@jbrowse/plugin-alignments 2.3.4 → 2.4.1

package/dist/LinearReadCloudDisplay/model.d.ts

@@ -2,7 +2,6 @@ import React from 'react';
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { ChainData } from '../shared/fetchChains';
-import { ExportSvgOptions } from '@jbrowse/plugin-linear-genome-view/src/LinearGenomeView';
 interface Filter {
     flagInclude: number;
     flagExclude: number;
@@ -21,14 +20,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
-            /**
-             * #property
-             */
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -44,11 +40,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
-        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        layout: any;
-        /**
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined; /**
          * #action
          */
+        layout: any;
         status: string;
         error: unknown;
         message: string | undefined;
@@ -56,21 +51,18 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
-        /**
-         * #action
-         */
         renderProps: any;
     } & {
         doReload(): void;
-        afterAttach(): void;
+        afterAttach(): void; /**
+         * #action
+         */
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, import("@jbrowse/core/util").Feature>; /**
-             * #getter
-             */
+            features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -171,6 +163,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -231,8 +224,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }[];
     renderProps(): any;
 } & {
-    renderSvg(opts: ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
+        theme: import("@mui/material").ThemeOptions;
     }): Promise<JSX.Element>;
 } & {
     loading: boolean;
@@ -304,14 +298,72 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #method
      */
-    renderSvg(opts: ExportSvgOptions): Promise<JSX.Element | undefined>;
+    renderSvg(opts: {
+        rasterizeLayers?: boolean;
+    }): Promise<JSX.Element | undefined>;
 } & {
     afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, {
+}, {
+    type: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    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>>;
+} & {
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
-    height: number;
     id: string;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/dist/LinearReadCloudDisplay/model.js

@@ -41,6 +41,11 @@ const fetchChains_1 = require("../shared/fetchChains");
 const drawFeats_1 = __importDefault(require("./drawFeats"));
 // async
 const FilterByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/FilterByTag'))));
+// stabilize clipid under test for snapshot
+function getId(id) {
+    const isJest = typeof jest === 'undefined';
+    return `cloud-clip-${isJest ? id : 'jest'}`;
+}
 /**
  * #stateModel LinearReadCloudDisplay
  * extends `BaseLinearDisplay`
@@ -213,9 +218,16 @@ function stateModelFactory(configSchema) {
                     const C2S = await Promise.resolve().then(() => __importStar(require('canvas2svg')));
                     const ctx = new C2S.default(width, height);
                     await (0, drawFeats_1.default)(self, ctx);
-                    str = (
-                    // eslint-disable-next-line react/no-danger
-                    react_1.default.createElement("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML } }));
+                    const clipid = getId(self.id);
+                    str = (react_1.default.createElement(react_1.default.Fragment, null,
+                        react_1.default.createElement("defs", null,
+                            react_1.default.createElement("clipPath", { id: clipid },
+                                react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
+                        react_1.default.createElement("g", { 
+                            /* eslint-disable-next-line react/no-danger */
+                            dangerouslySetInnerHTML: {
+                                __html: ctx.getSvg().innerHTML,
+                            }, clipPath: `url(#${clipid})` })));
                 }
                 return react_1.default.createElement("g", null, str);
             },

package/dist/LinearReadCloudDisplay/model.js.map

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package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -10,13 +10,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #property
-             */
+            refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -37,17 +35,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         status: string;
         error: unknown;
         message: string | undefined;
-        maxHeightReached: boolean; /**
-         * #action
-         */
+        maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void; /**
-         * #action
-         */
+        doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
@@ -156,9 +150,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
-            rendererTypeName: string; /**
-             * #method
-             */
+            rendererTypeName: string;
             error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
@@ -183,6 +175,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -245,6 +238,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
+        theme: import("@mui/material").ThemeOptions;
     }): Promise<JSX.Element>;
 } & {
     message: string | undefined;
@@ -344,6 +338,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     afterAttach(): void;
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
+        theme: import("@mui/material").ThemeOptions;
     }): Promise<JSX.Element>;
 } & {
     modificationTagMap: Record<string, string> | undefined;

package/dist/MismatchParser/index.js

@@ -287,18 +287,17 @@ function getModificationTypes(mm) {
     const mods = mm.split(';');
     return mods
         .filter(mod => !!mod)
-        .map(mod => {
+        .flatMap(mod => {
         const [basemod] = mod.split(',');
         const matches = basemod.match(modificationRegex);
         if (!matches) {
             throw new Error(`bad format for MM tag: ${mm}`);
         }
-        const [, , , typestr] = matches;
+        const typestr = matches[3];
         // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
         // split, and they can also be chemical codes (ChEBI) e.g. C+16061
         return typestr.split(/(\d+|.)/).filter(f => !!f);
-    })
-        .flat();
+    });
 }
 exports.getModificationTypes = getModificationTypes;
 function getOrientedCigar(flip, cigar) {
@@ -313,8 +312,7 @@ function getOrientedCigar(flip, cigar) {
             else if (op === 'I') {
                 op = 'D';
             }
-            ret.push(len);
-            ret.push(op);
+            ret.push(len, op);
         }
         return ret;
     }

package/dist/MismatchParser/index.js.map

@@ -1 +1 @@
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package/dist/NestedFrequencyTable.js

