@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/esm/LinearReadArcsDisplay/model.d.ts

@@ -1,17 +1,8 @@
-import React from 'react';
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { IFilter } from '../shared';
-import { ChainData } from '../shared/fetchChains';
-/**
- * #stateModel LinearReadArcsDisplay
- * the arc display is a non-block-based track, so draws to a single canvas and
- * can connect multiple regions
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
+import type React from 'react';
+import type { ChainData } from '../shared/fetchChains';
+import type { ColorBy, FilterBy } from '../shared/types';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Instance } from 'mobx-state-tree';
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -24,22 +15,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearReadArcsDisplay">;
     configuration: AnyConfigurationSchemaType;
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-            tag: import("mobx-state-tree").ISimpleType<string>;
-            value: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
     lineWidth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     jitter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        type: import("mobx-state-tree").ISimpleType<string>;
-        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        extra: import("mobx-state-tree").IType<any, any, any>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
     drawInter: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawLongRange: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
@@ -131,6 +110,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
 } & {
@@ -140,83 +120,29 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     lastDrawnBpPerPx: number;
     ref: HTMLCanvasElement | null;
 } & {
-    /**
-     * #action
-     */
+    readonly colorBy: any;
+    readonly filterBy: any;
+} & {
     setLastDrawnOffsetPx(n: number): void;
-    /**
-     * #action
-     */
     setLastDrawnBpPerPx(n: number): void;
-    /**
-     * #action
-     */
     setLoading(f: boolean): void;
-    /**
-     * #action
-     */
     reload(): void;
-    /**
-     * #action
-     * internal, a reference to a HTMLCanvas because we use a autorun to draw
-     * the canvas
-     */
     setRef(ref: HTMLCanvasElement | null): void;
-    /**
-     * #action
-     */
-    setColorScheme(s: {
+    setColorScheme(colorBy: {
         type: string;
     }): void;
-    /**
-     * #action
-     */
     setChainData(args: ChainData): void;
-    /**
-     * #action
-     */
     setDrawInter(f: boolean): void;
-    /**
-     * #action
-     */
     setDrawLongRange(f: boolean): void;
-    /**
-     * #action
-     */
-    setFilterBy(filter: IFilter): void;
-    /**
-     * #action
-     * thin, bold, extrabold, etc
-     */
+    setFilterBy(filter: FilterBy): void;
     setLineWidth(n: number): void;
-    /**
-     * #action
-     * jitter val, helpful to jitter the x direction so you see better
-     * evidence when e.g. 100 long reads map to same x position
-     */
     setJitter(n: number): void;
 } & {
-    /**
-     * #getter
-     */
     readonly drawn: boolean;
-    /**
-     * #getter
-     */
     readonly lineWidthSetting: any;
-    /**
-     * #getter
-     */
     readonly jitterVal: number;
 } & {
-    /**
-     * #method
-     * only used to tell system it's ready for export
-     */
     renderProps(): any;
-    /**
-     * #method
-     */
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -259,9 +185,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         checked?: undefined;
     })[];
 } & {
-    /**
-     * #method
-     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<React.ReactNode>;

