@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/dist/LinearPileupDisplay/model.js

@@ -15,93 +15,61 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
-const tracks_1 = require("@jbrowse/core/util/tracks");
 const util_1 = require("@jbrowse/core/util");
-// icons
-const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const ColorLens_1 = __importDefault(require("@mui/icons-material/ColorLens"));
 const SwapVert_1 = __importDefault(require("@mui/icons-material/SwapVert"));
+const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
 const Workspaces_1 = __importDefault(require("@mui/icons-material/Workspaces"));
-const ColorLens_1 = __importDefault(require("@mui/icons-material/ColorLens"));
-// locals
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const SharedLinearPileupDisplayMixin_1 = require("./SharedLinearPileupDisplayMixin");
-const util_2 = require("../util");
 const getUniqueModifications_1 = require("../shared/getUniqueModifications");
-// lazies
+const util_2 = require("../util");
 const SortByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SortByTagDialog'))));
 const GroupByDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/GroupByDialog'))));
-/**
- * #stateModel LinearPileupDisplay
- * #category display
- * extends
- * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
- */
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearPileupDisplay', (0, SharedLinearPileupDisplayMixin_1.SharedLinearPileupDisplayMixin)(configSchema), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearPileupDisplay'),
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        /**
-         * #property
-         */
         showSoftClipping: false,
-        /**
-         * #property
-         */
         mismatchAlpha: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
         sortedBy: mobx_state_tree_1.types.frozen(),
     }))
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         sortReady: false,
-        /**
-         * #volatile
-         */
         currSortBpPerPx: 0,
-        /**
-         * #volatile
-         */
         visibleModifications: mobx_1.observable.map({}),
-        /**
-         * #volatile
-         */
         modificationsReady: false,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setCurrSortBpPerPx(n) {
             self.currSortBpPerPx = n;
         },
-        /**
-         * #action
-         */
         updateVisibleModifications(uniqueModifications) {
             uniqueModifications.forEach(value => {
                 if (!self.visibleModifications.has(value.type)) {
@@ -112,39 +80,21 @@ function stateModelFactory(configSchema) {
                 }
             });
         },
-        /**
-         * #action
-         */
         setModificationsReady(flag) {
             self.modificationsReady = flag;
         },
-        /**
-         * #action
-         */
         setSortReady(flag) {
             self.sortReady = flag;
         },
-        /**
-         * #action
-         */
         clearSelected() {
             self.sortedBy = undefined;
         },
-        /**
-         * #action
-         */
         toggleSoftClipping() {
             self.showSoftClipping = !self.showSoftClipping;
         },
-        /**
-         * #action
-         */
         toggleMismatchAlpha() {
             self.mismatchAlpha = !self.mismatchAlpha;
         },
-        /**
-         * #action
-         */
         setSortedBy(type, tag) {
             const { centerLineInfo } = (0, util_1.getContainingView)(self);
             if (!centerLineInfo) {
@@ -164,23 +114,14 @@ function stateModelFactory(configSchema) {
                 tag,
             };
         },
-        /**
-         * #action
-         * overrides base from SharedLinearPileupDisplay to make sortReady false
-         * since changing feature height destroys the sort-induced layout
-         */
         setFeatureHeight(n) {
             self.sortReady = false;
             self.featureHeight = n;
         },
     }))
         .actions(self => {
-        // resets the sort object and refresh whole display on reload
         const superReload = self.reload;
         return {
-            /**
-             * #action
-             */
             reload() {
                 self.clearSelected();
                 superReload();
@@ -188,21 +129,16 @@ function stateModelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #getter
-         */
         get visibleModificationTypes() {
             return [...self.visibleModifications.keys()];
         },
-        /**
-         * #getter
-         */
         get rendererConfig() {
-            const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, } = self;
+            const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, hideSmallIndels, } = self;
             const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
             return self.rendererType.configSchema.create({
                 ...configBlob,
                 ...(featureHeight !== undefined ? { height: featureHeight } : {}),
+                ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
                 ...(noSpacing !== undefined ? { noSpacing } : {}),
                 ...(mismatchAlpha !== undefined ? { mismatchAlpha } : {}),
                 ...(trackMaxHeight !== undefined
@@ -214,15 +150,9 @@ function stateModelFactory(configSchema) {
         .views(self => {
         const { renderReady: superRenderReady } = self;
         return {
-            /**
-             * #getter
-             */
             get mismatchAlphaSetting() {
                 return (0, configuration_1.readConfObject)(self.rendererConfig, 'mismatchAlpha');
             },
-            /**
-             * #method
-             */
             renderReady() {
                 const view = (0, util_1.getContainingView)(self);
                 return (self.modificationsReady &&
@@ -234,9 +164,6 @@ function stateModelFactory(configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderPropsPre: superRenderPropsPre, renderProps: superRenderProps, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
         return {
-            /**
-             * #method
-             */
             renderPropsPre() {
                 const { sortedBy, showSoftClipping, visibleModifications } = self;
                 const superProps = superRenderPropsPre();
@@ -247,9 +174,6 @@ function stateModelFactory(configSchema) {
                     visibleModifications: Object.fromEntries(visibleModifications.toJSON()),
                 };
             },
-            /**
-             * #method
-             */
             renderProps() {
                 const { sortReady } = self;
                 const result = superRenderProps();
@@ -258,9 +182,6 @@ function stateModelFactory(configSchema) {
                     notReady: result.notReady || !sortReady,
                 };
             },
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -395,7 +316,10 @@ function stateModelFactory(configSchema) {
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(handleClose => [
                                 GroupByDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },
@@ -406,8 +330,6 @@ function stateModelFactory(configSchema) {
                         checked: self.showSoftClipping,
                         onClick: () => {
                             self.toggleSoftClipping();
-                            // if toggling from off to on, will break sort for this track
-                            // so clear it
                             if (self.showSoftClipping) {
                                 self.clearSelected();
                             }
@@ -445,8 +367,6 @@ function stateModelFactory(configSchema) {
                 if (sortedBy &&
                     (!sortReady || self.currSortBpPerPx === view.bpPerPx)) {
                     const { pos, refName, assemblyName } = sortedBy;
-                    // render just the sorted region first
-                    // @ts-expect-error
                     await self.rendererType.renderInClient(rpcManager, {
                         assemblyName,
                         regions: [

