@jbrowse/plugin-linear-genome-view 2.11.2 → 2.12.1

package/dist/LinearGenomeView/model.d.ts

@@ -62,16 +62,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     type: import("mobx-state-tree").IType<string | undefined, string, string>;
     offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
     bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-    displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        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]>;
-    } & {
-        assemblyName: import("mobx-state-tree").ISimpleType<string>;
-    }, {
-        setRefName(newRefName: string): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Region[], Region[], Region[]>, [undefined]>;
     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>;
@@ -94,15 +85,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     volatileWidth: number | undefined;
     minimumBlockWidth: number;
-    draggingTrackId: string | undefined;
+    draggingTrackId: undefined | string;
     volatileError: unknown;
     afterDisplayedRegionsSetCallbacks: Function[];
     scaleFactor: number;
     trackRefs: Record<string, HTMLDivElement>;
     coarseDynamicBlocks: BaseBlock[];
     coarseTotalBp: number;
-    leftOffset: BpOffset | undefined;
-    rightOffset: BpOffset | undefined;
+    leftOffset: undefined | BpOffset;
+    rightOffset: undefined | BpOffset;
 } & {
     /**
      * #getter
@@ -336,7 +327,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
+    setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
     /**
      * #action
      */
@@ -365,15 +356,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         start: number;
         end: number;
         type: string;
-        regionNumber?: number | undefined;
-        reversed?: boolean | undefined;
+        regionNumber?: number;
+        reversed?: boolean;
         refName: string;
         assemblyName: string;
         key: string;
         offsetPx: number;
         widthPx: number;
-        variant?: string | undefined;
-        isLeftEndOfDisplayedRegion?: boolean | undefined;
+        variant?: string;
+        isLeftEndOfDisplayedRegion?: boolean;
     }[];
     /**
      * #action
@@ -585,7 +576,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         offset: number;
         start: number;
         end: number;
-        reversed: boolean;
+        reversed?: boolean;
     };
     /**
      * #getter
@@ -599,7 +590,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         offset: number;
         start: number;
         end: number;
-        reversed: boolean;
+        reversed?: boolean;
     } | undefined;
 } & {
     afterCreate(): void;
@@ -612,16 +603,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     type: import("mobx-state-tree").IType<string | undefined, string, string>;
     offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
     bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-    displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        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]>;
-    } & {
-        assemblyName: import("mobx-state-tree").ISimpleType<string>;
-    }, {
-        setRefName(newRefName: string): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Region[], Region[], Region[]>, [undefined]>;
     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>;

package/dist/LinearGenomeView/model.js

@@ -26,7 +26,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderToSvg = exports.ZoomControls = exports.SearchBox = exports.RefNameAutocomplete = exports.LinearGenomeView = exports.ReactComponent = exports.stateModelFactory = exports.WIDGET_HEIGHT = exports.SPACING = exports.INTER_REGION_PADDING_WIDTH = exports.RESIZE_HANDLE_HEIGHT = exports.SCALE_BAR_HEIGHT = exports.HEADER_OVERVIEW_HEIGHT = exports.HEADER_BAR_HEIGHT = void 0;
+exports.renderToSvg = exports.ZoomControls = exports.SearchBox = exports.RefNameAutocomplete = exports.LinearGenomeView = exports.ReactComponent = exports.WIDGET_HEIGHT = exports.SPACING = exports.INTER_REGION_PADDING_WIDTH = exports.RESIZE_HANDLE_HEIGHT = exports.SCALE_BAR_HEIGHT = exports.HEADER_OVERVIEW_HEIGHT = exports.HEADER_BAR_HEIGHT = void 0;
+exports.stateModelFactory = stateModelFactory;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
@@ -120,7 +121,7 @@ function stateModelFactory(pluginManager) {
          * advised to use the entire set of chromosomes if your assembly is very
          * fragmented
          */
-        displayedRegions: mobx_state_tree_1.types.array(mst_1.Region),
+        displayedRegions: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), []),
         /**
          * #property
          * array of currently displayed tracks state models instances
@@ -317,7 +318,7 @@ function stateModelFactory(pluginManager) {
          * #getter
          */
         get totalBp() {
-            return self.displayedRegions.reduce((a, b) => a + b.end - b.start, 0);
+            return (0, util_1.sum)(self.displayedRegions.map(r => r.end - r.start));
         },
         /**
          * #getter
@@ -1418,7 +1419,6 @@ function stateModelFactory(pluginManager) {
         };
     });
 }
-exports.stateModelFactory = stateModelFactory;
 var LinearGenomeView_1 = require("./components/LinearGenomeView");
 Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_1).default; } });
 Object.defineProperty(exports, "LinearGenomeView", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_1).default; } });

package/dist/LinearGenomeView/svgcomponents/SVGBackground.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SVGBackground;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
@@ -10,4 +11,3 @@ function SVGBackground({ width, height, shift, }) {
     const theme = (0, material_1.useTheme)();
     return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
 }
-exports.default = SVGBackground;

package/dist/LinearGenomeView/svgcomponents/SVGHeader.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SVGHeader;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
@@ -55,4 +56,3 @@ function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
         react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight + y})` },
             react_1.default.createElement(SVGRuler_1.default, { model: model, fontSize: fontSize }))));
 }
-exports.default = SVGHeader;

