@jbrowse/plugin-linear-comparative-view 2.6.1

package/dist/LinearSyntenyDisplay/drawSynteny.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.drawMouseoverSynteny = exports.drawRef = exports.getId = exports.MAX_COLOR_RANGE = void 0;
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./components/util");
+exports.MAX_COLOR_RANGE = 255 * 255 * 255; // max color range
+function makeColor(idx) {
+    const r = Math.floor(idx / (255 * 255)) % 255;
+    const g = Math.floor(idx / 255) % 255;
+    const b = idx % 255;
+    return `rgb(${r},${g},${b})`;
+}
+const colorMap = {
+    I: '#ff03',
+    N: '#0a03',
+    D: '#00f3',
+    X: 'brown',
+    M: '#f003',
+    '=': '#f003',
+};
+const lineLimit = 3;
+const oobLimit = 1600;
+function getId(r, g, b, unitMultiplier) {
+    return Math.floor((r * 255 * 255 + g * 255 + b - 1) / unitMultiplier);
+}
+exports.getId = getId;
+function drawRef(model, ctx1, ctx3) {
+    var _a;
+    const view = (0, util_1.getContainingView)(model);
+    const drawCurves = view.drawCurves;
+    const drawCIGAR = view.drawCIGAR;
+    const height = view.middleComparativeHeight;
+    const width = view.width;
+    const bpPerPxs = view.views.map(v => v.bpPerPx);
+    if (ctx3) {
+        ctx3.imageSmoothingEnabled = false;
+    }
+    ctx1.beginPath();
+    const featPos = model.featPositions;
+    const offsets = view.views.map(v => v.offsetPx);
+    const unitMultiplier = Math.floor(exports.MAX_COLOR_RANGE / featPos.length);
+    // this loop is optimized to draw many thin lines with a single ctx.stroke
+    // call, a separate loop below draws larger boxes
+    ctx1.fillStyle = colorMap.M;
+    ctx1.strokeStyle = colorMap.M;
+    for (let i = 0; i < featPos.length; i++) {
+        const { p11, p12, p21, p22 } = featPos[i];
+        const x11 = p11.offsetPx - offsets[0];
+        const x12 = p12.offsetPx - offsets[0];
+        const x21 = p21.offsetPx - offsets[1];
+        const x22 = p22.offsetPx - offsets[1];
+        const l1 = Math.abs(x12 - x11);
+        const l2 = Math.abs(x22 - x21);
+        const y1 = 0;
+        const y2 = height;
+        const mid = (y2 - y1) / 2;
+        // drawing a line if the results are thin results in much less pixellation
+        // than filling in a thin polygon
+        if (l1 <= lineLimit &&
+            l2 <= lineLimit &&
+            x21 < width + oobLimit &&
+            x21 > -oobLimit) {
+            ctx1.moveTo(x11, y1);
+            if (drawCurves) {
+                ctx1.bezierCurveTo(x11, mid, x21, mid, x21, y2);
+            }
+            else {
+                ctx1.lineTo(x21, y2);
+            }
+        }
+    }
+    ctx1.stroke();
+    // this loop only draws small lines as a polyline, the polyline calls
+    // ctx.stroke once is much more efficient than calling stroke() many times
+    ctx1.fillStyle = colorMap.M;
+    ctx1.strokeStyle = colorMap.M;
+    for (let i = 0; i < featPos.length; i++) {
+        const { p11, p12, p21, p22, f, cigar } = featPos[i];
+        const x11 = p11.offsetPx - offsets[0];
+        const x12 = p12.offsetPx - offsets[0];
+        const x21 = p21.offsetPx - offsets[1];
+        const x22 = p22.offsetPx - offsets[1];
+        const l1 = Math.abs(x12 - x11);
+        const l2 = Math.abs(x22 - x21);
+        const minX = Math.min(x21, x22);
+        const maxX = Math.max(x21, x22);
+        const y1 = 0;
+        const y2 = height;
+        const mid = (y2 - y1) / 2;
+        if (!(l1 <= lineLimit && l2 <= lineLimit) &&
+            (0, util_1.doesIntersect2)(minX, maxX, -oobLimit, view.width + oobLimit)) {
+            const s1 = f.get('strand');
+            const k1 = s1 === -1 ? x12 : x11;
+            const k2 = s1 === -1 ? x11 : x12;
+            // rev1/rev2 flip the direction of the CIGAR drawing in horizontally flipped
+            // modes. somewhat heuristically determined, but tested for
+            const rev1 = k1 < k2 ? 1 : -1;
+            const rev2 = (x21 < x22 ? 1 : -1) * s1;
+            // cx1/cx2 are the current x positions on top and bottom rows
+            let cx1 = k1;
+            let cx2 = s1 === -1 ? x22 : x21;
+            if ((cigar === null || cigar === void 0 ? void 0 : cigar.length) && drawCIGAR) {