@@ -22,12 +22,7 @@ class NestedFrequencyTable {
         if (!amount) {
             amount = 1;
         }
-        if (!slotName) {
-            slotName = 'default';
-        }
-        else {
-            slotName = slotName.toString();
-        }
+        slotName = slotName ? slotName.toString() : 'default';
         if (this.categories[slotName]) {
             this.categories[slotName] = Math.max(0, this.categories[slotName] - amount);
             return this.categories[slotName];
@@ -39,12 +34,7 @@ class NestedFrequencyTable {
         if (!amount) {
             amount = 1;
         }
-        if (!slotName) {
-            slotName = 'default';
-        }
-        else {
-            slotName = slotName.toString();
-        }
+        slotName = slotName ? slotName.toString() : 'default';
         this.categories[slotName] = (this.categories[slotName] || 0) + amount;
         return this.categories[slotName];
     }
@@ -58,7 +48,7 @@ class NestedFrequencyTable {
         if (typeof path === 'string') {
             path = path.split('/');
         }
-        if (!path.length) {
+        if (path.length === 0) {
             return this;
         }
         const slotName = path[0].toString();

package/dist/NestedFrequencyTable.js.map

@@ -1 +1 @@
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package/dist/PileupRPC/rpcMethods.d.ts

@@ -1,4 +1,3 @@
-import PileupGetReducedFeatures from './methods/GetReducedFeatures';
-import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag';
-import PileupGetVisibleModifications from './methods/GetVisibleModifications';
-export { PileupGetReducedFeatures, PileupGetVisibleModifications, PileupGetGlobalValueForTag, };
+export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures';
+export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications';
+export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag';

package/dist/PileupRPC/rpcMethods.js

@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PileupGetGlobalValueForTag = exports.PileupGetVisibleModifications = exports.PileupGetReducedFeatures = void 0;
-const GetReducedFeatures_1 = __importDefault(require("./methods/GetReducedFeatures"));
-exports.PileupGetReducedFeatures = GetReducedFeatures_1.default;
-const GetGlobalValueForTag_1 = __importDefault(require("./methods/GetGlobalValueForTag"));
-exports.PileupGetGlobalValueForTag = GetGlobalValueForTag_1.default;
-const GetVisibleModifications_1 = __importDefault(require("./methods/GetVisibleModifications"));
-exports.PileupGetVisibleModifications = GetVisibleModifications_1.default;
+var GetReducedFeatures_1 = require("./methods/GetReducedFeatures");
+Object.defineProperty(exports, "PileupGetReducedFeatures", { enumerable: true, get: function () { return __importDefault(GetReducedFeatures_1).default; } });
+var GetVisibleModifications_1 = require("./methods/GetVisibleModifications");
+Object.defineProperty(exports, "PileupGetVisibleModifications", { enumerable: true, get: function () { return __importDefault(GetVisibleModifications_1).default; } });
+var GetGlobalValueForTag_1 = require("./methods/GetGlobalValueForTag");
+Object.defineProperty(exports, "PileupGetGlobalValueForTag", { enumerable: true, get: function () { return __importDefault(GetGlobalValueForTag_1).default; } });
 //# sourceMappingURL=rpcMethods.js.map

package/dist/PileupRPC/rpcMethods.js.map

@@ -1 +1 @@
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+{"version":3,"file":"rpcMethods.js","sourceRoot":"","sources":["../../src/PileupRPC/rpcMethods.ts"],"names":[],"mappings":";;;;;;AAAA,mEAAkF;AAAzE,+IAAA,OAAO,OAA4B;AAC5C,6EAA4F;AAAnF,yJAAA,OAAO,OAAiC;AACjD,uEAAsF;AAA7E,mJAAA,OAAO,OAA8B"}

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="react" />
 import { Theme } from '@mui/material/styles';
-import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import BoxRendererType, { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { Region, Feature } from '@jbrowse/core/util';
 import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
@@ -100,7 +100,7 @@ export default class PileupRenderer extends BoxRendererType {
         canvasWidth: number;
     }): void;
     drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
-    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }: {
+    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, theme, canvasWidth, }: {
         ctx: CanvasRenderingContext2D;
         feat: LayoutFeature;
         renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
@@ -110,8 +110,9 @@ export default class PileupRenderer extends BoxRendererType {
         charHeight: number;
         defaultColor: boolean;
         canvasWidth: number;
+        theme: Theme;
     }): void;
-    drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, }: {
+    drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, theme, }: {
         ctx: CanvasRenderingContext2D;
         feat: LayoutFeature;
         renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
@@ -129,6 +130,7 @@ export default class PileupRenderer extends BoxRendererType {
         charWidth: number;
         charHeight: number;
         canvasWidth: number;
+        theme: Theme;
     }): void;
     drawSoftClipping({ ctx, feat, renderArgs, config, theme, canvasWidth, }: {
         ctx: CanvasRenderingContext2D;
@@ -175,4 +177,4 @@ export default class PileupRenderer extends BoxRendererType {
     }>;
     createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }
-export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };
+export { type RenderArgs, type RenderResults, type RenderArgsSerialized, type ResultsSerialized, type ResultsDeserialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';