@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/dist/LinearSNPCoverageDisplay/models/model.js

@@ -13,173 +13,254 @@ const Tooltip_1 = __importDefault(require("../components/Tooltip"));
 const shared_1 = require("../../shared");
 // using a map because it preserves order
 const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
-const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.types
-    .compose('LinearSNPCoverageDisplay', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
-    type: mobx_state_tree_1.types.literal('LinearSNPCoverageDisplay'),
-    drawInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-    drawIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-    drawArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-    filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
-        flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
-        flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
-        readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({ tag: mobx_state_tree_1.types.string, value: mobx_state_tree_1.types.string })),
-    }), {}),
-    colorBy: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
-        type: mobx_state_tree_1.types.string,
-        tag: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-    })),
-}))
-    .volatile(() => ({
-    modificationTagMap: mobx_1.observable.map({}),
-}))
-    .actions(self => ({
-    setConfig(configuration) {
-        self.configuration = configuration;
-    },
-    setFilterBy(filter) {
-        self.filterBy = (0, mobx_state_tree_1.cast)(filter);
-    },
-    setColorBy(colorBy) {
-        self.colorBy = (0, mobx_state_tree_1.cast)(colorBy);
-    },
-    updateModificationColorMap(uniqueModifications) {
-        const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
-        let i = 0;
-        uniqueModifications.forEach(value => {
-            if (!self.modificationTagMap.has(value)) {
-                const newColor = colorPalette[i++];
-                self.modificationTagMap.set(value, newColor);
-            }
-        });
-    },
-}))
-    .views(self => {
-    const { renderProps: superRenderProps } = self;
-    return {
-        get rendererConfig() {
-            var _a, _b, _c;
-            const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
-            return self.rendererType.configSchema.create({
-                ...configBlob,
-                drawInterbaseCounts: (_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : configBlob.drawInterbaseCounts,
-                drawIndicators: (_b = self.drawIndicators) !== null && _b !== void 0 ? _b : configBlob.drawIndicators,
-                drawArcs: (_c = self.drawArcs) !== null && _c !== void 0 ? _c : configBlob.drawArcs,
-            }, (0, mobx_state_tree_1.getEnv)(self));
+/**
+ * #stateModel LinearSNPCoverageDisplay
+ * extends `LinearWiggleDisplay`
+ */
+function stateModelFactory(pluginManager, configSchema) {
+    return mobx_state_tree_1.types
+        .compose('LinearSNPCoverageDisplay', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('LinearSNPCoverageDisplay'),
+        /**
+         * #property
+         */
+        drawInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        /**
+         * #property
+         */
+        drawIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        /**
+         * #property
+         */
+        drawArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        /**
+         * #property
+         */
+        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
+            flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
+            flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
+            readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+            tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({ tag: mobx_state_tree_1.types.string, value: mobx_state_tree_1.types.string })),
+        }), {}),
+        /**
+         * #property
+         */
+        colorBy: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
+            type: mobx_state_tree_1.types.string,
+            tag: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        })),
+    }))
+        .volatile(() => ({
+        modificationTagMap: mobx_1.observable.map({}),
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setConfig(configuration) {
+            self.configuration = configuration;
         },
-        get drawArcsSetting() {
-            var _a;
-            return ((_a = self.drawArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawArcs'));
+        /**
+         * #action
+         */
+        setFilterBy(filter) {
+            self.filterBy = (0, mobx_state_tree_1.cast)(filter);
         },
-        get drawInterbaseCountsSetting() {
-            var _a;
-            return ((_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawInterbaseCounts'));
+        /**
+         * #action
+         */
+        setColorBy(colorBy) {
+            self.colorBy = (0, mobx_state_tree_1.cast)(colorBy);
         },
-        get drawIndicatorsSetting() {
-            var _a;
-            return ((_a = self.drawIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawIndicators'));
-        },
-        get modificationsReady() {
-            var _a;
-            return ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) === 'modifications'
-                ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap)))
-                    .length > 0
-                : true;
-        },
-        renderProps() {
-            const superProps = superRenderProps();
-            const { colorBy, filterBy, modificationTagMap } = self;
-            return {
-                ...superProps,
-                notReady: superProps.notReady || !this.modificationsReady,
-                modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
-                // must use getSnapshot because otherwise changes to e.g. just the
-                // colorBy.type are not read
-                colorBy: colorBy ? (0, mobx_state_tree_1.getSnapshot)(colorBy) : undefined,
-                filterBy: filterBy ? (0, mobx_state_tree_1.getSnapshot)(filterBy) : undefined,
-            };
-        },
-    };
-})
-    .actions(self => ({
-    toggleDrawIndicators() {
-        self.drawIndicators = !self.drawIndicatorsSetting;
-    },
-    toggleDrawInterbaseCounts() {
-        self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
-    },
-    toggleDrawArcs() {
-        self.drawArcs = !self.drawArcsSetting;
-    },
-    afterAttach() {
-        (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-            try {
-                const { colorBy } = self;
-                const view = (0, util_1.getContainingView)(self);
-                if (!view.initialized ||
-                    !self.estimatedStatsReady ||
-                    self.regionTooLarge) {
-                    return;
-                }
-                const { staticBlocks } = view;
-                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                    const adapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
-                    self.updateModificationColorMap(await (0, shared_1.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks));
+        /**
+         * #action
+         */
+        updateModificationColorMap(uniqueModifications) {
+            const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
+            let i = 0;
+            uniqueModifications.forEach(value => {
+                if (!self.modificationTagMap.has(value)) {
+                    const newColor = colorPalette[i++];
+                    self.modificationTagMap.set(value, newColor);
                 }
-            }
-            catch (error) {
-                console.error(error);
-                self.setError(error);
-            }
