npm - jbrowse-plugin-msaview - Versions diffs - 2.2.1 → 2.2.3 - Mend

jbrowse-plugin-msaview 2.2.1 → 2.2.3

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 (132) hide show

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.d.ts ADDED Viewed

@@ -0,0 +1,10 @@
+import { BaseAdapter, BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export default class BgzipFastaMsaAdapter extends BaseAdapter {
+    configureP: Promise<BaseFeatureDataAdapter> | undefined;
+    refNamesP: Promise<string[]> | undefined;
+    configurePre(): Promise<BaseFeatureDataAdapter>;
+    configure(): Promise<BaseFeatureDataAdapter>;
+    getMSARefs(): Promise<string[]>;
+    getMSAList(): Promise<string[]>;
+    getMSA(id: string): Promise<import("@jbrowse/core/util").Feature[]>;
+}

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js ADDED Viewed

@@ -0,0 +1,64 @@
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { firstValueFrom, toArray } from 'rxjs';
+export default class BgzipFastaMsaAdapter extends BaseAdapter {
+    async configurePre() {
+        const getSubAdapter = this.getSubAdapter;
+        if (getSubAdapter) {
+            const adapter = await getSubAdapter({
+                ...readConfObject(this.config),
+                type: 'BgzipFastaAdapter',
+            });
+            return adapter.dataAdapter;
+        }
+        else {
+            throw new Error('no get subadapter');
+        }
+    }
+    configure() {
+        this.configureP ??= this.configurePre().catch((e) => {
+            this.configureP = undefined;
+            throw e;
+        });
+        return this.configureP;
+    }
+    async getMSARefs() {
+        this.refNamesP ??= this.configure()
+            .then(adapter => adapter.getRefNames())
+            .catch((e) => {
+            this.refNamesP = undefined;
+            throw e;
+        });
+        return this.refNamesP;
+    }
+    async getMSAList() {
+        const refNames = await this.getMSARefs();
+        const list = new Set();
+        const val = this.getConf('msaRegex');
+        const re = new RegExp(val);
+        for (let i = 0, l = refNames.length; i < l; i++) {
+            list.add(refNames[i].split(re)[0]);
+        }
+        return [...list];
+    }
+    async getMSA(id) {
+        const adapter = await this.configure();
+        const refNames = await adapter.getRefNames();
+        const rows = [];
+        for (let i = 0, l = refNames.length; i < l; i++) {
+            const refName = refNames[i];
+            if (refName.startsWith(id)) {
+                rows.push(refName);
+            }
+        }
+        return firstValueFrom(adapter
+            .getFeaturesInMultipleRegions(rows.map(refName => ({
+            refName,
+            start: 0,
+            end: 1_000_000_000,
+            assemblyName: '',
+        })))
+            .pipe(toArray()));
+    }
+}
+//# sourceMappingURL=BgzipFastaMsaAdapter.js.map

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"BgzipFastaMsaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EACL,WAAW,GAEZ,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,MAAM,CAAC,OAAO,OAAO,oBAAqB,SAAQ,WAAW;IAK3D,KAAK,CAAC,YAAY;QAChB,MAAM,aAAa,GAAG,IAAI,CAAC,aAAa,CAAA;QACxC,IAAI,aAAa,EAAE,CAAC;YAClB,MAAM,OAAO,GAAG,MAAM,aAAa,CAAC;gBAClC,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC9B,IAAI,EAAE,mBAAmB;aAC1B,CAAC,CAAA;YAEF,OAAO,OAAO,CAAC,WAAqC,CAAA;QACtD,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;IACD,SAAS;QACP,IAAI,CAAC,UAAU,KAAK,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YAC3D,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;YAC3B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,UAAU;QACd,IAAI,CAAC,SAAS,KAAK,IAAI,CAAC,SAAS,EAAE;aAChC,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC;aACtC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YACpB,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;YAC1B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACJ,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,KAAK,CAAC,UAAU;QACd,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,UAAU,EAAE,CAAA;QACxC,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAA;QAC9B,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;QACpC,MAAM,EAAE,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;QAC1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAChD,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,CAAE,CAAC,CAAA;QACtC,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,CAAA;IAClB,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,EAAU;QACrB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,WAAW,EAAE,CAAA;QAC5C,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAChD,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;YAC5B,IAAI,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC,EAAE,CAAC;gBAC3B,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACpB,CAAC;QACH,CAAC;QACD,OAAO,cAAc,CACnB,OAAO;aACJ,4BAA4B,CAC3B,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YACnB,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,aAAa;YAClB,YAAY,EAAE,EAAE;SACjB,CAAC,CAAC,CACJ;aACA,IAAI,CAAC,OAAO,EAAE,CAAC,CACnB,CAAA;IACH,CAAC;CACF"}

