npm - @jbrowse/plugin-wiggle - Versions diffs - 2.1.5 → 2.1.6 - Mend

@jbrowse/plugin-wiggle 2.1.5 → 2.1.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (27) hide show

package/dist/BigWigAdapter/BigWigAdapter.js CHANGED Viewed

@@ -25,17 +25,17 @@ class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return this.setupP;
     }
     async getRefNames(opts) {
-        const { header: { refsByName }, } = await this.setup(opts);
-        return Object.keys(refsByName);
+        const { header } = await this.setup(opts);
+        return Object.keys(header.refsByName);
     }
     async refIdToName(refId) {
         var _a;
-        const { header: { refsByNumber }, } = await this.setup();
-        return (_a = refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name;
+        const { header } = await this.setup();
+        return (_a = header.refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name;
     }
     async getGlobalStats(opts) {
-        const { header: { totalSummary }, } = await this.setup(opts);
-        return (0, stats_1.rectifyStats)(totalSummary);
+        const { header } = await this.setup(opts);
+        return (0, stats_1.rectifyStats)(header.totalSummary);
     }
     getFeatures(region, opts = {}) {
         const { refName, start, end } = region;

package/dist/BigWigAdapter/BigWigAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -119,7 +119,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -239,7 +239,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly maxScore: any;
     readonly minScore: any;
 } & {
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     readonly filled: any;
     readonly summaryScoreModeSetting: any;

package/dist/LinearWiggleDisplay/models/model.js CHANGED Viewed

@@ -206,7 +206,7 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
             ...(negColor !== undefined ? { negColor } : {}),
             ...(posColor !== undefined ? { posColor } : {}),
             ...(minSize !== undefined ? { minSize } : {}),
-        }, (0, mobx_state_tree_1.getEnv)(self));
+        }, (0, util_1.getEnv)(self));
     },
 }))
     .views(self => {

package/dist/LinearWiggleDisplay/models/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/MultiLinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -126,7 +126,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -254,7 +254,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly maxScore: number;
     readonly minScore: number;
 } & {
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     readonly needsScalebar: boolean;
     readonly needsFullHeightScalebar: boolean;

package/dist/MultiLinearWiggleDisplay/models/model.js CHANGED Viewed

@@ -238,7 +238,7 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
             ...(negColor !== undefined ? { negColor } : {}),
             ...(posColor !== undefined ? { posColor } : {}),
             ...(minSize !== undefined ? { minSize } : {}),
-        }, (0, mobx_state_tree_1.getEnv)(self));
+        }, (0, util_1.getEnv)(self));
     },
 }))
     .views(self => ({

package/dist/MultiLinearWiggleDisplay/models/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js CHANGED Viewed

@@ -80,7 +80,7 @@ function MultiWiggleWidget({ model }) {
                     bigWigs = JSON.parse(val);
                 }
                 catch (e) {
-                    bigWigs = val.split('\n');
+                    bigWigs = val.split(/\n|\r\n|\r/);
                 }
                 const obj = typeof bigWigs[0] === 'string'
                     ? { bigWigs }

package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/index.d.ts CHANGED Viewed

@@ -173,7 +173,7 @@ export default class WigglePlugin extends Plugin {
                 readonly adapterConfig: any;
                 readonly parentTrack: any;
                 renderProps(): any;
-                readonly rendererType: any;
+                readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
                 readonly DisplayMessageComponent: import("react").FC<any> | undefined;
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -293,7 +293,11 @@ export default class WigglePlugin extends Plugin {
                 readonly maxScore: any;
                 readonly minScore: any;
             } & {
-                readonly rendererConfig: any;
+                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>;
             } & {
                 readonly filled: any;
                 readonly summaryScoreModeSetting: any;
@@ -466,7 +470,7 @@ export default class WigglePlugin extends Plugin {
                 readonly adapterConfig: any;
                 readonly parentTrack: any;
                 renderProps(): any;
-                readonly rendererType: any;
+                readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
                 readonly DisplayMessageComponent: import("react").FC<any> | undefined;
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -586,7 +590,11 @@ export default class WigglePlugin extends Plugin {
                 readonly maxScore: any;
                 readonly minScore: any;
             } & {
-                readonly rendererConfig: any;
+                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>;
             } & {
                 readonly filled: any;
                 readonly summaryScoreModeSetting: any;
@@ -783,7 +791,7 @@ export default class WigglePlugin extends Plugin {
             readonly adapterConfig: any;
             readonly parentTrack: any;
             renderProps(): any;
-            readonly rendererType: any;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
             readonly DisplayMessageComponent: import("react").FC<any> | undefined;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -903,7 +911,11 @@ export default class WigglePlugin extends Plugin {
             readonly maxScore: any;
             readonly minScore: any;
         } & {
-            readonly rendererConfig: any;
+            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>;
         } & {
             readonly filled: any;
             readonly summaryScoreModeSetting: any;