-        }, { delay: 1000 }));
-    },
-}))
-    .views(self => {
-    const { trackMenuItems: superTrackMenuItems } = self;
-    return {
-        get TooltipComponent() {
-            return Tooltip_1.default;
+            });
         },
-        get adapterConfig() {
-            const subadapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
-            return {
-                type: 'SNPCoverageAdapter',
-                subadapter,
-            };
+    }))
+        .views(self => {
+        const { renderProps: superRenderProps } = self;
+        return {
+            /**
+             * #getter
+             */
+            get rendererConfig() {
+                var _a, _b, _c;
+                const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
+                return self.rendererType.configSchema.create({
+                    ...configBlob,
+                    drawInterbaseCounts: (_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : configBlob.drawInterbaseCounts,
+                    drawIndicators: (_b = self.drawIndicators) !== null && _b !== void 0 ? _b : configBlob.drawIndicators,
+                    drawArcs: (_c = self.drawArcs) !== null && _c !== void 0 ? _c : configBlob.drawArcs,
+                }, (0, mobx_state_tree_1.getEnv)(self));
+            },
+            /**
+             * #getter
+             */
+            get drawArcsSetting() {
+                var _a;
+                return ((_a = self.drawArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawArcs'));
+            },
+            /**
+             * #getter
+             */
+            get drawInterbaseCountsSetting() {
+                var _a;
+                return ((_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawInterbaseCounts'));
+            },
+            /**
+             * #getter
+             */
+            get drawIndicatorsSetting() {
+                var _a;
+                return ((_a = self.drawIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawIndicators'));
+            },
+            /**
+             * #getter
+             */
+            get modificationsReady() {
+                var _a;
+                return ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) === 'modifications'
+                    ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap)))
+                        .length > 0
+                    : true;
+            },
+            /**
+             * #method
+             */
+            renderProps() {
+                const superProps = superRenderProps();
+                const { colorBy, filterBy, modificationTagMap } = self;
+                return {
+                    ...superProps,
+                    notReady: superProps.notReady || !this.modificationsReady,
+                    modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
+                    // must use getSnapshot because otherwise changes to e.g. just the
+                    // colorBy.type are not read
+                    colorBy: colorBy ? (0, mobx_state_tree_1.getSnapshot)(colorBy) : undefined,
+                    filterBy: filterBy ? (0, mobx_state_tree_1.getSnapshot)(filterBy) : undefined,
+                };
+            },
+        };
+    })
+        .actions(self => ({
+        /**
+         * #action
+         */
+        toggleDrawIndicators() {
+            self.drawIndicators = !self.drawIndicatorsSetting;
         },
-        get rendererTypeName() {
-            return rendererTypes.get('snpcoverage');
+        /**
+         * #action
+         */
+        toggleDrawInterbaseCounts() {
+            self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
         },
-        get needsScalebar() {
-            return true;
+        /**
+         * #action
+         */
+        toggleDrawArcs() {
+            self.drawArcs = !self.drawArcsSetting;
         },
-        contextMenuItems() {
-            return [];
-        },
-        trackMenuItems() {
-            return [
-                ...superTrackMenuItems(),
-                {
-                    label: 'Draw insertion/clipping indicators',
-                    type: 'checkbox',
-                    checked: self.drawIndicatorsSetting,
-                    onClick: () => self.toggleDrawIndicators(),
-                },
-                {
-                    label: 'Draw insertion/clipping counts',
-                    type: 'checkbox',
-                    checked: self.drawInterbaseCountsSetting,
-                    onClick: () => self.toggleDrawInterbaseCounts(),
-                },
-                {
-                    label: 'Draw arcs',
-                    type: 'checkbox',
-                    checked: self.drawArcsSetting,
-                    onClick: () => self.toggleDrawArcs(),
-                },
-            ];
+        afterAttach() {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
+                try {
+                    const { colorBy } = self;
+                    const view = (0, util_1.getContainingView)(self);
+                    if (!view.initialized ||
+                        !self.estimatedStatsReady ||
+                        self.regionTooLarge) {
+                        return;
+                    }
+                    const { staticBlocks } = view;
+                    if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+                        const adapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
+                        self.updateModificationColorMap(await (0, shared_1.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks));
+                    }
+                }
+                catch (error) {
+                    console.error(error);
+                    self.setError(error);
+                }
+            }, { delay: 1000 }));
         },
-    };
-});
+    }))
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems } = self;
+        return {
+            /**
+             * #getter
+             */
+            get TooltipComponent() {
+                return Tooltip_1.default;
+            },
+            /**
+             * #getter
+             */
+            get adapterConfig() {
+                const subadapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
+                return {
+                    type: 'SNPCoverageAdapter',
+                    subadapter,
+                };
+            },
+            /**
+             * #getter
+             */
+            get rendererTypeName() {
+                return rendererTypes.get('snpcoverage');
+            },
+            /**
+             * #getter
+             */
+            get needsScalebar() {
+                return true;
+            },
+            /**
+             * #method
+             */
+            contextMenuItems() {
+                return [];
+            },
+            /**
+             * #method
+             */
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Draw insertion/clipping indicators',
+                        type: 'checkbox',
+                        checked: self.drawIndicatorsSetting,
+                        onClick: () => self.toggleDrawIndicators(),
+                    },
+                    {
+                        label: 'Draw insertion/clipping counts',
+                        type: 'checkbox',
+                        checked: self.drawInterbaseCountsSetting,
+                        onClick: () => self.toggleDrawInterbaseCounts(),
+                    },
+                    {
+                        label: 'Draw arcs',
+                        type: 'checkbox',
+                        checked: self.drawArcsSetting,
+                        onClick: () => self.toggleDrawArcs(),
+                    },
+                ];
+            },
+        };
+    });
+}
 exports.default = stateModelFactory;
 //# sourceMappingURL=model.js.map

