
294
- readonly refNameColors: string[];
295
- } & {
296
- readonly refNames: string[] | undefined;
297
- } & {
298
- getCanonicalRefName(refName: string): string | undefined;
299
- getRefNameColor(refName: string): string | undefined; /**
300
- * #property
301
- */
302
- isValidRefName(refName: string): boolean;
303
- } & {
304
- setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
305
- setError(e: unknown): void;
306
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
307
- setRefNameAliases(aliases: {
308
- [x: string]: string | undefined;
309
- }, lcAliases: {
310
- [x: string]: string | undefined;
311
- }): void;
312
- setCytobands(cytobands: Feature[]): void;
313
- setLoadingP(p?: Promise<void> | undefined): void;
314
- load(): Promise<void>;
315
- loadPre(): Promise<void>;
316
- } & {
317
- getAdapterMapEntry(adapterConf: {
318
- [x: string]: unknown;
319
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
320
- getRefNameMapForAdapter(adapterConf: {
321
- [x: string]: unknown;
322
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
323
- [x: string]: string | undefined;
324
- }>;
325
- getReverseRefNameMapForAdapter(adapterConf: {
326
- [x: string]: unknown;
327
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
328
- [x: string]: string | undefined;
329
- }>;
330
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
200
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
331
201
  }): Promise<void>;
332
- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
202
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
333
203
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
334
204
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
335
205
  } & {
@@ -337,12 +207,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
337
207
  bpToPx({ refName, coord, regionNumber, }: {
338
208
  refName: string;
339
209
  coord: number;
340
- regionNumber?: number | undefined;
210
+ regionNumber?: number;
341
211
  }): {
342
212
  index: number;
343
213
  offsetPx: number;
344
214
  } | undefined;
345
- centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
215
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
346
216
  pxToBp(px: number): {
347
217
  coord: number;
348
218
  index: number;
@@ -352,7 +222,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
352
222
  offset: number;
353
223
  start: number;
354
224
  end: number;
355
- reversed?: boolean | undefined;
225
+ reversed?: boolean;
356
226
  };
357
227
  readonly centerLineInfo: {
358
228
  coord: number;
@@ -363,7 +233,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
363
233
  offset: number;
364
234
  start: number;
365
235
  end: number;
366
- reversed?: boolean | undefined;
236
+ reversed?: boolean;
367
237
  } | undefined;
368
238
  } & {
369
239
  afterCreate(): void;
package/dist/BreakpointSplitView/model.js CHANGED
@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
26
26
  return (mod && mod.__esModule) ? mod : { "default": mod };
27
27
  };
28
28
  Object.defineProperty(exports, "__esModule", { value: true });
29
+ exports.default = stateModelFactory;
29
30
  const react_1 = require("react");
30
31
  const mobx_state_tree_1 = require("mobx-state-tree");
31
32
  const mobx_1 = require("mobx");
@@ -307,4 +308,3 @@ function stateModelFactory(pluginManager) {
307
308
  },
308
309
  }));
309
310
  }
310
- exports.default = stateModelFactory;
package/dist/BreakpointSplitView/svgcomponents/SVGBackground.js CHANGED
@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
+ exports.default = SVGBackground;
6
7
  const react_1 = __importDefault(require("react"));
7
8
  const material_1 = require("@mui/material");
8
9
  const util_1 = require("@jbrowse/core/util");
@@ -10,4 +11,3 @@ function SVGBackground({ width, height, shift, }) {
10
11
  const theme = (0, material_1.useTheme)();
11
12
  return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
12
13
  }
13
- exports.default = SVGBackground;
package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js CHANGED
@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.renderToSvg = void 0;
6
+ exports.renderToSvg = renderToSvg;
7
7
  const react_1 = __importDefault(require("react"));
8
8
  const mobx_1 = require("mobx");
9
9
  const util_1 = require("@jbrowse/core/util");
@@ -65,4 +65,3 @@ async function renderToSvg(model, opts) {
65
65
  react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }))),
66
66
