@jbrowse/plugin-alignments 2.2.0 → 2.2.2

package/esm/LinearSNPCoverageDisplay/models/model.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="react" />
-import { AnyConfigurationSchemaType, AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
+import { AnyConfigurationSchemaType, AnyConfigurationModel } from '@jbrowse/core/configuration';
 /**
  * #stateModel LinearSNPCoverageDisplay
  * extends `LinearWiggleDisplay`
@@ -43,9 +43,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     } & {
         doReload(): void;
         afterAttach(): void;
-        setStatus(message: string): void; /**
-         * #action
-         */
+        setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
@@ -68,9 +66,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
-     * #getter
-     */
+    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -156,11 +152,16 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }, {
             rendererTypeName: string;
             error: unknown;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+         * #getter
+         */
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
+    /**
+     * #method
+     */
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
@@ -343,7 +344,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {
-    modificationTagMap: import("mobx").ObservableMap<any, any>;
+    modificationTagMap: Record<string, string> | undefined;
 } & {
     /**
      * #action
@@ -424,6 +425,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             featureUnderMouse: import("@jbrowse/core/util").Feature;
         };
         height: number;
+        /**
+         * #action
+         */
         offsetMouseCoord: [number, number];
         clientMouseCoord: [number, number];
         clientRect?: DOMRect | undefined;
@@ -457,5 +461,5 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         onClick: () => void;
     })[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;
+export type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;
 export default stateModelFactory;

package/esm/LinearSNPCoverageDisplay/models/model.js

@@ -1,5 +1,6 @@
 import { addDisposer, types, cast, getEnv, getSnapshot } from 'mobx-state-tree';
-import { observable, autorun } from 'mobx';
+import clone from 'clone';
+import { autorun } from 'mobx';
 import { getConf, readConfObject, } from '@jbrowse/core/configuration';
 import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle';
 import { getContainingView } from '@jbrowse/core/util';
@@ -49,7 +50,7 @@ function stateModelFactory(pluginManager, configSchema) {
         })),
     }))
         .volatile(() => ({
-        modificationTagMap: observable.map({}),
+        modificationTagMap: undefined,
     }))
         .actions(self => ({
         /**
@@ -76,12 +77,14 @@ function stateModelFactory(pluginManager, configSchema) {
         updateModificationColorMap(uniqueModifications) {
             const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
             let i = 0;
+            const newMap = clone(self.modificationTagMap) || {};
             uniqueModifications.forEach(value => {
-                if (!self.modificationTagMap.has(value)) {
+                if (!newMap[value]) {
                     const newColor = colorPalette[i++];
-                    self.modificationTagMap.set(value, newColor);
+                    newMap[value] = newColor;
                 }
             });
+            self.modificationTagMap = newMap;
         },
     }))
         .views(self => {
@@ -127,8 +130,7 @@ function stateModelFactory(pluginManager, configSchema) {
             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
+                    ? self.modificationTagMap !== undefined
                     : true;
             },
             /**
@@ -140,7 +142,7 @@ function stateModelFactory(pluginManager, configSchema) {
                 return {
                     ...superProps,
                     notReady: superProps.notReady || !this.modificationsReady,
-                    modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
+                    modificationTagMap: modificationTagMap,
                     // must use getSnapshot because otherwise changes to e.g. just the
                     // colorBy.type are not read
                     colorBy: colorBy ? getSnapshot(colorBy) : undefined,

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

@@ -1 +1 @@
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package/esm/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/esm/PileupRPC/rpcMethods.js

@@ -1,7 +1,8 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { renameRegionsIfNeeded } from '@jbrowse/core/util';
 import { toArray } from 'rxjs/operators';
+// locals
 import { getTagAlt } from '../util';
 import { getModificationTypes } from '../BamAdapter/MismatchParser';
 export class PileupGetGlobalValueForTag extends RpcMethodType {
@@ -20,9 +21,11 @@ export class PileupGetGlobalValueForTag extends RpcMethodType {
         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 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 getAdapter(pm, sessionId, adapterConfig))
+            .dataAdapter;
         const features = dataAdapter.getFeaturesInMultipleRegions(regions);
         const featuresArray = await features.pipe(toArray()).toPromise();
         const uniqueValues = new Set();
@@ -52,9 +55,11 @@ export class PileupGetVisibleModifications extends RpcMethodType {
         return super.serializeArguments(renamedArgs, rpcDriverClassName);
     }
     async execute(args, rpcDriverClassName) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { adapterConfig, sessionId, regions } = deserializedArgs;
-        const dataAdapter = (await 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 getAdapter(pm, sessionId, adapterConfig))
+            .dataAdapter;
         const features = dataAdapter.getFeaturesInMultipleRegions(regions);
         const featuresArray = await features.pipe(toArray()).toPromise();
         const uniqueValues = new Set();

package/esm/PileupRPC/rpcMethods.js.map

@@ -1 +1 @@
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package/esm/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/esm/PileupRenderer/PileupRenderer.js

