jbrowse-plugin-msaview 3.1.0 → 3.2.0

package/dist/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.js

@@ -50,7 +50,7 @@ const BlastAutomaticPanel = observer(function ({ handleClose, feature, model, ch
                     React.createElement(Typography, null, "Previous BLAST Results")),
                 React.createElement(AccordionDetails, null,
                     React.createElement(CachedBlastResults, { model: model, handleClose: handleClose, feature: feature })))) : null),
-        React.createElement(SubmitCancelActions, { submitDisabled: !proteinSequence, onSubmit: () => {
+        React.createElement(SubmitCancelActions, { model: model, submitDisabled: !proteinSequence, onSubmit: () => {
                 try {
                     if (selectedTranscript) {
                         setLaunchViewError(undefined);

package/dist/LaunchMsaView/components/BlastQuery/BlastManualPanel.js

@@ -79,7 +79,7 @@ const BlastManualPanel = observer(function ({ handleClose, feature, model, child
                             setTreeText(event.target.value);
                         } }),
                     React.createElement(QueryRowSelector, { ...queryRow })))),
-        React.createElement(SubmitCancelActions, { submitDisabled: !selectedTranscript || !msaText.trim(), onSubmit: () => {
+        React.createElement(SubmitCancelActions, { model: model, submitDisabled: !selectedTranscript || !msaText.trim(), onSubmit: () => {
                 try {
                     if (selectedTranscript) {
                         setLaunchViewError(undefined);

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

@@ -1,7 +1,9 @@
 import { getSession } from '@jbrowse/core/util';
+import { launchMsaView } from '../../../utils/launchMsaView';
+import { readLaunchPlacement } from '../../../utils/workspaces';
 export function blastLaunchView({ newViewTitle, view, feature, blastParams, }) {
-    getSession(view).addView('MsaView', {
-        type: 'MsaView',
+    launchMsaView(getSession(view), {
+        placement: readLaunchPlacement(),
         displayName: newViewTitle,
         connectedViewId: view.id,
         connectedFeature: feature.toJSON(),
@@ -12,8 +14,8 @@ export function blastLaunchView({ newViewTitle, view, feature, blastParams, }) {
     });
 }
 export function blastLaunchViewFromCache({ newViewTitle, view, cached, connectedFeature, }) {
-    getSession(view).addView('MsaView', {
-        type: 'MsaView',
+    launchMsaView(getSession(view), {
+        placement: readLaunchPlacement(),
         displayName: newViewTitle,
         connectedViewId: view.id,
         connectedFeature,

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

@@ -58,7 +58,7 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
                     } })))),
             React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection }),
             React.createElement(QueryRowSelector, { ...queryRow })),
-        React.createElement(SubmitCancelActions, { submitDisabled: !selectedTranscript ||
+        React.createElement(SubmitCancelActions, { model: model, submitDisabled: !selectedTranscript ||
                 (inputMethod === 'file' && !msaFileLocation) ||
                 (inputMethod === 'text' && !msaText.trim()), onSubmit: () => {
                 try {

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

@@ -1,7 +1,9 @@
 import { getSession } from '@jbrowse/core/util';
+import { launchMsaView } from '../../../utils/launchMsaView';
+import { readLaunchPlacement } from '../../../utils/workspaces';
 export function launchView({ newViewTitle, view, feature, msaFilehandle, treeFilehandle, querySeqName, data, }) {
-    getSession(view).addView('MsaView', {
-        type: 'MsaView',
+    launchMsaView(getSession(view), {
+        placement: readLaunchPlacement(),
         displayName: newViewTitle,
         connectedViewId: view.id,
         connectedFeature: feature.toJSON(),

package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js

@@ -40,7 +40,7 @@ const OrthologPanel = observer(function ({ handleClose, feature, model, }) {
                         setMaxSpecies(event.target.value);
                     }, error: !rowCountValid, helperText: "the closest N species NCBI has" })),
             React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection })),
-        React.createElement(SubmitCancelActions, { submitDisabled: !proteinSequence || !rowCountValid, onSubmit: () => {
+        React.createElement(SubmitCancelActions, { model: model, submitDisabled: !proteinSequence || !rowCountValid, onSubmit: () => {
                 try {
                     if (selectedTranscript) {
                         setLaunchViewError(undefined);

package/dist/LaunchMsaView/components/OrthologQuery/orthologLaunchView.js

@@ -1,7 +1,9 @@
 import { getSession } from '@jbrowse/core/util';
+import { launchMsaView } from '../../../utils/launchMsaView';
+import { readLaunchPlacement } from '../../../utils/workspaces';
 export function orthologLaunchView({ newViewTitle, view, feature, orthologParams, }) {
-    getSession(view).addView('MsaView', {
-        type: 'MsaView',
+    launchMsaView(getSession(view), {
+        placement: readLaunchPlacement(),
         displayName: newViewTitle,
         connectedViewId: view.id,
         connectedFeature: feature.toJSON(),