  react_1.default.createElement("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)" }, model.matchedTracks.map(track => (react_1.default.createElement(Overlay_1.default, { parentRef: { current: null }, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }))))))), createRootFn);
67
67
  }
68
- exports.renderToSvg = renderToSvg;
package/dist/BreakpointSplitView/svgcomponents/util.js CHANGED
@@ -1,13 +1,13 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.getTrackOffsets = exports.getTrackNameMaxLen = void 0;
3
+ exports.getTrackNameMaxLen = getTrackNameMaxLen;
4
+ exports.getTrackOffsets = getTrackOffsets;
4
5
  const util_1 = require("@jbrowse/core/util");
5
6
  // locals
6
7
  const tracks_1 = require("@jbrowse/core/util/tracks");
7
8
  function getTrackNameMaxLen(views, fontSize, session) {
8
9
  return (0, util_1.max)(views.flatMap(view => view.tracks.map(t => (0, util_1.measureText)((0, tracks_1.getTrackName)(t.configuration, session), fontSize))), 0);
9
10
  }
10
- exports.getTrackNameMaxLen = getTrackNameMaxLen;
11
11
  function getTrackOffsets(view, textOffset, extra = 0) {
12
12
  const offsets = {};
13
13
  let curr = textOffset;
@@ -17,4 +17,3 @@ function getTrackOffsets(view, textOffset, extra = 0) {
17
17
  }
18
18
  return offsets;
19
19
  }
20
- exports.getTrackOffsets = getTrackOffsets;
package/dist/BreakpointSplitView/util.js CHANGED
@@ -1,6 +1,9 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.intersect = exports.useNextFrame = exports.yPos = exports.getPxFromCoordinate = void 0;
3
+ exports.useNextFrame = void 0;
4
+ exports.getPxFromCoordinate = getPxFromCoordinate;
5
+ exports.yPos = yPos;
6
+ exports.intersect = intersect;
4
7
  const react_1 = require("react");
5
8
  const util_1 = require("@jbrowse/core/util");
6
9
  const [, TOP, , BOTTOM] = [0, 1, 2, 3];
@@ -17,7 +20,6 @@ function getPxFromCoordinate(view, refName, coord) {
17
20
  var _a;
18
21
  return (((_a = view.bpToPx({ refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
19
22
  }
20
- exports.getPxFromCoordinate = getPxFromCoordinate;
21
23
  // get's the yposition of a layout record in a track
22
24
  function yPos(trackId, level, views, tracks, c, getYPosOverride) {
23
25
  const display = tracks[level].displays[0];
@@ -33,7 +35,6 @@ function yPos(trackId, level, views, tracks, c, getYPosOverride) {
33
35
  heightFromSpecificLevel(views, trackId, level, getYPosOverride) +
34
36
  display.scrollTop);
35
37
  }
36
- exports.yPos = yPos;
37
38
  // we combo a useEffect and useState combo to force rerender on snap changing.
38
39
  // the setup of this being a useEffect+useState makes it re-render once the
39
40
  // useEffect is called, which is generally the "next frame". If we removed the
@@ -53,4 +54,3 @@ function intersect(cb, a1 = [], a2 = [], ...rest) {
53
54
  const a12 = a1.filter(value => ids.has(cb(value)));
54
55
  return rest.length === 0 ? a12 : intersect(cb, a12, ...rest);
55
56
  }
56
- exports.intersect = intersect;
package/esm/BreakpointSplitView/model.d.ts CHANGED
@@ -74,17 +74,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
74
74
  } & {
75
75
  volatileWidth: number | undefined;
76
76
  minimumBlockWidth: number;
77
- draggingTrackId: string | undefined;
77
+ draggingTrackId: undefined | string;
78
78
  volatileError: unknown;
79
- afterDisplayedRegionsSetCallbacks: Function[]; /**
80
- * #action
81
- */
79
+ afterDisplayedRegionsSetCallbacks: Function[];
82
80
  scaleFactor: number;
83
81
  trackRefs: Record<string, HTMLDivElement>;
84
82
  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
85
83
  coarseTotalBp: number;
86
- leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
87
- rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
84
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
85
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
88
86
  } & {
89
87
  readonly trackLabelsSetting: any;
90
88
  readonly width: number;
@@ -133,8 +131,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
133
131
  removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
134
132
  scrollTo(offsetPx: number): number;
135
133
  zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
136
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
137
- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
134
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
135
+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
138
136