package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js

@@ -3,7 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SVGTracks = exports.SVGRuler = exports.renderToSvg = void 0;
+exports.SVGTracks = exports.SVGRuler = void 0;
+exports.renderToSvg = renderToSvg;
 /* eslint-disable react-refresh/only-export-components */
 const react_1 = __importDefault(require("react"));
 const mobx_1 = require("mobx");
@@ -48,7 +49,6 @@ async function renderToSvg(model, opts) {
                         react_1.default.createElement(SVGHeader_1.default, { model: model, fontSize: fontSize, rulerHeight: rulerHeight, cytobandHeight: cytobandHeight })),
                     react_1.default.createElement(SVGTracks_1.default, { textHeight: textHeight, fontSize: fontSize, model: model, displayResults: displayResults, offset: offset, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset }))))), createRootFn);
 }
-exports.renderToSvg = renderToSvg;
 var SVGRuler_1 = require("./SVGRuler");
 Object.defineProperty(exports, "SVGRuler", { enumerable: true, get: function () { return __importDefault(SVGRuler_1).default; } });
 var SVGTracks_2 = require("./SVGTracks");

package/dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.js

@@ -3,10 +3,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SVGRegionSeparators;
 const react_1 = __importDefault(require("react"));
 // SVG component, region separator
 function SVGRegionSeparators({ model, height, }) {
     const { dynamicBlocks, offsetPx, interRegionPaddingWidth } = model;
     return (react_1.default.createElement(react_1.default.Fragment, null, dynamicBlocks.contentBlocks.slice(1).map(block => (react_1.default.createElement("rect", { key: block.key, x: block.offsetPx - offsetPx - interRegionPaddingWidth, width: interRegionPaddingWidth, y: 0, height: height, fill: "grey" })))));
 }
-exports.default = SVGRegionSeparators;

package/dist/LinearGenomeView/svgcomponents/SVGRuler.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SVGRuler;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
@@ -49,4 +50,3 @@ function SVGRuler({ model, fontSize, }) {
                             react_1.default.createElement(Ruler, { hideText: !renderRuler, start: start, end: end, bpPerPx: bpPerPx, reversed: reversed }))))));
         })));
 }
-exports.default = SVGRuler;

package/dist/LinearGenomeView/svgcomponents/SVGScalebar.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SVGScalebar;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
@@ -21,4 +22,3 @@ function SVGScalebar({ model, fontSize, }) {
         react_1.default.createElement("line", { x1: x1, x2: x1, y1: 5, y2: 15, stroke: c }),
         react_1.default.createElement("text", { x: x, y: y, textAnchor: "middle", dominantBaseline: "hanging", fontSize: fontSize, fill: c }, displayBp)));
 }
-exports.default = SVGScalebar;

package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SVGTrackLabel;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
@@ -14,4 +15,3 @@ function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x,
     const name = (0, util_1.coarseStripHTML)(trackName);
     return trackLabels !== 'none' ? (react_1.default.createElement("g", null, trackLabels === 'left' ? (react_1.default.createElement("text", { x: trackLabelOffset - 40, y: 20, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", textAnchor: "end" }, name)) : (react_1.default.createElement("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging" }, name)))) : null;
 }
-exports.default = SVGTrackLabel;

package/dist/LinearGenomeView/svgcomponents/SVGTracks.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SVGTracks;
 const react_1 = __importDefault(require("react"));
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const util_1 = require("@jbrowse/core/util");
@@ -26,4 +27,3 @@ function SVGTracks({ displayResults, model, offset, textHeight, fontSize, trackL
             react_1.default.createElement(SVGTrackLabel_1.default, { trackName: trackName, fontSize: fontSize, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset, x: x })));
     })));
 }
-exports.default = SVGTracks;

package/dist/LinearGenomeView/svgcomponents/util.js

@@ -1,9 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.totalHeight = void 0;
+exports.totalHeight = totalHeight;
 const util_1 = require("@jbrowse/core/util");
 function totalHeight(tracks, textHeight, trackLabels) {
     return (0, util_1.sum)(tracks.map(t => t.displays[0].height +
         (['none', 'left'].includes(trackLabels) ? 0 : textHeight)));
 }
-exports.totalHeight = totalHeight;

package/dist/LinearGenomeView/util.d.ts

@@ -23,9 +23,9 @@ export declare function makeTicks(start: number, end: number, bpPerPx: number, e
 export declare function generateLocations(regions: ParsedLocString[] | undefined, assemblyManager: AssemblyManager, assemblyName?: string): Promise<{
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
-    end?: number | undefined;
-    start?: number | undefined;
-    reversed?: boolean | undefined;
+    end?: number;
+    start?: number;
+    reversed?: boolean;
     refName: string;
 }[]>;
 /**

package/dist/LinearGenomeView/util.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseLocStrings = exports.generateLocations = exports.makeTicks = exports.chooseGridPitch = void 0;
+exports.chooseGridPitch = chooseGridPitch;
+exports.makeTicks = makeTicks;
+exports.generateLocations = generateLocations;
+exports.parseLocStrings = parseLocStrings;
 const util_1 = require("@jbrowse/core/util");
 /**
  * Given a scale ( bp/px ) and minimum distances (px) between major and minor
@@ -33,7 +36,6 @@ function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     }
     return { majorPitch, minorPitch };
 }
-exports.chooseGridPitch = chooseGridPitch;
 function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
     const gridPitch = chooseGridPitch(bpPerPx, 60, 15);
     let minBase = start;
@@ -64,7 +66,6 @@ function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
     }
     return ticks;
 }
-exports.makeTicks = makeTicks;
 /**
  * Generate location objects for a set of parsed locstrings, which includes
  * translating the refNames to assembly-canonical refNames and adding the
@@ -102,7 +103,6 @@ async function generateLocations(regions = [], assemblyManager, assemblyName) {
         };
     }));
 }
-exports.generateLocations = generateLocations;
 /**
  * Parses locString or space separated set of locStrings into location objects
  * Example inputs:
@@ -141,4 +141,3 @@ function parseLocStrings(input, assemblyName, isValidRefName) {
         }
     }
 }
-exports.parseLocStrings = parseLocStrings;