@jbrowse/plugin-alignments 2.10.0 → 2.10.2

package/esm/LinearPileupDisplay/model.js

@@ -12,8 +12,8 @@ import SortIcon from '@mui/icons-material/Sort';
 import { SharedLinearPileupDisplayMixin } from './SharedLinearPileupDisplayMixin';
 import { observable } from 'mobx';
 // async
-const SortByTagDlg = lazy(() => import('./components/SortByTag'));
-const ModificationsDlg = lazy(() => import('./components/ColorByModifications'));
+const SortByTagDialog = lazy(() => import('./components/SortByTag'));
+const ModificationsDialog = lazy(() => import('./components/ColorByModifications'));
 /**
  * #stateModel LinearPileupDisplay
  * #category display
@@ -237,7 +237,7 @@ function stateModelFactory(configSchema) {
                                 label: 'Sort by tag...',
                                 onClick: () => {
                                     getSession(self).queueDialog(handleClose => [
-                                        SortByTagDlg,
+                                        SortByTagDialog,
                                         { model: self, handleClose },
                                     ]);
                                 },
@@ -259,7 +259,7 @@ function stateModelFactory(configSchema) {
                                 label: 'Modifications or methylation',
                                 onClick: () => {
                                     getSession(self).queueDialog(doneCallback => [
-                                        ModificationsDlg,
+                                        ModificationsDialog,
                                         { model: self, handleClose: doneCallback },
                                     ]);
                                 },

package/esm/LinearReadArcsDisplay/model.d.ts

@@ -61,7 +61,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & import("mobx-state-tree").IStateTreeNode<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>>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+             * #property
+             */
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -80,7 +82,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         } & 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>>;
         }, {
@@ -90,17 +94,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
-    readonly parentTrack: any; /**
-     * #action
-     */
+    readonly parentTrack: any;
     renderProps(): 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[];
-    regionCannotBeRendered(): null; /**
-     * #getter
-     */
+    regionCannotBeRendered(): null;
 } & {
     setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void; /**

package/esm/LinearReadArcsDisplay/model.js

@@ -10,7 +10,7 @@ import FilterListIcon from '@mui/icons-material/ClearAll';
 // locals
 import { FilterModel } from '../shared';
 // async
-const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
+const FilterByTagDialog = lazy(() => import('../shared/FilterByTag'));
 /**
  * #stateModel LinearReadArcsDisplay
  * the arc display is a non-block-based track, so draws to a single canvas and
@@ -192,7 +192,7 @@ function stateModelFactory(configSchema) {
                         icon: FilterListIcon,
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
-                                FilterByTagDlg,
+                                FilterByTagDialog,
                                 { model: self, handleClose },
                             ]);
                         },

package/esm/LinearReadCloudDisplay/model.d.ts

@@ -44,6 +44,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     message: string | undefined;
 } & {
     readonly RenderingComponent: React.FC<{
+        /**
+         * #stateModel LinearReadCloudDisplay
+         * it is not a block based track, hence not BaseLinearDisplay
+         * extends
+         * - [BaseDisplay](../basedisplay)
+         * - [TrackHeightMixin](../trackheightmixin)
+         * - [FeatureDensityMixin](../featuredensitymixin)
+         */
         model: {
             id: string;
             type: string;
@@ -55,9 +63,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & import("mobx-state-tree").IStateTreeNode<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>;
-            /**
-             * #property
-             */
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -78,7 +83,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<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>;
+            type: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             * internal, a reference to a HTMLCanvas because we use a autorun to draw
+             * the canvas
+             */
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -130,9 +139,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
-    /**
-     * #method
-     */
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
 } & {

package/esm/LinearReadCloudDisplay/model.js

@@ -10,7 +10,7 @@ import FilterListIcon from '@mui/icons-material/ClearAll';
 // locals
 import { FilterModel } from '../shared';
 // async
-const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
+const FilterByTagDialog = lazy(() => import('../shared/FilterByTag'));
 /**
  * #stateModel LinearReadCloudDisplay
  * it is not a block based track, hence not BaseLinearDisplay
@@ -142,7 +142,7 @@ function stateModelFactory(configSchema) {
                         icon: FilterListIcon,
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
-                                FilterByTagDlg,
+                                FilterByTagDialog,
                                 { model: self, handleClose },
                             ]);
                         },

package/esm/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import { observer } from 'mobx-react';
+import { toLocale } from '@jbrowse/core/util';
 import { Tooltip } from '@jbrowse/plugin-wiggle';
-const en = (n) => n.toLocaleString('en-US');
 const toP = (s = 0) => +(+s).toFixed(1);
 const pct = (n, total) => `${toP((n / (total || 1)) * 100)}%`;
 const TooltipContents = React.forwardRef(function TooltipContents2({ feature }, reactRef) {
@@ -9,7 +9,10 @@ const TooltipContents = React.forwardRef(function TooltipContents2({ feature },
     const end = feature.get('end');
     const name = feature.get('refName');
     const { refbase, all, total, ref, '-1': rn1, '1': r1, '0': r0, ...info } = feature.get('snpinfo');
-    const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]
+    const loc = [
+        name,
+        start === end ? toLocale(start) : `${toLocale(start)}..${toLocale(end)}`,
+    ]
         .filter(f => !!f)
         .join(':');
     return (React.createElement("div", { ref: reactRef },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.10.0",
+  "version": "2.10.2",
   "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": "223d8bfb68fd1bacaf22852639ad5920f1b7f43b"
+  "gitHead": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
 }

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-export default function SupplementaryAlignments(props: {
-    tag: string;
-    model: IAnyStateTreeNode;
-}): React.JSX.Element;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-export default function SupplementaryAlignments(props: {
-    tag: string;
-    model: IAnyStateTreeNode;
-}): React.JSX.Element;