@@ -79,7 +79,7 @@ export default class PileupRenderer extends BoxRendererType {
         if (showSoftClip) {
             const mismatches = feature.get('mismatches');
             const seq = feature.get('seq');
-            if (seq) {
+            if (seq && mismatches) {
                 for (let i = 0; i < mismatches.length; i += 1) {
                     const { type, start, cliplen = 0 } = mismatches[i];
                     if (type === 'softclip') {
@@ -515,6 +515,9 @@ export default class PileupRenderer extends BoxRendererType {
         const extraHorizontallyFlippedOffset = region.reversed
             ? 1 / bpPerPx + 1
             : -1;
+        if (!mismatches) {
+            return;
+        }
         // two pass rendering: first pass, draw all the mismatches except wide
         // insertion markers
         for (let i = 0; i < mismatches.length; i += 1) {
@@ -643,34 +646,35 @@ export default class PileupRenderer extends BoxRendererType {
             deletion: '#808080', // gray
         };
         // Display all bases softclipped off in lightened colors
-        if (seq) {
-            mismatches
-                .filter(mismatch => mismatch.type === 'softclip')
-                .forEach(mismatch => {
-                const softClipLength = mismatch.cliplen || 0;
-                const s = feature.get('start');
-                const softClipStart = mismatch.start === 0 ? s - softClipLength : s + mismatch.start;
-                for (let k = 0; k < softClipLength; k += 1) {
-                    const base = seq.charAt(k + mismatch.start);
-                    // If softclip length+start is longer than sequence, no need to
-                    // continue showing base
-                    if (!base) {
-                        return;
-                    }
-                    const [softClipLeftPx, softClipRightPx] = bpSpanPx(softClipStart + k, softClipStart + k + 1, region, bpPerPx);
-                    const softClipWidthPx = Math.max(minFeatWidth, Math.abs(softClipLeftPx - softClipRightPx));
-                    // Black accounts for IUPAC ambiguity code bases such as N that
-                    // show in soft clipping
-                    const baseColor = colorForBase[base] || '#000000';
-                    ctx.fillStyle = baseColor;
-                    fillRect(ctx, softClipLeftPx, topPx, softClipWidthPx, heightPx, canvasWidth);
-                    if (softClipWidthPx >= charWidth && heightPx >= charHeight - 5) {
-                        ctx.fillStyle = theme.palette.getContrastText(baseColor);
-                        ctx.fillText(base, softClipLeftPx + (softClipWidthPx - charWidth) / 2 + 1, topPx + heightPx);
-                    }
-                }
-            });
+        if (!(seq && mismatches)) {
+            return;
         }
+        mismatches
+            .filter(mismatch => mismatch.type === 'softclip')
+            .forEach(mismatch => {
+            const len = mismatch.cliplen || 0;
+            const s = feature.get('start');
+            const start = mismatch.start === 0 ? s - len : s + mismatch.start;
+            for (let k = 0; k < len; k += 1) {
+                const base = seq.charAt(k + mismatch.start);
+                // If softclip length+start is longer than sequence, no need to
+                // continue showing base
+                if (!base) {
+                    return;
+                }
+                const [leftPx, rightPx] = bpSpanPx(start + k, start + k + 1, region, bpPerPx);
+                const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
+                // Black accounts for IUPAC ambiguity code bases such as N that
+                // show in soft clipping
+                const baseColor = colorForBase[base] || '#000000';
+                ctx.fillStyle = baseColor;
+                fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
+                if (widthPx >= charWidth && heightPx >= charHeight - 5) {
+                    ctx.fillStyle = theme.palette.getContrastText(baseColor);
+                    ctx.fillText(base, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
+                }
+            }
+        });
     }
     makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
         const { layout, config, showSoftClip, colorBy, theme: configTheme, } = renderArgs;

package/esm/PileupRenderer/PileupRenderer.js.map

@@ -1 +1 @@
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package/esm/PileupRenderer/configSchema.js

@@ -22,7 +22,7 @@ const PileupRenderer = ConfigurationSchema('PileupRenderer', {
         type: 'stringEnum',
         model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),
         defaultValue: 'fr',
-        description: 'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
+        description: 'read sequencer orientation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
     },
     /**
      * #slot

package/esm/PileupRenderer/configSchema.js.map

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package/esm/PileupRenderer/index.js

@@ -2,11 +2,13 @@ import PileupRenderer from './PileupRenderer';
 import ReactComponent from './components/PileupRendering';
 import configSchema from './configSchema';
 export default function register(pluginManager) {
-    pluginManager.addRendererType(() => new PileupRenderer({
-        name: 'PileupRenderer',
-        ReactComponent,
-        configSchema,
-        pluginManager,
-    }));
+    pluginManager.addRendererType(() => {
+        return new PileupRenderer({
+            name: 'PileupRenderer',
+            ReactComponent,
+            configSchema,
+            pluginManager,
+        });
+    });
 }
 //# sourceMappingURL=index.js.map

package/esm/PileupRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":"AACA,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,cAAc,MAAM,8BAA8B,CAAA;AACzD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAAC,GAAG,EAAE;QACjC,OAAO,IAAI,cAAc,CAAC;YACxB,IAAI,EAAE,gBAAgB;YACtB,cAAc;YACd,YAAY;YACZ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -11,57 +11,6 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     freeResources(): void;
-    generateCoverageBins(features: Feature[], region: Region, opts: {
-        bpPerPx?: number;
-        colorBy?: {
-            type: string;
-            tag?: string;
-        };
-    }): Promise<{
-        bins: {
-            refbase?: string | undefined;
-            total: number;
-            all: number;
-            ref: number;
-            '-1': 0;
-            '0': 0;
-            '1': 0;
-            lowqual: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            cov: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            delskips: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            noncov: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-        }[];
-        skipmap: {
-            [key: string]: {
-                score: number;
-                feature: unknown;
-                start: number;
-                end: number;
-                strand: number;
-                xs: string;
-            };
-        };
-    }>;
 }
 declare const capabilities: string[];
 export { capabilities };