@jbrowse/plugin-alignments 2.2.2 → 2.3.1

package/dist/LinearPileupDisplay/model.js

@@ -41,11 +41,12 @@ const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
 const Sort_1 = __importDefault(require("@mui/icons-material/Sort"));
 const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
 const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
+// locals
 const LinearPileupDisplayBlurb_1 = __importDefault(require("./components/LinearPileupDisplayBlurb"));
 const shared_1 = require("../shared");
 // 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'))));
-const FilterByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/FilterByTag'))));
 const SortByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SortByTag'))));
 const SetFeatureHeightDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetFeatureHeight'))));
 const SetMaxHeightDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeight'))));
@@ -115,12 +116,7 @@ function stateModelFactory(configSchema) {
         /**
          * #property
          */
-        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
-            flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
-            flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
-            readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-            tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({ tag: mobx_state_tree_1.types.string, value: mobx_state_tree_1.types.string })),
-        }), {}),
+        filterBy: mobx_state_tree_1.types.optional(shared_1.FilterModel, {}),
     }))
         .volatile(() => ({
         colorTagMap: mobx_1.observable.map({}),
@@ -679,12 +675,31 @@ function stateModelFactory(configSchema) {
                     },
                     {
                         label: 'Set feature height',
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(doneCallback => [
-                                SetFeatureHeightDlg,
-                                { model: self, handleClose: doneCallback },
-                            ]);
-                        },
+                        subMenu: [
+                            {
+                                label: 'Normal',
+                                onClick: () => {
+                                    self.setFeatureHeight(7);
+                                    self.setNoSpacing(false);
+                                },
+                            },
+                            {
+                                label: 'Compact',
+                                onClick: () => {
+                                    self.setFeatureHeight(2);
+                                    self.setNoSpacing(true);
+                                },
+                            },
+                            {
+                                label: 'Manually set height',
+                                onClick: () => {
+                                    (0, util_1.getSession)(self).queueDialog(doneCallback => [
+                                        SetFeatureHeightDlg,
+                                        { model: self, handleClose: doneCallback },
+                                    ]);
+                                },
+                            },
+                        ],
                     },
                     {
                         label: 'Set max height',

package/dist/LinearPileupDisplay/model.js.map

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

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+import { LinearReadArcsDisplayModel } from '../model';
+declare const _default: ({ model, }: {
+    model: LinearReadArcsDisplayModel;
+}) => JSX.Element;
+export default _default;

package/dist/LinearReadArcsDisplay/components/ReactComponent.js

@@ -0,0 +1,49 @@
+"use strict";
+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 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 => ({
+    loading: {
+        paddingLeft: '0.6em',
+        backgroundColor: theme.palette.action.disabledBackground,
+        backgroundImage: 'repeating-linear-gradient(45deg, transparent, transparent 5px, rgba(255,255,255,.5) 5px, rgba(255,255,255,.5) 10px)',
+        height: '100%',
+        width: '100%',
+        pointerEvents: 'none',
+        textAlign: 'center',
+    },
+}));
+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-${model.drawn}`, ref: ref => {
+            if ((0, mobx_state_tree_1.isAlive)(model)) {
+                model.setRef(ref);
+            }
+        }, style: {
+            position: 'absolute',
+            left: -view.offsetPx + model.lastDrawnOffsetPx,
+            width: view.dynamicBlocks.totalWidthPx,
+            height: model.height,
+        }, width: view.dynamicBlocks.totalWidthPx * 2, height: model.height * 2 }));
+});
+exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
+    const view = (0, util_1.getContainingView)(model);
+    const { classes } = useStyles();
+    const err = model.error;
+    return err ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${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 }));
+});
+//# sourceMappingURL=ReactComponent.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../../src/LinearReadArcsDisplay/components/ReactComponent.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,qDAAyC;AACzC,uCAA0C;AAC1C,2CAAqC;AACrC,6CAAsD;AACtD,yCAAkD;AAClD,kFAG2C;AAO3C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,WAAW,EAAE,OAAO;QACpB,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,kBAAkB;QACxD,eAAe,EACb,qHAAqH;QACvH,MAAM,EAAE,MAAM;QACd,KAAK,EAAE,MAAM;QACb,aAAa,EAAE,MAAM;QACrB,SAAS,EAAE,QAAQ;KACpB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,IAAI,GAAG,IAAA,qBAAQ,EAAC,UAAU,EAC9B,KAAK,GAGN;IACC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,KAAK,CAAQ,CAAA;IAC5C,OAAO,CACL,yDACe,eAAe,KAAK,CAAC,KAAK,EAAE,EACzC,GAAG,EAAE,GAAG,CAAC,EAAE;YACT,IAAI,IAAA,yBAAO,EAAC,KAAK,CAAC,EAAE;gBAClB,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;aAClB;QACH,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,CAAC,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,iBAAiB;YAC9C,KAAK,EAAE,IAAI,CAAC,aAAa,CAAC,YAAY;YACtC,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,EACD,KAAK,EAAE,IAAI,CAAC,aAAa,CAAC,YAAY,GAAG,CAAC,EAC1C,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,CAAC,GACxB,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,kBAAe,IAAA,qBAAQ,EAAC,UAAU,EAChC,KAAK,GAGN;IACC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,KAAK,CAAC,CAAA;IACrC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,KAAK,CAAC,KAAK,CAAA;IACvB,OAAO,GAAG,CAAC,CAAC,CAAC,CACX,8BAAC,oCAAQ,IACP,OAAO,EAAE,GAAG,GAAG,EAAE,EACjB,QAAQ,EAAC,OAAO,EAChB,UAAU,EAAE,QAAQ,EACpB,MAAM,EAAE,KAAK,CAAC,MAAM,GACpB,CACH,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAClB,uCACE,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,KAAK,EAAE;YACL,KAAK,EAAE,IAAI,CAAC,aAAa,CAAC,YAAY;YACtC,MAAM,EAAE,EAAE;YACV,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC;SAClC;QAED,8BAAC,oBAAe,IAAC,OAAO,EAAE,KAAK,CAAC,OAAO,GAAI,CACvC,CACP,CAAC,CAAC,CAAC,CACF,8BAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI,CACvB,CAAA;AACH,CAAC,CAAC,CAAA"}

