@jbrowse/plugin-alignments 2.6.2 → 2.7.0

package/dist/shared/FilterByTag.js

@@ -70,7 +70,7 @@ function Bitmask(props) {
                 react_1.default.createElement("label", { htmlFor: key }, name)));
         })));
 }
-function FilterByTagDlg(props) {
+const FilterByTagDialog = (0, mobx_react_1.observer)(function (props) {
     var _a, _b;
     const { model, handleClose } = props;
     const { classes } = useStyles();
@@ -99,9 +99,7 @@ function FilterByTagDlg(props) {
                         react_1.default.createElement(Bitmask, { flag: flagExclude, setFlag: setFlagExclude })))),
             react_1.default.createElement(material_1.Paper, { className: classes.paper, variant: "outlined" },
                 react_1.default.createElement(material_1.Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
-                        maxLength: 2,
-                    }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '' }),
+                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: { maxLength: 2 }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '' }),
                 react_1.default.createElement(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value" })),
             react_1.default.createElement(material_1.Paper, { className: classes.paper, variant: "outlined" },
                 react_1.default.createElement(material_1.Typography, null, "Filter by read name"),
@@ -122,5 +120,5 @@ function FilterByTagDlg(props) {
                         handleClose();
                     } }, "Submit"),
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
-}
-exports.default = (0, mobx_react_1.observer)(FilterByTagDlg);
+});
+exports.default = FilterByTagDialog;

package/dist/shared/color.d.ts

@@ -1,3 +1,4 @@
+import { Instance } from 'mobx-state-tree';
 import { ChainStats } from './fetchChains';
 export declare const fillColor: {
     color_fwd_strand_not_proper: string;
@@ -53,3 +54,12 @@ export declare function getPairedInsertSizeAndOrientationColor(f1: {
 export declare function getPairedOrientationColor(f: {
     pair_orientation?: string;
 }): readonly [string, string];
+export interface ExtraColorBy {
+    custom?: Record<string, string>;
+}
+export declare const ColorByModel: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<string>;
+    tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    extra: import("mobx-state-tree").IType<any, any, any>;
+}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+export type IColorByModel = Instance<typeof ColorByModel>;

package/dist/shared/color.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getPairedOrientationColor = exports.getPairedInsertSizeAndOrientationColor = exports.getPairedInsertSizeColor = exports.strokeColor = exports.fillColor = void 0;
+exports.ColorByModel = exports.getPairedOrientationColor = exports.getPairedInsertSizeAndOrientationColor = exports.getPairedInsertSizeColor = exports.strokeColor = exports.fillColor = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("../util");
 exports.fillColor = {
     color_fwd_strand_not_proper: '#ECC8C8',
@@ -74,3 +75,8 @@ function getPairedOrientationColor(f) {
     ];
 }
 exports.getPairedOrientationColor = getPairedOrientationColor;
+exports.ColorByModel = 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),
+    extra: mobx_state_tree_1.types.frozen(),
+}));

package/dist/shared/fetchChains.js

@@ -4,6 +4,7 @@ exports.fetchChains = void 0;
 const util_1 = require("@jbrowse/core/util");
 const mobx_state_tree_1 = require("mobx-state-tree");
 async function fetchChains(self) {
+    // @ts-expect-error
     const { rpcSessionId: sessionId } = (0, util_1.getContainingTrack)(self);
     const { rpcManager } = (0, util_1.getSession)(self);
     const view = (0, util_1.getContainingView)(self);

package/dist/shared/index.d.ts

@@ -33,4 +33,13 @@ export declare const FilterModel: import("mobx-state-tree").IModelType<{
         value: import("mobx-state-tree").ISimpleType<string>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export interface IFilter {
+    flagExclude: number;
+    flagInclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
 export {};

package/dist/util.d.ts

@@ -5,15 +5,9 @@ import { IAutorunOptions } from 'mobx';
 export declare function getTag(feature: Feature, tag: string): any;
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {
-    fr: {
-        [key: string]: string;
-    };
-    rf: {
-        [key: string]: string;
-    };
-    ff: {
-        [key: string]: string;
-    };
+    fr: Record<string, string>;
+    rf: Record<string, string>;
+    ff: Record<string, string>;
 };
 export declare const pairMap: {
     readonly LR: "color_pair_lr";

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
-declare const _default: (props: {
+declare const AlignmentsFeatureDetails: (props: {
     model: IAnyStateTreeNode;
 }) => React.JSX.Element;
-export default _default;
+export default AlignmentsFeatureDetails;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -92,7 +92,7 @@ function PairLink({ locString, model, }) {
             navToLoc(locString, model);
         }, href: "#" }, locString));
 }
-export default observer(function AlignmentFeatureDetails(props) {
+const AlignmentsFeatureDetails = observer(function (props) {
     const { model } = props;
     const feat = clone(model.featureData);
     const SA = getTag('SA', feat);
@@ -103,3 +103,4 @@ export default observer(function AlignmentFeatureDetails(props) {
         SA ? React.createElement(SupplementaryAlignments, { model: model, tag: SA }) : null,
         feat.flags !== undefined ? (React.createElement(AlignmentFlags, { feature: feat, ...props })) : null));
 });
+export default AlignmentsFeatureDetails;

package/esm/AlignmentsFeatureDetail/util.d.ts

@@ -1,8 +1,6 @@
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTag(tag: string, feat: {
-    tags?: {
-        [key: string]: unknown;
-    };
+    tags?: Record<string, unknown>;
     [key: string]: unknown;
 }): unknown;
 export declare function navToLoc(locString: string, model: IAnyStateTreeNode): Promise<void>;

