jbrowse-plugin-msaview 2.3.8 → 2.4.1

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js

@@ -1,29 +1,18 @@
 import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import { useStyles } from './util';
+import { hasHoverPosition, useStyles } from './util';
 const GenomeMouseoverHighlight = observer(function ({ model, }) {
-    const session = getSession(model);
-    const { hovered, views } = session;
-    // Early return if no MSA view exists
+    const { hovered, views } = getSession(model);
     const hasMsaView = views.some(s => s.type === 'MsaView');
-    if (!hasMsaView) {
-        return null;
-    }
-    // Early return if no hover position
-    if (!hovered ||
-        typeof hovered !== 'object' ||
-        !('hoverPosition' in hovered)) {
-        return null;
-    }
-    return React.createElement(GenomeMouseoverHighlightRenderer, { model: model, hovered: hovered });
+    return hasMsaView && hasHoverPosition(hovered) ? (React.createElement(GenomeMouseoverHighlightRenderer, { model: model, hovered: hovered })) : null;
 });
 const GenomeMouseoverHighlightRenderer = observer(function ({ model, hovered, }) {
     const { classes } = useStyles();
     const { offsetPx } = model;
     const { coord, refName } = hovered.hoverPosition;
     const s = model.bpToPx({ refName, coord: coord - 1 });
-    const e = model.bpToPx({ refName, coord: coord });
+    const e = model.bpToPx({ refName, coord });
     if (s && e) {
         const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4);
         const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx;

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map

@@ -1 +1 @@
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+{"version":3,"file":"GenomeMouseoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/GenomeMouseoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAIpD,MAAM,wBAAwB,GAAG,QAAQ,CAAC,UAAU,EAClD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC5C,MAAM,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAAC,CAAA;IACxD,OAAO,UAAU,IAAI,gBAAgB,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAC/C,oBAAC,gCAAgC,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,OAAO,GAAI,CACrE,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,MAAM,gCAAgC,GAAG,QAAQ,CAAC,UAAU,EAC1D,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;IAEhD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;IACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAA;IAE1C,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;QAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;QACxD,OAAO,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS,EAAE,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GAAI,CAAA;IACtE,CAAC;IAED,OAAO,IAAI,CAAA;AACb,CAAC,CAAC,CAAA;AAEF,eAAe,wBAAwB,CAAA"}

package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -1,29 +1,27 @@
 import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import { useStyles } from './util';
-// Outer component: only re-renders when MSA view or highlights change
+import { hasHoverPosition, useStyles } from './util';
+import { getCanonicalRefName } from '../MsaViewPanel/util';
 const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, }) {
-    const { views } = getSession(model);
+    const { views, hovered } = getSession(model);
     const msaView = views.find(f => f.type === 'MsaView');
     const highlights = msaView?.connectedHighlights;
-    // Early return if no highlights - avoid all other work
-    if (!highlights || highlights.length === 0) {
-        return null;
-    }
-    return React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights });
+    // Suppress codon highlight while hovering the LGV — GenomeMouseoverHighlight
+    // handles the single-bp display in that case
+    return !hasHoverPosition(hovered) && highlights?.length ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: Array.from(highlights) })) : null;
 });
 // Inner component: handles the scroll-dependent rendering
 const MsaToGenomeHighlightRenderer = observer(function ({ model, highlights, }) {
     const { classes } = useStyles();
     const { assemblyManager } = getSession(model);
-    const assembly = assemblyManager.get(model.assemblyNames[0]);
     const { offsetPx } = model;
-    if (!assembly) {
-        return null;
-    }
     return (React.createElement(React.Fragment, null, highlights.map((r, idx) => {
-        const refName = assembly.getCanonicalRefName(r.refName) ?? r.refName;
+        const refName = getCanonicalRefName({
+            assemblyManager,
+            assemblyNames: model.assemblyNames,
+            refName: r.refName,
+        });
         const s = model.bpToPx({ refName, coord: r.start });
         const e = model.bpToPx({ refName, coord: r.end });
         if (s && e) {