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

@@ -58,7 +58,7 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
                 msaList ? (React.createElement("div", null,
                     React.createElement(SanitizedHTML, { html: selectedDataset.description }),
                     React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection }))) : null)) : null),
-        React.createElement(SubmitCancelActions, { submitDisabled: !selectedTranscript || !msaData?.length, onSubmit: () => {
+        React.createElement(SubmitCancelActions, { model: model, submitDisabled: !selectedTranscript || !msaData?.length, onSubmit: () => {
                 try {
                     if (selectedTranscript && msaData) {
                         const querySeqName = `${selectedId}_${assemblyNames[0]}`;

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

@@ -1,7 +1,9 @@
 import { getSession } from '@jbrowse/core/util';
+import { launchMsaView } from '../../../utils/launchMsaView';
+import { readLaunchPlacement } from '../../../utils/workspaces';
 export function preCalculatedLaunchView({ newViewTitle, view, feature, data, querySeqName, }) {
-    getSession(view).addView('MsaView', {
-        type: 'MsaView',
+    launchMsaView(getSession(view), {
+        placement: readLaunchPlacement(),
         displayName: newViewTitle,
         treeAreaWidth: 200,
         querySeqName,

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

@@ -1,8 +1,11 @@
 import React from 'react';
-export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, submitLabel, cancelLabel, }: {
+import type { AbstractTrackModel } from '@jbrowse/core/util';
+export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, submitLabel, cancelLabel, model, }: {
     onSubmit: () => void;
     onCancel: () => void;
     submitDisabled?: boolean;
     submitLabel?: string;
     cancelLabel?: string;
+    /** omitted by a panel that submits something other than a view launch */
+    model?: AbstractTrackModel;
 }): React.JSX.Element;

package/dist/LaunchMsaView/components/SubmitCancelActions.js

@@ -1,11 +1,35 @@
-import React from 'react';
-import { Button, DialogActions } from '@mui/material';
-export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, submitLabel = 'Submit', cancelLabel = 'Cancel', }) {
-    return (React.createElement(DialogActions, null,
-        React.createElement(Button, { color: "primary", variant: "contained", disabled: submitDisabled, onClick: () => {
-                onSubmit();
-            } }, submitLabel),
-        React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                onCancel();
-            } }, cancelLabel)));
+import React, { useState } from 'react';
+import { getSession } from '@jbrowse/core/util';
+import { Button, Checkbox, DialogActions, FormControlLabel, } from '@mui/material';
+import { readLaunchPlacement, sessionSupportsPlacement, writeLaunchPlacement, } from '../../utils/workspaces';
+/**
+ * Where the launch puts the view, offered wherever a launch is submitted.
+ *
+ * A checkbox rather than a menu of the three placements: the choice a reader
+ * has at this point is "beside the genome view or under it", and `newTab` is a
+ * spec's to state, not a thing to pick before you have seen the alignment.
+ *
+ * Absent entirely on a host that cannot tile — an embedded session, or a
+ * release that places views its own way — because the box would do nothing
+ * there and every launch would quietly ignore it.
+ */
+function PlacementToggle({ model }) {
+    const session = getSession(model);
+    const [sideBySide, setSideBySide] = useState(() => readLaunchPlacement() === 'splitRight');
+    return sessionSupportsPlacement(session) ? (React.createElement(FormControlLabel, { label: "Open beside the genome view", control: React.createElement(Checkbox, { checked: sideBySide, onChange: event => {
+                const { checked } = event.target;
+                setSideBySide(checked);
+                writeLaunchPlacement(checked ? 'splitRight' : 'stack');
+            } }) })) : null;
+}
+export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, submitLabel = 'Submit', cancelLabel = 'Cancel', model, }) {
+    return (React.createElement(DialogActions, { sx: { flexWrap: 'wrap', rowGap: 1 } },
+        model ? React.createElement(PlacementToggle, { model: model }) : null,
+        React.createElement("div", { style: { display: 'flex', gap: 8, marginLeft: 'auto' } },
+            React.createElement(Button, { sx: { flexShrink: 0 }, color: "primary", variant: "contained", disabled: submitDisabled, onClick: () => {
+                    onSubmit();
+                } }, submitLabel),
+            React.createElement(Button, { sx: { flexShrink: 0 }, color: "secondary", variant: "contained", onClick: () => {
+                    onCancel();
+                } }, cancelLabel))));
 }

