@jbrowse/plugin-linear-comparative-view 2.11.2 → 2.12.1

package/dist/LinearSyntenyDisplay/components/util.js

@@ -1,7 +1,15 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawBezierBox = exports.drawBox = exports.draw = exports.drawMatchSimple = void 0;
+exports.drawMatchSimple = drawMatchSimple;
+exports.draw = draw;
+exports.drawBox = drawBox;
+exports.drawBezierBox = drawBezierBox;
+exports.onSynClick = onSynClick;
+exports.onSynContextClick = onSynContextClick;
+exports.getTooltip = getTooltip;
 const util_1 = require("@jbrowse/core/util");
+// locals
+const drawSynteny_1 = require("../drawSynteny");
 function drawMatchSimple({ feature, ctx, offsets, cb, height, drawCurves, oobLimit, viewWidth, hideTiny, }) {
     const { p11, p12, p21, p22 } = feature;
     const x11 = p11.offsetPx - offsets[0];
@@ -40,7 +48,6 @@ function drawMatchSimple({ feature, ctx, offsets, cb, height, drawCurves, oobLim
         cb(ctx);
     }
 }
-exports.drawMatchSimple = drawMatchSimple;
 function draw(ctx, x1, x2, y1, x3, x4, y2, mid, drawCurves) {
     if (drawCurves) {
         drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid);
@@ -49,7 +56,6 @@ function draw(ctx, x1, x2, y1, x3, x4, y2, mid, drawCurves) {
         drawBox(ctx, x1, x2, y1, x3, x4, y2);
     }
 }
-exports.draw = draw;
 function drawBox(ctx, x1, x2, y1, x3, x4, y2) {
     ctx.beginPath();
     ctx.moveTo(x1, y1);
@@ -59,7 +65,6 @@ function drawBox(ctx, x1, x2, y1, x3, x4, y2) {
     ctx.closePath();
     ctx.fill();
 }
-exports.drawBox = drawBox;
 function drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid) {
     const len1 = Math.abs(x1 - x2);
     const len2 = Math.abs(x1 - x2);
@@ -80,4 +85,84 @@ function drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid) {
     ctx.closePath();
     ctx.fill();
 }
-exports.drawBezierBox = drawBezierBox;
+function onSynClick(event, model) {
+    const ref1 = model.clickMapCanvas;
+    const ref2 = model.cigarClickMapCanvas;
+    if (!ref1 || !ref2) {
+        return;
+    }
+    const rect = ref1.getBoundingClientRect();
+    const ctx1 = ref1.getContext('2d');
+    const ctx2 = ref2.getContext('2d');
+    if (!ctx1 || !ctx2) {
+        return;
+    }
+    const x = event.clientX - rect.left;
+    const y = event.clientY - rect.top;
+    const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data;
+    const unitMultiplier = Math.floor(drawSynteny_1.MAX_COLOR_RANGE / model.numFeats);
+    const id = (0, drawSynteny_1.getId)(r1, g1, b1, unitMultiplier);
+    const feat = model.featPositions[id];
+    if (feat) {
+        const { f } = feat;
+        model.setClickId(f.id());
+        const session = (0, util_1.getSession)(model);
+        if ((0, util_1.isSessionModelWithWidgets)(session)) {
+            session.showWidget(session.addWidget('SyntenyFeatureWidget', 'syntenyFeature', {
+                featureData: {
+                    feature1: f.toJSON(),
+                    feature2: f.get('mate'),
+                },
+            }));
+        }
+    }
+    return feat;
+}
+function onSynContextClick(event, model, setAnchorEl) {
+    event.preventDefault();
+    const ref1 = model.clickMapCanvas;
+    const ref2 = model.cigarClickMapCanvas;
+    if (!ref1 || !ref2) {
+        return;
+    }
+    const rect = ref1.getBoundingClientRect();
+    const ctx1 = ref1.getContext('2d');
+    const ctx2 = ref2.getContext('2d');
+    if (!ctx1 || !ctx2) {
+        return;
+    }
+    const { clientX, clientY } = event;
+    const x = clientX - rect.left;
+    const y = clientY - rect.top;
+    const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data;
+    const unitMultiplier = Math.floor(drawSynteny_1.MAX_COLOR_RANGE / model.numFeats);
+    const id = (0, drawSynteny_1.getId)(r1, g1, b1, unitMultiplier);
+    const f = model.featPositions[id];
+    if (f) {
+        model.setClickId(f.f.id());
+        setAnchorEl({ clientX, clientY, feature: f });
+    }
+}
+function getTooltip(f, cigarOp, cigarOpLen) {
+    // @ts-expect-error
+    const f1 = f.toJSON();
+    const f2 = f1.mate;
+    const l1 = f1.end - f1.start;
+    const l2 = f2.end - f2.start;
+    const identity = f1.identity;
+    const n1 = f1.name;
+    const n2 = f2.name;
+    return [
+        `Loc1: ${(0, util_1.assembleLocString)(f1)}`,
+        `Loc2: ${(0, util_1.assembleLocString)(f2)}`,
+        `Inverted: ${f1.strand === -1}`,
+        `Query len: ${l1.toLocaleString('en-US')}`,
+        `Target len: ${l2.toLocaleString('en-US')}`,
+        identity ? `Identity: ${identity.toPrecision(2)}` : '',
+        cigarOp ? `CIGAR operator: ${cigarOp}${cigarOpLen}` : '',
+        n1 ? `Name 1: ${n1}` : '',
+        n2 ? `Name 1: ${n2}` : '',
+    ]
+        .filter(f => !!f)
+        .join('<br/>');
+}

