@jbrowse/plugin-alignments 2.1.7 → 2.2.0

package/dist/LinearAlignmentsDisplay/models/model.js

@@ -11,32 +11,77 @@ const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
 const minDisplayHeight = 20;
-const stateModelFactory = (pluginManager, configSchema) => {
+/**
+ * #stateModel LinearAlignmentsDisplay
+ * extends `BaseDisplay`
+ */
+function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearAlignmentsDisplay', models_1.BaseDisplay, mobx_state_tree_1.types.model({
+        /**
+         * #property
+         * refers to LinearPileupDisplay sub-display model
+         */
         PileupDisplay: mobx_state_tree_1.types.maybe(pluginManager.getDisplayType('LinearPileupDisplay').stateModel),
+        /**
+         * #property
+         * refers to LinearSNPCoverageDisplay sub-display model
+         */
         SNPCoverageDisplay: mobx_state_tree_1.types.maybe(pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel),
+        /**
+         * #property
+         */
         snpCovHeight: 45,
+        /**
+         * #property
+         */
         type: mobx_state_tree_1.types.literal('LinearAlignmentsDisplay'),
+        /**
+         * #property
+         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+        /**
+         * #property
+         */
         height: 250,
+        /**
+         * #property
+         */
         showCoverage: true,
+        /**
+         * #property
+         */
         showPileup: true,
+        /**
+         * #property
+         */
         userFeatureScreenDensity: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
     }))
         .volatile(() => ({
         scrollTop: 0,
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         toggleCoverage() {
             self.showCoverage = !self.showCoverage;
         },
+        /**
+         * #action
+         */
         togglePileup() {
             self.showPileup = !self.showPileup;
         },
+        /**
+         * #action
+         */
         setScrollTop(scrollTop) {
             self.scrollTop = scrollTop;
         },
+        /**
+         * #action
+         */
         setSNPCoverageHeight(n) {
             self.snpCovHeight = n;
         },
@@ -44,6 +89,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         return {
+            /**
+             * #getter
+             */
             get pileupDisplayConfig() {
                 const conf = (0, configuration_1.getConf)(self, 'pileupDisplay');
                 const track = (0, util_1.getContainingTrack)(self);
@@ -54,28 +102,52 @@ const stateModelFactory = (pluginManager, configSchema) => {
                     displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
                 };
             },
+            /**
+             * #method
+             */
             getFeatureByID(blockKey, id) {
                 return self.PileupDisplay.getFeatureByID(blockKey, id);
             },
+            /**
+             * #method
+             */
             searchFeatureByID(id) {
                 return self.PileupDisplay.searchFeatureByID(id);
             },
+            /**
+             * #getter
+             */
             get features() {
                 return self.PileupDisplay.features;
             },
+            /**
+             * #getter
+             */
             get DisplayBlurb() {
                 var _a;
                 return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
             },
+            /**
+             * #getter
+             */
             get sortedBy() {
                 return self.PileupDisplay.sortedBy;
             },
+            /**
+             * #getter
+             */
             get sortedByPosition() {
                 return self.PileupDisplay.sortedByPosition;
             },
+            /**
+             * #getter
+             */
             get sortedByRefName() {
                 return self.PileupDisplay.sortedByRefName;
             },
+            /**
+             * #getter
+             */
             get snpCoverageDisplayConfig() {
                 const conf = (0, configuration_1.getConf)(self, 'snpCoverageDisplay');
                 const track = (0, util_1.getContainingTrack)(self);
@@ -86,6 +158,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
                     displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
                 };
             },
+            /**
+             * #method
+             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -104,6 +179,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
         };
     })
         .actions(self => ({
+        /**
+         * #action
+         */
         setSNPCoverageDisplay(displayConfig) {
             self.SNPCoverageDisplay = {
                 type: 'LinearSNPCoverageDisplay',
@@ -111,16 +189,25 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 height: self.snpCovHeight,
             };
         },
+        /**
+         * #action
+         */
         setUserFeatureScreenDensity(limit) {
             self.PileupDisplay.setUserFeatureScreenDensity(limit);
             self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit);
         },
+        /**
+         * #action
+         */
         setPileupDisplay(displayConfig) {
             self.PileupDisplay = {
                 type: 'LinearPileupDisplay',
                 configuration: displayConfig,
             };
         },
+        /**
+         * #action
+         */
         setHeight(displayHeight) {
             if (displayHeight > minDisplayHeight) {
                 self.height = displayHeight;
@@ -130,6 +217,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
             }
             return self.height;
         },
+        /**
+         * #action
+         */
         resizeHeight(distance) {
             const oldHeight = self.height;
             const newHeight = this.setHeight(self.height + distance);
@@ -170,6 +260,9 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 self.setSNPCoverageHeight(self.SNPCoverageDisplay.height);
             }));
         },
+        /**
+         * #action
+         */
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
             await (0, mobx_1.when)(() => self.PileupDisplay.ready);
@@ -181,6 +274,6 @@ const stateModelFactory = (pluginManager, configSchema) => {
                 }))));
         },
     }));
-};
+}
 exports.default = stateModelFactory;
 //# sourceMappingURL=model.js.map

package/dist/LinearAlignmentsDisplay/models/model.js.map

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package/dist/LinearPileupDisplay/configSchema.js

