@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/esm/LinearReadArcsDisplay/configSchema.d.ts

@@ -1,40 +1,32 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearReadArcsDisplay
- */
+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
-     */
     lineWidth: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     jitter: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
-    colorScheme: {
+    colorBy: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
+        defaultValue: {
+            type: string;
+        };
+    };
+    filterBy: {
+        type: string;
+        defaultValue: {
+            flagInclude: number;
+            flagExclude: number;
+        };
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     renderer: import("mobx-state-tree").IAnyModelType;

package/esm/LinearReadArcsDisplay/configSchema.js

@@ -1,55 +1,32 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
-import { types } from 'mobx-state-tree';
-/**
- * #config LinearReadArcsDisplay
- */
+import { defaultFilterFlags } from '../shared/util';
 function configSchemaF(pluginManager) {
     return ConfigurationSchema('LinearReadArcsDisplay', {
-        /**
-         * #slot
-         */
         maxFeatureScreenDensity: {
             type: 'number',
             description: 'maximum features per pixel that is displayed in the view',
             defaultValue: 5,
         },
-        /**
-         * #slot
-         */
         lineWidth: {
             type: 'number',
             description: 'set arc line width',
             defaultValue: 1,
         },
-        /**
-         * #slot
-         */
         jitter: {
             type: 'number',
             description: 'jitters the x position so e.g. if many reads map to exact same x position, jittering makes it easy to see that there are many of them',
             defaultValue: 0,
         },
-        /**
-         * #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' },
+        },
+        filterBy: {
+            type: 'frozen',
+            defaultValue: defaultFilterFlags,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
         explicitlyTyped: true,
     });

package/esm/LinearReadArcsDisplay/drawFeats.d.ts

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

package/esm/LinearReadArcsDisplay/drawFeats.js

@@ -1,13 +1,11 @@
 import { getContainingView, getSession } from '@jbrowse/core/util';
-// locals
-import { getPairedOrientationColor, getPairedInsertSizeColor, getPairedInsertSizeAndOrientationColor, } from '../shared/color';
 import { featurizeSA } from '../MismatchParser';
+import { getPairedInsertSizeAndOrientationColor, getPairedInsertSizeColor, getPairedOrientationColor, } from '../shared/color';
 import { hasPairedReads } from '../shared/util';
 function jitter(n) {
     return Math.random() * 2 * n - n;
 }
 function drawLineAtOffset(ctx, offset, height, color) {
-    // draws a vertical line off to middle of nowhere if the second end not found
     ctx.strokeStyle = color;
     ctx.beginPath();
     ctx.moveTo(offset, 0);
@@ -47,9 +45,6 @@ export function drawFeats(self, ctx, width, height) {
             const p = r1 - view.offsetPx;
             const p2 = r2 - view.offsetPx;
             const drawArcInsteadOfBezier = absrad > 10000;
-            // bezier (used for non-long-range arcs) requires moveTo before beginPath
-            // arc (used for long-range) requires moveTo after beginPath (or else a
-            // unwanted line at y=0 is rendered along with the arc)
             if (longRange && drawArcInsteadOfBezier) {
                 ctx.moveTo(p, 0);
                 ctx.beginPath();
@@ -97,8 +92,6 @@ export function drawFeats(self, ctx, width, height) {
             const destX = p + radius * 2;
             const destY = Math.min(height + jitter(jitterVal), absrad);
             if (longRange) {
-                // avoid drawing gigantic circles that glitch out the rendering,
-                // instead draw vertical lines
                 if (absrad > 100000) {
                     drawLineAtOffset(ctx, p + jitter(jitterVal), height, 'red');
                     drawLineAtOffset(ctx, p2 + jitter(jitterVal), height, 'red');
@@ -122,7 +115,6 @@ export function drawFeats(self, ctx, width, height) {
         }
     }
     for (const chain of chains) {
-        // chain.length === 1, singleton (other pairs/mates not in view)
         if (chain.length === 1 && drawLongRange) {
             const f = chain[0];
             if (hasPaired && !(f.flags & 8)) {

package/esm/LinearReadArcsDisplay/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/LinearReadArcsDisplay/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);