package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map

@@ -1 +1 @@
-{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAOlC,sEAAsE;AACtE,MAAM,oBAAoB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACnE,KAAK,GAGN;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACnC,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAEvC,CAAA;IAEb,MAAM,UAAU,GAAG,OAAO,EAAE,mBAAmB,CAAA;IAE/C,uDAAuD;IACvD,IAAI,CAAC,UAAU,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC3C,OAAO,IAAI,CAAA;IACb,CAAC;IAED,OAAO,oBAAC,4BAA4B,IAAC,KAAK,EAAE,KAAK,EAAE,UAAU,EAAE,UAAU,GAAI,CAAA;AAC/E,CAAC,CAAC,CAAA;AAEF,0DAA0D;AAC1D,MAAM,4BAA4B,GAAG,QAAQ,CAAC,UAAU,EACtD,KAAK,EACL,UAAU,GAIX;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,CAAE,CAAC,CAAA;IAC7D,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAE1B,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,IAAI,CAAA;IACb,CAAC;IAED,OAAO,CACL,0CACG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;QACzB,MAAM,OAAO,GAAG,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,OAAO,CAAA;QACpE,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAA;QACnD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;YACxD,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,EAC9C,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}
+{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AACpD,OAAO,EAAE,mBAAmB,EAAE,MAAM,sBAAsB,CAAA;AAO1D,MAAM,oBAAoB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACnE,KAAK,GAGN;IACC,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAEvC,CAAA;IACb,MAAM,UAAU,GAAG,OAAO,EAAE,mBAAmB,CAAA;IAE/C,6EAA6E;IAC7E,6CAA6C;IAC7C,OAAO,CAAC,gBAAgB,CAAC,OAAO,CAAC,IAAI,UAAU,EAAE,MAAM,CAAC,CAAC,CAAC,CACxD,oBAAC,4BAA4B,IAC3B,KAAK,EAAE,KAAK,EACZ,UAAU,EAAE,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,GAClC,CACH,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,0DAA0D;AAC1D,MAAM,4BAA4B,GAAG,QAAQ,CAAC,UAAU,EACtD,KAAK,EACL,UAAU,GAIX;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAE1B,OAAO,CACL,0CACG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;QACzB,MAAM,OAAO,GAAG,mBAAmB,CAAC;YAClC,eAAe;YACf,aAAa,EAAE,KAAK,CAAC,aAAa;YAClC,OAAO,EAAE,CAAC,CAAC,OAAO;SACnB,CAAC,CAAA;QACF,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAA;QACnD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;YACxD,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,EAC9C,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}

package/dist/AddHighlightModel/util.d.ts

@@ -1,3 +1,9 @@
+export declare function hasHoverPosition(hovered: unknown): hovered is {
+    hoverPosition: {
+        coord: number;
+        refName: string;
+    };
+};
 export declare const useStyles: (params: void, muiStyleOverridesParams?: {
     props: Record<string, unknown>;
     ownerState?: Record<string, unknown> | undefined;

package/dist/AddHighlightModel/util.js

@@ -1,4 +1,10 @@
 import { makeStyles } from 'tss-react/mui';
+export function hasHoverPosition(hovered) {
+    return (!!hovered &&
+        typeof hovered === 'object' &&
+        'hoverPosition' in hovered &&
+        !!hovered.hoverPosition);
+}
 export const useStyles = makeStyles()({
     highlight: {
         height: '100%',

package/dist/AddHighlightModel/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,CAAC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IACpC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,qBAAqB;QACjC,MAAM,EAAE,6BAA6B;QACrC,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,EAAE;QACV,SAAS,EAAE,QAAQ;QACnB,aAAa,EAAE,MAAM;QACrB,QAAQ,EAAE,QAAQ;KACnB;CACF,CAAC,CAAA"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,UAAU,gBAAgB,CAC9B,OAAgB;IAEhB,OAAO,CACL,CAAC,CAAC,OAAO;QACT,OAAO,OAAO,KAAK,QAAQ;QAC3B,eAAe,IAAI,OAAO;QAC1B,CAAC,CAAC,OAAO,CAAC,aAAa,CACxB,CAAA;AACH,CAAC;AAED,MAAM,CAAC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IACpC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,qBAAqB;QACjC,MAAM,EAAE,6BAA6B;QACrC,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,EAAE;QACV,SAAS,EAAE,QAAQ;QACnB,aAAa,EAAE,MAAM;QACrB,QAAQ,EAAE,QAAQ;KACnB;CACF,CAAC,CAAA"}