@@ -3,24 +3,38 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_state_tree_1 = require("mobx-state-tree");
+/**
+ * #config LinearPileupDisplay
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 function PileupConfigFactory(pluginManager) {
-    const PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema;
     // modify config schema to take in a sub coverage display
     return (0, configuration_1.ConfigurationSchema)('LinearPileupDisplay', {
+        /**
+         * #slot
+         */
         defaultRendering: {
             type: 'stringEnum',
             model: mobx_state_tree_1.types.enumeration('Rendering', ['pileup']),
             defaultValue: 'pileup',
         },
+        /**
+         * #slot
+         */
         renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
-            PileupRenderer: PileupRendererConfigSchema,
+            PileupRenderer: pluginManager.getRendererType('PileupRenderer').configSchema,
         }),
-        renderer: '',
+        /**
+         * #slot
+         */
         maxFeatureScreenDensity: {
             type: 'number',
             description: 'maximum features per pixel that is displayed in the view',
             defaultValue: 5,
         },
+        /**
+         * #slot
+         */
         colorScheme: {
             type: 'stringEnum',
             model: mobx_state_tree_1.types.enumeration('colorScheme', [
@@ -35,6 +49,9 @@ function PileupConfigFactory(pluginManager) {
             defaultValue: 'normal',
         },
     }, {
+        /**
+         * #baseConfiguration
+         */
         baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
         explicitlyTyped: true,
     });

package/dist/LinearPileupDisplay/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAiD;AAGjD;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,yDAAyD;IACzD,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAMD,kBAAe,mBAAmB,CAAA"}

package/dist/LinearPileupDisplay/model.d.ts

@@ -4,7 +4,10 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import { LinearPileupDisplayConfigModel } from './configSchema';
-declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel) => import("mobx-state-tree").IModelType<{
+/**
+ * #stateModel LinearPileupDisplay
+ */
+declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel): 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>>;
@@ -101,7 +104,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
+             * #action
+             */
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -218,25 +223,71 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     featureUnderMouseVolatile: Feature | undefined;
     ready: boolean;
 } & {
+    /**
+     * #action
+     */
     setReady(flag: boolean): void;
+    /**
+     * #action
+     */
     setMaxHeight(n: number): void;
+    /**
+     * #action
+     */
     setFeatureHeight(n: number): void;
+    /**
+     * #action
+     */
     setNoSpacing(flag: boolean): void;
+    /**
+     * #action
+     */
     setColorScheme(colorScheme: {
         type: string;
         tag?: string;
     }): void;
+    /**
+     * #action
+     */
     updateModificationColorMap(uniqueModifications: string[]): void;
+    /**
+     * #action
+     */
     updateColorTagMap(uniqueTag: string[]): void;
+    /**
+     * #action
+     */
     setFeatureUnderMouse(feat?: Feature): void;
 } & {
     afterAttach(): void;
+    /**
+     * #action
+     */
     selectFeature(feature: Feature): void;
+    /**
+     * #action
+     */
     clearSelected(): void;
+    /**
+     * #action
+     * uses copy-to-clipboard and generates notification
+     */
     copyFeatureToClipboard(feature: Feature): void;
+    /**
+     * #action
+     */
     toggleSoftClipping(): void;
+    /**
+     * #action
+     */
     toggleMismatchAlpha(): void;
+    /**
+     * #action
+     */
     setConfig(configuration: AnyConfigurationModel): void;
+    /**
+     * #action
+     */
     setSortedBy(type: string, tag?: string): void;
     setFilterBy(filter: {
         flagInclude: number;
@@ -248,26 +299,59 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         };
     }): void;
 } & {
+    /**
+     * #action
+     */
     reload(): void;
 } & {
+    /**
+     * #getter
+     */
     readonly maxHeight: any;
+    /**
+     * #getter
+     */
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    /**
+     * #getter
+     */
     readonly featureHeightSetting: any;
+    /**
+     * #getter
+     */
     readonly mismatchAlphaSetting: any;
+    /**
+     * #getter
+     */
     readonly featureUnderMouse: Feature | undefined;
 } & {
+    /**
+     * #getter
+     */
     readonly rendererTypeName: string;
+    /**
+     * #method
+     */
     contextMenuItems(): {
         label: string;
         icon: typeof ContentCopyIcon;
         onClick: () => void;
     }[];
+    /**
+     * #getter
+     */
     readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => JSX.Element | null;
+    /**
+     * #method
+     */
     renderProps(): any;
+    /**
+     * #method
+     */
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -325,8 +409,8 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     })[];
 }, import("mobx-state-tree")._NotCustomized, {
     type: string;
-    height: number;
     id: string;
+    height: number;
     rpcDriverName: string | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;