package/esm/LinearReadArcsDisplay/model.js

@@ -1,63 +1,22 @@
 import { lazy } from 'react';
-import { cast, types } from 'mobx-state-tree';
-import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
-import { getSession } from '@jbrowse/core/util';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes';
+import { getSession } from '@jbrowse/core/util';
 import { FeatureDensityMixin, TrackHeightMixin, } from '@jbrowse/plugin-linear-genome-view';
-// icons
-import PaletteIcon from '@mui/icons-material/Palette';
 import FilterListIcon from '@mui/icons-material/ClearAll';
-// locals
-import { FilterModel } from '../shared';
-// async
-const FilterByTagDialog = lazy(() => import('../shared/FilterByTagDialog'));
-/**
- * #stateModel LinearReadArcsDisplay
- * the arc display is a non-block-based track, so draws to a single canvas and
- * can connect multiple regions
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
+import PaletteIcon from '@mui/icons-material/Palette';
+import { types } from 'mobx-state-tree';
+const FilterByTagDialog = lazy(() => import('../shared/components/FilterByTagDialog'));
 function stateModelFactory(configSchema) {
     return types
         .compose('LinearReadArcsDisplay', BaseDisplay, TrackHeightMixin(), FeatureDensityMixin(), types.model({
-        /**
-         * #property
-         */
         type: types.literal('LinearReadArcsDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
-        filterBy: types.optional(FilterModel, {}),
-        /**
-         * #property
-         */
         lineWidth: types.maybe(types.number),
-        /**
-         * #property
-         */
         jitter: types.maybe(types.number),
-        /**
-         * #property
-         */
-        colorBy: types.maybe(types.model({
-            type: types.string,
-            tag: types.maybe(types.string),
-            extra: types.frozen(),
-        })),
-        /**
-         * #property
-         */
+        colorBySetting: types.frozen(),
+        filterBySetting: types.frozen(),
         drawInter: true,
-        /**
-         * #property
-         */
         drawLongRange: true,
     }))
         .volatile(() => ({
@@ -66,103 +25,67 @@ function stateModelFactory(configSchema) {
         lastDrawnOffsetPx: undefined,
         lastDrawnBpPerPx: 0,
         ref: null,
+    }))
+        .views(self => ({
+        get colorBy() {
+            var _a;
+            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : getConf(self, 'colorBy');
+        },
+        get filterBy() {
+            var _a;
+            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : getConf(self, 'filterBy');
+        },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setLastDrawnOffsetPx(n) {
             self.lastDrawnOffsetPx = n;
         },
-        /**
-         * #action
-         */
         setLastDrawnBpPerPx(n) {
             self.lastDrawnBpPerPx = n;
         },
-        /**
-         * #action
-         */
         setLoading(f) {
             self.loading = f;
         },
-        /**
-         * #action
-         */
         reload() {
             self.error = undefined;
         },
-        /**
-         * #action
-         * internal, a reference to a HTMLCanvas because we use a autorun to draw
-         * the canvas
-         */
         setRef(ref) {
             self.ref = ref;
         },
-        /**
-         * #action
-         */
-        setColorScheme(s) {
-            self.colorBy = cast(s);
+        setColorScheme(colorBy) {
+            self.colorBySetting = {
+                ...colorBy,
+            };
         },
-        /**
-         * #action
-         */
         setChainData(args) {
             self.chainData = args;
         },
-        /**
-         * #action
-         */
         setDrawInter(f) {
             self.drawInter = f;
         },
-        /**
-         * #action
-         */
         setDrawLongRange(f) {
             self.drawLongRange = f;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
-            self.filterBy = cast(filter);
+            self.filterBySetting = {
+                ...filter,
+            };
         },
-        /**
-         * #action
-         * thin, bold, extrabold, etc
-         */
         setLineWidth(n) {
             self.lineWidth = n;
         },
-        /**
-         * #action
-         * jitter val, helpful to jitter the x direction so you see better
-         * evidence when e.g. 100 long reads map to same x position
-         */
         setJitter(n) {
             self.jitter = n;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get drawn() {
             return self.lastDrawnOffsetPx !== undefined;
         },
-        /**
-         * #getter
-         */
         get lineWidthSetting() {
             var _a;
             return (_a = self.lineWidth) !== null && _a !== void 0 ? _a : getConf(self, 'lineWidth');
         },
-        /**
-         * #getter
-         */
         get jitterVal() {
             var _a;
             return (_a = self.jitter) !== null && _a !== void 0 ? _a : getConf(self, 'jitter');
@@ -171,19 +94,12 @@ function stateModelFactory(configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
-            /**
-             * #method
-             * only used to tell system it's ready for export
-             */
             renderProps() {
                 return {
                     ...superRenderProps(),
                     notReady: !self.chainData,
                 };
             },
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -300,18 +216,14 @@ function stateModelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #method
-         */
         async renderSvg(opts) {
-            const { renderSvg } = await import('../shared/renderSvg');
+            const { renderSvg } = await import('../shared/renderSvgUtil');
             const { drawFeats } = await import('./drawFeats');
             return renderSvg(self, opts, drawFeats);
         },
     }))
         .actions(self => ({
         afterAttach() {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;
             (async () => {
                 try {

package/esm/LinearReadArcsDisplay/util.d.ts

@@ -1,2 +1,2 @@
-import { ChainData } from '../shared/fetchChains';
+import type { ChainData } from '../shared/fetchChains';
 export declare function hasPairedReads(features: ChainData): boolean;

package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { LinearReadCloudDisplayModel } from '../model';
+import type { LinearReadCloudDisplayModel } from '../model';
 declare const LinearReadCloudReactComponent: ({ model, }: {
     model: LinearReadCloudDisplayModel;
 }) => React.JSX.Element;

package/esm/LinearReadCloudDisplay/components/ReactComponent.js

@@ -1,18 +1,14 @@
 import React, { useCallback } from 'react';
-import { observer } from 'mobx-react';
 import { getContainingView } from '@jbrowse/core/util';
-import BaseDisplayComponent from '../../shared/BaseDisplayComponent';
+import { observer } from 'mobx-react';
+import BaseDisplayComponent from '../../shared/components/BaseDisplayComponent';
 const Cloud = observer(function ({ model, }) {
     const view = getContainingView(model);
     const width = Math.round(view.dynamicBlocks.totalWidthPx);
     const height = model.height;
-    // biome-ignore lint/correctness/useExhaustiveDependencies:
     const cb = useCallback((ref) => {
         model.setRef(ref);
-    }, 
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-    [model, width, height]);
-    // note: the position absolute below avoids scrollbar from appearing on track
+    }, [model, width, height]);
     return (React.createElement("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
 const LinearReadCloudReactComponent = observer(function ({ model, }) {

package/esm/LinearReadCloudDisplay/configSchema.d.ts

@@ -1,31 +1,19 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearReadCloudDisplay
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     maxFeatureScreenDensity: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     featureHeight: {
         type: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
-    colorScheme: {
+    colorBy: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
+        defaultValue: {
+            type: string;
+        };
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     renderer: import("mobx-state-tree").IAnyModelType;