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.d.ts

@@ -6,6 +6,8 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
     configurePre(): Promise<BaseFeatureDataAdapter>;
     configure(): Promise<BaseFeatureDataAdapter>;
     getMSARefs(): Promise<string[]>;
+    getMsaRegex(): RegExp;
+    refNameToMsaId(refName: string): string;
     getMSAList(): Promise<string[]>;
     getMSA(id: string): Promise<import("@jbrowse/core/util").Feature[]>;
 }

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js

@@ -31,17 +31,21 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
         });
         return this.refNamesP;
     }
+    getMsaRegex() {
+        return new RegExp(this.getConf('msaRegex'));
+    }
+    refNameToMsaId(refName) {
+        return refName.split(this.getMsaRegex())[0];
+    }
     async getMSAList() {
         const refNames = await this.getMSARefs();
-        const val = this.getConf('msaRegex');
-        const re = new RegExp(val);
-        const list = new Set(refNames.map(name => name.split(re)[0]));
+        const list = new Set(refNames.map(name => this.refNameToMsaId(name)));
         return [...list];
     }
     async getMSA(id) {
         const adapter = await this.configure();
         const refNames = await adapter.getRefNames();
-        const rows = refNames.filter(refName => refName.startsWith(id));
+        const rows = refNames.filter(refName => this.refNameToMsaId(refName) === id);
         return firstValueFrom(adapter
             .getFeaturesInMultipleRegions(rows.map(refName => ({
             refName,

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js

@@ -1,18 +1,16 @@
 import React, { useState } from 'react';
-import { readConfObject } from '@jbrowse/core/configuration';
 import { Dialog } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import { Tab, Tabs } from '@mui/material';
-import EnsemblGeneTree from './EnsemblGeneTree/EnsemblGeneTree';
 import ManualMSALoader from './ManualMSALoader/ManualMSALoader';
 import NCBIBlastPanel from './NCBIBlastQuery/NCBIBlastPanel';
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
+import { readMsaDatasets } from './PreLoadedMSA/types';
 import TabPanel from './TabPanel';
 export default function LaunchMsaViewDialog({ handleClose, feature, model, }) {
     const session = getSession(model);
-    const { jbrowse } = session;
-    const datasets = readConfObject(jbrowse, ['msa', 'datasets']);
-    const hasPreloadedDatasets = datasets && datasets.length > 0;
+    const datasets = readMsaDatasets(session.jbrowse);
+    const hasPreloadedDatasets = !!datasets?.length;
     const [value, setValue] = useState('ncbi_blast');
     const handleChange = (_event, newValue) => {
         setValue(newValue);
@@ -21,14 +19,11 @@ export default function LaunchMsaViewDialog({ handleClose, feature, model, }) {
         React.createElement(Tabs, { value: value, onChange: handleChange },
             React.createElement(Tab, { label: "NCBI BLAST query", value: "ncbi_blast" }),
             hasPreloadedDatasets ? (React.createElement(Tab, { label: "Pre-loaded MSA datasets", value: "preloaded_msa" })) : null,
-            React.createElement(Tab, { label: "Ensembl GeneTree", value: "ensembl_genetree" }),
             React.createElement(Tab, { label: "Manual upload", value: "manual_msa" })),
         React.createElement(TabPanel, { value: value, index: "ncbi_blast" },
             React.createElement(NCBIBlastPanel, { handleClose: handleClose, feature: feature, model: model })),
         hasPreloadedDatasets ? (React.createElement(TabPanel, { value: value, index: "preloaded_msa" },
             React.createElement(PreLoadedMSA, { model: model, feature: feature, handleClose: handleClose }))) : null,
-        React.createElement(TabPanel, { value: value, index: "ensembl_genetree" },
-            React.createElement(EnsemblGeneTree, { model: model, feature: feature, handleClose: handleClose })),
         React.createElement(TabPanel, { value: value, index: "manual_msa" },
             React.createElement(ManualMSALoader, { model: model, feature: feature, handleClose: handleClose }))));
 }