package/dist/LinearSyntenyDisplay/drawSynteny.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawMouseoverSynteny = exports.drawRef = exports.getId = exports.MAX_COLOR_RANGE = void 0;
+exports.MAX_COLOR_RANGE = void 0;
+exports.getId = getId;
+exports.drawRef = drawRef;
+exports.drawMouseoverSynteny = drawMouseoverSynteny;
 const util_1 = require("@jbrowse/core/util");
 const util_2 = require("./components/util");
 exports.MAX_COLOR_RANGE = 255 * 255 * 255; // max color range
@@ -23,7 +26,6 @@ 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);
@@ -183,7 +185,6 @@ function drawRef(model, ctx1, ctx3) {
         });
     }
 }
-exports.drawRef = drawRef;
 function drawMouseoverSynteny(model) {
     var _a;
     const { clickId, mouseoverId } = model;
@@ -229,4 +230,3 @@ function drawMouseoverSynteny(model) {
         });
     }
 }
-exports.drawMouseoverSynteny = drawMouseoverSynteny;

package/dist/LinearSyntenyDisplay/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearSyntenyDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 // locals
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
@@ -44,4 +45,3 @@ function LinearSyntenyDisplayF(pluginManager) {
         });
     });
 }
-exports.default = LinearSyntenyDisplayF;

package/dist/LinearSyntenyDisplay/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
@@ -58,8 +57,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -82,19 +81,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
-    renderProps(): any; /**
-     * #getter
-     */
+    renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
-     * #getter
-     * used for synteny svg rendering
-     */
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -112,7 +106,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             configuration: {
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: unknown): any;
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                        [x: string]: any;
+                    } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+                } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
             } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
             height: number;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -138,8 +138,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: Function | undefined;
-                blockState?: Record<string, any> | undefined;
+                onHorizontalScroll?: Function;
+                blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{
                 model: {
@@ -162,19 +162,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: any;
-            renderProps(): any; /**
-             * #getter
-             */
+            renderProps(): any;
             readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            readonly DisplayMessageComponent: undefined | import("react").FC<any>;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
-             * #getter
-             * used for synteny svg rendering
-             */
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
             regionCannotBeRendered(): null;
         } & {
-            setMessage(arg?: string | undefined): void;
+            setMessage(arg?: string): void;
             setError(error?: unknown): void;
             setRpcDriverName(rpcDriverName: string): void;
             reload(): void;
@@ -213,8 +208,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: Function | undefined;
-                blockState?: Record<string, any> | undefined;
+                onHorizontalScroll?: Function;
+                blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{
                 model: {
@@ -237,19 +232,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: any;
-            renderProps(): any; /**
-             * #getter
-             */
+            renderProps(): any;
             readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            readonly DisplayMessageComponent: undefined | import("react").FC<any>;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
-             * #getter
-             * used for synteny svg rendering
-             */
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
             regionCannotBeRendered(): null;
         } & {
-            setMessage(arg?: string | undefined): void;
+            setMessage(arg?: string): void;
             setError(error?: unknown): void;
             setRpcDriverName(rpcDriverName: string): void;
             reload(): void;
@@ -265,7 +255,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setMessage(messageText: string): void;
     setRendered(args?: {
         features: Feature[];
-    } | undefined): void;
+    }): void;
     setError(error: unknown): void;
 } & {
     afterAttach(): void;

