@jbrowse/plugin-alignments 2.5.0 → 2.6.0

package/dist/LinearPileupDisplay/model.js

@@ -44,6 +44,8 @@ const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
 // locals
 const LinearPileupDisplayBlurb_1 = __importDefault(require("./components/LinearPileupDisplayBlurb"));
 const shared_1 = require("../shared");
+const util_2 = require("../util");
+const util_3 = require("../util");
 // async
 const FilterByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/FilterByTag'))));
 const ColorByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByTag'))));
@@ -58,6 +60,7 @@ const rendererTypes = new Map([
 ]);
 /**
  * #stateModel LinearPileupDisplay
+ * #category display
  * extends `BaseLinearDisplay`
  */
 function stateModelFactory(configSchema) {
@@ -123,14 +126,36 @@ function stateModelFactory(configSchema) {
         modificationTagMap: mobx_1.observable.map({}),
         featureUnderMouseVolatile: undefined,
         currSortBpPerPx: 0,
-        ready: false,
+        modificationsReady: false,
+        sortReady: false,
+        tagsReady: false,
+    }))
+        .views(self => ({
+        get autorunReady() {
+            const view = (0, util_1.getContainingView)(self);
+            return (view.initialized &&
+                self.featureDensityStatsReady &&
+                !self.regionTooLarge);
+        },
     }))
         .actions(self => ({
         /**
          * #action
          */
-        setReady(flag) {
-            self.ready = flag;
+        setModificationsReady(flag) {
+            self.modificationsReady = flag;
+        },
+        /**
+         * #action
+         */
+        setTagsReady(flag) {
+            self.tagsReady = flag;
+        },
+        /**
+         * #action
+         */
+        setSortReady(flag) {
+            self.sortReady = flag;
         },
         /**
          * #action
@@ -162,18 +187,16 @@ function stateModelFactory(configSchema) {
         setColorScheme(colorScheme) {
             self.colorTagMap = mobx_1.observable.map({}); // clear existing mapping
             self.colorBy = (0, mobx_state_tree_1.cast)(colorScheme);
-            self.ready = false;
+            self.tagsReady = false;
+            self.modificationsReady = false;
         },
         /**
          * #action
          */
         updateModificationColorMap(uniqueModifications) {
-            const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
             uniqueModifications.forEach(value => {
                 if (!self.modificationTagMap.has(value)) {
-                    const totalKeys = [...self.modificationTagMap.keys()].length;
-                    const newColor = colorPalette[totalKeys];
-                    self.modificationTagMap.set(value, newColor);
+                    self.modificationTagMap.set(value, util_2.modificationColors[value] || (0, util_3.randomColor)());
                 }
             });
         },
@@ -199,8 +222,7 @@ function stateModelFactory(configSchema) {
             uniqueTag.forEach(value => {
                 if (!self.colorTagMap.has(value)) {
                     const totalKeys = [...self.colorTagMap.keys()].length;
-                    const newColor = colorPalette[totalKeys];
-                    self.colorTagMap.set(value, newColor);
+                    self.colorTagMap.set(value, colorPalette[totalKeys]);
                 }
             });
         },
@@ -210,99 +232,6 @@ function stateModelFactory(configSchema) {
         setFeatureUnderMouse(feat) {
             self.featureUnderMouseVolatile = feat;
         },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-                try {
-                    const { rpcManager } = (0, util_1.getSession)(self);
-                    const view = (0, util_1.getContainingView)(self);
-                    const { sortedBy, colorBy, parentTrack, adapterConfig, rendererType, } = self;
-                    if (!view.initialized ||
-                        !self.featureDensityStatsReady ||
-                        self.regionTooLarge) {
-                        return;
-                    }
-                    const { staticBlocks, bpPerPx } = view;
-                    // continually generate the vc pairing, set and rerender if any
-                    // new values seen
-                    if (colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) {
-                        self.updateColorTagMap(await (0, shared_1.getUniqueTagValues)(self, colorBy, staticBlocks));
-                    }
-                    if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                        const adapter = (0, configuration_1.getConf)(parentTrack, ['adapter']);
-                        self.updateModificationColorMap(await (0, shared_1.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks));
-                    }
-                    if (sortedBy) {
-                        const { pos, refName, assemblyName } = sortedBy;
-                        // render just the sorted region first
-                        // @ts-expect-error
-                        await self.rendererType.renderInClient(rpcManager, {
-                            assemblyName,
-                            regions: [
