jbrowse-plugin-mafviewer 1.0.6 → 1.1.1

package/dist/LinearMafDisplay/stateModel.js

@@ -0,0 +1,276 @@
+import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
+import { getEnv, getSession } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { ascending } from 'd3-array';
+import { cluster, hierarchy } from 'd3-hierarchy';
+import { autorun } from 'mobx';
+import { addDisposer, isAlive, types } from 'mobx-state-tree';
+import SetRowHeightDialog from './components/SetRowHeight';
+import { maxLength, setBrLength, } from './types';
+import { normalize } from '../util';
+/**
+ * #stateModel LinearMafDisplay
+ * extends LinearBasicDisplay
+ */
+export default function stateModelFactory(configSchema, pluginManager) {
+    const LinearGenomePlugin = pluginManager.getPlugin('LinearGenomeViewPlugin');
+    const { BaseLinearDisplay } = LinearGenomePlugin.exports;
+    return types
+        .compose('LinearMafDisplay', BaseLinearDisplay, types.model({
+        /**
+         * #property
+         */
+        type: types.literal('LinearMafDisplay'),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+        /**
+         * #property
+         */
+        rowHeight: 15,
+        /**
+         * #property
+         */
+        rowProportion: 0.8,
+        /**
+         * #property
+         */
+        showAllLetters: false,
+        /**
+         * #property
+         */
+        mismatchRendering: true,
+        /**
+         * #property
+         */
+        showBranchLen: false,
+        /**
+         * #property
+         */
+        treeAreaWidth: 80,
+    }))
+        .volatile(() => ({
+        /**
+         * #volatile
+         */
+        prefersOffset: true,
+        /**
+         * #volatile
+         */
+        volatileSamples: [],
+        /**
+         * #volatile
+         */
+        tree: undefined,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setRowHeight(n) {
+            self.rowHeight = n;
+        },
+        /**
+         * #action
+         */
+        setRowProportion(n) {
+            self.rowProportion = n;
+        },
+        /**
+         * #action
+         */
+        setShowAllLetters(f) {
+            self.showAllLetters = f;
+        },
+        /**
+         * #action
+         */
+        setMismatchRendering(f) {
+            self.mismatchRendering = f;
+        },
+        /**
+         * #action
+         */
+        setSamples({ samples, tree }) {
+            self.volatileSamples = samples;
+            self.tree = tree;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get rendererTypeName() {
+            return 'LinearMafRenderer';
+        },
+        /**
+         * #getter
+         */
+        get rendererConfig() {
+            const configBlob = getConf(self, ['renderer']) || {};
+            const config = configBlob;
+            return self.rendererType.configSchema.create({
+                ...config,
+                type: 'LinearMafRenderer',
+            }, getEnv(self));
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get root() {
+            return self.tree
+                ? hierarchy(self.tree, d => d.children)
+                    // todo: investigate whether needed, typescript says children always true
+                    .sum(d => (d.children ? 0 : 1))
+                    .sort((a, b) => ascending(a.data.length || 1, b.data.length || 1))
+                : undefined;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         * generates a new tree that is clustered with x,y positions
+         */
+        get hierarchy() {
+            const r = self.root;
+            if (r) {
+                const width = self.treeAreaWidth;
+                const clust = cluster()
+                    .size([this.totalHeight, width])
+                    .separation(() => 1);
+                clust(r);
+                setBrLength(r, (r.data.length = 0), width / maxLength(r));
+                return r;
+            }
+            else {
+                return undefined;
+            }
+        },
+        /**
+         * #getter
+         */
+        get samples() {
+            return this.rowNames ? normalize(this.rowNames) : self.volatileSamples;
+        },
+        /**
+         * #getter
+         */
+        get totalHeight() {
+            return this.samples.length * self.rowHeight;
+        },
+        /**
+         * #getter
+         */
+        get leaves() {
+            return self.root?.leaves();
+        },
+        /**
+         * #getter
+         */
+        get rowNames() {
+            return this.leaves?.map(n => n.data.name);
+        },
+    }))
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+        return {
+            /**
+             * #getter
+             */
+            get treeWidth() {
+                return self.hierarchy ? self.treeAreaWidth : 0;
+            },
+            /**
+             * #method
+             */
+            renderProps() {
+                const { showAllLetters, rendererConfig, samples, rowHeight, rowProportion, mismatchRendering, } = self;
+                return {
+                    ...superRenderProps(),
+                    config: rendererConfig,
+                    samples,
+                    rowHeight,
+                    rowProportion,
+                    showAllLetters,
+                    mismatchRendering,
+                };
+            },
+            /**
+             * #method
+             */
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Set row height',
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                SetRowHeightDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Show all letters',
+                        type: 'checkbox',
+                        checked: self.showAllLetters,
+                        onClick: () => {
+                            self.setShowAllLetters(!self.showAllLetters);
+                        },
+                    },
+                    {
+                        label: 'Draw mismatches as single color',
+                        type: 'checkbox',
+                        checked: !self.mismatchRendering,
+                        onClick: () => {
+                            self.setMismatchRendering(!self.mismatchRendering);
+                        },
+                    },
+                ];
+            },
+        };
+    })
+        .actions(self => ({
+        afterCreate() {
+            addDisposer(self, autorun(async () => {
+                try {
+                    const { rpcManager } = getSession(self);
+                    const sessionId = getRpcSessionId(self);
+                    const results = (await rpcManager.call(sessionId, 'MafGetSamples', {
+                        sessionId,
+                        adapterConfig: self.adapterConfig,
+                        statusCallback: (message) => {
+                            if (isAlive(self)) {
+                                self.setMessage(message);
+                            }
+                        },
+                    }));
+                    self.setSamples(results);
+                }
+                catch (e) {
+                    console.error(e);
+                    getSession(self).notifyError(`${e}`, e);
+                }
+            }));
+        },
+    }))
+        .actions(self => {
+        const { renderSvg: superRenderSvg } = self;
+        return {
+            /**
+             * #action
+             */
+            async renderSvg(opts) {
+                const { renderSvg } = await import('./renderSvg');
+                return renderSvg(self, opts, superRenderSvg);
+            },
+        };
+    });
+}
+//# sourceMappingURL=stateModel.js.map

