@jbrowse/plugin-alignments 2.10.2 → 2.10.3

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -37,8 +37,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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;
+    type: "BaseFeatureWidget";
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/dist/BamAdapter/BamAdapter.js

@@ -65,14 +65,13 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             const idToName = [];
             const nameToId = {};
             samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
-                sqLine.data.forEach(item => {
-                    if (item.tag === 'SN') {
-                        // this is the ref name
-                        const refName = item.value;
-                        nameToId[refName] = refId;
-                        idToName[refId] = refName;
-                    }
-                });
+                const SN = sqLine.data.find(item => item.tag === 'SN');
+                if (SN) {
+                    // this is the ref name
+                    const refName = SN.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                }
             });
             return { idToName, nameToId };
         });

package/dist/CramAdapter/CramAdapter.js

@@ -22,12 +22,6 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre() {
         const cramLocation = this.getConf('cramLocation');
         const craiLocation = this.getConf('craiLocation');
-        if (!cramLocation) {
-            throw new Error('missing cramLocation argument');
-        }
-        if (!craiLocation) {
-            throw new Error('missing craiLocation argument');
-        }
         const pm = this.pluginManager;
         const cram = new cram_1.IndexedCramFile({
             cramFilehandle: (0, io_1.openLocation)(cramLocation, pm),
@@ -40,6 +34,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             throw new Error('Error getting subadapter');
         }
         const seqConf = this.getConf('sequenceAdapter');
+        if (!seqConf) {
+            throw new Error('no sequenceAdapter supplied to CramAdapter config');
+        }
         const subadapter = await this.getSubAdapter(seqConf);
         return {
             cram,
@@ -86,8 +83,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             return chunkSeq.slice(trimStart, trimStart + trimLength);
         })
             .join('');
-        if (sequence.length !== end - start) {
-            throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
+        const qlen = end - start;
+        if (sequence.length !== qlen) {
+            throw new Error(`fetching ${refName}:${(0, util_1.toLocale)(start - 1)}-${(0, util_1.toLocale)(end)} returned ${(0, util_1.toLocale)(sequence.length)} bases, should have returned ${(0, util_1.toLocale)(qlen)}`);
         }
         return sequence;
     }
@@ -104,14 +102,12 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             samHeader
                 .filter(l => l.tag === 'SQ')
                 .forEach((sqLine, refId) => {
-                sqLine.data.forEach(item => {
-                    if (item.tag === 'SN') {
-                        // this is the ref name
-                        const refName = item.value;
-                        nameToId[refName] = refId;
-                        idToName[refId] = refName;
-                    }
-                });
+                const SN = sqLine.data.find(item => item.tag === 'SN');
+                if (SN) {
+                    const refName = SN.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                }
             });
             const readGroups = samHeader
                 .filter(l => l.tag === 'RG')
@@ -161,7 +157,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { signal, filterBy, statusCallback = () => { } } = opts || {};
         const { refName, start, end, originalRefName } = region;
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { cram } = await this.setup(opts);
+            const { cram, samHeader } = await this.setup(opts);
             const refId = this.refNameToId(refName);
             if (refId === undefined) {
                 console.warn('Unknown refName', refName);
@@ -183,7 +179,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     }
                     if (tagFilter) {
                         const v = tagFilter.tag === 'RG'
-                            ? (_a = this.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
+                            ? (_a = samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
                             : record.tags[tagFilter.tag];
                         if (!(tagFilter.value === '*'
                             ? v !== undefined

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -46,8 +46,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -453,8 +460,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/dist/LinearPileupDisplay/model.d.ts

@@ -43,8 +43,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

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

@@ -42,8 +42,17 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode; /**
+                 * #property
+                 */
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/dist/shared/BaseDisplayComponent.js

@@ -9,6 +9,7 @@ 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 material_1 = require("@mui/material");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     loading: {
         backgroundColor: theme.palette.background.default,
@@ -24,7 +25,8 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
 }));
 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: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : regionTooLarge ? (model.regionCannotBeRendered()) : (react_1.default.createElement(DataDisplay, { model: model }, children));
+    return error ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: react_1.default.createElement(material_1.Tooltip, { title: "Reload" },
+            react_1.default.createElement(material_1.Button, { "data-testid": "reload_button", onClick: () => model.reload() }, "Reload")) })) : regionTooLarge ? (model.regionCannotBeRendered()) : (react_1.default.createElement(DataDisplay, { model: model }, children));
 });
 const DataDisplay = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { drawn, loading } = model;

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -37,8 +37,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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;
+    type: "BaseFeatureWidget";
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/esm/BamAdapter/BamAdapter.js