package/dist/LinearReadArcsDisplay/configSchema.d.ts

@@ -0,0 +1,6 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #config LinearReadArcsDisplay
+ */
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchemaF;

package/dist/LinearReadArcsDisplay/configSchema.js

@@ -0,0 +1,52 @@
+"use strict";
+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
+ */
+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
+         */
+        colorScheme: {
+            type: 'stringEnum',
+            model: mobx_state_tree_1.types.enumeration('colorScheme', [
+                'strand',
+                'normal',
+                'insertSize',
+                'insertSizeAndOrientation',
+                'mappingQuality',
+                'tag',
+            ]),
+            description: 'color scheme to use',
+            defaultValue: 'normal',
+        },
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
+        explicitlyTyped: true,
+    });
+}
+exports.default = configSchemaF;
+//# sourceMappingURL=configSchema.js.map

package/dist/LinearReadArcsDisplay/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/LinearReadArcsDisplay/drawFeats.d.ts

@@ -0,0 +1,14 @@
+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;
+}, ctx: CanvasRenderingContext2D): Promise<void>;

package/dist/LinearReadArcsDisplay/drawFeats.js

@@ -0,0 +1,162 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.hasPairedReads = void 0;
+const util_1 = require("@jbrowse/core/util");
+// locals
+const color_1 = require("../shared/color");
+const MismatchParser_1 = require("../MismatchParser");
+function hasPairedReads(features) {
+    for (const f of features.chains.values()) {
+        if (f[0].flags & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+exports.hasPairedReads = hasPairedReads;
+async function drawFeats(self, ctx) {
+    var _a;
+    const { chainData } = self;
+    if (!chainData) {
+        return;
+    }
+    const displayHeight = self.height;
+    const view = (0, util_1.getContainingView)(self);
+    const { assemblyManager } = (0, util_1.getSession)(self);
+    self.setLastDrawnOffsetPx(view.offsetPx);
+    ctx.lineWidth = self.lineWidthSetting;
+    const { chains, stats } = chainData;
+    const hasPaired = hasPairedReads(chainData);
+    const assemblyName = view.assemblyNames[0];
+    const asm = assemblyManager.get(assemblyName);
+    const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
+    function draw(k1, k2, longRange) {
+        const s1 = k1.strand;
+        const s2 = k2.strand;
+        const f1 = s1 === -1;
+        const f2 = s2 === -1;
+        const p1 = f1 ? k1.start : k1.end;
+        const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start;
+        const r1 = view.bpToPx({ refName: k1.refName, coord: p1 });
+        const r2 = view.bpToPx({ refName: k2.refName, coord: p2 });
+        if (r1 && r2) {
+            const radius = (r2.offsetPx - r1.offsetPx) / 2;
+            const absrad = Math.abs(radius);
+            const p = r1.offsetPx - view.offsetPx;
+            // 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) {
+                ctx.moveTo(p, 0);
+                ctx.beginPath();
+            }
+            else {
+                ctx.beginPath();
+                ctx.moveTo(p, 0);
+            }
+            if (longRange) {
+                ctx.strokeStyle = 'red';
+            }
+            else {
+                if (hasPaired) {
+                    if (type === 'insertSizeAndOrientation') {
+                        ctx.strokeStyle = (0, color_1.getInsertSizeAndOrientationColor)(k1, k2, stats);
+                    }
+                    else if (type === 'orientation') {
+                        ctx.strokeStyle = (0, color_1.getOrientationColor)(k1);
+                    }
+                    else if (type === 'insertSize') {
+                        ctx.strokeStyle = (0, color_1.getInsertSizeColor)(k1, k2, stats) || 'grey';
+                    }
+                    else if (type === 'gradient') {
+                        ctx.strokeStyle = `hsl(${Math.log10(Math.abs(p1 - p2)) * 10},50%,50%)`;
+                    }
+                }
+                else {
+                    if (type === 'orientation' || type === 'insertSizeAndOrientation') {
+                        if (s1 === -1 && s2 === 1) {
+                            ctx.strokeStyle = 'navy';
+                        }
+                        else if (s1 === 1 && s2 === -1) {