-                                {
-                                    start: pos,
-                                    end: pos + 1,
-                                    refName,
-                                    assemblyName,
-                                },
-                            ],
-                            adapterConfig: adapterConfig,
-                            rendererType: rendererType.name,
-                            sessionId: (0, tracks_1.getRpcSessionId)(self),
-                            layoutId: view.id,
-                            timeout: 1000000,
-                            ...self.renderProps(),
-                        });
-                        self.setReady(true);
-                        self.setCurrSortBpPerPx(bpPerPx);
-                    }
-                    else {
-                        self.setReady(true);
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    self.setError(e);
-                }
-            }, { 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);
-                try {
-                    const featureId = self.featureIdUnderMouse;
-                    if (((_a = self.featureUnderMouse) === null || _a === void 0 ? void 0 : _a.id()) !== featureId) {
-                        if (!featureId) {
-                            self.setFeatureUnderMouse(undefined);
-                        }
-                        else {
-                            const sessionId = (0, tracks_1.getRpcSessionId)(self);
-                            const view = (0, util_1.getContainingView)(self);
-                            const { feature } = (await session.rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
-                                featureId,
-                                sessionId,
-                                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 (self.featureIdUnderMouse === feature.uniqueId) {
-                                self.setFeatureUnderMouse(new util_1.SimpleFeature(feature));
-                            }
-                        }
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    session.notify(`${e}`, 'error');
-                }
-            }));
-        },
         /**
          * #action
          */
@@ -361,6 +290,7 @@ function stateModelFactory(configSchema) {
             if (centerBp < 0 || !refName) {
                 return;
             }
+            self.sortReady = false;
             self.sortedBy = {
                 type,
                 pos: centerBp,
@@ -368,7 +298,6 @@ function stateModelFactory(configSchema) {
                 assemblyName,
                 tag,
             };
-            self.ready = false;
         },
         setFilterBy(filter) {
             self.filterBy = (0, mobx_state_tree_1.cast)(filter);
@@ -430,6 +359,15 @@ function stateModelFactory(configSchema) {
         get featureUnderMouse() {
             return self.featureUnderMouseVolatile;
         },
+        /**
+         * #getter
+         */
+        get renderReady() {
+            const view = (0, util_1.getContainingView)(self);
+            return (self.modificationsReady &&
+                self.tagsReady &&
+                self.currSortBpPerPx === view.bpPerPx);
+        },
     }))
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
@@ -450,7 +388,7 @@ function stateModelFactory(configSchema) {
              */
             contextMenuItems() {
                 const feat = self.contextMenuFeature;
-                const contextMenuItems = feat
+                return feat
                     ? [
                         {
                             label: 'Open feature details',
@@ -473,7 +411,6 @@ function stateModelFactory(configSchema) {
                         },
                     ]
                     : [];
-                return contextMenuItems;
             },
             /**
              * #getter
@@ -484,19 +421,16 @@ function stateModelFactory(configSchema) {
             /**
              * #method
              */
-            renderProps() {
-                const view = (0, util_1.getContainingView)(self);
-                const { colorTagMap, modificationTagMap, sortedBy, colorBy, filterBy, rpcDriverName, currSortBpPerPx, ready, } = self;
+            renderPropsPre() {
+                const { colorTagMap, modificationTagMap, sortedBy, colorBy, filterBy, rpcDriverName, } = self;
                 const superProps = superRenderProps();
                 return {
                     ...superProps,
-                    notReady: superProps.notReady ||
-                        !ready ||
-                        (sortedBy && currSortBpPerPx !== view.bpPerPx),
+                    notReady: superProps.notReady || !self.renderReady,
                     rpcDriverName,
                     displayModel: self,
-                    sortedBy,
-                    colorBy,
+                    sortedBy: sortedBy ? (0, mobx_state_tree_1.getSnapshot)(sortedBy) : undefined,
+                    colorBy: colorBy ? (0, mobx_state_tree_1.getSnapshot)(colorBy) : undefined,
                     filterBy: JSON.parse(JSON.stringify(filterBy)),