package/dist/BgzipFastaMsaAdapter/configSchema.d.ts ADDED Viewed

@@ -0,0 +1,7 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    msaRegex: {
+        type: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration").AnyConfigurationSchemaType, undefined>>;

package/dist/BgzipFastaMsaAdapter/configSchema.js ADDED Viewed

@@ -0,0 +1,13 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default function configSchemaF(pluginManager) {
+    const base = pluginManager.getAdapterType('BgzipFastaAdapter');
+    return ConfigurationSchema('BgzipFastaMsaAdapter', {
+        msaRegex: {
+            type: 'string',
+            defaultValue: '_',
+        },
+    }, {
+        baseConfiguration: base?.configSchema,
+    });
+}
+//# sourceMappingURL=configSchema.js.map

package/dist/BgzipFastaMsaAdapter/configSchema.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BgzipFastaMsaAdapter/configSchema.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,aAA4B;IAChE,MAAM,IAAI,GAAG,aAAa,CAAC,cAAc,CAAC,mBAAmB,CAAC,CAAA;IAC9D,OAAO,mBAAmB,CACxB,sBAAsB,EACtB;QACE,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,GAAG;SAClB;KACF,EACD;QACE,iBAAiB,EAAE,IAAI,EAAE,YAAY;KACtC,CACF,CAAA;AACH,CAAC"}

package/dist/BgzipFastaMsaAdapter/index.d.ts ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import PluginManager from '@jbrowse/core/PluginManager';
2	+ export default function BgzipFastaMsaAdapterF(pluginManager: PluginManager): PluginManager;

package/dist/BgzipFastaMsaAdapter/index.js ADDED Viewed

@@ -0,0 +1,15 @@
+import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
+import configSchemaF from './configSchema';
+export default function BgzipFastaMsaAdapterF(pluginManager) {
+    return pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'BgzipFastaMsaAdapter',
+            configSchema: configSchemaF(pluginManager),
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+            getAdapterClass: () => import('./BgzipFastaMsaAdapter').then(t => t.default),
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/BgzipFastaMsaAdapter/index.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipFastaMsaAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,MAAM,CAAC,OAAO,UAAU,qBAAqB,CAAC,aAA4B;IACxE,OAAO,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QACvC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,YAAY,EAAE,aAAa,CAAC,aAAa,CAAC;YAC1C,eAAe,EAAE;gBACf,aAAa,EAAE,IAAI;aACpB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,wBAAwB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACxD,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts CHANGED Viewed

@@ -6,5 +6,5 @@ export declare function useGeneTree(geneId: string): {
         treeMetadata: string;
     } | undefined;
     isTreeLoading: boolean;
-    treeError: unknown;
+    treeError: any;
 };

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js CHANGED Viewed

@@ -1,27 +1,7 @@
-import { useEffect, useState } from 'react';
+import useSWR from 'swr';
 import { geneTreeFetcher } from './ensemblGeneTreeUtils';
 export function useGeneTree(geneId) {
-    const [treeData, setTreeData] = useState();
-    const [isTreeLoading, setIsTreeLoading] = useState(false);
-    const [treeError, setTreeError] = useState();
-    useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
-            try {
-                setIsTreeLoading(true);
-                const result = await geneTreeFetcher(geneId);
-                setTreeData(result);
-            }
-            catch (e) {
-                console.error(e);
-                setTreeError(e);
-            }
-            finally {
-                setIsTreeLoading(false);
-            }
-        })();
-    }, [geneId]);
-    return { treeData, isTreeLoading, treeError };
+    const { data, error, isLoading } = useSWR(() => (geneId ? ['geneTree', geneId] : null), ([, geneId]) => geneTreeFetcher(geneId));
+    return { treeData: data, isTreeLoading: isLoading, treeError: error };
 }
 //# sourceMappingURL=useGeneTree.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/util.d.ts CHANGED Viewed

