@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -15,144 +15,111 @@ 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.SharedLinearPileupDisplayMixin = SharedLinearPileupDisplayMixin;
 const react_1 = require("react");
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const configuration_1 = require("@jbrowse/core/configuration");
 const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
-const tracks_1 = require("@jbrowse/core/util/tracks");
+const Icons_1 = require("@jbrowse/core/ui/Icons");
 const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-// icons
-const Icons_1 = require("@jbrowse/core/ui/Icons");
-const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
 const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
-// locals
-const LinearPileupDisplayBlurb_1 = __importDefault(require("./components/LinearPileupDisplayBlurb"));
+const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const util_2 = require("../util");
+const LinearPileupDisplayBlurb_1 = __importDefault(require("./components/LinearPileupDisplayBlurb"));
 const getUniqueTags_1 = require("../shared/getUniqueTags");
-const util_3 = require("../shared/util");
-// lazies
 const FilterByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/FilterByTagDialog'))));
 const ColorByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByTagDialog'))));
 const SetFeatureHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetFeatureHeightDialog'))));
 const SetMaxHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeightDialog'))));
-// using a map because it preserves order
 const rendererTypes = new Map([
     ['pileup', 'PileupRenderer'],
     ['svg', 'SvgFeatureRenderer'],
 ]);
-/**
- * #stateModel SharedLinearPileupDisplayMixin
- * #category display
- * extends `BaseLinearDisplay`
- */
 function SharedLinearPileupDisplayMixin(configSchema) {
     return mobx_state_tree_1.types
         .compose(plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        /**
-         * #property
-         */
         featureHeight: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        /**
-         * #property
-         */
         noSpacing: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
         fadeLikelihood: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
         trackMaxHeight: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        /**
-         * #property
-         */
-        colorBy: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
-        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), util_3.defaultFilterFlags),
-        /**
-         * #property
-         */
+        colorBySetting: mobx_state_tree_1.types.frozen(),
+        filterBySetting: mobx_state_tree_1.types.frozen(),
         jexlFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string), []),
+        hideSmallIndelsSetting: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
     }))
         .volatile(() => ({
         colorTagMap: mobx_1.observable.map({}),
         featureUnderMouseVolatile: undefined,
         tagsReady: false,
+    }))
+        .views(self => ({
+        get colorBy() {
+            var _a;
+            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
+        },
+        get filterBy() {
+            var _a;
+            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
+        },
     }))
         .views(self => ({
         get autorunReady() {
             const view = (0, util_1.getContainingView)(self);
-            return (view.initialized &&
-                self.featureDensityStatsReady &&
-                !self.regionTooLarge);
+            return view.initialized && self.statsReadyAndRegionNotTooLarge;
+        },
+        get hideSmallIndels() {
+            return self.hideSmallIndelsSetting;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setTagsReady(flag) {
             self.tagsReady = flag;
         },
-        /**
-         * #action
-         */
         setMaxHeight(n) {
             self.trackMaxHeight = n;
         },
-        /**
-         * #action
-         */
         setFeatureHeight(n) {
             self.featureHeight = n;
         },
-        /**
-         * #action
-         */
         setNoSpacing(flag) {
             self.noSpacing = flag;
         },
-        /**
-         * #action
-         */
         setColorScheme(colorScheme) {
             self.colorTagMap = mobx_1.observable.map({});
-            self.colorBy = {
+            self.colorBySetting = {
                 ...colorScheme,
             };
             if (colorScheme.tag) {
                 self.tagsReady = false;
             }
         },
-        /**
-         * #action
-         */
         updateColorTagMap(uniqueTag) {
-            // pale color scheme
-            // https://cran.r-project.org/web/packages/khroma/vignettes/tol.html
-            // e.g. "tol_light"
             const colorPalette = [
                 '#BBCCEE',
                 'pink',
@@ -172,15 +139,9 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                 }
             });
         },
-        /**
-         * #action
-         */
         setFeatureUnderMouse(feat) {
             self.featureUnderMouseVolatile = feat;
         },
-        /**
-         * #action
-         */
         selectFeature(feature) {
             const session = (0, util_1.getSession)(self);
             if ((0, util_1.isSessionModelWithWidgets)(session)) {
@@ -193,82 +154,53 @@ function SharedLinearPileupDisplayMixin(configSchema) {
             }
             session.setSelection(feature);
         },
-        /**
-         * #action
-         * uses copy-to-clipboard and generates notification
-         */
         copyFeatureToClipboard(feature) {
             const { uniqueId, ...rest } = feature.toJSON();
             const session = (0, util_1.getSession)(self);
             (0, copy_to_clipboard_1.default)(JSON.stringify(rest, null, 4));
             session.notify('Copied to clipboard', 'success');
         },
-        /**
-         * #action
-         */
         setConfig(conf) {
             self.configuration = conf;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
-            self.filterBy = {
+            self.filterBySetting = {
                 ...filter,
             };
         },
-        /**
-         * #action
-         */
         setJexlFilters(filters) {
             self.jexlFilters = (0, mobx_state_tree_1.cast)(filters);