                     colorTagMap: Object.fromEntries(colorTagMap.toJSON()),
                     modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
@@ -560,6 +494,19 @@ function stateModelFactory(configSchema) {
                     },
                 };
             },
+            // renderProps and renderPropsPre are separated due to sortReady
+            // causing a infinite loop in the sort autorun, since the sort autorun
+            // uses renderProps
+            /**
+             * #method
+             */
+            renderProps() {
+                const pre = this.renderPropsPre();
+                return {
+                    ...pre,
+                    notReady: pre.notReady || !self.sortReady,
+                };
+            },
             /**
              * #method
              */
@@ -716,7 +663,106 @@ function stateModelFactory(configSchema) {
                 ];
             },
         };
-    });
+    })
+        .actions(self => ({
+        afterAttach() {
+            (0, util_2.createAutorun)(self, async () => {
+                const view = (0, util_1.getContainingView)(self);
+                if (!self.autorunReady) {
+                    return;
+                }
+                const { colorBy } = self;
+                const { staticBlocks } = view;
+                if (colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) {
+                    const vals = await (0, shared_1.getUniqueTagValues)(self, colorBy, staticBlocks);
+                    self.updateColorTagMap(vals);
+                }
+                self.setTagsReady(true);
+            }, { delay: 1000 });
+            (0, util_2.createAutorun)(self, async () => {
+                if (!self.autorunReady) {
+                    return;
+                }
+                const { parentTrack, colorBy } = self;
+                const { staticBlocks } = (0, util_1.getContainingView)(self);
+                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+                    const adapter = (0, configuration_1.getConf)(parentTrack, ['adapter']);
+                    const vals = await (0, shared_1.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks);
+                    self.updateModificationColorMap(vals);
+                }
+                self.setModificationsReady(true);
+            });
+            (0, util_2.createAutorun)(self, async () => {
+                const { rpcManager } = (0, util_1.getSession)(self);
+                const view = (0, util_1.getContainingView)(self);
+                if (!self.autorunReady) {
+                    return;
+                }
+                const { sortedBy, adapterConfig, rendererType } = self;
+                const { bpPerPx } = view;
+                if (sortedBy) {
+                    const { pos, refName, assemblyName } = sortedBy;
+                    // render just the sorted region first
+                    // @ts-expect-error
+                    await self.rendererType.renderInClient(rpcManager, {
+                        assemblyName,
+                        regions: [
+                            {
+                                start: pos,
+                                end: pos + 1,
+                                refName,
+                                assemblyName,
+                            },
+                        ],
+                        adapterConfig,
+                        rendererType: rendererType.name,
+                        sessionId: (0, tracks_1.getRpcSessionId)(self),
+                        layoutId: view.id,
+                        timeout: 1000000,
+                        ...self.renderPropsPre(),
+                    });
+                }
+                self.setCurrSortBpPerPx(bpPerPx);
+                self.setSortReady(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);
+                try {
+                    const featureId = self.featureIdUnderMouse;
+                    if (((_a = self.featureUnderMouse) === null || _a === void 0 ? void 0 : _a.id()) !== featureId) {
+                        if (!featureId) {
+                            self.setFeatureUnderMouse(undefined);
+                        }
+                        else {
+                            const sessionId = (0, tracks_1.getRpcSessionId)(self);
+                            const view = (0, util_1.getContainingView)(self);
+                            const { feature } = (await session.rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                                featureId,
+                                sessionId,
+                                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 (self.featureIdUnderMouse === feature.uniqueId) {
+                                self.setFeatureUnderMouse(new util_1.SimpleFeature(feature));
+                            }
+                        }
+                    }
+                }
+                catch (e) {
+                    console.error(e);
+                    session.notify(`${e}`, 'error');
+                }
+            }));
+        },
+    }));
 }
 exports.default = stateModelFactory;
 //# sourceMappingURL=model.js.map