  setNewView(bpPerPx: number, offsetPx: number): void;
139
137
  horizontallyFlip(): void;
140
138
  showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -147,30 +145,30 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
147
145
  moveTrack(movingId: string, targetId: string): void;
148
146
  closeView(): void;
149
147
  toggleTrack(trackId: string): boolean;
150
- setTrackLabels(setting: "hidden" | "offset" | "overlapping"): void;
148
+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
151
149
  setShowCenterLine(b: boolean): void;
152
150
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
153
151
  activateTrackSelector(): import("@jbrowse/core/util").Widget;
154
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
152
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
155
153
  start: number;
156
154
  end: number;
157
155
  type: string;
158
- regionNumber?: number | undefined;
159
- reversed?: boolean | undefined;
156
+ regionNumber?: number;
157
+ reversed?: boolean;
160
158
  refName: string;
161
159
  assemblyName: string;
162
160
  key: string;
163
161
  offsetPx: number;
164
162
  widthPx: number;
165
- variant?: string | undefined;
166
- isLeftEndOfDisplayedRegion?: boolean | undefined;
163
+ variant?: string;
164
+ isLeftEndOfDisplayedRegion?: boolean;
167
165
  }[];
168
166
  afterDisplayedRegionsSet(cb: Function): void;
169
167
  horizontalScroll(distance: number): number;
170
168
  center(): void;
171
169
  showAllRegions(): void;
172
- showAllRegionsInAssembly(assemblyName?: string | undefined): void;
173
- setDraggingTrackId(idx?: string | undefined): void;
170
+ showAllRegionsInAssembly(assemblyName?: string): void;
171
+ setDraggingTrackId(idx?: string): void;
174
172
  setScaleFactor(factor: number): void;
175
173
  clearView(): void;
176
174
  exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
@@ -195,141 +193,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
195
193
  setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
196
194
  afterAttach(): void;
197
195
  } & {
198
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
199
- navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
196
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
197
+ navToLocString(input: string, optAssemblyName?: string): Promise<void>;
200
198
  navToSearchString({ input, assembly, }: {
201
199
  input: string;
202
- assembly: {
203
- configuration: any;
204
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
205
- error: unknown;
206
- loaded: boolean;
207
- loadingP: Promise<void> | undefined;
208
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
209
- refNameAliases: {
210
- [x: string]: string | undefined;
211
- } | undefined;
212
- lowerCaseRefNameAliases: {
213
- [x: string]: string | undefined;
214
- } | undefined;
215
- cytobands: Feature[] | undefined;
216
- } & {
217
- getConf(arg: string): any;
218
- } & {
219
- readonly initialized: boolean;
220
- readonly name: string;
221
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
222
- readonly aliases: string[];
223
- readonly displayName: string | undefined;
224
- hasName(name: string): boolean;
225
- readonly allAliases: string[];
226
- readonly allRefNames: string[] | undefined;
227
- readonly lowerCaseRefNames: string[] | undefined;
228
- readonly allRefNamesWithLowerCase: string[] | undefined;
229
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
230
- readonly refNameColors: string[];
231
- } & {
232
- readonly refNames: string[] | undefined;
233
- } & {
234
- getCanonicalRefName(refName: string): string | undefined;
235
- getRefNameColor(refName: string): string | undefined; /**
236
- * #property
237
- */
238
- isValidRefName(refName: string): boolean;
239
- } & {
240
- setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
241
- setError(e: unknown): void;
242
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
243
- setRefNameAliases(aliases: {
244
- [x: string]: string | undefined;
245
- }, lcAliases: {
246
- [x: string]: string | undefined;
247
- }): void;
248
- setCytobands(cytobands: Feature[]): void;
249
- setLoadingP(p?: Promise<void> | undefined): void;
250
- load(): Promise<void>;
251
- loadPre(): Promise<void>;
252
- } & {
253
- getAdapterMapEntry(adapterConf: {
254
- [x: string]: unknown;
255
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
256
- getRefNameMapForAdapter(adapterConf: {
257
- [x: string]: unknown;
258