         },
+        setHideSmallIndels(arg) {
+            self.hideSmallIndelsSetting = arg;
+        },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get rendererConfig() {
-            const { featureHeight, noSpacing, trackMaxHeight, rendererTypeName } = self;
+            const { featureHeight: height, noSpacing, hideSmallIndels, trackMaxHeight: maxHeight, rendererTypeName, } = self;
             const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
             return self.rendererType.configSchema.create({
                 ...configBlob,
-                ...(featureHeight !== undefined ? { height: featureHeight } : {}),
+                ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
+                ...(height !== undefined ? { height } : {}),
                 ...(noSpacing !== undefined ? { noSpacing } : {}),
-                ...(trackMaxHeight !== undefined
-                    ? { maxHeight: trackMaxHeight }
-                    : {}),
+                ...(maxHeight !== undefined ? { maxHeight } : {}),
             }, (0, util_1.getEnv)(self));
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get maxHeight() {
             return (0, configuration_1.readConfObject)(self.rendererConfig, 'maxHeight');
         },
-        /**
-         * #getter
-         */
         get featureHeightSetting() {
             return (0, configuration_1.readConfObject)(self.rendererConfig, 'height');
         },
-        /**
-         * #getter
-         */
         get featureUnderMouse() {
             return self.featureUnderMouseVolatile;
         },
-        /**
-         * #getter
-         */
         renderReady() {
             return self.tagsReady;
         },
-        /**
-         * #getter
-         */
         get filters() {
             return new serializableFilterChain_1.default({ filters: self.jexlFilters });
         },
@@ -276,9 +208,6 @@ function SharedLinearPileupDisplayMixin(configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
-            /**
-             * #getter
-             */
             get rendererTypeName() {
                 const viewName = (0, configuration_1.getConf)(self, 'defaultRendering');
                 const rendererType = rendererTypes.get(viewName);
@@ -287,9 +216,6 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                 }
                 return rendererType;
             },
-            /**
-             * #method
-             */
             contextMenuItems() {
                 const feat = self.contextMenuFeature;
                 return feat
@@ -312,15 +238,9 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                     ]
                     : [];
             },
-            /**
-             * #getter
-             */
             get DisplayBlurb() {
                 return LinearPileupDisplayBlurb_1.default;
             },
-            /**
-             * #method
-             */
             renderPropsPre() {
                 const { colorTagMap, colorBy, filterBy, rpcDriverName } = self;
                 const superProps = superRenderProps();
@@ -363,7 +283,6 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                     onClick() {
                         self.clearFeatureSelection();
                     },
-                    // similar to click but opens a menu with further options
                     async onFeatureContextMenu(_, featureId) {
                         const session = (0, util_1.getSession)(self);
                         const { rpcManager } = session;
@@ -392,9 +311,6 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                     },
                 };
             },
-            /**
-             * #method
-             */
             colorSchemeSubMenuItems() {
                 return [
                     {
@@ -459,9 +375,6 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                     },
                 ];
             },
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -497,6 +410,15 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                             },
                         ],
                     },
+                    {
+                        label: 'Hide small indels (<10bp)',
+                        priority: -1,
+                        type: 'checkbox',
+                        checked: self.hideSmallIndels,
+                        onClick: () => {
+                            self.setHideSmallIndels(!self.hideSmallIndels);
+                        },
+                    },
                     {
                         label: 'Set max height...',
                         priority: -1,
@@ -556,9 +478,6 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                     self.setTagsReady(true);
                 }
             }, { delay: 1000 });
-            // autorun synchronizes featureUnderMouse with featureIdUnderMouse
-            // asynchronously. this is needed due to how we do not serialize all
-            // features from the BAM/CRAM over the rpc
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
                 var _a;
                 const session = (0, util_1.getSession)(self);
@@ -577,10 +496,6 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                                 layoutId: view.id,
                                 rendererType: 'PileupRenderer',
                             }));
-                            // check featureIdUnderMouse is still the same as the
-                            // feature.id that was returned e.g. that the user hasn't
-                            // moused over to a new position during the async operation
-                            // above
                             if ((0, mobx_state_tree_1.isAlive)(self) &&
                                 feature &&
                                 self.featureIdUnderMouse === feature.uniqueId) {
@@ -595,5 +510,16 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                 }
             }));
         },
-    }));
+    }))
+        .preProcessSnapshot(snap => {
+        if (snap) {
+            const { colorBy, colorBySetting, filterBySetting, filterBy, ...rest } = snap;
+            return {
+                ...rest,
+                filterBySetting: filterBySetting || filterBy,
+                colorBySetting: colorBySetting || colorBy,
+            };
+        }
+        return snap;
+    });
 }