@@ -1,4 +1 @@
-export declare function jsonfetch<T>(url: string, arg?: RequestInit): Promise<T>;
-export declare function textfetch(url: string, arg?: RequestInit): Promise<string>;
-export declare function fetchWithLocalStorageCache<T>(key: string, fetchFn: () => Promise<T>): Promise<T>;
-export declare function unzipfetch(url: string, arg?: RequestInit): Promise<string>;
+export { fetchWithLocalStorageCache, jsonfetch, textfetch, unzipfetch, } from '../../../utils/fetch';

package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js CHANGED Viewed

@@ -1,38 +1,2 @@
-import { ungzip } from 'pako';
-export async function jsonfetch(url, arg) {
-    const res = await fetch(url, arg);
-    if (!res.ok) {
-        throw new Error(`HTTP ${res.status} from ${url}: ${await res.text()}`);
-    }
-    return res.json();
-}
-export async function textfetch(url, arg) {
-    const res = await fetch(url, arg);
-    if (!res.ok) {
-        throw new Error(`HTTP ${res.status} from ${url}`);
-    }
-    return res.text();
-}
-export async function fetchWithLocalStorageCache(key, fetchFn) {
-    const cachedData = localStorage.getItem(key);
-    if (cachedData) {
-        try {
-            return JSON.parse(cachedData);
-        }
-        catch (error) {
-            console.error(`Error parsing cached data for ${key}:`, error);
-            // Continue to fetch fresh data if parsing fails
-        }
-    }
-    const data = await fetchFn();
-    localStorage.setItem(key, JSON.stringify(data));
-    return data;
-}
-export async function unzipfetch(url, arg) {
-    const res = await fetch(url, arg);
-    if (!res.ok) {
-        throw new Error(`HTTP ${res.status} from ${url}: ${await res.text()}`);
-    }
-    return ungzip(await res.arrayBuffer(), { to: 'string' });
-}
+export { fetchWithLocalStorageCache, jsonfetch, textfetch, unzipfetch, } from '../../../utils/fetch';
 //# sourceMappingURL=util.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/LaunchMsaViewDialog.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 import React from 'react';
 import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-export default function LaunchProteinViewDialog({ handleClose, feature, model, }: {
+export default function LaunchMsaViewDialog({ handleClose, feature, model, }: {
     handleClose: () => void;
     feature: Feature;
     model: AbstractTrackModel;

package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js CHANGED Viewed

@@ -6,25 +6,30 @@ import ManualMSALoader from './ManualMSALoader/ManualMSALoader';
 import NCBIBlastPanel from './NCBIBlastQuery/NCBIBlastPanel';
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
 import TabPanel from './TabPanel';
-export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
-    const [value, setValue] = useState(0);
-    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch MSA view", open: true, onClose: () => {
-            handleClose();
-        } },
-        React.createElement(Tabs, { value: value, onChange: (_, val) => {
-                setValue(val);
-            } },
-            React.createElement(Tab, { label: "NCBI BLAST query", value: 0 }),
-            React.createElement(Tab, { label: "UCSC 100-way dataset", value: 1 }),
-            React.createElement(Tab, { label: "Ensembl GeneTree", value: 2 }),
-            React.createElement(Tab, { label: "Manually open MSA/tree", value: 3 })),
-        React.createElement(TabPanel, { value: value, index: 0 },
+const TABS = {
+    NCBI_BLAST: 0,
+    PRELOADED_MSA: 1,
+    ENSEMBL_GENETREE: 2,
+    MANUAL_MSA: 3,
+};
+export default function LaunchMsaViewDialog({ handleClose, feature, model, }) {
+    const [value, setValue] = useState(TABS.NCBI_BLAST);
+    const handleChange = (_event, newValue) => {
+        setValue(newValue);
+    };
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch MSA view", open: true, onClose: handleClose },
+        React.createElement(Tabs, { value: value, onChange: handleChange },
+            React.createElement(Tab, { label: "NCBI BLAST query", value: TABS.NCBI_BLAST }),
+            React.createElement(Tab, { label: "Pre-loaded MSA datasets", value: TABS.PRELOADED_MSA }),
+            React.createElement(Tab, { label: "Ensembl GeneTree", value: TABS.ENSEMBL_GENETREE }),
+            React.createElement(Tab, { label: "Manually open MSA dataset", value: TABS.MANUAL_MSA })),
+        React.createElement(TabPanel, { value: value, index: TABS.NCBI_BLAST },
             React.createElement(NCBIBlastPanel, { handleClose: handleClose, feature: feature, model: model })),
-        React.createElement(TabPanel, { value: value, index: 1 },
+        React.createElement(TabPanel, { value: value, index: TABS.PRELOADED_MSA },
             React.createElement(PreLoadedMSA, { model: model, feature: feature, handleClose: handleClose })),
-        React.createElement(TabPanel, { value: value, index: 2 },
+        React.createElement(TabPanel, { value: value, index: TABS.ENSEMBL_GENETREE },
             React.createElement(EnsemblGeneTree, { model: model, feature: feature, handleClose: handleClose })),
-        React.createElement(TabPanel, { value: value, index: 3 },
+        React.createElement(TabPanel, { value: value, index: TABS.MANUAL_MSA },
             React.createElement(ManualMSALoader, { model: model, feature: feature, handleClose: handleClose }))));
 }
 //# sourceMappingURL=LaunchMsaViewDialog.js.map

