@jbrowse/plugin-alignments 2.1.6 → 2.2.0

package/esm/LinearSNPCoverageDisplay/models/model.js

@@ -8,173 +8,254 @@ import Tooltip from '../components/Tooltip';
 import { getUniqueModificationValues } from '../../shared';
 // using a map because it preserves order
 const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
-const stateModelFactory = (pluginManager, configSchema) => types
-    .compose('LinearSNPCoverageDisplay', linearWiggleDisplayModelFactory(pluginManager, configSchema), types.model({
-    type: types.literal('LinearSNPCoverageDisplay'),
-    drawInterbaseCounts: types.maybe(types.boolean),
-    drawIndicators: types.maybe(types.boolean),
-    drawArcs: types.maybe(types.boolean),
-    filterBy: types.optional(types.model({
-        flagInclude: types.optional(types.number, 0),
-        flagExclude: types.optional(types.number, 1540),
-        readName: types.maybe(types.string),
-        tagFilter: types.maybe(types.model({ tag: types.string, value: types.string })),
-    }), {}),
-    colorBy: types.maybe(types.model({
-        type: types.string,
-        tag: types.maybe(types.string),
-    })),
-}))
-    .volatile(() => ({
-    modificationTagMap: observable.map({}),
-}))
-    .actions(self => ({
-    setConfig(configuration) {
-        self.configuration = configuration;
-    },
-    setFilterBy(filter) {
-        self.filterBy = cast(filter);
-    },
-    setColorBy(colorBy) {
-        self.colorBy = 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 = 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,
-            }, getEnv(self));
+/**
+ * #stateModel LinearSNPCoverageDisplay
+ * extends `LinearWiggleDisplay`
+ */
+function stateModelFactory(pluginManager, configSchema) {
+    return types
+        .compose('LinearSNPCoverageDisplay', linearWiggleDisplayModelFactory(pluginManager, configSchema), types.model({
+        /**
+         * #property
+         */
+        type: types.literal('LinearSNPCoverageDisplay'),
+        /**
+         * #property
+         */
+        drawInterbaseCounts: types.maybe(types.boolean),
+        /**
+         * #property
+         */
+        drawIndicators: types.maybe(types.boolean),
+        /**
+         * #property
+         */
+        drawArcs: types.maybe(types.boolean),
+        /**
+         * #property
+         */
+        filterBy: types.optional(types.model({
+            flagInclude: types.optional(types.number, 0),
+            flagExclude: types.optional(types.number, 1540),
+            readName: types.maybe(types.string),
+            tagFilter: types.maybe(types.model({ tag: types.string, value: types.string })),
+        }), {}),
+        /**
+         * #property
+         */
+        colorBy: types.maybe(types.model({
+            type: types.string,
+            tag: types.maybe(types.string),
+        })),
+    }))
+        .volatile(() => ({
+        modificationTagMap: observable.map({}),
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setConfig(configuration) {
+            self.configuration = configuration;
         },
-        get drawArcsSetting() {
-            var _a;
-            return ((_a = self.drawArcs) !== null && _a !== void 0 ? _a : readConfObject(this.rendererConfig, 'drawArcs'));
+        /**
+         * #action
+         */
+        setFilterBy(filter) {
+            self.filterBy = cast(filter);
         },
-        get drawInterbaseCountsSetting() {
-            var _a;
-            return ((_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : readConfObject(this.rendererConfig, 'drawInterbaseCounts'));
+        /**
+         * #action
+         */
+        setColorBy(colorBy) {
+            self.colorBy = cast(colorBy);
         },
-        get drawIndicatorsSetting() {
-            var _a;
-            return ((_a = self.drawIndicators) !== null && _a !== void 0 ? _a : 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 ? getSnapshot(colorBy) : undefined,
-                filterBy: filterBy ? getSnapshot(filterBy) : undefined,
-            };
-        },
-    };
-})
-    .actions(self => ({
-    toggleDrawIndicators() {
-        self.drawIndicators = !self.drawIndicatorsSetting;
-    },
-    toggleDrawInterbaseCounts() {
-        self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
-    },
-    toggleDrawArcs() {
-        self.drawArcs = !self.drawArcsSetting;
-    },
-    afterAttach() {
-        addDisposer(self, autorun(async () => {
-            try {
-                const { colorBy } = self;
-                const view = 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 = getConf(self.parentTrack, 'adapter');
-                    self.updateModificationColorMap(await 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;
+            });
         },
-        get adapterConfig() {
-            const subadapter = getConf(self.parentTrack, 'adapter');
-            return {
-                type: 'SNPCoverageAdapter',
-                subadapter,
-            };
+    }))
+        .views(self => {
+        const { renderProps: superRenderProps } = self;
+        return {
+            /**
+             * #getter
+             */
+            get rendererConfig() {
+                var _a, _b, _c;
+                const configBlob = 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,
+                }, getEnv(self));
+            },
+            /**
+             * #getter
+             */
+            get drawArcsSetting() {
+                var _a;
+                return ((_a = self.drawArcs) !== null && _a !== void 0 ? _a : readConfObject(this.rendererConfig, 'drawArcs'));
+            },
+            /**
+             * #getter
+             */
+            get drawInterbaseCountsSetting() {
+                var _a;
+                return ((_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : readConfObject(this.rendererConfig, 'drawInterbaseCounts'));
+            },
+            /**
+             * #getter
+             */
+            get drawIndicatorsSetting() {
+                var _a;
+                return ((_a = self.drawIndicators) !== null && _a !== void 0 ? _a : 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 ? getSnapshot(colorBy) : undefined,
+                    filterBy: filterBy ? 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() {
+            addDisposer(self, autorun(async () => {
+                try {
+                    const { colorBy } = self;
+                    const view = 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 = getConf(self.parentTrack, 'adapter');
+                        self.updateModificationColorMap(await 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;
+            },
+            /**
+             * #getter
+             */
+            get adapterConfig() {
+                const subadapter = 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(),
+                    },
+                ];
+            },
+        };
+    });
+}
 export default stateModelFactory;
 //# sourceMappingURL=model.js.map

