@jbrowse/plugin-alignments 2.7.2 → 2.9.0

package/dist/AlignmentsFeatureDetail/index.d.ts

@@ -10,6 +10,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
@@ -18,7 +19,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
-    setExtra(type?: string | undefined, trackId?: string | undefined): void;
+    setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
     setError(e: unknown): void;
 } & {
     afterCreate(): void;
@@ -34,6 +35,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: "BaseFeatureWidget";
     id: string;
@@ -41,6 +43,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;
     trackType: string | undefined;
+    maxDepth: number | undefined;
     formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;

package/dist/AlignmentsTrack/configSchemaF.d.ts

@@ -58,6 +58,11 @@ export default function configSchemaFactory(pluginManager: PluginManager): impor
             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: {

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -233,14 +233,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined; /**
-     * #property
-     */
+    featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
 } & {
-    /**
-     * #property
-     */
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -530,7 +530,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                             // feature.id that was returned e.g. that the user hasn't
                             // moused over to a new position during the async operation
                             // above
-                            if (self.featureIdUnderMouse === feature.uniqueId) {
+                            if (self.featureIdUnderMouse === (feature === null || feature === void 0 ? void 0 : feature.uniqueId)) {
                                 self.setFeatureUnderMouse(new util_1.SimpleFeature(feature));
                             }
                         }

package/dist/LinearPileupDisplay/model.d.ts

@@ -244,16 +244,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined; /**
-     * #getter
-     */
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    clearFeatureSelection(): void; /**
-     * #method
-     */
+    clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {

package/dist/LinearSNPCoverageDisplay/models/configSchema.js

@@ -39,7 +39,7 @@ function SNPCoverageConfigFactory(pluginManager) {
          */
         scaleType: {
             type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
+            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']), // todo zscale
             description: 'The type of scale to use',
             defaultValue: 'linear',
         },

package/dist/shared/BaseDisplayComponent.js

@@ -9,22 +9,19 @@ const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view"
 const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const util_1 = require("@jbrowse/core/util");
-const useStyles = (0, mui_1.makeStyles)()(theme => {
-    const bg = theme.palette.action.disabledBackground;
-    return {
-        loading: {
-            backgroundColor: theme.palette.background.default,
-            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
-            position: 'absolute',
-            bottom: 0,
-            height: 50,
-            width: 300,
-            right: 0,
-            pointerEvents: 'none',
-            textAlign: 'center',
-        },
-    };
-});
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    loading: {
+        backgroundColor: theme.palette.background.default,
+        backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,
+        position: 'absolute',
+        bottom: 0,
+        height: 50,
+        width: 300,
+        right: 0,
+        pointerEvents: 'none',
+        textAlign: 'center',
+    },
+}));
 const BaseDisplayComponent = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { error, regionTooLarge } = model;
     return error ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : regionTooLarge ? (model.regionCannotBeRendered()) : (react_1.default.createElement(DataDisplay, { model: model }, children));

package/esm/AlignmentsFeatureDetail/index.d.ts

@@ -10,6 +10,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
@@ -18,7 +19,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
-    setExtra(type?: string | undefined, trackId?: string | undefined): void;
+    setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
     setError(e: unknown): void;
 } & {
     afterCreate(): void;
@@ -34,6 +35,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: "BaseFeatureWidget";
     id: string;
@@ -41,6 +43,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;
     trackType: string | undefined;
+    maxDepth: number | undefined;
     formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;

package/esm/AlignmentsTrack/configSchemaF.d.ts

@@ -58,6 +58,11 @@ export default function configSchemaFactory(pluginManager: PluginManager): impor
             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: {

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -233,14 +233,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined; /**
-     * #property
-     */
+    featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
 } & {
-    /**
-     * #property
-     */
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -501,7 +501,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                             // feature.id that was returned e.g. that the user hasn't
                             // moused over to a new position during the async operation
                             // above
-                            if (self.featureIdUnderMouse === feature.uniqueId) {
+                            if (self.featureIdUnderMouse === (feature === null || feature === void 0 ? void 0 : feature.uniqueId)) {
                                 self.setFeatureUnderMouse(new SimpleFeature(feature));
                             }
                         }

package/esm/LinearPileupDisplay/model.d.ts

@@ -244,16 +244,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined; /**
-     * #getter
-     */
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    clearFeatureSelection(): void; /**
-     * #method
-     */
+    clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {

package/esm/LinearSNPCoverageDisplay/models/configSchema.js

@@ -37,7 +37,7 @@ export default function SNPCoverageConfigFactory(pluginManager) {
          */
         scaleType: {
             type: 'stringEnum',
-            model: types.enumeration('Scale type', ['linear', 'log']),
+            model: types.enumeration('Scale type', ['linear', 'log']), // todo zscale
             description: 'The type of scale to use',
             defaultValue: 'linear',
         },

package/esm/shared/BaseDisplayComponent.js

@@ -4,22 +4,19 @@ import { BlockMsg, } from '@jbrowse/plugin-linear-genome-view';
 import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
 import { getContainingView } from '@jbrowse/core/util';
-const useStyles = makeStyles()(theme => {
-    const bg = theme.palette.action.disabledBackground;
-    return {
-        loading: {
-            backgroundColor: theme.palette.background.default,
-            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
-            position: 'absolute',
-            bottom: 0,
-            height: 50,
-            width: 300,
-            right: 0,
-            pointerEvents: 'none',
-            textAlign: 'center',
-        },
-    };
-});
+const useStyles = makeStyles()(theme => ({
+    loading: {
+        backgroundColor: theme.palette.background.default,
+        backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,
+        position: 'absolute',
+        bottom: 0,
+        height: 50,
+        width: 300,
+        right: 0,
+        pointerEvents: 'none',
+        textAlign: 'center',
+    },
+}));
 const BaseDisplayComponent = observer(function ({ model, children, }) {
     const { error, regionTooLarge } = model;
     return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.7.2",
+  "version": "2.9.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "9052b295f2d322e729254457ed9fe2231fb22cce"
+  "gitHead": "a50b6f67cf8c8f3c65a7b8cd858de2fcca1f2909"
 }