package/dist/LinearMafDisplay/stateModel.js.map

@@ -0,0 +1 @@
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package/dist/LinearMafDisplay/types.d.ts

@@ -0,0 +1,17 @@
+import type { HierarchyNode } from 'd3-hierarchy';
+export interface NodeWithIds {
+    id: string;
+    name: string;
+    children: NodeWithIds[];
+    length?: number;
+    noTree?: boolean;
+}
+export interface NodeWithIdsAndLength {
+    id: string;
+    name: string;
+    children: NodeWithIdsAndLength[];
+    noTree?: boolean;
+    length: number;
+}
+export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
+export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;

package/dist/LinearMafDisplay/types.js

@@ -0,0 +1,16 @@
+import { max } from 'd3-array';
+// basically same as maxLength from https://observablehq.com/@d3/tree-of-life
+export function maxLength(d) {
+    return ((d.data.length || 0) + (d.children ? max(d.children, maxLength) || 0 : 0));
+}
+// basically same as setRadius from https://observablehq.com/@d3/tree-of-life
+export function setBrLength(d, y0, k) {
+    // @ts-expect-error
+    d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
+    if (d.children) {
+        d.children.forEach(d => {
+            setBrLength(d, y0, k);
+        });
+    }
+}
+//# sourceMappingURL=types.js.map

package/dist/LinearMafDisplay/types.js.map

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package/dist/LinearMafRenderer/LinearMafRenderer.d.ts

@@ -0,0 +1,45 @@
+import { FeatureRendererType } from '@jbrowse/core/pluggableElementTypes';
+import { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { Feature, Region } from '@jbrowse/core/util';
+interface Sample {
+    id: string;
+    color?: string;
+}
+interface RenderArgs extends RenderArgsDeserialized {
+    samples: Sample[];
+    rowHeight: number;
+    rowProportion: number;
+    showAllLetters: boolean;
+    mismatchRendering: boolean;
+}
+export default class LinearMafRenderer extends FeatureRendererType {
+    getExpandedRegion(region: Region): {
+        start: number;
+        end: number;
+        refName: string;
+        reversed?: boolean | undefined;
+        assemblyName: string;
+    };
+    render(renderProps: RenderArgs): Promise<{
+        width: number;
+        height: number;
+        canvasRecordedData: any;
+        features: Map<string, Feature>;
+        reactElement?: React.ReactElement;
+        html?: string;
+    } | {
+        width: number;
+        height: number;
+        reactElement: import("react/jsx-runtime").JSX.Element;
+        features: Map<string, Feature>;
+        html?: string;
+    } | {
+        width: number;
+        height: number;
+        imageData: any;
+        features: Map<string, Feature>;
+        reactElement?: React.ReactElement;
+        html?: string;
+    }>;
+}
+export {};