package/dist/LinearPileupDisplay/model.js.map

@@ -1 +1 @@
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package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts

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

package/dist/LinearReadArcsDisplay/components/ReactComponent.js

@@ -1,52 +1,49 @@
 "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 = __importDefault(require("react"));
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mui_1 = require("tss-react/mui");
+const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const util_1 = require("@jbrowse/core/util");
-const ui_1 = require("@jbrowse/core/ui");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const useStyles = (0, mui_1.makeStyles)()(theme => {
-    const bg = theme.palette.action.disabledBackground;
-    return {
-        loading: {
-            paddingLeft: '0.6em',
-            backgroundColor: theme.palette.background.default,
-            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
-            height: '100%',
-            width: '100%',
-            pointerEvents: 'none',
-            textAlign: 'center',
-        },
-    };
-});
+const BaseDisplayComponent_1 = __importDefault(require("../../shared/BaseDisplayComponent"));
 const Arcs = (0, mobx_react_1.observer)(function ({ model, }) {
     const view = (0, util_1.getContainingView)(model);
-    return (react_1.default.createElement("canvas", { "data-testid": `Arc-display-${model.drawn}`, ref: ref => {
-            if ((0, mobx_state_tree_1.isAlive)(model)) {
-                model.setRef(ref);
-            }
-        }, style: {
-            position: 'absolute',
-            left: -view.offsetPx + model.lastDrawnOffsetPx,
-            width: view.dynamicBlocks.totalWidthPx,
-            height: model.height,
-        }, width: view.dynamicBlocks.totalWidthPx * 2, height: model.height * 2 }));
+    const width = Math.round(view.dynamicBlocks.totalWidthPx);
+    const height = model.height;
+    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 }));
 });
 exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
-    const view = (0, util_1.getContainingView)(model);
-    const { classes } = useStyles();
-    const err = model.error;
-    return err ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${err}`, severity: "error", buttonText: 'Reload', action: model.reload })) : model.loading ? (react_1.default.createElement("div", { className: classes.loading, style: {
-            width: view.dynamicBlocks.totalWidthPx,
-            height: 20,
-            position: 'absolute',
-            left: Math.max(0, -view.offsetPx),
-        } },
-        react_1.default.createElement(ui_1.LoadingEllipses, { message: model.message }))) : (react_1.default.createElement(Arcs, { model: model }));
+    return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
+        react_1.default.createElement(Arcs, { model: model })));
 });
 //# sourceMappingURL=ReactComponent.js.map

package/dist/LinearReadArcsDisplay/components/ReactComponent.js.map

@@ -1 +1 @@
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package/dist/LinearReadArcsDisplay/configSchema.d.ts

@@ -44,9 +44,6 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     fetchSizeLimit: {
         type: string;
         defaultValue: number;

package/dist/LinearReadArcsDisplay/drawFeats.d.ts

@@ -1,15 +1,2 @@
-import { ChainData } from '../shared/fetchChains';
-export declare function hasPairedReads(features: ChainData): boolean;
-export default function drawFeats(self: {
-    setLastDrawnOffsetPx: (n: number) => void;
-    drawInter?: boolean;
-    drawLongRange?: boolean;
-    setError: (e: unknown) => void;
-    colorBy?: {
-        type: string;
-    };
-    height: number;
-    chainData?: ChainData;
-    lineWidthSetting: number;
-    jitterVal: number;
-}, ctx: CanvasRenderingContext2D): Promise<void>;
+import { LinearReadArcsDisplayModel } from './model';
+export declare function drawFeats(self: LinearReadArcsDisplayModel, ctx: CanvasRenderingContext2D, width: number, height: number): void;