+                // continuingFlag skips drawing commands on very small CIGAR features
+                let continuingFlag = false;
+                // px1/px2 are the previous x positions on the top and bottom rows
+                let px1 = 0;
+                let px2 = 0;
+                const unitMultiplier2 = Math.floor(exports.MAX_COLOR_RANGE / cigar.length);
+                for (let j = 0; j < cigar.length; j += 2) {
+                    const idx = j * unitMultiplier2 + 1;
+                    const len = +cigar[j];
+                    const op = cigar[j + 1];
+                    if (!continuingFlag) {
+                        px1 = cx1;
+                        px2 = cx2;
+                    }
+                    const d1 = len / bpPerPxs[0];
+                    const d2 = len / bpPerPxs[1];
+                    if (op === 'M' || op === '=' || op === 'X') {
+                        cx1 += d1 * rev1;
+                        cx2 += d2 * rev2;
+                    }
+                    else if (op === 'D' || op === 'N') {
+                        cx1 += d1 * rev1;
+                    }
+                    else if (op === 'I') {
+                        cx2 += d2 * rev2;
+                    }
+                    // check that we are even drawing in view here, e.g. that all
+                    // points are not all less than 0 or greater than width
+                    if (!(Math.max(px1, px2, cx1, cx2) < 0 ||
+                        Math.min(px1, px2, cx1, cx2) > width)) {
+                        // if it is a small feature and not the last element of the
+                        // CIGAR (which could skip rendering it entire if we did turn
+                        // it on), then turn on continuing flag
+                        const isNotLast = j < cigar.length - 2;
+                        if (Math.abs(cx1 - px1) <= 1 &&
+                            Math.abs(cx2 - px2) <= 1 &&
+                            isNotLast) {
+                            continuingFlag = true;
+                        }
+                        else {
+                            continuingFlag = false;
+                            // allow rendering the dominant color when using continuing
+                            // flag if the last element of continuing was a large
+                            // feature, else just use match
+                            ctx1.fillStyle =
+                                colorMap[(continuingFlag && d1 > 1) || d2 > 1 ? op : 'M'];
+                            (0, util_2.draw)(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
+                            if (ctx3) {
+                                ctx3.fillStyle = makeColor(idx);
+                                (0, util_2.draw)(ctx3, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
+                            }
+                        }
+                    }
+                }
+            }
+            else {
+                (0, util_2.draw)(ctx1, x11, x12, y1, x22, x21, y2, mid, drawCurves);
+            }
+        }
+    }
+    // draw click map
+    const ctx2 = (_a = model.clickMapCanvas) === null || _a === void 0 ? void 0 : _a.getContext('2d');
+    if (!ctx2) {
+        return;
+    }
+    ctx2.imageSmoothingEnabled = false;
+    ctx2.clearRect(0, 0, width, height);
+    for (let i = 0; i < featPos.length; i++) {
+        const feature = featPos[i];
+        const idx = i * unitMultiplier + 1;
+        ctx2.fillStyle = makeColor(idx);
+        // too many click map false positives with colored stroked lines
+        (0, util_2.drawMatchSimple)({
+            cb: ctx => ctx.fill(),
+            feature,
+            ctx: ctx2,
+            drawCurves,
+            offsets,
+            oobLimit,
+            viewWidth: view.width,
+            hideTiny: true,
+            height,
+        });
+    }
+}
+exports.drawRef = drawRef;
+function drawMouseoverSynteny(model) {
+    var _a;
+    const { clickId, mouseoverId } = model;
+    const highResolutionScaling = 1;
+    const view = (0, util_1.getContainingView)(model);
+    const drawCurves = view.drawCurves;
+    const height = view.middleComparativeHeight;
+    const width = view.width;
+    const ctx = (_a = model.mouseoverCanvas) === null || _a === void 0 ? void 0 : _a.getContext('2d');