package/dist/LinearMafRenderer/LinearMafRenderer.js

@@ -0,0 +1,183 @@
+import { FeatureRendererType } from '@jbrowse/core/pluggableElementTypes';
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { featureSpanPx, renderToAbstractCanvas, } from '@jbrowse/core/util';
+import { getColorBaseMap, getContrastBaseMap } from './util';
+function makeImageData({ ctx, renderArgs, }) {
+    const { regions, bpPerPx, rowHeight, showAllLetters, theme: configTheme, mismatchRendering, samples, rowProportion, features, } = renderArgs;
+    const region = regions[0];
+    const h = rowHeight * rowProportion;
+    const theme = createJBrowseTheme(configTheme);
+    const colorForBase = getColorBaseMap(theme);
+    const contrastForBase = getContrastBaseMap(theme);
+    const sampleToRowMap = new Map(samples.map((s, i) => [s.id, i]));
+    const scale = 1 / bpPerPx;
+    const f = 0.4;
+    const h2 = rowHeight / 2;
+    const hp2 = h / 2;
+    const offset = (rowHeight - h) / 2;
+    // sample as alignments
+    ctx.font = 'bold 10px Courier New,monospace';
+    for (const feature of features.values()) {
+        const [leftPx] = featureSpanPx(feature, region, bpPerPx);
+        const vals = feature.get('alignments');
+        const seq = feature.get('seq').toLowerCase();
+        for (const [sample, val] of Object.entries(vals)) {
+            const origAlignment = val.data;
+            const alignment = origAlignment.toLowerCase();
+            const row = sampleToRowMap.get(sample);
+            if (row === undefined) {
+                continue;
+            }
+            const t = rowHeight * row;
+            // gaps
+            ctx.beginPath();
+            ctx.fillStyle = 'black';
+            for (let i = 0, o = 0; i < alignment.length; i++) {
+                if (seq[i] !== '-') {
+                    if (alignment[i] === '-') {
+                        const l = leftPx + scale * o;
+                        ctx.moveTo(l, t + h2);
+                        ctx.lineTo(l + scale + f, t + h2);
+                    }
+                    o++;
+                }
+            }
+            ctx.stroke();
+            if (!showAllLetters) {
+                // matches
+                ctx.beginPath();
+                ctx.fillStyle = 'lightgrey';
+                for (let i = 0, o = 0; i < alignment.length; i++) {
+                    if (seq[i] !== '-') {
+                        const c = alignment[i];
+                        const l = leftPx + scale * o;
+                        if (seq[i] === c && c !== '-') {
+                            ctx.rect(l, offset + t, scale + f, h);
+                        }
+                        o++;
+                    }
+                }
+                ctx.fill();
+            }
+            // mismatches
+            for (let i = 0, o = 0; i < alignment.length; i++) {
+                const c = alignment[i];
+                if (seq[i] !== '-') {
+                    if (c !== '-') {
+                        const l = leftPx + scale * o;
+                        if (seq[i] !== c && c !== ' ') {
+                            ctx.fillStyle = mismatchRendering
+                                ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                                    (colorForBase[c] ?? 'black')
+                                : 'orange';
+                            ctx.fillRect(l, offset + t, scale + f, h);
+                        }
+                        else if (showAllLetters) {
+                            ctx.fillStyle = mismatchRendering
+                                ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                                    (colorForBase[c] ?? 'black')
+                                : 'lightblue';
+                            ctx.fillRect(l, offset + t, scale + f, h);
+                        }
+                    }
+                    o++;
+                }
+            }
+            // font
+            const charSizeW = 10;
+            if (scale >= charSizeW) {
+                for (let i = 0, o = 0; i < alignment.length; i++) {
+                    if (seq[i] !== '-') {
+                        const l = leftPx + scale * o;
+                        const offset = (scale - charSizeW) / 2 + 1;
+                        const c = alignment[i];
+                        if ((showAllLetters || seq[i] !== c) && c !== '-') {
+                            ctx.fillStyle = mismatchRendering
+                                ? (contrastForBase[c] ?? 'white')
+                                : 'black';
+                            ctx.fillText(origAlignment[i] || '', l + offset, hp2 + t + 3);
+                        }
+                        o++;
+                    }
+                }
+            }
+        }
+    }
+    // second pass for insertions, has slightly improved look since the
+    // insertions are always 'on top' of the other features
+    for (const feature of features.values()) {
+        const [leftPx] = featureSpanPx(feature, region, bpPerPx);
+        const vals = feature.get('alignments');
+        const seq = feature.get('seq').toLowerCase();
+        for (const [sample, val] of Object.entries(vals)) {
+            const origAlignment = val.data;
+            const alignment = origAlignment.toLowerCase();
+            const row = sampleToRowMap.get(sample);
+            if (row === undefined) {
+                continue;
+            }
+            const t = rowHeight * row;
+            ctx.beginPath();
+            ctx.fillStyle = 'purple';
+            for (let i = 0, o = 0; i < alignment.length; i++) {
+                let ins = '';
+                while (seq[i] === '-') {
+                    if (alignment[i] !== '-' && alignment[i] !== ' ') {
+                        ins += alignment[i];
+                    }
+                    i++;
+                }
+                if (ins.length > 0) {
+                    const l = leftPx + scale * o - 1;
+                    ctx.rect(l, offset + t + 1, 1, h - 1);
+                    ctx.rect(l - 2, offset + t, 5, 1);
+                    ctx.rect(l - 2, offset + t + h - 1, 5, 1);
+                }
+                o++;
+            }
+            ctx.fill();
+        }
+    }
+}
+export default class LinearMafRenderer extends FeatureRendererType {
+    getExpandedRegion(region) {
+        const { start, end } = region;
+        const bpExpansion = 1;
+        return {
+            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+            ...region,
+            start: Math.floor(Math.max(start - bpExpansion, 0)),
+            end: Math.ceil(end + bpExpansion),
+        };
+    }
+    async render(renderProps) {
+        const { regions, bpPerPx, samples, rowHeight } = renderProps;
+        const region = regions[0];
+        const height = samples.length * (rowHeight + 1) + 100;
+        const width = (region.end - region.start) / bpPerPx;
+        const features = await this.getFeatures(renderProps);
+        const res = await renderToAbstractCanvas(width, height, renderProps, ctx => {
+            makeImageData({
+                ctx,
+                renderArgs: {
+                    ...renderProps,
+                    features,
+                },
+            });
+            return undefined;
+        });
+        const results = await super.render({
+            ...renderProps,
+            ...res,
+            width,
+            height,
+        });
+        return {
+            ...results,
+            ...res,
+            width,
+            height,
+        };
+    }
+}
+//# sourceMappingURL=LinearMafRenderer.js.map