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

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+{"version":3,"file":"LaunchMsaViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/LaunchMsaViewDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAEzC,OAAO,eAAe,MAAM,mCAAmC,CAAA;AAC/D,OAAO,cAAc,MAAM,iCAAiC,CAAA;AAC5D,OAAO,YAAY,MAAM,sCAAsC,CAAA;AAC/D,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AACtD,OAAO,QAAQ,MAAM,YAAY,CAAA;AAIjC,MAAM,CAAC,OAAO,UAAU,mBAAmB,CAAC,EAC1C,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,QAAQ,GAAG,eAAe,CAAC,OAAO,CAAC,OAAO,CAAC,CAAA;IACjD,MAAM,oBAAoB,GAAG,CAAC,CAAC,QAAQ,EAAE,MAAM,CAAA;IAE/C,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,YAAY,CAAC,CAAA;IAEhD,MAAM,YAAY,GAAG,CAAC,MAA4B,EAAE,QAAgB,EAAE,EAAE;QACtE,QAAQ,CAAC,QAAQ,CAAC,CAAA;IACpB,CAAC,CAAA;IAED,OAAO,CACL,oBAAC,MAAM,IAAC,QAAQ,EAAC,IAAI,EAAC,KAAK,EAAC,iBAAiB,EAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QACrE,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,YAAY;YACxC,oBAAC,GAAG,IAAC,KAAK,EAAC,kBAAkB,EAAC,KAAK,EAAC,YAAY,GAAG;YAClD,oBAAoB,CAAC,CAAC,CAAC,CACtB,oBAAC,GAAG,IAAC,KAAK,EAAC,yBAAyB,EAAC,KAAK,EAAC,eAAe,GAAG,CAC9D,CAAC,CAAC,CAAC,IAAI;YACR,oBAAC,GAAG,IAAC,KAAK,EAAC,eAAe,EAAC,KAAK,EAAC,YAAY,GAAG,CAC3C;QACP,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAC,YAAY;YACxC,oBAAC,cAAc,IACb,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,GACZ,CACO;QACV,oBAAoB,CAAC,CAAC,CAAC,CACtB,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAC,eAAe;YAC3C,oBAAC,YAAY,IACX,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACO,CACZ,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAC,YAAY;YACxC,oBAAC,eAAe,IACd,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACO,CACJ,CACV,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js

@@ -43,8 +43,8 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
     const [msaFileLocation, setMsaFileLocation] = useState();
     const [treeFileLocation, setTreeFileLocation] = useState();
     const [querySeqName, setQuerySeqName] = useState('');
-    const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: error2, } = useTranscriptSelection({ feature, view });
-    const e = launchViewError ?? error2;
+    const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error, } = useTranscriptSelection({ feature, view });
+    const e = launchViewError ?? error;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             e ? React.createElement(ErrorMessage, { error: e }) : null,
@@ -73,16 +73,13 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
                     (inputMethod === 'file' && !msaFileLocation) ||
                     (inputMethod === 'text' && !msaText.trim()), onClick: () => {
                     try {
-                        if (!selectedTranscript) {
-                            return;
-                        }
                         setLaunchViewError(undefined);
                         launchView({
                             session,
                             newViewTitle: getGeneDisplayName(selectedTranscript),
                             view,
                             feature: selectedTranscript,
-                            querySeqName: querySeqName.trim() || undefined,
+                            querySeqName: querySeqName.trim(),
                             ...(inputMethod === 'file'
                                 ? {
                                     msaFilehandle: msaFileLocation,
@@ -91,15 +88,15 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
                                 : {
                                     data: {
                                         msa: msaText,
-                                        tree: treeText || undefined,
+                                        tree: treeText,
                                     },
                                 }),
                         });
                         handleClose();
                     }
-                    catch (e) {
-                        console.error(e);
-                        setLaunchViewError(e);
+                    catch (err) {
+                        console.error(err);
+                        setLaunchViewError(err);
                     }
                 } }, "Submit"),
             React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {

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

@@ -1 +1 @@
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+{"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,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAClE,OAAO,EACL,KAAK,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,MAAM,YAAY,CAAA;AAC/C,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AASlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;IACD,cAAc,EAAE;QACd,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,QAAQ,EAAE,GAAG;KACd;IACD,QAAQ,EAAE;QACR,YAAY,EAAE,EAAE;KACjB;IACD,cAAc,EAAE;QACd,SAAS,EAAE,EAAE;KACd;IACD,YAAY,EAAE;QACZ,SAAS,EAAE,EAAE;KACd;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,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACpD,MAAM,EACJ,OAAO,EACP,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,GACN,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAE7C,MAAM,CAAC,GAAG,eAAe,IAAI,KAAK,CAAA;IAClC,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,SAAS,EAAE,OAAO,CAAC,cAAc,IACnC,WAAW,KAAK,MAAM,CAAC,CAAC,CAAC,CACxB,6BAAK,SAAS,EAAE,OAAO,CAAC,aAAa;gBACnC,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,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,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,UAAU,EAAE,UAAU,EACtB,kBAAkB,EAAE,kBAAkB,EACtC,kBAAkB,EAAE,aAAa,EACjC,eAAe,EAAE,eAAe,GAChC;YAEF,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,cAAc,EACnB,SAAS,QACT,QAAQ,QACR,SAAS,EAAE,OAAO,CAAC,cAAc,EACjC,WAAW,EAAC,6DAA6D,EACzE,UAAU,EAAC,uGAAuG,EAClH,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACrC,CAAC,GACD;YAED,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CACtB,oBAAC,KAAK,IAAC,QAAQ,EAAC,SAAS,EAAC,SAAS,EAAE,OAAO,CAAC,YAAY,8JAIjD,CACT,CAAC,CAAC,CAAC,IAAI,CACM;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,QAAQ,EACN,CAAC,kBAAkB;oBACnB,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,IAAI,CAAC;wBACH,kBAAkB,CAAC,SAAS,CAAC,CAAA;wBAC7B,UAAU,CAAC;4BACT,OAAO;4BACP,YAAY,EAAE,kBAAkB,CAAC,kBAAkB,CAAC;4BACpD,IAAI;4BACJ,OAAO,EAAE,kBAAmB;4BAC5B,YAAY,EAAE,YAAY,CAAC,IAAI,EAAE;4BACjC,GAAG,CAAC,WAAW,KAAK,MAAM;gCACxB,CAAC,CAAC;oCACE,aAAa,EAAE,eAAe;oCAC9B,cAAc,EAAE,gBAAgB;iCACjC;gCACH,CAAC,CAAC;oCACE,IAAI,EAAE;wCACJ,GAAG,EAAE,OAAO;wCACZ,IAAI,EAAE,QAAQ;qCACf;iCACF,CAAC;yBACP,CAAC,CAAA;wBAEF,WAAW,EAAE,CAAA;oBACf,CAAC;oBAAC,OAAO,GAAG,EAAE,CAAC;wBACb,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;wBAClB,kBAAkB,CAAC,GAAG,CAAC,CAAA;oBACzB,CAAC;gBACH,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