+    const offsets = view.views.map(v => v.offsetPx);
+    if (!ctx) {
+        return;
+    }
+    ctx.resetTransform();
+    ctx.scale(highResolutionScaling, highResolutionScaling);
+    ctx.clearRect(0, 0, width, height);
+    const feature1 = model.featMap[mouseoverId || ''];
+    if (feature1) {
+        ctx.fillStyle = 'rgb(0,0,0,0.1)';
+        (0, util_2.drawMatchSimple)({
+            cb: ctx => ctx.fill(),
+            feature: feature1,
+            ctx,
+            oobLimit,
+            viewWidth: view.width,
+            drawCurves,
+            offsets,
+            height,
+        });
+    }
+    const feature2 = model.featMap[clickId || ''];
+    if (feature2) {
+        ctx.strokeStyle = 'rgb(0, 0, 0, 0.9)';
+        (0, util_2.drawMatchSimple)({
+            cb: ctx => ctx.stroke(),
+            feature: feature2,
+            ctx,
+            oobLimit,
+            viewWidth: view.width,
+            drawCurves,
+            offsets,
+            height,
+        });
+    }
+}
+exports.drawMouseoverSynteny = drawMouseoverSynteny;
+//# sourceMappingURL=drawSynteny.js.map

package/dist/LinearSyntenyDisplay/drawSynteny.js.map

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package/dist/LinearSyntenyDisplay/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/LinearSyntenyDisplay/index.js

@@ -0,0 +1,47 @@
+"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 DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+// locals
+const configSchemaF_1 = __importDefault(require("./configSchemaF"));
+const model_1 = __importDefault(require("./model"));
+const react_1 = require("react");
+exports.default = (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchemaF_1.default)(pluginManager);
+        return new DisplayType_1.default({
+            name: 'LinearSyntenyDisplay',
+            configSchema,
+            stateModel: (0, model_1.default)(configSchema),
+            trackType: 'SyntenyTrack',
+            viewType: 'LinearSyntenyView',
+            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Component')))),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/dist/LinearSyntenyDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearSyntenyDisplay/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kGAAyE;AAGzE,SAAS;AACT,oEAA2C;AAC3C,oDAAuC;AACvC,iCAA4B;AAE5B,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,uBAAa,EAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,mBAAmB;YAC7B,cAAc,EAAE,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,wBAAwB,GAAC,CAAC;SAC7D,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/LinearSyntenyDisplay/model.d.ts

@@ -0,0 +1,333 @@
+/// <reference types="react" />
+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
+interface Pos {
+    offsetPx: number;
+}
+interface FeatPos {
+    p11: Pos;
+    p12: Pos;
+    p21: Pos;
+    p22: Pos;
+    f: Feature;
+    cigar: string[];
+}
+/**
+ * #stateModel LinearSyntenyDisplay
+ * extends `LinearComparativeDisplay` model
+ */
+declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
+    configuration: AnyConfigurationSchemaType;
+    height: import("mobx-state-tree").IType<number | undefined, number, number>;
+} & {
+    /**
+     * #property
+     */
+    type: import("mobx-state-tree").ISimpleType<"LinearSyntenyDisplay">;
+    /**
+     * #property
+     */
+    configuration: AnyConfigurationSchemaType;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+    message: string | undefined;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+         * #action
+         */
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): null;
+} & {
+    setMessage(arg?: string | undefined): void;
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    renderInProgress: AbortController | undefined;
+    features: Feature[] | undefined;
+    message: string | undefined;
+} & {
+    renderProps(): {
+        rpcDriverName: string | undefined;
+        displayModel: {
+            id: string;
+            type: "LinearComparativeDisplay";
+            rpcDriverName: string | undefined;
+            configuration: {
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: unknown): any;
