@jbrowse/plugin-breakpoint-split-view 2.10.1 → 2.10.3

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Files changed (9) hide show
  1. package/dist/BreakpointSplitView/components/ExportSvgDialog.d.ts +1 -1
  2. package/dist/BreakpointSplitView/components/ExportSvgDialog.js +2 -2
  3. package/dist/BreakpointSplitView/components/Translocations.js +16 -3
  4. package/dist/BreakpointSplitView/model.d.ts +15 -8
  5. package/esm/BreakpointSplitView/components/ExportSvgDialog.d.ts +1 -1
  6. package/esm/BreakpointSplitView/components/ExportSvgDialog.js +1 -1
  7. package/esm/BreakpointSplitView/components/Translocations.js +16 -3
  8. package/esm/BreakpointSplitView/model.d.ts +15 -8
  9. package/package.json +2 -2
package/dist/BreakpointSplitView/components/ExportSvgDialog.d.ts CHANGED
@@ -1,6 +1,6 @@
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  import React from 'react';
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  import { ExportSvgOptions } from '../model';
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- export default function ExportSvgDlg({ model, handleClose, }: {
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+ export default function ExportSvgDialog({ model, handleClose, }: {
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  model: {
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  exportSvg(opts: ExportSvgOptions): Promise<void>;
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  };
package/dist/BreakpointSplitView/components/ExportSvgDialog.js CHANGED
@@ -35,7 +35,7 @@ function LoadingMessage() {
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  function useSvgLocal(key, val) {
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  return (0, util_1.useLocalStorage)('svg-' + key, val);
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  }
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- function ExportSvgDlg({ model, handleClose, }) {
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+ function ExportSvgDialog({ model, handleClose, }) {
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  const session = (0, util_1.getSession)(model);
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  const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
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  const [rasterizeLayers, setRasterizeLayers] = (0, react_1.useState)(offscreenCanvas);
@@ -80,4 +80,4 @@ function ExportSvgDlg({ model, handleClose, }) {
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  }
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  } }, "Submit"))));
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  }
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- exports.default = ExportSvgDlg;
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+ exports.default = ExportSvgDialog;
package/dist/BreakpointSplitView/components/Translocations.js CHANGED
@@ -31,6 +31,17 @@ const mobx_state_tree_1 = require("mobx-state-tree");
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  const util_2 = require("./util");
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  const util_3 = require("../util");
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  const [LEFT] = [0, 1, 2, 3];
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+ function str(s) {
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+ if (s === '+') {
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+ return 1;
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+ }
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+ else if (s === '-') {
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+ return -1;
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+ }
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+ else {
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+ return 0;
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+ }
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+ }
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  const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, parentRef: ref, getTrackYPosOverride, }) {
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  const { views } = model;
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  const session = (0, util_1.getSession)(model);
@@ -57,6 +68,7 @@ const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, pa
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  return null;
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  }
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  return (react_1.default.createElement("g", { fill: "none", stroke: "green", strokeWidth: 5, "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
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+ var _a, _b;
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  // we follow a path in the list of chunks, not from top to bottom,
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  // just in series following x1,y1 -> x2,y2
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  const ret = [];
@@ -69,7 +81,8 @@ const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, pa
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  const info = f1.get('INFO');
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  const chr2 = info.CHR2[0];
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  const end2 = info.END[0];
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- const [myDirection, mateDirection] = info.STRANDS[0].split('');
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+ const res = (_b = (_a = info.STRANDS) === null || _a === void 0 ? void 0 : _a[0]) === null || _b === void 0 ? void 0 : _b.split(''); // not all files have STRANDS
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+ const [myDirection, mateDirection] = res !== null && res !== void 0 ? res : ['.', '.'];
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  const r = (0, util_3.getPxFromCoordinate)(views[level2], chr2, end2);
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  if (r) {
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  const c2 = [r, 0, r + 1, 0];
@@ -84,7 +97,7 @@ const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, pa
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  yOffset;
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  const path = [
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  'M', // move to
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- x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1),
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+ x1 - 20 * str(myDirection) * (reversed1 ? -1 : 1),
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  y1,
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  'L', // line to
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  x1,
@@ -93,7 +106,7 @@ const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, pa
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  x2,
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  y2,
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  'L', // line to
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- x2 - 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1),
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+ x2 - 20 * str(mateDirection) * (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: () => {
package/dist/BreakpointSplitView/model.d.ts CHANGED
@@ -70,6 +70,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ highlight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
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  }, {
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  width: number;
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  } & {
@@ -81,16 +82,21 @@ 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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+ /**
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+ * #action
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+ */
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  draggingTrackId: string | undefined;
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  volatileError: unknown;
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  afterDisplayedRegionsSetCallbacks: Function[];
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- scaleFactor: number;
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+ scaleFactor: number; /**
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+ * #action
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+ */
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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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+ coarseTotalBp: number; /**
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  * #action
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  */
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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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  } & {
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  readonly trackLabelsSetting: any;
@@ -130,10 +136,11 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  setShowCytobands(flag: boolean): void;
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  setWidth(newWidth: number): void;
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  setError(error: unknown): void;
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- toggleHeader(): void;
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- toggleHeaderOverview(): void;
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- toggleNoTracksActive(): void;
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- toggleShowGridlines(): void;
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+ setHideHeader(b: boolean): void;
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+ setHideHeaderOverview(b: boolean): void;
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+ setHideNoTracksActive(b: boolean): void;
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+ setShowGridlines(b: boolean): void;
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+ setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): 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;
@@ -147,7 +154,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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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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- toggleCenterLine(): 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): {
package/esm/BreakpointSplitView/components/ExportSvgDialog.d.ts CHANGED
@@ -1,6 +1,6 @@
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  import React from 'react';