@@ -7,7 +7,7 @@ import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import CachedBlastResults from './CachedBlastResults';
 import { blastLaunchView } from './blastLaunchView';
-import { msaAlgorithms } from './consts';
+import { blastDatabaseOptions, blastPrograms, msaAlgorithms } from './consts';
 import { useCachedBlastResults } from './useCachedBlastResults';
 import TextField2 from '../../../components/TextField2';
 import { getGeneDisplayName, getGeneIdentifiers, getTranscriptDisplayName, } from '../../util';
@@ -34,8 +34,6 @@ const useStyles = makeStyles()({
         marginTop: 20,
     },
 });
-const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
-const blastPrograms = ['blastp', 'quick-blastp'];
 const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
     const { classes } = useStyles();
     const view = getContainingView(model);
@@ -52,8 +50,7 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
             children,
             e ? React.createElement(ErrorMessage, { error: e }) : null,
             React.createElement(TextField2, { variant: "outlined", label: "BLAST database", className: classes.selectField, select: true, value: selectedBlastDatabase, onChange: event => {
-                    const newDb = event.target
-                        .value;
+                    const newDb = event.target.value;
                     setSelectedBlastDatabase(newDb);
                     if (newDb === 'nr_cluster_seq') {
                         setSelectedBlastProgram('blastp');

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

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

@@ -43,9 +43,6 @@ const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, c
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     handleClose();
-                } }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
                 } }, "Close"))));
 });
 export default NCBIBlastManualPanel;

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

@@ -1 +1 @@
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+{"version":3,"file":"NCBIBlastManualPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,iBAAiB,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChF,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,YAAY,MAAM,kCAAkC,CAAA;AAC3D,OAAO,EAAE,oBAAoB,EAAE,MAAM,YAAY,CAAA;AACjD,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAKlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;IACD,QAAQ,EAAE;QACR,SAAS,EAAE,WAAW;QACtB,MAAM,EAAE,EAAE;QACV,QAAQ,EAAE,GAAG;KACd;IACD,QAAQ,EAAE;QACR,SAAS,EAAE,EAAE;KACd;CACF,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,WAAW,EACX,OAAO,EACP,KAAK,EACL,QAAQ,EACR,OAAO,GAOR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EACJ,OAAO,EACP,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,GACN,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAE7C,MAAM,EAAE,GAAG,oBAAoB,CAAC,eAAe,CAAC,CAAA;IAChD,MAAM,IAAI,GAAG,GAAG,OAAO,6DAA6D,EAAE,EAAE,CAAA;IACxF,MAAM,KAAK,GAAG,GAAG,OAAO,6DAA6D,QAAQ,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAA;IAEvG,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,QAAQ;YACR,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAE9C,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,OAAO,EAChB,UAAU,EAAE,UAAU,EACtB,kBAAkB,EAAE,kBAAkB,EACtC,kBAAkB,EAAE,aAAa,EACjC,eAAe,EAAE,eAAe,GAChC;YAED,eAAe,CAAC,CAAC,CAAC,CACjB,6BAAK,SAAS,EAAE,OAAO,CAAC,QAAQ;;gBACV,oBAAC,YAAY,IAAC,IAAI,EAAE,IAAI,IAAG,KAAK,CAAgB,CAChE,CACP,CAAC,CAAC,CAAC,IAAI;YAER,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,QAAQ,2UAM1B,CACC;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,YAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts

@@ -1,4 +1,4 @@
-import type { JBrowsePluginMsaViewModel } from '../../../MsaViewPanel/model';
+import type { BlastParams } from '../../../MsaViewPanel/model';
 import type { CachedBlastResult } from '../../../utils/blastCache';
 import type { Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
@@ -6,10 +6,10 @@ export declare function blastLaunchView({ newViewTitle, view, feature, blastPara
     newViewTitle: string;
     view: LinearGenomeViewModel;
     feature: Feature;
-    blastParams: Record<string, unknown>;
-}): JBrowsePluginMsaViewModel;
+    blastParams: BlastParams;
+}): void;
 export declare function blastLaunchViewFromCache({ newViewTitle, view, cached, }: {
     newViewTitle: string;
     view: LinearGenomeViewModel;
     cached: CachedBlastResult;
-}): JBrowsePluginMsaViewModel;
+}): void;

package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js

@@ -1,6 +1,6 @@
 import { getSession } from '@jbrowse/core/util';
 export function blastLaunchView({ newViewTitle, view, feature, blastParams, }) {
-    return getSession(view).addView('MsaView', {
+    getSession(view).addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         connectedViewId: view.id,
@@ -12,7 +12,7 @@ export function blastLaunchView({ newViewTitle, view, feature, blastParams, }) {
     });
 }
 export function blastLaunchViewFromCache({ newViewTitle, view, cached, }) {
-    return getSession(view).addView('MsaView', {
+    getSession(view).addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         connectedViewId: view.id,