package/dist/LinearSNPCoverageDisplay/models/model.js.map

@@ -1 +1 @@
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package/dist/PileupRPC/rpcMethods.d.ts

@@ -1,6 +1,6 @@
 import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { Region } from '@jbrowse/core/util';
 import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { Region } from '@jbrowse/core/util/types';
 import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
 export declare class PileupGetGlobalValueForTag extends RpcMethodType {
     name: string;

package/dist/PileupRPC/rpcMethods.js

@@ -4,10 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PileupGetVisibleModifications = exports.PileupGetGlobalValueForTag = void 0;
-const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const util_1 = require("@jbrowse/core/util");
 const operators_1 = require("rxjs/operators");
+// locals
 const util_2 = require("../util");
 const MismatchParser_1 = require("../BamAdapter/MismatchParser");
 class PileupGetGlobalValueForTag extends RpcMethodType_1.default {
@@ -26,9 +27,11 @@ class PileupGetGlobalValueForTag extends RpcMethodType_1.default {
         return super.serializeArguments(renamedArgs, rpcDriverClassName);
     }
     async execute(args, rpcDriverClassName) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { adapterConfig, sessionId, regions, tag } = deserializedArgs;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const pm = this.pluginManager;
+        const deArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId, regions, tag } = deArgs;
+        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig))
+            .dataAdapter;
         const features = dataAdapter.getFeaturesInMultipleRegions(regions);
         const featuresArray = await features.pipe((0, operators_1.toArray)()).toPromise();
         const uniqueValues = new Set();
@@ -59,9 +62,11 @@ class PileupGetVisibleModifications extends RpcMethodType_1.default {
         return super.serializeArguments(renamedArgs, rpcDriverClassName);
     }
     async execute(args, rpcDriverClassName) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { adapterConfig, sessionId, regions } = deserializedArgs;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const pm = this.pluginManager;
+        const deArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId, regions } = deArgs;
+        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig))
+            .dataAdapter;
         const features = dataAdapter.getFeaturesInMultipleRegions(regions);
         const featuresArray = await features.pipe((0, operators_1.toArray)()).toPromise();
         const uniqueValues = new Set();

package/dist/PileupRPC/rpcMethods.js.map

@@ -1 +1 @@
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package/dist/PileupRenderer/PileupLayoutSession.d.ts

@@ -11,7 +11,7 @@ export interface PileupLayoutSessionProps {
     sortedBy: unknown;
     showSoftClip: unknown;
 }
-declare type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
+type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
 interface CachedPileupLayout {
     layout: MyMultiLayout;
     config: AnyConfigurationModel;

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -41,7 +41,7 @@ interface LayoutFeature {
 }
 export default class PileupRenderer extends BoxRendererType {
     supportsSVG: boolean;
-    getCharWidthHeight(ctx: CanvasRenderingContext2D): {
+    getCharWidthHeight(): {
         charWidth: number;
         charHeight: number;
     };