package/dist/LinearMafRenderer/LinearMafRenderer.js.map

@@ -0,0 +1 @@
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package/dist/LinearMafRenderer/components/ReactComponent.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+declare const LinearMafRendering: (props: {
+    width: number;
+    height: number;
+}) => React.JSX.Element;
+export default LinearMafRendering;

package/dist/LinearMafRenderer/components/ReactComponent.js

@@ -0,0 +1,8 @@
+import React from 'react';
+import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+const LinearMafRendering = observer(function (props) {
+    return React.createElement(PrerenderedCanvas, { ...props });
+});
+export default LinearMafRendering;
+//# sourceMappingURL=ReactComponent.js.map

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

@@ -0,0 +1 @@
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package/dist/LinearMafRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default configSchema;

package/dist/LinearMafRenderer/configSchema.js

@@ -0,0 +1,13 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config LinearMafRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = ConfigurationSchema('LinearMafRenderer', {}, {
+    /**
+     * #baseConfiguration
+     */
+    explicitlyTyped: true,
+});
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/dist/LinearMafRenderer/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,mBAAmB,EACnB,EAAE,EACF;IACE;;OAEG;IACH,eAAe,EAAE,IAAI;CACtB,CACF,CAAA;AAED,eAAe,YAAY,CAAA"}

package/dist/LinearMafRenderer/index.d.ts

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

package/dist/LinearMafRenderer/index.js

@@ -0,0 +1,12 @@
+import LinearMafRenderer from './LinearMafRenderer';
+import ReactComponent from './components/ReactComponent';
+import configSchema from './configSchema';
+export default function LinearMafRendererF(pluginManager) {
+    pluginManager.addRendererType(() => new LinearMafRenderer({
+        name: 'LinearMafRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+    }));
+}
+//# sourceMappingURL=index.js.map

package/dist/LinearMafRenderer/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/index.ts"],"names":[],"mappings":"AAEA,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,cAAc,MAAM,6BAA6B,CAAA;AACxD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,iBAAiB,CAAC;QACpB,IAAI,EAAE,mBAAmB;QACzB,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/LinearMafRenderer/util.d.ts

@@ -0,0 +1,10 @@
+import { Theme } from '@mui/material';
+export declare function getContrastBaseMap(theme: Theme): {
+    [k: string]: string;
+};
+export declare function getColorBaseMap(theme: Theme): {
+    a: string;
+    c: string;
+    g: string;
+    t: string;
+};

package/dist/LinearMafRenderer/util.js

@@ -0,0 +1,16 @@
+export function getContrastBaseMap(theme) {
+    return Object.fromEntries(Object.entries(getColorBaseMap(theme)).map(([key, value]) => [
+        key,
+        theme.palette.getContrastText(value),
+    ]));
+}
+export function getColorBaseMap(theme) {
+    const { bases } = theme.palette;
+    return {
+        a: bases.A.main,
+        c: bases.C.main,
+        g: bases.G.main,
+        t: bases.T.main,
+    };
+}
+//# sourceMappingURL=util.js.map