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 { ColorBy, FilterBy } from '../shared/types';
-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>;
@@ -24,10 +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").IType<FilterBy, FilterBy, FilterBy>, [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").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    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>;
 }, {
@@ -54,17 +45,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: () => void;
-        blockState? /**
-         * #property
-         */: Record<string, any>;
+        blockState?: Record<string, any>;
     }>;
-    readonly DisplayBlurb: React.
-    /**
-     * #property
-     */
-    FC /**
-     * #property
-     */<{
+    readonly DisplayBlurb: React.FC<{
         model: {
             id: string;
             type: string;
@@ -75,9 +58,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree" /**
-             * #action
-             */).ISimpleType<string>;
+            type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -89,10 +70,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: undefined | React.FC /**
-     * #action
-     * thin, bold, extrabold, etc
-     */<any>;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
@@ -132,8 +110,9 @@ 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;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     loading: boolean;
     chainData: ChainData | undefined;
@@ -141,83 +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(colorBy: {
         type: string;
     }): void;
-    /**
-     * #action
-     */
     setChainData(args: ChainData): void;
-    /**
-     * #action
-     */
     setDrawInter(f: boolean): void;
-    /**
-     * #action
-     */
     setDrawLongRange(f: boolean): void;
-    /**
-     * #action
-     */
     setFilterBy(filter: FilterBy): void;
-    /**
-     * #action
-     * thin, bold, extrabold, etc
-     */
     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">> & {
@@ -260,9 +185,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         checked?: undefined;
     })[];
 } & {
-    /**
-     * #method
-     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<React.ReactNode>;

package/esm/LinearReadArcsDisplay/model.js

@@ -1,58 +1,22 @@
 import { lazy } from 'react';
-import { 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';
-import { defaultFilterFlags } from '../shared/util';
-// lazies
+import PaletteIcon from '@mui/icons-material/Palette';
+import { types } from 'mobx-state-tree';
 const FilterByTagDialog = lazy(() => import('../shared/components/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)
- */
 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(types.frozen(), defaultFilterFlags),
-        /**
-         * #property
-         */
         lineWidth: types.maybe(types.number),
-        /**
-         * #property
-         */
         jitter: types.maybe(types.number),
-        /**
-         * #property
-         */
-        colorBy: types.frozen(),
-        /**
-         * #property
-         */
+        colorBySetting: types.frozen(),
+        filterBySetting: types.frozen(),
         drawInter: true,
-        /**
-         * #property
-         */
         drawLongRange: true,
     }))
         .volatile(() => ({
@@ -61,107 +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(colorBy) {
-            self.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 = {
+            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');
@@ -170,19 +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(),
@@ -299,9 +216,6 @@ function stateModelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #method
-         */
         async renderSvg(opts) {
             const { renderSvg } = await import('../shared/renderSvgUtil');
             const { drawFeats } = await import('./drawFeats');
@@ -310,7 +224,6 @@ function stateModelFactory(configSchema) {
     }))
         .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

@@ -1,6 +1,5 @@
-import React from 'react';
-import { LinearReadCloudDisplayModel } from '../model';
+import type { LinearReadCloudDisplayModel } from '../model';
 declare const LinearReadCloudReactComponent: ({ model, }: {
     model: LinearReadCloudDisplayModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default LinearReadCloudReactComponent;

package/esm/LinearReadCloudDisplay/components/ReactComponent.js

@@ -1,22 +1,18 @@
-import React, { useCallback } from 'react';
-import { observer } from 'mobx-react';
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useCallback } from 'react';
 import { getContainingView } from '@jbrowse/core/util';
+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
-    return (React.createElement("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
+    }, [model, width, height]);
+    return (_jsx("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
 const LinearReadCloudReactComponent = observer(function ({ model, }) {
-    return (React.createElement(BaseDisplayComponent, { model: model },
-        React.createElement(Cloud, { model: model })));
+    return (_jsx(BaseDisplayComponent, { model: model, children: _jsx(Cloud, { model: model }) }));
 });
 export default LinearReadCloudReactComponent;

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;