+            } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+            height: number;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & {
+            readonly RenderingComponent: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: Function | undefined;
+                blockState?: Record<string, any> | undefined;
+            }>;
+            readonly DisplayBlurb: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+                 * #action
+                 */
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: any;
+            renderProps(): any;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            regionCannotBeRendered(): null;
+        } & {
+            setMessage(arg?: string | undefined): void;
+            setError(error?: unknown): void;
+            setRpcDriverName(rpcDriverName: string): void;
+            reload(): void;
+        } & {
+            renderInProgress: AbortController | undefined;
+            features: Feature[] | undefined;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        } & {
+            type: import("mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
+            configuration: AnyConfigurationSchemaType;
+            height: import("mobx-state-tree").IType<number | undefined, number, number>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & {
+            readonly RenderingComponent: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: Function | undefined;
+                blockState?: Record<string, any> | undefined;
+            }>;
+            readonly DisplayBlurb: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+                 * #action
+                 */
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: any;
+            renderProps(): any;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            regionCannotBeRendered(): null;
+        } & {
+            setMessage(arg?: string | undefined): void;
+            setError(error?: unknown): void;
+            setRpcDriverName(rpcDriverName: string): void;
+            reload(): void;
+        } & {
+            renderInProgress: AbortController | undefined;
+            features: Feature[] | undefined;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        highResolutionScaling: number;
+    };
+} & {
+    setLoading(abortController: AbortController): void;
+    setMessage(messageText: string): void;
+    setRendered(args?: {
+        features: Feature[];
+    } | undefined): void;
+    setError(error: unknown): void;
+} & {
+    afterAttach(): void;
+} & {
+    mainCanvas: HTMLCanvasElement | null;
+    clickMapCanvas: HTMLCanvasElement | null;
+    cigarClickMapCanvas: HTMLCanvasElement | null;
+    mouseoverCanvas: HTMLCanvasElement | null;
+    featPositions: FeatPos[];
+    mouseoverId: string | undefined;
+    clickId: string | undefined;
+    cigarMouseoverId: number;
+} & {
+    /**
+     * #action
+     */
+    setFeatPositions(arg: FeatPos[]): void;
+    /**
+     * #action
+     */
+    setMainCanvasRef(ref: HTMLCanvasElement | null): void;
+    /**
+     * #action
+     */
+    setClickMapCanvasRef(ref: HTMLCanvasElement | null): void;
+    /**
+     * #action
+     */
+    setCigarClickMapCanvasRef(ref: HTMLCanvasElement | null): void;
+    /**
+     * #action
+     */
+    setMouseoverCanvasRef(ref: HTMLCanvasElement | null): void;
+    /**
+     * #action
+     */
+    setMouseoverId(arg?: string): void;
+    /**
+     * #action
+     */
+    setCigarMouseoverId(arg: number): void;
+    /**
+     * #action
+     */
+    setClickId(arg?: string): void;
+} & {
+    /**
+     * #getter
+     */
+    readonly adapterConfig: any;
+    /**
+     * #getter
+     */
+    readonly trackIds: string[];
+    /**
+     * #getter
+     */
+    readonly numFeats: number;
+    /**
+     * #getter
+     * used for synteny svg rendering
+     */
+    readonly ready: boolean;
+    /**
+     * #getter
+     */
+    readonly featMap: {
+        [k: string]: FeatPos;
+    };
+} & {
+    afterAttach(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type LinearSyntenyDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type LinearSyntenyDisplayModel = Instance<LinearSyntenyDisplayStateModel>;
+export default stateModelFactory;