package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map

@@ -1 +1 @@
-{"version":3,"file":"blastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAO/C,MAAM,UAAU,eAAe,CAAC,EAC9B,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,WAAW,GAMZ;IACC,OAAO,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QACzC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;QAClC,eAAe,EAAE,IAAI;QACrB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,WAAW;KACZ,CAA8B,CAAA;AACjC,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,YAAY,EACZ,IAAI,EACJ,MAAM,GAKP;IACC,OAAO,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QACzC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,eAAe,EAAE,IAAI;QACrB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,IAAI,EAAE;YACJ,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,YAAY,EAAE,MAAM,CAAC,YAAY;SAClC;KACF,CAA8B,CAAA;AACjC,CAAC"}
+{"version":3,"file":"blastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAO/C,MAAM,UAAU,eAAe,CAAC,EAC9B,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,WAAW,GAMZ;IACC,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QAClC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;QAClC,eAAe,EAAE,IAAI;QACrB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,WAAW;KACZ,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,YAAY,EACZ,IAAI,EACJ,MAAM,GAKP;IACC,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QAClC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,eAAe,EAAE,IAAI;QACrB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,IAAI,EAAE;YACJ,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,YAAY,EAAE,MAAM,CAAC,YAAY;SAClC;KACF,CAAC,CAAA;AACJ,CAAC"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts

@@ -1,3 +1,7 @@
 export declare const BASE_BLAST_URL = "https://blast.ncbi.nlm.nih.gov/Blast.cgi";
 export declare const msaAlgorithms: readonly ["clustalo", "muscle", "kalign", "mafft"];
 export type MsaAlgorithm = (typeof msaAlgorithms)[number];
+export declare const blastDatabaseOptions: readonly ["nr", "nr_cluster_seq"];
+export type BlastDatabase = (typeof blastDatabaseOptions)[number];
+export declare const blastPrograms: readonly ["blastp", "quick-blastp"];
+export type BlastProgram = (typeof blastPrograms)[number];

package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js

@@ -1,3 +1,5 @@
 export const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi';
 export const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
+export const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
+export const blastPrograms = ['blastp', 'quick-blastp'];
 //# sourceMappingURL=consts.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map

@@ -1 +1 @@
-{"version":3,"file":"consts.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,cAAc,GAAG,0CAA0C,CAAA;AACxE,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,CAAU,CAAA"}
+{"version":3,"file":"consts.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,cAAc,GAAG,0CAA0C,CAAA;AAExE,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,CAAU,CAAA;AAG/E,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC,IAAI,EAAE,gBAAgB,CAAU,CAAA;AAGrE,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,QAAQ,EAAE,cAAc,CAAU,CAAA"}

