@jbrowse/plugin-linear-comparative-view 2.6.1 → 2.6.3

package/esm/LinearComparativeView/model.d.ts

@@ -32,19 +32,18 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>; /**
-             * #getter
-             */
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
+            /**
+             * #property
+             */
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
         hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>; /**
-         * #getter
-         */
+        hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -72,9 +71,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
-        rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined; /**
-         * #action
-         */
+        rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
     } & {
         readonly width: number;
         readonly interRegionPaddingWidth: number;
@@ -89,9 +86,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         readonly scaleBarHeight: number;
         readonly headerHeight: number;
         readonly trackHeights: number;
-        /**
-         * #action
-         */
         readonly trackHeightsWithResizeHandles: number;
         readonly height: number;
         readonly totalBp: number;
@@ -120,12 +114,12 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         toggleNoTracksActive(): void;
         toggleShowGridlines(): void;
         scrollTo(offsetPx: number): number;
-        zoomTo(bpPerPx: number, offset?: number | undefined, centerAtOffset?: boolean | undefined): number;
+        zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
-        showTrack(trackId: string, initialSnapshot?: {} | undefined, displayInitialSnapshot?: {} | undefined): any;
+        showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
         hideTrack(trackId: string): number;
     } & {
         moveTrack(movingId: string, targetId: string): void;
@@ -156,7 +150,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setDraggingTrackId(idx?: string | undefined): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions | undefined): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {

package/esm/LinearComparativeView/model.js

@@ -315,4 +315,3 @@ function stateModelFactory(pluginManager) {
     }));
 }
 export default stateModelFactory;
-//# sourceMappingURL=model.js.map

package/esm/LinearReadVsRef/LinearReadVsRef.js

@@ -255,4 +255,3 @@ export default function ReadVsRefDialog({ track, feature: preFeature, handleClos
             React.createElement(Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel"),
             React.createElement(Button, { disabled: !primaryFeature, variant: "contained", color: "primary", onClick: onSubmit }, "Submit"))));
 }
-//# sourceMappingURL=LinearReadVsRef.js.map

package/esm/LinearReadVsRef/index.js

@@ -46,4 +46,3 @@ export default function (pm) {
         return pluggableElement;
     });
 }
-//# sourceMappingURL=index.js.map

package/esm/LinearSyntenyDisplay/afterAttach.js

@@ -101,4 +101,3 @@ export function doAfterAttach(self) {
         self.setFeatPositions(map);
     }, { fireImmediately: true }));
 }
-//# sourceMappingURL=afterAttach.js.map

package/esm/LinearSyntenyDisplay/components/Component.js

@@ -56,4 +56,3 @@ const ServerSideRenderedBlockContent = observer(function ({ model, }) {
     return React.createElement(LinearSyntenyRendering, { model: model });
 });
 export default ServerSideRenderedBlockContent;
-//# sourceMappingURL=Component.js.map

package/esm/LinearSyntenyDisplay/components/LinearSyntenyRendering.js

@@ -129,4 +129,3 @@ export default observer(function LinearSyntenyRendering({ model, }) {
             }, width: width, height: height }),
         model.mouseoverId && tooltip && currX && currY ? (React.createElement(SyntenyTooltip, { x: currX, y: currY, title: tooltip })) : null));
 });
-//# sourceMappingURL=LinearSyntenyRendering.js.map

package/esm/LinearSyntenyDisplay/components/SyntenyTooltip.js

@@ -55,4 +55,3 @@ const SyntenyTooltip = observer(function ({ x, y, title, }) {
             React.createElement(SanitizedHTML, { html: title })))) : null;
 });
 export default SyntenyTooltip;
-//# sourceMappingURL=SyntenyTooltip.js.map

package/esm/LinearSyntenyDisplay/components/util.js

@@ -74,4 +74,3 @@ export function drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid) {
     ctx.closePath();
     ctx.fill();
 }
-//# sourceMappingURL=util.js.map

package/esm/LinearSyntenyDisplay/configSchemaF.js

@@ -28,4 +28,3 @@ function configSchemaFactory(pluginManager) {
     });
 }
 export default configSchemaFactory;
-//# sourceMappingURL=configSchemaF.js.map

package/esm/LinearSyntenyDisplay/drawSynteny.js

@@ -226,4 +226,3 @@ export function drawMouseoverSynteny(model) {
         });
     }
 }
-//# sourceMappingURL=drawSynteny.js.map

package/esm/LinearSyntenyDisplay/index.js

@@ -16,4 +16,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/LinearSyntenyDisplay/model.js