package/dist/LinearPileupDisplay/components/ColorByTagDialog.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 interface Tag {
     type: string;
     tag: string;
@@ -8,5 +7,5 @@ declare const ColorByTagDialog: ({ model, handleClose, }: {
         setColorScheme: (arg: Tag) => void;
     };
     handleClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default ColorByTagDialog;

package/dist/LinearPileupDisplay/components/ColorByTagDialog.js

@@ -1,49 +1,20 @@
 "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;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const ColorByTagDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
     const [tag, setTag] = (0, react_1.useState)('');
     const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by tag" },
-        react_1.default.createElement(material_1.DialogContent, { style: { overflowX: 'hidden' } },
-            react_1.default.createElement(material_1.Typography, null, "Enter tag to color by: "),
-            react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."),
-            react_1.default.createElement(material_1.TextField, { value: tag, onChange: event => {
-                    setTag(event.target.value);
-                }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", slotProps: {
-                    htmlInput: { maxLength: 2 },
-                } }),
-            react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
-                        model.setColorScheme({ type: 'tag', tag });
-                        handleClose();
-                    }, disabled: !validTag }, "Submit"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel")))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by tag", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { style: { overflowX: 'hidden' }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Enter tag to color by: " }), (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "textSecondary", children: "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc." }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: tag, onChange: event => {
+                        setTag(event.target.value);
+                    }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", slotProps: {
+                        htmlInput: { maxLength: 2 },
+                    } }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
+                                model.setColorScheme({ type: 'tag', tag });
+                                handleClose();
+                            }, disabled: !validTag, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose, children: "Cancel" })] })] }) }));
 });
 exports.default = ColorByTagDialog;

package/dist/LinearPileupDisplay/components/GroupByDialog.d.ts

@@ -1,11 +1,10 @@
-import React from 'react';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
 declare const GroupByTagDialog: (props: {
     model: {
         adapterConfig: AnyConfigurationModel;
         configuration: AnyConfigurationModel;
     } & IAnyStateTreeNode;
     handleClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default GroupByTagDialog;