package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js CHANGED Viewed

@@ -6,7 +6,7 @@ import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Ra
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { launchView } from './launchView';
-import TextField2 from '../../../TextField2';
+import TextField2 from '../../../components/TextField2';
 import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
 import { useFeatureSequence } from '../useFeatureSequence';

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"ManualMSALoader.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAIL,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,KAAK,EACL,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAA;AACzC,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,kBAAkB,EAAE,KAAK,EAAE,qBAAqB,EAAE,MAAM,YAAY,CAAA;AAC7E,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,uBAAuB,CAAA;AAI1D,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAEF,MAAM,eAAe,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACtD,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,EAAW,CAAA;IACjE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAkB,MAAM,CAAC,CAAA;IACvE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC5C,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtE,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxE,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,aAAa,KAAK,KAAK,CAAC,GAAG,CAAC,CAAC,CAAA;IAC7D,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAE,CAAA;IAC7E,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,kBAAkB,CAAC;QAC5D,IAAI;QACJ,OAAO,EAAE,kBAAkB;KAC5B,CAAC,CAAA;IAEF,MAAM,CAAC,GAAG,eAAe,IAAI,MAAM,CAAA;IACnC,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACtC,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;gBAC/B,oBAAC,UAAU,IACT,GAAG,QACH,KAAK,EAAE,WAAW,EAClB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,cAAc,CAAC,KAAK,CAAC,MAAM,CAAC,KAAwB,CAAC,CAAA;oBACvD,CAAC;oBAED,oBAAC,gBAAgB,IACf,KAAK,EAAC,MAAM,EACZ,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,YAAY,GAClB;oBACF,oBAAC,gBAAgB,IACf,KAAK,EAAC,MAAM,EACZ,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,YAAY,GAClB,CACS,CACD;YAEd,6BAAK,KAAK,EAAE,EAAE,YAAY,EAAE,EAAE,EAAE,IAC7B,WAAW,KAAK,MAAM,CAAC,CAAC,CAAC,CACxB,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,GAAG,EAAE;gBAC3B,oBAAC,YAAY,IACX,IAAI,EAAC,6EAA6E,EAClF,MAAM,QACN,QAAQ,EAAE,eAAe,EACzB,WAAW,EAAE,kBAAkB,GAC/B;gBACF,oBAAC,YAAY,IACX,IAAI,EAAC,oDAAoD,EACzD,MAAM,QACN,QAAQ,EAAE,gBAAgB,EAC1B,WAAW,EAAE,mBAAmB,GAChC,CACE,CACP,CAAC,CAAC,CAAC,CACF;gBACE,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,KAAK,EACV,SAAS,QACT,OAAO,EAAE,CAAC,EACV,KAAK,EAAE,EAAE,YAAY,EAAE,MAAM,EAAE,EAC/B,OAAO,EAAE,EAAE,EACX,SAAS,QACT,WAAW,EAAC,gBAAgB,EAC5B,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAChC,CAAC,GACD;gBACF,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,MAAM,EACX,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,WAAW,EAAC,8BAA8B,EAC1C,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,GACD,CACD,CACJ,CACG;YAEN,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,OAAO,EAChB,oBAAoB,EAAE,aAAa,EACnC,kBAAkB,EAAE,gBAAgB,EACpC,eAAe,EAAE,eAAe,GAChC,CACY;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,QAAQ,EACN,CAAC,GAAG;oBACJ,CAAC,WAAW,KAAK,MAAM,IAAI,CAAC,eAAe,CAAC;oBAC5C,CAAC,WAAW,KAAK,MAAM,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,EAE7C,OAAO,EAAE,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,CAAC;oBAAA,CAAC,KAAK,IAAI,EAAE;wBACX,IAAI,CAAC;4BACH,IAAI,CAAC,GAAG,EAAE,CAAC;gCACT,OAAM;4BACR,CAAC;4BAED,kBAAkB,CAAC,SAAS,CAAC,CAAA;4BAC7B,UAAU,CAAC;gCACT,OAAO;gCACP,YAAY,EAAE,kBAAkB,CAAC,GAAG,CAAC;gCACrC,IAAI;gCACJ,OAAO,EAAE,GAAG;gCACZ,IAAI,EACF,WAAW,KAAK,MAAM;oCACpB,CAAC,CAAC;wCACE,GAAG,EAAE,eAAe;4CAClB,CAAC,CAAC,MAAM,YAAY,CAAC,eAAe,CAAC,CAAC,QAAQ,CAC1C,MAAM,CACP;4CACH,CAAC,CAAC,EAAE;wCACN,IAAI,EAAE,gBAAgB;4CACpB,CAAC,CAAC,MAAM,YAAY,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAC3C,MAAM,CACP;4CACH,CAAC,CAAC,SAAS;qCACd;oCACH,CAAC,CAAC;wCACE,GAAG,EAAE,OAAO;wCACZ,IAAI,EAAE,QAAQ;qCACf;6BACR,CAAC,CAAA;4BAEF,WAAW,EAAE,CAAA;wBACf,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,kBAAkB,CAAC,CAAC,CAAC,CAAA;wBACvB,CAAC;oBACH,CAAC,CAAC,EAAE,CAAA;gBACN,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js CHANGED Viewed