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  import { ExportSvgOptions } from '../model';
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- export default function ExportSvgDlg({ model, handleClose, }: {
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+ export default function ExportSvgDialog({ model, handleClose, }: {
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  model: {
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  exportSvg(opts: ExportSvgOptions): Promise<void>;
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  };
package/esm/BreakpointSplitView/components/ExportSvgDialog.js CHANGED
@@ -10,7 +10,7 @@ function LoadingMessage() {
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  function useSvgLocal(key, val) {
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  return useLocalStorage('svg-' + key, val);
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  }
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- export default function ExportSvgDlg({ model, handleClose, }) {
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+ export default function ExportSvgDialog({ model, handleClose, }) {
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  const session = getSession(model);
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  const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
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  const [rasterizeLayers, setRasterizeLayers] = useState(offscreenCanvas);
package/esm/BreakpointSplitView/components/Translocations.js CHANGED
@@ -6,6 +6,17 @@ import { getSnapshot } from 'mobx-state-tree';
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  import { getMatchedTranslocationFeatures } from './util';
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  import { yPos, getPxFromCoordinate, useNextFrame } from '../util';
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  const [LEFT] = [0, 1, 2, 3];
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+ function str(s) {
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+ if (s === '+') {
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+ return 1;
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+ }
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+ else if (s === '-') {
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+ return -1;
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+ }
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+ else {
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+ return 0;
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+ }
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+ }
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  const Translocations = observer(function ({ model, trackId, parentRef: ref, getTrackYPosOverride, }) {
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  const { views } = model;
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  const session = getSession(model);
@@ -32,6 +43,7 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
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  return null;
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  }
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  return (React.createElement("g", { fill: "none", stroke: "green", strokeWidth: 5, "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
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+ var _a, _b;
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  // we follow a path in the list of chunks, not from top to bottom,
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  // just in series following x1,y1 -> x2,y2
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  const ret = [];
@@ -44,7 +56,8 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
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  const info = f1.get('INFO');
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  const chr2 = info.CHR2[0];
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  const end2 = info.END[0];
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- const [myDirection, mateDirection] = info.STRANDS[0].split('');
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+ const res = (_b = (_a = info.STRANDS) === null || _a === void 0 ? void 0 : _a[0]) === null || _b === void 0 ? void 0 : _b.split(''); // not all files have STRANDS
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+ const [myDirection, mateDirection] = res !== null && res !== void 0 ? res : ['.', '.'];
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  const r = getPxFromCoordinate(views[level2], chr2, end2);
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  if (r) {
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  const c2 = [r, 0, r + 1, 0];
@@ -59,7 +72,7 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
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  yOffset;
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  const path = [
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  'M', // move to
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- x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1),
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+ x1 - 20 * str(myDirection) * (reversed1 ? -1 : 1),
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  y1,
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  'L', // line to
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  x1,
@@ -68,7 +81,7 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
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  x2,
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  y2,
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  'L', // line to
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- x2 - 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1),
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+ x2 - 20 * str(mateDirection) * (reversed2 ? -1 : 1),
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  y2,
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  ].join(' ');
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  ret.push(React.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
package/esm/BreakpointSplitView/model.d.ts CHANGED
@@ -70,6 +70,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ highlight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
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  }, {
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  width: number;
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  } & {
@@ -81,16 +82,21 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
81
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  } & {
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  volatileWidth: number | undefined;
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  minimumBlockWidth: number;
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+ /**
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+ * #action
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+ */
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  draggingTrackId: string | undefined;
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  volatileError: unknown;
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  afterDisplayedRegionsSetCallbacks: Function[];
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- scaleFactor: number;
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+ scaleFactor: number; /**
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+ * #action
93
+ */
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  trackRefs: Record<string, HTMLDivElement>;
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  coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
90
- coarseTotalBp: number;
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- leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined; /**
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+ coarseTotalBp: number; /**
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  * #action
93
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  */
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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;
95
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  } & {
96
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  readonly trackLabelsSetting: any;
@@ -130,10 +136,11 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
130
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  setShowCytobands(flag: boolean): void;
131
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  setWidth(newWidth: number): void;
132
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  setError(error: unknown): void;
133
- toggleHeader(): void;
134
- toggleHeaderOverview(): void;
135
- toggleNoTracksActive(): void;
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- toggleShowGridlines(): void;
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+ setHideHeader(b: boolean): void;
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+ setHideHeaderOverview(b: boolean): void;
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+ setHideNoTracksActive(b: boolean): void;
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+ setShowGridlines(b: boolean): void;
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+ setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): 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;
@@ -147,7 +154,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  closeView(): void;
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  toggleTrack(trackId: string): boolean;
149
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  setTrackLabels(setting: "hidden" | "offset" | "overlapping"): void;
150
- toggleCenterLine(): void;
157
+ setShowCenterLine(b: boolean): void;
151
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  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
152
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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): {
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-breakpoint-split-view",
3
- "version": "2.10.1",
3
+ "version": "2.10.3",
4
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  "description": "JBrowse 2 breakpoint detail split view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -58,5 +58,5 @@
58
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  "publishConfig": {
59
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  "access": "public"
60
60
  },
61
- "gitHead": "442b5f87efddfdf4ccf520b4d9dd01ddd370cb07"
61
+ "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
62
62
  }