@jbrowse/plugin-linear-genome-view 4.3.0 → 5.0.0-beta.2

package/esm/BaseLinearDisplay/util.js

@@ -1,71 +0,0 @@
-import { SimpleFeature, mergeIntervals } from '@jbrowse/core/util';
-export async function fetchFeatureByIdRpc({ rpcManager, sessionId, trackId, rendererType, featureId, parentFeatureId, }) {
-    const lookupId = parentFeatureId || featureId;
-    const { feature: featureData } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
-        featureId: lookupId,
-        sessionId,
-        trackInstanceId: trackId,
-        rendererType,
-    }));
-    if (!featureData) {
-        return undefined;
-    }
-    const feature = new SimpleFeature(featureData);
-    if (parentFeatureId) {
-        return findSubfeatureById(feature, featureId);
-    }
-    return feature;
-}
-export function findSubfeatureById(feature, targetId) {
-    const subfeatures = feature.get('subfeatures');
-    if (subfeatures) {
-        for (const sub of subfeatures) {
-            if (sub.id() === targetId) {
-                return sub;
-            }
-            const found = findSubfeatureById(sub, targetId);
-            if (found) {
-                return found;
-            }
-        }
-    }
-    return undefined;
-}
-export function featureHasExonsOrCDS(feature) {
-    const subs = feature.get('subfeatures') ?? [];
-    return subs.some((f) => f.get('type') === 'exon' || f.get('type') === 'CDS');
-}
-export function hasExonsOrCDS(transcripts) {
-    return transcripts.some(t => featureHasExonsOrCDS(t));
-}
-export function hasIntrons(transcripts) {
-    const subs = transcripts.flatMap(transcript => transcript
-        .get('subfeatures')
-        ?.filter((f) => f.get('type') === 'exon' || f.get('type') === 'CDS') ?? []);
-    if (subs.length < 2) {
-        return false;
-    }
-    const merged = mergeIntervals(subs.map((f) => ({ start: f.get('start'), end: f.get('end') })), 0);
-    return merged.length > 1;
-}
-export function getTranscripts(feature) {
-    if (!feature) {
-        return [];
-    }
-    return featureHasExonsOrCDS(feature)
-        ? [feature]
-        : (feature.get('subfeatures') ?? []);
-}
-export function drawCanvasImageData(canvas, imageData) {
-    if (!canvas || !imageData) {
-        return false;
-    }
-    const ctx = canvas.getContext('2d');
-    if (!ctx) {
-        return false;
-    }
-    ctx.resetTransform();
-    ctx.clearRect(0, 0, canvas.width, canvas.height);
-    ctx.drawImage(imageData, 0, 0);
-    return true;
-}

package/esm/BasicTrack/configSchema.d.ts

@@ -1,85 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    name: {
-        description: string;
-        type: string;
-        defaultValue: string;
-    };
-    assemblyNames: {
-        description: string;
-        type: string;
-        defaultValue: string[];
-    };
-    description: {
-        description: string;
-        type: string;
-        defaultValue: string;
-    };
-    category: {
-        description: string;
-        type: string;
-        defaultValue: never[];
-    };
-    metadata: {
-        type: string;
-        description: string;
-        defaultValue: {};
-    };
-    rpcDriverName: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        indexingAttributes: {
-            type: string;
-            description: string;
-            defaultValue: string[];
-        };
-        indexingFeatureTypesToExclude: {
-            type: string;
-            description: string;
-            defaultValue: string[];
-        };
-        textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        feature: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        subfeatures: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        depth: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-        maxDepth: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        config: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        hideUris: {
-            type: string;
-            defaultValue: boolean;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, "trackId">>;
-export default configSchema;

package/esm/BasicTrack/configSchema.js

@@ -1,8 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
-function x() { }
-const configSchema = (pluginManager) => ConfigurationSchema('BasicTrack', {}, {
-    baseConfiguration: createBaseTrackConfig(pluginManager),
-    explicitIdentifier: 'trackId',
-});
-export default configSchema;

package/esm/BasicTrack/index.d.ts

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

package/esm/BasicTrack/index.js

@@ -1,12 +0,0 @@
-import { TrackType, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes';
-import configSchemaF from "./configSchema.js";
-export default function BasicTrackF(pm) {
-    pm.addTrackType(() => {
-        const configSchema = configSchemaF(pm);
-        return new TrackType({
-            name: 'BasicTrack',
-            configSchema,
-            stateModel: createBaseTrackModel(pm, 'BasicTrack', configSchema),
-        });
-    });
-}

package/esm/LinearBareDisplay/configSchema.d.ts

@@ -1,32 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("@jbrowse/mobx-state-tree").IAnyModelType;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
-export { configSchemaFactory };

package/esm/LinearBareDisplay/configSchema.js

@@ -1,11 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { baseLinearDisplayConfigSchema } from "../BaseLinearDisplay/index.js";
-function configSchemaFactory(pluginManager) {
-    return ConfigurationSchema('LinearBareDisplay', {
-        renderer: pluginManager.pluggableConfigSchemaType('renderer'),
-    }, {
-        baseConfiguration: baseLinearDisplayConfigSchema,
-        explicitlyTyped: true,
-    });
-}
-export { configSchemaFactory };

package/esm/LinearBareDisplay/index.d.ts

@@ -1,4 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function LinearBareDisplayF(pluginManager: PluginManager): void;
-export { configSchemaFactory } from './configSchema.ts';
-export { stateModelFactory } from './model.ts';

package/esm/LinearBareDisplay/index.js

@@ -1,20 +0,0 @@
-import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
-import { configSchemaFactory } from "./configSchema.js";
-import { stateModelFactory } from "./model.js";
-import { BaseLinearDisplayComponent } from "../BaseLinearDisplay//index.js";
-export default function LinearBareDisplayF(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = configSchemaFactory(pluginManager);
-        return new DisplayType({
-            name: 'LinearBareDisplay',
-            configSchema,
-            displayName: 'Bare feature display',
-            stateModel: stateModelFactory(configSchema),
-            trackType: 'BasicTrack',
-            viewType: 'LinearGenomeView',
-            ReactComponent: BaseLinearDisplayComponent,
-        });
-    });
-}
-export { configSchemaFactory } from "./configSchema.js";
-export { stateModelFactory } from "./model.js";