@@ -5,7 +5,7 @@ import { Button, DialogActions, DialogContent, MenuItem, Typography, } from '@mu
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { blastLaunchView } from './blastLaunchView';
-import TextField2 from '../../../TextField2';
+import TextField2 from '../../../components/TextField2';
 import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
 import { useFeatureSequence } from '../useFeatureSequence';
@@ -28,9 +28,9 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
     const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] = useState('clustalo');
     const options = getTranscriptFeatures(feature);
     const [selectedTranscriptId, setSelectedTranscriptId] = useState(getId(options[0]));
-    const [selectedBlastProgram, setSelectedBlastProgram] = useState('blastp');
+    const [selectedBlastProgram, setSelectedBlastProgram] = useState('quick-blastp');
     const selectedTranscript = options.find(val => getId(val) === selectedTranscriptId);
-    const { error, proteinSequence } = useFeatureSequence({
+    const { error: proteinSequenceError, proteinSequence } = useFeatureSequence({
         view,
         feature: selectedTranscript,
     });
@@ -39,22 +39,26 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
             setSelectedBlastProgram('blastp');
         }
     }, [selectedBlastDatabase]);
-    const e = error ?? launchViewError;
+    const e = proteinSequenceError ?? launchViewError;
+    const style = { width: 150 };
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             children,
             e ? React.createElement(ErrorMessage, { error: e }) : null,
-            React.createElement(TextField2, { variant: "outlined", label: "BLAST database", style: { width: 150 }, select: true, value: selectedBlastDatabase, onChange: event => {
+            React.createElement(TextField2, { variant: "outlined", label: "BLAST database", style: style, select: true, value: selectedBlastDatabase, onChange: event => {
                     setSelectedBlastDatabase(event.target.value);
                 } }, blastDatabaseOptions.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
-            React.createElement(TextField2, { variant: "outlined", label: "MSA Algorithm", style: { width: 150 }, select: true, value: selectedMsaAlgorithm, onChange: event => {
+            React.createElement(TextField2, { variant: "outlined", label: "MSA Algorithm", style: style, select: true, value: selectedMsaAlgorithm, onChange: event => {
                     setSelectedMsaAlgorithm(event.target.value);
                 } }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
             React.createElement("div", { style: { display: 'flex' } },
-                React.createElement(TextField2, { variant: "outlined", label: "BLAST program", disabled: selectedBlastDatabase === 'nr_cluster_seq', style: { width: 150 }, select: true, value: selectedBlastProgram, onChange: event => {
+                React.createElement(TextField2, { variant: "outlined", label: "BLAST program", disabled: selectedBlastDatabase === 'nr_cluster_seq', style: style, select: true, value: selectedBlastProgram, onChange: event => {
                         setSelectedBlastProgram(event.target.value);
                     } }, blastPrograms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
-                selectedBlastDatabase === 'nr_cluster_seq' ? (React.createElement(Typography, { variant: "subtitle2", style: { marginLeft: 4, alignContent: 'center' } }, "Can only use blastp on nr_cluster_seq")) : null),
+                selectedBlastDatabase === 'nr_cluster_seq' ? (React.createElement(Typography, { variant: "subtitle2", style: {
+                        marginLeft: 4,
+                        alignContent: 'center',
+                    } }, "Can only use blastp on nr_cluster_seq")) : null),
             React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: selectedTranscriptId, onTranscriptChange: setSelectedTranscriptId, proteinSequence: proteinSequence }),
             React.createElement(Typography, { style: { marginTop: 20 } }, "This panel will automatically submit a query to NCBI. Using blastp can take 10+ minutes to run, quick-blastp is generally a lot faster but is not available for the clustered database. After completion, all the hits will be run through a multiple sequence alignment. Note: we are not able to currently run NCBI COBALT automatically on the BLAST results, even though that is the method NCBI uses on their website. If you need a COBALT alignment, please use the manual approach of submitting BLAST yourself and downloading the resulting files")),
         React.createElement(DialogActions, null,