@@ -60,14 +60,13 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             const idToName = [];
             const nameToId = {};
             samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
-                sqLine.data.forEach(item => {
-                    if (item.tag === 'SN') {
-                        // this is the ref name
-                        const refName = item.value;
-                        nameToId[refName] = refId;
-                        idToName[refId] = refName;
-                    }
-                });
+                const SN = sqLine.data.find(item => item.tag === 'SN');
+                if (SN) {
+                    // this is the ref name
+                    const refName = SN.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                }
             });
             return { idToName, nameToId };
         });

package/esm/CramAdapter/CramAdapter.js

@@ -1,6 +1,6 @@
 import { CraiIndex, IndexedCramFile } from '@gmod/cram';
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { checkAbortSignal, updateStatus, } from '@jbrowse/core/util';
+import { checkAbortSignal, updateStatus, toLocale, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { toArray } from 'rxjs/operators';
@@ -17,12 +17,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     async configurePre() {
         const cramLocation = this.getConf('cramLocation');
         const craiLocation = this.getConf('craiLocation');
-        if (!cramLocation) {
-            throw new Error('missing cramLocation argument');
-        }
-        if (!craiLocation) {
-            throw new Error('missing craiLocation argument');
-        }
         const pm = this.pluginManager;
         const cram = new IndexedCramFile({
             cramFilehandle: openLocation(cramLocation, pm),
@@ -35,6 +29,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
             throw new Error('Error getting subadapter');
         }
         const seqConf = this.getConf('sequenceAdapter');
+        if (!seqConf) {
+            throw new Error('no sequenceAdapter supplied to CramAdapter config');
+        }
         const subadapter = await this.getSubAdapter(seqConf);
         return {
             cram,
@@ -81,8 +78,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
             return chunkSeq.slice(trimStart, trimStart + trimLength);
         })
             .join('');
-        if (sequence.length !== end - start) {
-            throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
+        const qlen = end - start;
+        if (sequence.length !== qlen) {
+            throw new Error(`fetching ${refName}:${toLocale(start - 1)}-${toLocale(end)} returned ${toLocale(sequence.length)} bases, should have returned ${toLocale(qlen)}`);
         }
         return sequence;
     }
@@ -99,14 +97,12 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
             samHeader
                 .filter(l => l.tag === 'SQ')
                 .forEach((sqLine, refId) => {
-                sqLine.data.forEach(item => {
-                    if (item.tag === 'SN') {
-                        // this is the ref name
-                        const refName = item.value;
-                        nameToId[refName] = refId;
-                        idToName[refId] = refName;
-                    }
-                });
+                const SN = sqLine.data.find(item => item.tag === 'SN');
+                if (SN) {
+                    const refName = SN.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                }
             });
             const readGroups = samHeader
                 .filter(l => l.tag === 'RG')
@@ -156,7 +152,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         const { signal, filterBy, statusCallback = () => { } } = opts || {};
         const { refName, start, end, originalRefName } = region;
         return ObservableCreate(async (observer) => {
-            const { cram } = await this.setup(opts);
+            const { cram, samHeader } = await this.setup(opts);
             const refId = this.refNameToId(refName);
             if (refId === undefined) {
                 console.warn('Unknown refName', refName);
@@ -178,7 +174,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
                     }
                     if (tagFilter) {
                         const v = tagFilter.tag === 'RG'
-                            ? (_a = this.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
+                            ? (_a = samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
                             : record.tags[tagFilter.tag];
                         if (!(tagFilter.value === '*'
                             ? v !== undefined

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -46,8 +46,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -453,8 +460,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/esm/LinearPileupDisplay/model.d.ts

@@ -43,8 +43,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

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

@@ -42,8 +42,17 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode; /**
+                 * #property
+                 */
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/esm/shared/BaseDisplayComponent.js

@@ -4,6 +4,7 @@ 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';
+import { Button, Tooltip } from '@mui/material';
 const useStyles = makeStyles()(theme => ({
     loading: {
         backgroundColor: theme.palette.background.default,
@@ -19,7 +20,8 @@ const useStyles = makeStyles()(theme => ({
 }));
 const BaseDisplayComponent = observer(function ({ model, children, }) {
     const { error, regionTooLarge } = model;
-    return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));
+    return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", action: React.createElement(Tooltip, { title: "Reload" },
+            React.createElement(Button, { "data-testid": "reload_button", onClick: () => model.reload() }, "Reload")) })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));
 });
 const DataDisplay = observer(function ({ model, children, }) {
     const { drawn, loading } = model;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.10.2",
+  "version": "2.10.3",
   "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": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
+  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
 }