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -1,5 +1,4 @@
 import React, { useState } from 'react';
-import { readConfObject } from '@jbrowse/core/configuration';
 import { ErrorMessage, LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui';
 import { getContainingView, getEnv, getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
@@ -13,6 +12,7 @@ import { useTranscriptSelection } from '../useTranscriptSelection';
 import { swrFlags } from './consts';
 import { fetchMSA, fetchMSAList } from './fetchMSAData';
 import { preCalculatedLaunchView } from './preCalculatedLaunchView';
+import { readMsaDatasets } from './types';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -28,30 +28,19 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
     const { pluginManager } = getEnv(model);
     const { assemblyNames } = view;
     const [viewError, setViewError] = useState();
-    const { jbrowse } = session;
-    const datasets = readConfObject(jbrowse, ['msa', 'datasets']);
+    const datasets = readMsaDatasets(session.jbrowse);
     const [selectedDatasetId, setSelectedDatasetId] = useState(datasets?.[0]?.datasetId);
     const selectedDataset = datasets?.find(d => d.datasetId === selectedDatasetId);
-    const { data: msaList, isLoading: msaListLoading, error: msaListFetchError, } = useSWR(selectedDatasetId ? `${selectedDatasetId}-msa-list` : 'none-msa-list', () => selectedDataset
-        ? fetchMSAList({
-            config: selectedDataset.adapter,
-            pluginManager,
-        })
-        : undefined, swrFlags);
+    const { data: msaList, isLoading: msaListLoading, error: msaListFetchError, } = useSWR(selectedDataset ? `${selectedDataset.datasetId}-msa-list` : null, () => fetchMSAList({ config: selectedDataset.adapter, pluginManager }), swrFlags);
     const { options: transcripts, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view, validIds: msaList });
-    const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedId && selectedDatasetId
-        ? `${selectedDatasetId}-${selectedId}-${msaList?.length}-msa`
-        : 'none-msa', () => selectedId && selectedDataset && msaList
-        ? fetchMSA({
-            msaId: selectedId,
-            config: selectedDataset.adapter,
-            pluginManager,
-        })
-        : undefined, swrFlags);
+    const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedId && selectedDataset && msaList
+        ? `${selectedDataset.datasetId}-${selectedId}-${msaList.length}-msa`
+        : null, () => fetchMSA({
+        msaId: selectedId,
+        config: selectedDataset.adapter,
+        pluginManager,
+    }), swrFlags);
     const e = msaListFetchError ?? msaDataFetchError ?? proteinSequenceError ?? viewError;
-    if (e) {
-        console.error(e);
-    }
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             e ? React.createElement(ErrorMessage, { error: e }) : null,

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/PreLoadedMSA/types.d.ts

@@ -5,3 +5,4 @@ export interface Dataset {
     description?: string;
     adapter: AnyConfigurationModel;
 }
+export declare function readMsaDatasets(jbrowse: AnyConfigurationModel): Dataset[] | undefined;

package/dist/LaunchMsaView/components/PreLoadedMSA/types.js

@@ -1,2 +1,5 @@
-export {};
+import { readConfObject } from '@jbrowse/core/configuration';
+export function readMsaDatasets(jbrowse) {
+    return readConfObject(jbrowse, ['msa', 'datasets']);
+}
 //# sourceMappingURL=types.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/types.js.map

@@ -1 +1 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/types.ts"],"names":[],"mappings":""}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/types.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAW5D,MAAM,UAAU,eAAe,CAAC,OAA8B;IAC5D,OAAO,cAAc,CAAC,OAAO,EAAE,CAAC,KAAK,EAAE,UAAU,CAAC,CAA0B,CAAA;AAC9E,CAAC"}

package/dist/LaunchMsaView/components/types.d.ts

@@ -5,7 +5,4 @@ export interface Feat {
 }
 export interface SeqState {
     seq: string;
-    upstream?: string;
-    downstream?: string;
-    error?: unknown;
 }

package/dist/LaunchMsaView/components/useFeatureSequence.d.ts

@@ -1,13 +1,13 @@
 import type { Feature } from '@jbrowse/core/util';
-export declare function useFeatureSequence({ view, feature, upDownBp, forceLoad, }: {
+export declare function useFeatureSequence({ view, feature, }: {
     view: {
         assemblyNames?: string[];
     } | undefined;
     feature?: Feature;
-    upDownBp?: number;
-    forceLoad?: boolean;
 }): {
     proteinSequence: string;
-    sequence: import("./types").SeqState | undefined;
+    sequence: {
+        seq: string;
+    } | undefined;
     error: any;
 };

package/dist/LaunchMsaView/components/useFeatureSequence.js

@@ -1,13 +1,11 @@
 import { getProteinSequenceFromFeature } from './calculateProteinSequence';
 import { useSWRFeatureSequence } from './useSWRFeatureSequence';
-export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
+export function useFeatureSequence({ view, feature, }) {
     const { sequence, error } = useSWRFeatureSequence({
         view,
         feature,
-        upDownBp,
-        forceLoad,
     });
-    const proteinSequence = sequence && !('error' in sequence) && feature
+    const proteinSequence = sequence && feature
         ? getProteinSequenceFromFeature({
             seq: sequence.seq,
             feature,