package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { LinearReadArcsDisplayModel } from '../model';
+import type { LinearReadArcsDisplayModel } from '../model';
 declare const LinearReadArcsReactComponent: ({ model, }: {
     model: LinearReadArcsDisplayModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default LinearReadArcsReactComponent;

package/dist/LinearReadArcsDisplay/components/ReactComponent.js

@@ -1,50 +1,23 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
 const BaseDisplayComponent_1 = __importDefault(require("../../shared/components/BaseDisplayComponent"));
 const Arcs = (0, mobx_react_1.observer)(function ({ model, }) {
     const view = (0, util_1.getContainingView)(model);
     const width = Math.round(view.dynamicBlocks.totalWidthPx);
     const height = model.height;
-    // biome-ignore lint/correctness/useExhaustiveDependencies:
     const cb = (0, react_1.useCallback)((ref) => {
         model.setRef(ref);
-    }, 
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-    [model, width, height]);
-    // note: the position absolute below avoids scrollbar from appearing on track
-    return (react_1.default.createElement("canvas", { "data-testid": "arc-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
+    }, [model, width, height]);
+    return ((0, jsx_runtime_1.jsx)("canvas", { "data-testid": "arc-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
 const LinearReadArcsReactComponent = (0, mobx_react_1.observer)(function ({ model, }) {
-    return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
-        react_1.default.createElement(Arcs, { model: model })));
+    return ((0, jsx_runtime_1.jsx)(BaseDisplayComponent_1.default, { model: model, children: (0, jsx_runtime_1.jsx)(Arcs, { model: model }) }));
 });
 exports.default = LinearReadArcsReactComponent;

package/dist/LinearReadArcsDisplay/configSchema.d.ts

@@ -1,40 +1,32 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearReadArcsDisplay
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     maxFeatureScreenDensity: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     lineWidth: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     jitter: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
-    colorScheme: {
+    colorBy: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
+        defaultValue: {
+            type: string;
+        };
+    };
+    filterBy: {
+        type: string;
+        defaultValue: {
+            flagInclude: number;
+            flagExclude: number;
+        };
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     renderer: import("mobx-state-tree").IAnyModelType;