package/esm/LinearReadCloudDisplay/configSchema.js

@@ -1,46 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
-import { types } from 'mobx-state-tree';
-/**
- * #config LinearReadCloudDisplay
- */
 function configSchemaF(pluginManager) {
     return ConfigurationSchema('LinearReadCloudDisplay', {
-        /**
-         * #slot
-         */
         maxFeatureScreenDensity: {
             type: 'number',
             description: 'maximum features per pixel that is displayed in the view',
             defaultValue: 5,
         },
-        /**
-         * #slot
-         */
         featureHeight: {
             type: 'number',
             defaultValue: 7,
         },
-        /**
-         * #slot
-         */
-        colorScheme: {
-            type: 'stringEnum',
-            model: types.enumeration('colorScheme', [
-                'strand',
-                'normal',
-                'insertSize',
-                'insertSizeAndOrientation',
-                'mappingQuality',
-                'tag',
-            ]),
-            description: 'color scheme to use',
-            defaultValue: 'normal',
+        colorBy: {
+            type: 'frozen',
+            defaultValue: { type: 'insertSizeAndOrientation' },
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
         explicitlyTyped: true,
     });

package/esm/LinearReadCloudDisplay/drawFeats.d.ts

@@ -1,2 +1,2 @@
-import { LinearReadCloudDisplayModel } from './model';
+import type { LinearReadCloudDisplayModel } from './model';
 export declare function drawFeats(self: LinearReadCloudDisplayModel, ctx: CanvasRenderingContext2D): void;

package/esm/LinearReadCloudDisplay/drawFeats.js

@@ -1,7 +1,7 @@
 import { getContainingView, getSession } from '@jbrowse/core/util';
-import { hasPairedReads } from '../shared/util';
-import { drawPairChains } from './drawPairChains';
 import { drawLongReadChains } from './drawLongReadChains';
+import { drawPairChains } from './drawPairChains';
+import { hasPairedReads } from '../shared/util';
 export function drawFeats(self, ctx) {
     const { chainData } = self;
     if (!chainData) {

package/esm/LinearReadCloudDisplay/drawLongReadChains.d.ts

@@ -1,7 +1,7 @@
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { ChainData } from '../shared/fetchChains';
-import { LinearReadCloudDisplayModel } from './model';
+import type { LinearReadCloudDisplayModel } from './model';
+import type { ChainData } from '../shared/fetchChains';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function drawLongReadChains({ ctx, self, chainData, view, asm, }: {
     ctx: CanvasRenderingContext2D;
     self: LinearReadCloudDisplayModel;

package/esm/LinearReadCloudDisplay/drawLongReadChains.js

@@ -1,7 +1,7 @@
 import { getConf } from '@jbrowse/core/configuration';
 import { max, min } from '@jbrowse/core/util';
-import { fillColor, strokeColor } from '../shared/color';
 import { fillRectCtx, strokeRectCtx } from './util';
+import { fillColor, strokeColor } from '../shared/color';
 export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     var _a, _b, _c, _d, _e;
     const distances = [];
@@ -9,8 +9,6 @@ export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     const { chains } = chainData;
     const { height } = self;
     const featureHeight = getConf(self, 'featureHeight');
-    // get bounds on the 'distances' (pixel span that a particular split long
-    // read 'chain' would have in view)
     for (const chain of chains) {
         let minX = Number.MAX_VALUE;
         let maxX = Number.MIN_VALUE;
@@ -31,7 +29,6 @@ export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     const minD = Math.max(Math.log(min(distances)) - 1, 0);
     const scaler = (height - 20) / (maxD - minD);
     const halfHeight = featureHeight / 2 - 0.5;
-    // draw split long read 'chains' as connected entities
     for (let i = 0; i < chains.length; i++) {
         const chain = chains[i];
         const w = distances[i];

package/esm/LinearReadCloudDisplay/drawPairChains.d.ts

@@ -1,7 +1,7 @@
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
-import { LinearReadCloudDisplayModel } from './model';
+import type { LinearReadCloudDisplayModel } from './model';
+import type { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function drawPairChains({ ctx, self, chainData, view, asm, }: {
     ctx: CanvasRenderingContext2D;
     self: LinearReadCloudDisplayModel;

package/esm/LinearReadCloudDisplay/drawPairChains.js

@@ -9,9 +9,6 @@ export function drawPairChains({ ctx, self, chainData, view, asm, }) {
     const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
     const { chains, stats } = chainData;
     for (const chain of chains) {
-        // if we're looking at a paired read (flag 1) then assume it is just
-        // two reads (some small cases may defy this assumption such as
-        // secondary alignments but this may be uncommon)
         if (chain.length > 1) {
             const v0 = chain[0];
             const v1 = chain[1];

package/esm/LinearReadCloudDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function register(pluginManager: PluginManager): void;

package/esm/LinearReadCloudDisplay/index.js

@@ -1,8 +1,7 @@
+import { lazy } from 'react';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-// locals
 import configSchemaF from './configSchema';
 import stateModelF from './model';
-import { lazy } from 'react';
 export default function register(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);