package/esm/BamAdapter/BamAdapter.d.ts

@@ -2,6 +2,7 @@ import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
+import { IFilter } from '../shared';
 interface Header {
     idToName: string[];
     nameToId: Record<string, number>;
@@ -29,15 +30,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: {
-            flagInclude: number;
-            flagExclude: number;
-            tagFilter: {
-                tag: string;
-                value: unknown;
-            };
-            readName: string;
-        };
+        filterBy: IFilter;
     }): import("rxjs").Observable<Feature>;
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
         bytes: number;

package/esm/CramAdapter/CramAdapter.d.ts

@@ -2,20 +2,12 @@ import { IndexedCramFile, CramRecord } from '@gmod/cram';
 import { BaseFeatureDataAdapter, BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region, Feature } from '@jbrowse/core/util';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+import { IFilter } from '../shared';
 interface Header {
     idToName?: string[];
     nameToId?: Record<string, number>;
     readGroups?: (string | undefined)[];
 }
-interface FilterBy {
-    flagInclude: number;
-    flagExclude: number;
-    tagFilter: {
-        tag: string;
-        value: unknown;
-    };
-    readName: string;
-}
 export default class CramAdapter extends BaseFeatureDataAdapter {
     samHeader: Header;
     private setupP?;
@@ -30,7 +22,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         cram: IndexedCramFile;
         sequenceAdapter: BaseSequenceAdapter;
     }>;
-    getHeader(opts?: BaseOptions): Promise<string | undefined>;
+    getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private seqFetch;
     private setupPre;
     private setup;
@@ -41,7 +33,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: FilterBy;
+        filterBy: IFilter;
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
     cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;

package/esm/CramAdapter/CramAdapter.js

@@ -5,6 +5,7 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
+// locals
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
 export default class CramAdapter extends BaseFeatureDataAdapter {
     constructor() {
@@ -49,7 +50,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         }
         return this.configureP;
     }
-    async getHeader(opts) {
+    async getHeader(_opts) {
         const { cram } = await this.configure();
         return cram.cram.getHeaderText();
     }

package/esm/CramAdapter/util.js

@@ -8,9 +8,7 @@ export function readFeaturesToMismatches(readFeatures, start, qual) {
     let refPos = 0;
     let sublen = 0;
     let lastPos = start;
-    for (let i = 0; i < readFeatures.length; i++) {
-        const f = readFeatures[i];
-        const { code, pos, data, sub, ref } = f;
+    for (const { refPos: p, code, pos, data, sub, ref } of readFeatures) {
         sublen = refPos - lastPos;
         lastPos = refPos;
         if (sublen && insLen > 0) {
@@ -22,7 +20,7 @@ export function readFeaturesToMismatches(readFeatures, start, qual) {
             };
             insLen = 0;
         }
-        refPos = f.refPos - 1 - start;
+        refPos = p - 1 - start;
         if (code === 'X') {
             // substitution
             mismatches[j++] = {
@@ -130,8 +128,7 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
     let sublen = 0;
     let insLen = 0;
     if (readFeatures !== undefined) {
-        for (let i = 0; i < readFeatures.length; i++) {
-            const { code, refPos, sub, data } = readFeatures[i];
+        for (const { code, refPos, sub, data } of readFeatures) {
             sublen = refPos - lastPos;
             seq += ref.slice(lastPos - refStart, refPos - refStart);
             lastPos = refPos;

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -1,7 +1,6 @@
 import React from 'react';
 import { AlignmentsDisplayModel } from '../models/model';
-declare function AlignmentsDisplay({ model }: {
+declare const AlignmentsDisplay: ({ model, }: {
     model: AlignmentsDisplayModel;
-}): React.JSX.Element | null;
-declare const _default: typeof AlignmentsDisplay;
-export default _default;
+}) => React.JSX.Element | null;
+export default AlignmentsDisplay;

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -10,7 +10,7 @@ const useStyles = makeStyles()({
         zIndex: 2,
     },
 });
-function AlignmentsDisplay({ model }) {
+const AlignmentsDisplay = observer(function AlignmentsDisplay({ model, }) {
     var _a;
     const { PileupDisplay, SNPCoverageDisplay } = model;
     const { classes } = useStyles();
@@ -30,5 +30,5 @@ function AlignmentsDisplay({ model }) {
                 top,
             } },
             React.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
-}
-export default observer(AlignmentsDisplay);
+});
+export default AlignmentsDisplay;

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

@@ -55,10 +55,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined; /**
-             * #property
-             * refers to LinearPileupDisplay sub-display model
-             */
+            message: string | undefined;
         } & IStateTreeNode<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>;
@@ -69,14 +66,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
-    readonly adapterConfig: any; /**
-     * #stateModel LinearAlignmentsDisplay
-     * extends `BaseDisplay`
-     */
+    readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    readonly DisplayMessageComponent: React.FC<any> | undefined; /**
+     * #action
+     */
     trackMenuItems(): MenuItem[];
     readonly viewMenuActions: MenuItem[];
     regionCannotBeRendered(): null;

package/esm/LinearAlignmentsDisplay/models/model.js

@@ -1,3 +1,4 @@
+/* eslint-disable react-refresh/only-export-components */
 import React from 'react';
 import { autorun, when } from 'mobx';
 import { addDisposer, getSnapshot, isAlive, types, } from 'mobx-state-tree';