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js CHANGED Viewed

@@ -4,7 +4,7 @@ import { getContainingView, shorten2 } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import ExternalLink from '../../../ExternalLink';
+import ExternalLink from '../../../components/ExternalLink';
 import { getId, getTranscriptFeatures } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
 import { useFeatureSequence } from '../useFeatureSequence';

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js CHANGED Viewed

@@ -11,18 +11,19 @@ export default function NCBIBlastPanel({ handleClose, model, feature, }) {
     const [lookupMethod, setLookupMethod] = useState('automatic');
     const [baseUrl, setBaseUrl] = useLocalStorage('msa-blastRootUrl', BASE_BLAST_URL);
     const [settingsOpen, setSettingsOpen] = useState(false);
+    const Panel = lookupMethod === 'automatic'
+        ? NCBIBlastAutomaticPanel
+        : NCBIBlastManualPanel;
     return (React.createElement(React.Fragment, null,
         React.createElement(IconButton, { style: { float: 'right' }, size: "small", onClick: () => {
                 setSettingsOpen(true);
             } },
             React.createElement(SettingsIcon, null)),
-        lookupMethod === 'automatic' ? (React.createElement(NCBIBlastAutomaticPanel, { model: model, feature: feature, handleClose: handleClose, baseUrl: baseUrl },
-            React.createElement(NCBIBlastMethodSelector, { lookupMethod: lookupMethod, setLookupMethod: setLookupMethod }))) : null,
-        lookupMethod === 'manual' ? (React.createElement(NCBIBlastManualPanel, { model: model, feature: feature, handleClose: handleClose, baseUrl: baseUrl },
-            React.createElement(NCBIBlastMethodSelector, { lookupMethod: lookupMethod, setLookupMethod: setLookupMethod }))) : null,
-        settingsOpen ? (React.createElement(NCBISettingsDialog, { baseUrl: baseUrl, handleClose: arg => {
-                if (arg) {
-                    setBaseUrl(arg);
+        React.createElement(Panel, { model: model, feature: feature, handleClose: handleClose, baseUrl: baseUrl },
+            React.createElement(NCBIBlastMethodSelector, { lookupMethod: lookupMethod, setLookupMethod: setLookupMethod })),
+        settingsOpen ? (React.createElement(NCBISettingsDialog, { baseUrl: baseUrl, handleClose: newUrl => {
+                if (newUrl) {
+                    setBaseUrl(newUrl);
                 }
                 setSettingsOpen(false);
             } })) : null));

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js CHANGED Viewed

@@ -1,7 +1,7 @@
 import React, { useState } from 'react';
 import { Button, Dialog, DialogActions, DialogContent, DialogTitle, } from '@mui/material';
 import { BASE_BLAST_URL } from './consts';
-import TextField2 from '../../../TextField2';
+import TextField2 from '../../../components/TextField2';
 export default function NCBISettingsDialog({ handleClose, baseUrl, }) {
     const [tempBaseUrl, setTempBaseUrl] = useState(baseUrl);
     return (React.createElement(Dialog, { open: true, maxWidth: "lg", onClose: () => {

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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