package/esm/BigWigAdapter/BigWigAdapter.js CHANGED Viewed

@@ -23,17 +23,17 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
         return this.setupP;
     }
     async getRefNames(opts) {
-        const { header: { refsByName }, } = await this.setup(opts);
-        return Object.keys(refsByName);
+        const { header } = await this.setup(opts);
+        return Object.keys(header.refsByName);
     }
     async refIdToName(refId) {
         var _a;
-        const { header: { refsByNumber }, } = await this.setup();
-        return (_a = refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name;
+        const { header } = await this.setup();
+        return (_a = header.refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name;
     }
     async getGlobalStats(opts) {
-        const { header: { totalSummary }, } = await this.setup(opts);
-        return rectifyStats(totalSummary);
+        const { header } = await this.setup(opts);
+        return rectifyStats(header.totalSummary);
     }
     getFeatures(region, opts = {}) {
         const { refName, start, end } = region;

package/esm/BigWigAdapter/BigWigAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/LinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -119,7 +119,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -239,7 +239,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly maxScore: any;
     readonly minScore: any;
 } & {
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     readonly filled: any;
     readonly summaryScoreModeSetting: any;

package/esm/LinearWiggleDisplay/models/model.js CHANGED Viewed

@@ -1,9 +1,9 @@
 import React, { lazy } from 'react';
 import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
-import { getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
+import { getEnv, getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
 import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
 import { when } from 'mobx';
-import { isAlive, types, getEnv } from 'mobx-state-tree';
+import { isAlive, types } from 'mobx-state-tree';
 import { axisPropsFromTickScale } from 'react-d3-axis-mod';
 import { getNiceDomain, getScale, getStats, statsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
 import Tooltip from '../components/Tooltip';

package/esm/LinearWiggleDisplay/models/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/MultiLinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -126,7 +126,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -254,7 +254,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly maxScore: number;
     readonly minScore: number;
 } & {
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     readonly needsScalebar: boolean;
     readonly needsFullHeightScalebar: boolean;

package/esm/MultiLinearWiggleDisplay/models/model.js CHANGED Viewed

@@ -1,11 +1,11 @@
 import React, { lazy } from 'react';
-import { addDisposer, getEnv, isAlive, types } from 'mobx-state-tree';
+import { addDisposer, isAlive, types } from 'mobx-state-tree';
 import { autorun, when } from 'mobx';
 import { axisPropsFromTickScale } from 'react-d3-axis-mod';
 import deepEqual from 'fast-deep-equal';
 // jbrowse imports
 import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
-import { getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
+import { getSession, getEnv, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { set1 as colors } from '@jbrowse/core/ui/colors';
 import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';

package/esm/MultiLinearWiggleDisplay/models/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js CHANGED Viewed

@@ -55,7 +55,7 @@ export default function MultiWiggleWidget({ model }) {
                     bigWigs = JSON.parse(val);
                 }
                 catch (e) {
-                    bigWigs = val.split('\n');
+                    bigWigs = val.split(/\n|\r\n|\r/);
                 }
                 const obj = typeof bigWigs[0] === 'string'
                     ? { bigWigs }

package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/index.d.ts CHANGED Viewed