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

@@ -1 +1 @@
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package/esm/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;
     };

package/esm/PileupRenderer/PileupRenderer.js

@@ -67,7 +67,7 @@ export default class PileupRenderer extends BoxRendererType {
     }
     // get width and height of chars the height is an approximation: width
     // letter M is approximately the height
-    getCharWidthHeight(ctx) {
+    getCharWidthHeight() {
         const charWidth = measureText('A');
         const charHeight = measureText('M') - 2;
         return { charWidth, charHeight };
@@ -116,8 +116,7 @@ export default class PileupRenderer extends BoxRendererType {
         const { config, showSoftClip } = renderArgs;
         const maxClippingSize = readConfObject(config, 'maxClippingSize');
         const { start, end } = region;
-        const len = end - start;
-        const bpExpansion = Math.max(len, showSoftClip ? Math.round(maxClippingSize) : 0);
+        const bpExpansion = showSoftClip ? Math.round(maxClippingSize) : 0;
         return {
             // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...region,
@@ -634,7 +633,7 @@ export default class PileupRenderer extends BoxRendererType {
         const minFeatWidth = readConfObject(config, 'minSubfeatureWidth');
         const mismatches = feature.get('mismatches');
         const seq = feature.get('seq');
-        const { charWidth, charHeight } = this.getCharWidthHeight(ctx);
+        const { charWidth, charHeight } = this.getCharWidthHeight();
         const { bases } = theme.palette;
         const colorForBase = {
             A: bases.A.main,
@@ -689,7 +688,7 @@ export default class PileupRenderer extends BoxRendererType {
             throw new Error('invalid layout object');
         }
         ctx.font = 'bold 10px Courier New,monospace';
-        const { charWidth, charHeight } = this.getCharWidthHeight(ctx);
+        const { charWidth, charHeight } = this.getCharWidthHeight();
         const drawSNPsMuted = shouldDrawSNPsMuted(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
         const drawIndels = shouldDrawIndels(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
         for (let i = 0; i < layoutRecords.length; i++) {
@@ -776,12 +775,12 @@ export default class PileupRenderer extends BoxRendererType {
         const features = await this.getFeatures(renderProps);
         const layout = this.createLayoutInWorker(renderProps);
         const { regions, bpPerPx } = renderProps;
+        const [region] = regions;
         const layoutRecords = this.layoutFeats({
             ...renderProps,
             features,
             layout,
         });
-        const [region] = regions;
         // only need reference sequence if there are features and only for some
         // cases
         const regionSequence = features.size && shouldFetchReferenceSequence((_a = renderProps.colorBy) === null || _a === void 0 ? void 0 : _a.type)