package/dist/LinearReadArcsDisplay/configSchema.js

@@ -2,56 +2,33 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 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 LinearReadArcsDisplay
- */
+const util_1 = require("../shared/util");
 function configSchemaF(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearReadArcsDisplay', {
-        /**
-         * #slot
-         */
         maxFeatureScreenDensity: {
             type: 'number',
             description: 'maximum features per pixel that is displayed in the view',
             defaultValue: 5,
         },
-        /**
-         * #slot
-         */
         lineWidth: {
             type: 'number',
             description: 'set arc line width',
             defaultValue: 1,
         },
-        /**
-         * #slot
-         */
         jitter: {
             type: 'number',
             description: 'jitters the x position so e.g. if many reads map to exact same x position, jittering makes it easy to see that there are many of them',
             defaultValue: 0,
         },
-        /**
-         * #slot
-         */
-        colorScheme: {
-            type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('colorScheme', [
-                'strand',
-                'normal',
-                'insertSize',
-                'insertSizeAndOrientation',
-                'mappingQuality',
-                'tag',
-            ]),
-            description: 'color scheme to use',
-            defaultValue: 'normal',
+        colorBy: {
+            type: 'frozen',
+            defaultValue: { type: 'insertSizeAndOrientation' },
+        },
+        filterBy: {
+            type: 'frozen',
+            defaultValue: util_1.defaultFilterFlags,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
         explicitlyTyped: true,
     });

package/dist/LinearReadArcsDisplay/drawFeats.d.ts

@@ -1,2 +1,2 @@
-import { LinearReadArcsDisplayModel } from './model';
+import type { LinearReadArcsDisplayModel } from './model';
 export declare function drawFeats(self: LinearReadArcsDisplayModel, ctx: CanvasRenderingContext2D, width: number, height: number): void;

package/dist/LinearReadArcsDisplay/drawFeats.js

@@ -2,15 +2,13 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.drawFeats = drawFeats;
 const util_1 = require("@jbrowse/core/util");
-// locals
-const color_1 = require("../shared/color");
 const MismatchParser_1 = require("../MismatchParser");
+const color_1 = require("../shared/color");
 const util_2 = require("../shared/util");
 function jitter(n) {
     return Math.random() * 2 * n - n;
 }
 function drawLineAtOffset(ctx, offset, height, color) {
-    // draws a vertical line off to middle of nowhere if the second end not found
     ctx.strokeStyle = color;
     ctx.beginPath();
     ctx.moveTo(offset, 0);
@@ -50,9 +48,6 @@ function drawFeats(self, ctx, width, height) {
             const p = r1 - view.offsetPx;
             const p2 = r2 - view.offsetPx;
             const drawArcInsteadOfBezier = absrad > 10000;
-            // bezier (used for non-long-range arcs) requires moveTo before beginPath
-            // arc (used for long-range) requires moveTo after beginPath (or else a
-            // unwanted line at y=0 is rendered along with the arc)
             if (longRange && drawArcInsteadOfBezier) {
                 ctx.moveTo(p, 0);
                 ctx.beginPath();
@@ -100,8 +95,6 @@ function drawFeats(self, ctx, width, height) {
             const destX = p + radius * 2;
             const destY = Math.min(height + jitter(jitterVal), absrad);
             if (longRange) {
-                // avoid drawing gigantic circles that glitch out the rendering,
-                // instead draw vertical lines
                 if (absrad > 100000) {
                     drawLineAtOffset(ctx, p + jitter(jitterVal), height, 'red');
                     drawLineAtOffset(ctx, p2 + jitter(jitterVal), height, 'red');
@@ -125,7 +118,6 @@ function drawFeats(self, ctx, width, height) {
         }
     }
     for (const chain of chains) {
-        // chain.length === 1, singleton (other pairs/mates not in view)
         if (chain.length === 1 && drawLongRange) {
             const f = chain[0];
             if (hasPaired && !(f.flags & 8)) {

package/dist/LinearReadArcsDisplay/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/LinearReadArcsDisplay/index.js

@@ -15,23 +15,32 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = register;
+const react_1 = require("react");
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-// locals
 const configSchema_1 = __importDefault(require("./configSchema"));
 const model_1 = __importDefault(require("./model"));
-const react_1 = require("react");
 function register(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);