@@ -148,4 +148,3 @@ function stateModelFactory(configSchema) {
     }));
 }
 export default stateModelFactory;
-//# sourceMappingURL=model.js.map

package/esm/LinearSyntenyView/components/ExportSvgDialog.js

@@ -57,4 +57,3 @@ export default function ExportSvgDlg({ model, handleClose, }) {
                     }
                 } }, "Submit"))));
 }
-//# sourceMappingURL=ExportSvgDialog.js.map

package/esm/LinearSyntenyView/components/Icons.js

@@ -8,4 +8,3 @@ export function StraightLines(props) {
     return (React.createElement(SvgIcon, { ...props },
         React.createElement("path", { fill: "currentColor", d: "M22 12L17 22L7.1 6.04L4.24 12H2L7 2L16.9 17.96L19.76 12H22Z" })));
 }
-//# sourceMappingURL=Icons.js.map

package/esm/LinearSyntenyView/components/ImportCustomTrack.js

@@ -149,4 +149,3 @@ const OpenTrack = observer(({ sessionTrackData, assembly1, assembly2, setSession
                         React.createElement(FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => setBed2Location(loc) }))))) : (React.createElement(FileSelector, { name: value ? value + ' location' : '', description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) }))))));
 });
 export default OpenTrack;
-//# sourceMappingURL=ImportCustomTrack.js.map

package/esm/LinearSyntenyView/components/ImportForm.js

@@ -96,4 +96,3 @@ export default observer(function ({ model, }) {
                                 React.createElement(Button, { onClick: onOpenClick, variant: "contained", color: "primary" }, "Launch"))))),
                 React.createElement(TrackSelector, { setShowTrackId: setShowTrackId, assembly2: assembly2, assembly1: assembly1, setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, model: model })))));
 });
-//# sourceMappingURL=ImportForm.js.map

package/esm/LinearSyntenyView/components/ImportSyntenyTrackSelector.js

@@ -35,4 +35,3 @@ const Selector = observer(({ model, assembly1, assembly2, setShowTrackId, }) =>
         filteredTracks.length ? (React.createElement(Select, { value: value, onChange: event => setValue(event.target.value) }, filteredTracks.map(track => (React.createElement(MenuItem, { key: track.trackId, value: track.trackId }, getTrackName(track, session)))))) : (React.createElement(ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
 });
 export default Selector;
-//# sourceMappingURL=ImportSyntenyTrackSelector.js.map

package/esm/LinearSyntenyView/components/LinearSyntenyView.js

@@ -7,4 +7,3 @@ const LinearSyntenyView = observer(({ model }) => {
     return !model.initialized ? (React.createElement(ImportForm, { model: model })) : (React.createElement(LinearComparativeViewComponent, { model: model }));
 });
 export default LinearSyntenyView;
-//# sourceMappingURL=LinearSyntenyView.js.map

package/esm/LinearSyntenyView/index.js

@@ -11,4 +11,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/LinearSyntenyView/model.d.ts

@@ -125,12 +125,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         toggleNoTracksActive(): void;
         toggleShowGridlines(): void;
         scrollTo(offsetPx: number): number;
-        zoomTo(bpPerPx: number, offset?: number | undefined, centerAtOffset?: boolean | undefined): number;
+        zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
-        showTrack(trackId: string, initialSnapshot?: {} | undefined, displayInitialSnapshot?: {} | undefined): any;
+        showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
         hideTrack(trackId: string): number;
     } & {
         moveTrack(movingId: string, targetId: string): void;
@@ -161,7 +161,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setDraggingTrackId(idx?: string | undefined): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions | undefined): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {
@@ -375,12 +375,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         toggleNoTracksActive(): void;
         toggleShowGridlines(): void;
         scrollTo(offsetPx: number): number;
-        zoomTo(bpPerPx: number, offset?: number | undefined, centerAtOffset?: boolean | undefined): number;
+        zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
-        showTrack(trackId: string, initialSnapshot?: {} | undefined, displayInitialSnapshot?: {} | undefined): any;
+        showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
         hideTrack(trackId: string): number;
     } & {
         moveTrack(movingId: string, targetId: string): void;
@@ -411,7 +411,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setDraggingTrackId(idx?: string | undefined): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions | undefined): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {
@@ -563,12 +563,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         toggleNoTracksActive(): void;
         toggleShowGridlines(): void;
         scrollTo(offsetPx: number): number;
-        zoomTo(bpPerPx: number, offset?: number | undefined, centerAtOffset?: boolean | undefined): number;
+        zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
-        showTrack(trackId: string, initialSnapshot?: {} | undefined, displayInitialSnapshot?: {} | undefined): any;
+        showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
         hideTrack(trackId: string): number;
     } & {
         moveTrack(movingId: string, targetId: string): void;
@@ -599,7 +599,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setDraggingTrackId(idx?: string | undefined): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions | undefined): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {

package/esm/LinearSyntenyView/model.js

@@ -138,4 +138,3 @@ export default function stateModelFactory(pluginManager) {
         };
     });
 }
-//# sourceMappingURL=model.js.map

package/esm/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
+import Color from 'color';
 export default function SVGBackground({ width, height, shift, }) {
     const theme = useTheme();
-    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: Color(theme.palette.background.default).hex() }));
 }
-//# sourceMappingURL=SVGBackground.js.map

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -75,4 +75,3 @@ export async function renderToSvg(model, opts) {
                         React.createElement(SVGRuler, { model: displayResults[1].view, fontSize: fontSize })),
                     React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, offset: offset, trackLabelOffset: trackLabelOffset }))))));
 }
-//# sourceMappingURL=SVGLinearSyntenyView.js.map

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -35,4 +35,3 @@ const BreakpointAlignmentsFeatureDetail = observer(
         React.createElement(CustomFeatureDetails, { feature: feature2 })));
 });
 export default BreakpointAlignmentsFeatureDetail;
-//# sourceMappingURL=SyntenyFeatureDetail.js.map

package/esm/SyntenyFeatureDetail/index.js

@@ -27,4 +27,3 @@ export default (pluginManager) => {
         ReactComponent: lazy(() => import('./SyntenyFeatureDetail')),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/SyntenyTrack/configSchema.js

@@ -11,4 +11,3 @@ const configSchema = (pluginManager) => ConfigurationSchema('SyntenyTrack', {},
     baseConfiguration: createBaseTrackConfig(pluginManager),
 });
 export default configSchema;
-//# sourceMappingURL=configSchema.js.map

package/esm/SyntenyTrack/index.js

@@ -11,4 +11,3 @@ export default (pm) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/index.js

@@ -38,4 +38,3 @@ export default class extends Plugin {
         }
     }
 }
-//# sourceMappingURL=index.js.map

package/esm/util.js

@@ -66,4 +66,3 @@ function bpToPx(view, { refName, coord }) {
 export function interstitialYPos(cond, height) {
     return cond ? 0 : height;
 }
-//# sourceMappingURL=util.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,13 +32,14 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@mui/icons-material": "^5.0.1",
     "@popperjs/core": "^2.0.0",
     "clone": "^2.1.2",
+    "color": "^3.1.3",
     "copy-to-clipboard": "^3.3.1",
     "file-saver": "^2.0.0",
     "react-popper": "^2.0.0"
@@ -63,5 +63,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }

package/dist/LGVSyntenyDisplay/configSchemaF.js.map

@@ -1 +0,0 @@
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package/dist/LGVSyntenyDisplay/index.js.map

@@ -1 +0,0 @@
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package/dist/LGVSyntenyDisplay/model.js.map

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package/dist/LaunchLinearSyntenyView.js.map

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package/dist/LinearComparativeDisplay/stateModelFactory.js.map

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package/dist/LinearComparativeView/components/Header.js.map

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package/dist/LinearComparativeView/components/LinearComparativeView.js.map

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package/dist/LinearComparativeView/components/Rubberband.js.map

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package/dist/LinearComparativeView/index.js.map

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package/dist/LinearComparativeView/model.js.map

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package/dist/LinearReadVsRef/LinearReadVsRef.js.map

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package/dist/LinearReadVsRef/index.js.map

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package/dist/LinearSyntenyDisplay/afterAttach.js.map

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package/dist/LinearSyntenyDisplay/components/SyntenyTooltip.js.map

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package/dist/LinearSyntenyDisplay/components/util.js.map

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