package/dist/LinearSyntenyView/components/ExportSvgDialog.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = ExportSvgDialog;
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
@@ -85,4 +86,3 @@ function ExportSvgDialog({ model, handleClose, }) {
                     }
                 } }, "Submit"))));
 }
-exports.default = ExportSvgDialog;

package/dist/LinearSyntenyView/components/Icons.js

@@ -3,16 +3,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StraightLines = exports.Curves = void 0;
+exports.Curves = Curves;
+exports.StraightLines = StraightLines;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 function Curves(props) {
     return (react_1.default.createElement(material_1.SvgIcon, { ...props },
         react_1.default.createElement("path", { fill: "currentColor", d: "M16.5,21C13.5,21 12.31,16.76 11.05,12.28C10.14,9.04 9,5 7.5,5C4.11,5 4,11.93 4,12H2C2,11.63 2.06,3 7.5,3C10.5,3 11.71,7.25 12.97,11.74C13.83,14.8 15,19 16.5,19C19.94,19 20.03,12.07 20.03,12H22.03C22.03,12.37 21.97,21 16.5,21Z" })));
 }
-exports.Curves = Curves;
 function StraightLines(props) {
     return (react_1.default.createElement(material_1.SvgIcon, { ...props },
         react_1.default.createElement("path", { fill: "currentColor", d: "M22 12L17 22L7.1 6.04L4.24 12H2L7 2L16.9 17.96L19.76 12H22Z" })));
 }
-exports.StraightLines = StraightLines;

package/dist/LinearSyntenyView/components/ImportForm/index.js

@@ -93,6 +93,7 @@ const LinearSyntenyViewImportForm = (0, mobx_react_1.observer)(function ({ model
                 };
             })));
             model.views.forEach(view => view.setWidth(model.width));
+            model.views.forEach(view => view.showAllRegions());
             if (sessionTrackData) {
                 session.addTrackConf(sessionTrackData);
                 model.toggleTrack(sessionTrackData.trackId);

package/dist/LinearSyntenyView/components/ImportForm/util.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.extName = exports.basename = exports.stripGz = exports.getName = void 0;
+exports.getName = getName;
+exports.stripGz = stripGz;
+exports.basename = basename;
+exports.extName = extName;
 function getName(sessionTrackData) {
     return sessionTrackData
         ? // @ts-expect-error
@@ -11,17 +14,13 @@ function getName(sessionTrackData) {
                 sessionTrackData.name
         : undefined;
 }
-exports.getName = getName;
 function stripGz(fileName) {
     return fileName.endsWith('.gz') ? fileName.slice(0, -3) : fileName;
 }
-exports.stripGz = stripGz;
 function basename(str) {
     return str.split('#')[0].split('?')[0].split('/').pop();
 }
-exports.basename = basename;
 function extName(str) {
     const r = str.split('.').pop();
     return r ? `.${r}` : '';
 }
-exports.extName = extName;

package/dist/LinearSyntenyView/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearSyntenyViewF;
 const react_1 = require("react");
 const model_1 = __importDefault(require("./model"));
 const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
@@ -39,4 +40,3 @@ function LinearSyntenyViewF(pluginManager) {
         });
     });
 }
-exports.default = LinearSyntenyViewF;