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

package/esm/LinearSyntenyDisplay/components/util.js

@@ -1,4 +1,6 @@
-import { doesIntersect2 } from '@jbrowse/core/util';
+import { assembleLocString, doesIntersect2, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
+// locals
+import { getId, MAX_COLOR_RANGE } from '../drawSynteny';
 export function drawMatchSimple({ feature, ctx, offsets, cb, height, drawCurves, oobLimit, viewWidth, hideTiny, }) {
     const { p11, p12, p21, p22 } = feature;
     const x11 = p11.offsetPx - offsets[0];
@@ -74,3 +76,84 @@ export function drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid) {
     ctx.closePath();
     ctx.fill();
 }
+export 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(MAX_COLOR_RANGE / model.numFeats);
+    const id = getId(r1, g1, b1, unitMultiplier);
+    const feat = model.featPositions[id];
+    if (feat) {
+        const { f } = feat;
+        model.setClickId(f.id());
+        const session = getSession(model);
+        if (isSessionModelWithWidgets(session)) {
+            session.showWidget(session.addWidget('SyntenyFeatureWidget', 'syntenyFeature', {
+                featureData: {
+                    feature1: f.toJSON(),
+                    feature2: f.get('mate'),
+                },
+            }));
+        }
+    }
+    return feat;
+}
+export 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(MAX_COLOR_RANGE / model.numFeats);
+    const id = getId(r1, g1, b1, unitMultiplier);
+    const f = model.featPositions[id];
+    if (f) {
+        model.setClickId(f.f.id());
+        setAnchorEl({ clientX, clientY, feature: f });
+    }
+}
+export 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: ${assembleLocString(f1)}`,
+        `Loc2: ${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/esm/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/esm/LinearSyntenyView/components/ImportForm/index.js

@@ -65,6 +65,7 @@ const LinearSyntenyViewImportForm = 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);