npm - jbrowse-plugin-msaview - Versions diffs - 2.3.8 → 2.4.0 - Mend

jbrowse-plugin-msaview 2.3.8 → 2.4.0

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 (120) hide show

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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,aAGlC,CAAA;IAED,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 CHANGED Viewed

@@ -1,17 +1,14 @@
 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';
 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, }) {

package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map CHANGED Viewed

	@@ -1 +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"}
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,gBAAgB,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAOpD,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,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"}

package/dist/AddHighlightModel/util.d.ts CHANGED Viewed

@@ -1,3 +1,6 @@
+export declare function hasHoverPosition(hovered: unknown): hovered is {
+    hoverPosition: unknown;
+};
 export declare const useStyles: (params: void, muiStyleOverridesParams?: {
     props: Record<string, unknown>;
     ownerState?: Record<string, unknown> | undefined;

package/dist/AddHighlightModel/util.js CHANGED Viewed

@@ -1,4 +1,7 @@
 import { makeStyles } from 'tss-react/mui';
+export function hasHoverPosition(hovered) {
+    return !!hovered && typeof hovered === 'object' && 'hoverPosition' in hovered;
+}
 export const useStyles = makeStyles()({
     highlight: {
         height: '100%',

package/dist/AddHighlightModel/util.js.map CHANGED Viewed

	@@ -1 +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"}
1	+ {"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,CAAC,CAAC,OAAO,IAAI,OAAO,OAAO,KAAK,QAAQ,IAAI,eAAe,IAAI,OAAO,CAAA;AAC/E,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/LaunchMsaView/components/LaunchMsaViewDialog.js CHANGED Viewed

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/types.ts"],"names":[],"mappings":""}
1	+ {"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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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,

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"useFeatureSequence.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/useFeatureSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,6BAA6B,EAAE,MAAM,4BAA4B,CAAA;AAC1E,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAI/D,MAAM,UAAU,kBAAkB,CAAC,EACjC,IAAI,EACJ,OAAO,GAIR;IACC,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,qBAAqB,CAAC;QAChD,IAAI;QACJ,OAAO;KACR,CAAC,CAAA;IAEF,MAAM,eAAe,GACnB,QAAQ,IAAI,OAAO;QACjB,CAAC,CAAC,6BAA6B,CAAC;YAC5B,GAAG,EAAE,QAAQ,CAAC,GAAG;YACjB,OAAO;SACR,CAAC;QACJ,CAAC,CAAC,EAAE,CAAA;IAER,OAAO;QACL,eAAe;QACf,QAAQ;QACR,KAAK;KACN,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/useSWRFeatureSequence.d.ts CHANGED Viewed

@@ -1,13 +1,12 @@
-import type { SeqState } from './types';
 import type { Feature } from '@jbrowse/core/util';
-export declare function useSWRFeatureSequence({ view, feature, upDownBp, forceLoad, }: {
+export declare function useSWRFeatureSequence({ view, feature, }: {
     view: {
         assemblyNames?: string[];
     } | undefined;
     feature?: Feature;
-    upDownBp?: number;
-    forceLoad?: boolean;
 }): {
-    sequence: SeqState | undefined;
+    sequence: {
+        seq: string;
+    } | undefined;
     error: any;
 };