+                            ctx.strokeStyle = 'green';
+                        }
+                        else {
+                            ctx.strokeStyle = 'grey';
+                        }
+                    }
+                    else if (type === 'gradient') {
+                        ctx.strokeStyle = `hsl(${Math.log10(Math.abs(p1 - p2)) * 10},50%,50%)`;
+                    }
+                }
+            }
+            const destX = p + radius * 2;
+            const destY = Math.min(displayHeight, absrad);
+            if (longRange) {
+                ctx.arc(p + radius, 0, absrad, 0, Math.PI);
+            }
+            else {
+                ctx.bezierCurveTo(p, destY, destX, destY, destX, 0);
+            }
+            ctx.stroke();
+        }
+        else if (r1 && self.drawInter) {
+            // draws a vertical line off to middle of nowhere if the second end not found
+            const p = r1.offsetPx - view.offsetPx;
+            ctx.strokeStyle = 'purple';
+            ctx.beginPath();
+            ctx.moveTo(p, 0);
+            ctx.lineTo(p, displayHeight);
+            ctx.stroke();
+        }
+    }
+    for (let i = 0; i < chains.length; i++) {
+        let chain = chains[i];
+        if (chain.length === 1 && self.drawLongRange) {
+            // singleton feature
+            const f = chain[0];
+            // special case where we look at RPOS/RNEXT
+            if (hasPaired) {
+                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+                const refName = (asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(f.next_ref)) || f.next_ref;
+                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+                const coord = f.next_pos;
+                draw(f, {
+                    refName,
+                    start: coord,
+                    end: coord,
+                    strand: f.strand,
+                }, true);
+            }
+            // special case where we look at SA
+            else {
+                const suppAlns = (0, MismatchParser_1.featurizeSA)(f.SA, f.id, f.strand, f.name);
+                const features = [f, ...suppAlns].sort((a, b) => a.clipPos - b.clipPos);
+                for (let i = 0; i < features.length - 1; i++) {
+                    const f = features[i];
+                    const v1 = features[i + 1];
+                    draw(f, {
+                        refName: (asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(v1.refName)) || v1.refName,
+                        start: v1.start,
+                        end: v1.end,
+                        strand: v1.strand,
+                    }, true);
+                }
+            }
+        }
+        else {
+            if (!hasPaired) {
+                chain.sort((a, b) => a.clipPos - b.clipPos);
+                chain = chain.filter(f => !(f.flags & 256));
+            }
+            else {
+                // ignore split/supplementary reads for hasPaired=true for now
+                chain = chain.filter(f => !(f.flags & 2048));
+            }
+            for (let i = 0; i < chain.length - 1; i++) {
+                draw(chain[i], chain[i + 1], false);
+            }
+        }
+    }
+}
+exports.default = drawFeats;
+//# sourceMappingURL=drawFeats.js.map

package/dist/LinearReadArcsDisplay/drawFeats.js.map

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package/dist/LinearReadArcsDisplay/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/dist/LinearReadArcsDisplay/index.js

@@ -0,0 +1,27 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+// locals
+const ReactComponent_1 = __importDefault(require("./components/ReactComponent"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
+function register(pluginManager) {
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchema_1.default)(pluginManager);
+        return new DisplayType_1.default({
+            name: 'LinearReadArcsDisplay',
+            displayName: 'Arc display',
+            configSchema,
+            stateModel: (0, model_1.default)(configSchema),
+            trackType: 'AlignmentsTrack',
+            viewType: 'LinearGenomeView',
+            subDisplay: { type: 'LinearAlignmentsDisplay', lowerPanel: true },
+            ReactComponent: ReactComponent_1.default,
+        });
+    });
+}
+exports.default = register;
+//# sourceMappingURL=index.js.map

package/dist/LinearReadArcsDisplay/index.js.map

@@ -0,0 +1 @@
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