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
259
- [x: string]: string | undefined;
260
- }>;
261
- getReverseRefNameMapForAdapter(adapterConf: {
262
- [x: string]: unknown;
263
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
264
- [x: string]: string | undefined;
265
- }>;
266
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
267
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
268
- }, {
269
- error: unknown;
270
- loaded: boolean;
271
- loadingP: Promise<void> | undefined;
272
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
273
- refNameAliases: {
274
- [x: string]: string | undefined;
275
- } | undefined;
276
- lowerCaseRefNameAliases: {
277
- [x: string]: string | undefined;
278
- } | undefined;
279
- cytobands: Feature[] | undefined;
280
- } & {
281
- getConf(arg: string): any;
282
- } & {
283
- readonly initialized: boolean;
284
- readonly name: string;
285
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
286
- readonly aliases: string[];
287
- readonly displayName: string | undefined;
288
- hasName(name: string): boolean;
289
- readonly allAliases: string[];
290
- readonly allRefNames: string[] | undefined;
291
- readonly lowerCaseRefNames: string[] | undefined;
292
- readonly allRefNamesWithLowerCase: string[] | undefined;
293
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
294
- readonly refNameColors: string[];
295
- } & {
296
- readonly refNames: string[] | undefined;
297
- } & {
298
- getCanonicalRefName(refName: string): string | undefined;
299
- getRefNameColor(refName: string): string | undefined; /**
300
- * #property
301
- */
302
- isValidRefName(refName: string): boolean;
303
- } & {
304
- setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
305
- setError(e: unknown): void;
306
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
307
- setRefNameAliases(aliases: {
308
- [x: string]: string | undefined;
309
- }, lcAliases: {
310
- [x: string]: string | undefined;
311
- }): void;
312
- setCytobands(cytobands: Feature[]): void;
313
- setLoadingP(p?: Promise<void> | undefined): void;
314
- load(): Promise<void>;
315
- loadPre(): Promise<void>;
316
- } & {
317
- getAdapterMapEntry(adapterConf: {
318
- [x: string]: unknown;
319
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
320
- getRefNameMapForAdapter(adapterConf: {
321
- [x: string]: unknown;
322
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
323
- [x: string]: string | undefined;
324
- }>;
325
- getReverseRefNameMapForAdapter(adapterConf: {
326
- [x: string]: unknown;
327
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
328
- [x: string]: string | undefined;
329
- }>;
330
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
200
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
331
201
  }): Promise<void>;
332
- navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
202
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
333
203
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
334
204
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
335
205
  } & {
@@ -337,12 +207,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
337
207
  bpToPx({ refName, coord, regionNumber, }: {
338
208
  refName: string;
339
209
  coord: number;
340
- regionNumber?: number | undefined;
210
+ regionNumber?: number;
341
211
  }): {
342
212
  index: number;
343
213
  offsetPx: number;
344
214
  } | undefined;
345
- centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
215
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
346
216
  pxToBp(px: number): {
347
217
  coord: number;
348
218
  index: number;
@@ -352,7 +222,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
352
222
  offset: number;
353
223
  start: number;
354
224
  end: number;
355
- reversed?: boolean | undefined;
225
+ reversed?: boolean;
356
226
  };
357
227
  readonly centerLineInfo: {
358
228
  coord: number;
@@ -363,7 +233,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
363
233
  offset: number;
364
234
  start: number;
365
235
  end: number;
366
- reversed?: boolean | undefined;
236
+ reversed?: boolean;
367
237
  } | undefined;
368
238
  } & {
369
239
  afterCreate(): void;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-breakpoint-split-view",
3
- "version": "2.12.0",
3
+ "version": "2.12.2",
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": "935f2602d29abc737bb1f493a922b6218d023ae2"
61
+ "gitHead": "1ec66736ce048a1637f52b7a7ef2eb02d956b771"
62
62
  }