@@ -173,7 +173,7 @@ export default class WigglePlugin extends Plugin {
                 readonly adapterConfig: any;
                 readonly parentTrack: any;
                 renderProps(): any;
-                readonly rendererType: any;
+                readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
                 readonly DisplayMessageComponent: import("react").FC<any> | undefined;
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -293,7 +293,11 @@ export default class WigglePlugin extends Plugin {
                 readonly maxScore: any;
                 readonly minScore: any;
             } & {
-                readonly rendererConfig: any;
+                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>;
             } & {
                 readonly filled: any;
                 readonly summaryScoreModeSetting: any;
@@ -466,7 +470,7 @@ export default class WigglePlugin extends Plugin {
                 readonly adapterConfig: any;
                 readonly parentTrack: any;
                 renderProps(): any;
-                readonly rendererType: any;
+                readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
                 readonly DisplayMessageComponent: import("react").FC<any> | undefined;
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -586,7 +590,11 @@ export default class WigglePlugin extends Plugin {
                 readonly maxScore: any;
                 readonly minScore: any;
             } & {
-                readonly rendererConfig: any;
+                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>;
             } & {
                 readonly filled: any;
                 readonly summaryScoreModeSetting: any;
@@ -783,7 +791,7 @@ export default class WigglePlugin extends Plugin {
             readonly adapterConfig: any;
             readonly parentTrack: any;
             renderProps(): any;
-            readonly rendererType: any;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
             readonly DisplayMessageComponent: import("react").FC<any> | undefined;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -903,7 +911,11 @@ export default class WigglePlugin extends Plugin {
             readonly maxScore: any;
             readonly minScore: any;
         } & {
-            readonly rendererConfig: any;
+            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>;
         } & {
             readonly filled: any;
             readonly summaryScoreModeSetting: any;

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "2.1.5",
+  "version": "2.1.6",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bbi": "^2.0.2",
+    "@gmod/bbi": "^2.0.3",
     "@mui/icons-material": "^5.0.2",
     "@popperjs/core": "^2.11.0",
     "clone": "^2.1.2",
@@ -70,5 +70,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "bc5253ecdddeceeb999fffebf6dc6cf5f444e1c9"
+  "gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
 }

package/src/BigWigAdapter/BigWigAdapter.ts CHANGED Viewed

@@ -50,24 +50,18 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
   }
   public async getRefNames(opts?: BaseOptions) {
-    const {
-      header: { refsByName },
-    } = await this.setup(opts)
-    return Object.keys(refsByName)
+    const { header } = await this.setup(opts)
+    return Object.keys(header.refsByName)
   }
   public async refIdToName(refId: number) {
-    const {
-      header: { refsByNumber },
-    } = await this.setup()
-    return refsByNumber[refId]?.name
+    const { header } = await this.setup()
+    return header.refsByNumber[refId]?.name
   }
   public async getGlobalStats(opts?: BaseOptions) {
-    const {
-      header: { totalSummary },
-    } = await this.setup(opts)
-    return rectifyStats(totalSummary as UnrectifiedFeatureStats)
+    const { header } = await this.setup(opts)
+    return rectifyStats(header.totalSummary as UnrectifiedFeatureStats)
   }
   public getFeatures(region: Region, opts: WiggleOptions = {}) {

package/src/LinearWiggleDisplay/models/model.tsx CHANGED Viewed

@@ -6,6 +6,7 @@ import {
   readConfObject,
 } from '@jbrowse/core/configuration'
 import {
+  getEnv,
   getSession,
   getContainingView,
   isSelectionContainer,
@@ -15,7 +16,7 @@ import {
   LinearGenomeViewModel,
 } from '@jbrowse/plugin-linear-genome-view'
 import { when } from 'mobx'
-import { isAlive, types, getEnv, Instance } from 'mobx-state-tree'
+import { isAlive, types, Instance } from 'mobx-state-tree'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { Feature } from '@jbrowse/core/util/simpleFeature'

package/src/MultiLinearWiggleDisplay/models/model.tsx CHANGED Viewed

@@ -1,5 +1,5 @@
 import React, { lazy } from 'react'
-import { addDisposer, getEnv, isAlive, types, Instance } from 'mobx-state-tree'
+import { addDisposer, isAlive, types, Instance } from 'mobx-state-tree'
 import { autorun, when } from 'mobx'
 import { axisPropsFromTickScale } from 'react-d3-axis-mod'
 import deepEqual from 'fast-deep-equal'
@@ -13,6 +13,7 @@ import {
 } from '@jbrowse/core/configuration'
 import {
   getSession,
+  getEnv,
   getContainingView,
   isSelectionContainer,
   Feature,

package/src/MultiWiggleAddTrackWidget/AddTrackWorkflow.tsx CHANGED Viewed

@@ -86,7 +86,7 @@ export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) {
           try {
             bigWigs = JSON.parse(val)
           } catch (e) {
-            bigWigs = val.split('\n')
+            bigWigs = val.split(/\n|\r\n|\r/)
           }
           const obj =
             typeof bigWigs[0] === 'string'