@jbrowse/plugin-alignments 2.17.0 → 2.18.0

package/dist/LinearReadCloudDisplay/model.js

@@ -27,47 +27,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const configuration_1 = require("@jbrowse/core/configuration");
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-// icons
-const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
 const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
-const util_2 = require("../shared/util");
-// async
+const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
+const mobx_state_tree_1 = require("mobx-state-tree");
 const FilterByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/FilterByTagDialog'))));
-/**
- * #stateModel LinearReadCloudDisplay
- * it is not a block based track, hence not BaseLinearDisplay
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearReadCloudDisplay', pluggableElementTypes_1.BaseDisplay, (0, plugin_linear_genome_view_1.TrackHeightMixin)(), (0, plugin_linear_genome_view_1.FeatureDensityMixin)(), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearReadCloudDisplay'),
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        /**
-         * #property
-         */
-        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), util_2.defaultFilterFlags),
-        /**
-         * #property
-         */
-        colorBy: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
+        filterBySetting: mobx_state_tree_1.types.frozen(),
+        colorBySetting: mobx_state_tree_1.types.frozen(),
         drawSingletons: true,
     }))
         .volatile(() => ({
@@ -76,62 +50,46 @@ function stateModelFactory(configSchema) {
         lastDrawnOffsetPx: undefined,
         lastDrawnBpPerPx: 0,
         ref: null,
+    }))
+        .views(self => ({
+        get colorBy() {
+            var _a;
+            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
+        },
+        get filterBy() {
+            var _a;
+            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
+        },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setDrawSingletons(f) {
             self.drawSingletons = f;
         },
-        /**
-         * #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;
         },
         setColorScheme(colorBy) {
-            self.colorBy = {
+            self.colorBySetting = {
                 ...colorBy,
             };
         },
-        /**
-         * #action
-         */
         setChainData(args) {
             self.chainData = args;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
-            self.filterBy = {
+            self.filterBySetting = {
                 ...filter,
             };
         },
@@ -144,17 +102,12 @@ function stateModelFactory(configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
-            // we don't use a server side renderer, so this fills in minimal
-            // info so as not to crash
             renderProps() {
                 return {
                     ...superRenderProps(),
                     notReady: !self.chainData,
                 };
             },
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -208,9 +161,6 @@ function stateModelFactory(configSchema) {
                     },
                 ];
             },
-            /**
-             * #method
-             */
             async renderSvg(opts) {
                 const { renderSvg } = await Promise.resolve().then(() => __importStar(require('../shared/renderSvgUtil')));
                 const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeats')));
@@ -220,7 +170,6 @@ function stateModelFactory(configSchema) {
     })
         .actions(self => ({
         afterAttach() {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;
             (async () => {
                 try {

package/dist/LinearReadCloudDisplay/util.js

@@ -2,7 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fillRectCtx = fillRectCtx;
 exports.strokeRectCtx = strokeRectCtx;
-// avoid drawing negative width features for SVG exports
 function fillRectCtx(x, y, width, height, ctx, fillColor) {
     if (width < 0) {
         x += width;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 declare const SNPCoverageTooltip: (props: {
     model: {

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -4,9 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
 const util_1 = require("@jbrowse/core/util");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(() => ({
     td: {

package/dist/LinearSNPCoverageDisplay/configSchema.d.ts

@@ -1,60 +1,55 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     autoscale: {
         type: string;
         defaultValue: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
     };
-    /**
-     * #slot
-     */
     minScore: {
         type: string;
         defaultValue: number;
         description: string;
     };
-    /**
-     * #slot
-     */
     maxScore: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     scaleType: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */ inverted: {
+    inverted: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     multiTicks: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    colorBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            type: string;
+        };
+    };
+    filterBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            flagInclude: number;
+            flagExclude: number;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;

package/dist/LinearSNPCoverageDisplay/configSchema.js

@@ -4,74 +4,58 @@ exports.default = SNPCoverageConfigFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_state_tree_1 = require("mobx-state-tree");
-/**
- * #config LinearSNPCoverageDisplay
- *
- * extends
- * - [BaseLinearDisplay](../baselineardisplay)
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const util_1 = require("../shared/util");
+function x() { }
 function SNPCoverageConfigFactory(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearSNPCoverageDisplay', {
-        /**
-         * #slot
-         */
         autoscale: {
             type: 'stringEnum',
             defaultValue: 'local',
             model: mobx_state_tree_1.types.enumeration('Autoscale type', ['local']),
             description: 'performs local autoscaling (no other options for SNP Coverage available)',
         },
-        /**
-         * #slot
-         */
         minScore: {
             type: 'number',
             defaultValue: Number.MIN_VALUE,
             description: 'minimum value for the y-scale',
         },
-        /**
-         * #slot
-         */
         maxScore: {
             type: 'number',
             description: 'maximum value for the y-scale',
             defaultValue: Number.MAX_VALUE,
         },
-        /**
-         * #slot
-         */
         scaleType: {
             type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']), // todo zscale
+            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
             description: 'The type of scale to use',
             defaultValue: 'linear',
         },
-        /**
-         * #slot
-         */ inverted: {
+        inverted: {
             type: 'boolean',
             description: 'draw upside down',
             defaultValue: false,
         },
-        /**
-         * #slot
-         */
         multiTicks: {
             type: 'boolean',
             description: 'Display multiple values for the ticks',
             defaultValue: false,
         },
-        /**
-         * #slot
-         */
         renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
             SNPCoverageRenderer: pluginManager.getRendererType('SNPCoverageRenderer').configSchema,
         }),
+        colorBy: {
+            type: 'frozen',
+            description: 'color scheme to use',
+            defaultValue: {
+                type: 'normal',
+            },
+        },
+        filterBy: {
+            type: 'frozen',
+            description: 'default filters to use',
+            defaultValue: util_1.defaultFilterFlags,
+        },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });

package/dist/LinearSNPCoverageDisplay/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/dist/LinearSNPCoverageDisplay/index.js

@@ -4,9 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = register;
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-// locals
+const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 const configSchema_1 = __importDefault(require("./configSchema"));
 const model_1 = __importDefault(require("./model"));
 function register(pluginManager) {

package/dist/LinearSNPCoverageDisplay/model.d.ts

@@ -1,11 +1,6 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { ColorBy, FilterBy } from '../shared/types';
-/**
- * #stateModel LinearSNPCoverageDisplay
- * extends
- * - [LinearWiggleDisplay](../linearwiggledisplay)
- */
+import type { ColorBy, FilterBy } from '../shared/types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 declare function stateModelFactory(pluginManager: PluginManager, 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>;
@@ -18,21 +13,12 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: 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>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -56,15 +42,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -118,33 +98,12 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
-    /**
-     * #property
-     */
     drawInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
     drawIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
     drawArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<FilterBy, FilterBy, FilterBy>, [undefined]>;
-    /**
-     * #property
-     */
-    colorBy: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    /**
-     * #property
-     */
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
 }, never, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;