package/dist/LaunchMsaView/components/SubmitCancelActions.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/LaunchMsaView/components/SubmitCancelActions.test.js

@@ -0,0 +1,55 @@
+// @vitest-environment jsdom
+import React from 'react';
+import { cleanup, render, screen } from '@testing-library/react';
+import { afterEach, beforeEach, expect, test, vi } from 'vitest';
+import SubmitCancelActions from './SubmitCancelActions';
+import { LAUNCH_PLACEMENT_KEY } from '../../utils/workspaces';
+// getSession walks the MST tree, and this component only wants the two actions
+// off the far end of that walk
+vi.mock('@jbrowse/core/util', () => ({
+    getSession: (model) => model.session,
+}));
+function trackModel(session) {
+    return { session };
+}
+const tiling = { setUseWorkspaces() { }, setPendingMove() { } };
+beforeEach(() => {
+    localStorage.clear();
+});
+afterEach(() => {
+    cleanup();
+});
+function toggle() {
+    return screen.queryByRole('checkbox');
+}
+test('a host that can tile offers the choice, checked by default', () => {
+    render(React.createElement(SubmitCancelActions, { model: trackModel(tiling), onSubmit: () => { }, onCancel: () => { } }));
+    expect(toggle()).toBeTruthy();
+    expect(toggle().checked).toBe(true);
+    expect(localStorage.getItem(LAUNCH_PLACEMENT_KEY)).toBeNull();
+});
+// the box would do nothing on an embedded session, and a control that silently
+// does nothing is worse than one that is not there
+test('a host that cannot tile does not offer it', () => {
+    render(React.createElement(SubmitCancelActions, { model: trackModel({}), onSubmit: () => { }, onCancel: () => { } }));
+    expect(toggle()).toBeNull();
+    expect(screen.getByText('Submit')).toBeTruthy();
+});
+test('a panel that launches nothing passes no model, and gets no box', () => {
+    render(React.createElement(SubmitCancelActions, { onSubmit: () => { }, onCancel: () => { } }));
+    expect(toggle()).toBeNull();
+});
+test('clicking it writes the placement the next launch will read', () => {
+    render(React.createElement(SubmitCancelActions, { model: trackModel(tiling), onSubmit: () => { }, onCancel: () => { } }));
+    toggle().click();
+    expect(localStorage.getItem(LAUNCH_PLACEMENT_KEY)).toBe('stack');
+    expect(toggle().checked).toBe(false);
+    toggle().click();
+    expect(localStorage.getItem(LAUNCH_PLACEMENT_KEY)).toBe('splitRight');
+    expect(toggle().checked).toBe(true);
+});
+test('a stored choice is what the box opens on', () => {
+    localStorage.setItem(LAUNCH_PLACEMENT_KEY, 'stack');
+    render(React.createElement(SubmitCancelActions, { model: trackModel(tiling), onSubmit: () => { }, onCancel: () => { } }));
+    expect(toggle().checked).toBe(false);
+});

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -1,3 +1,4 @@
+import { launchMsaView } from '../utils/launchMsaView';
 export default function LaunchMsaViewExtensionPointF(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-MsaView', (args) => {
         const { session, data, msaFileLocation, msaIndexedLocation, msaName, treeFileLocation, querySeqName, ...rest } = args;
@@ -14,8 +15,7 @@ export default function LaunchMsaViewExtensionPointF(pluginManager) {
         // directly, and so is orthologParams (the model's own autorun picks it up).
         // Only sources needing launch-time resolution go through `init`: msaUrl
         // (AlphaFold sniff) and the name-indexed bgzip block (no native loader).
-        session.addView('MsaView', {
-            type: 'MsaView',
+        launchMsaView(session, {
             ...rest,
             data,
             ...(treeFileLocation

package/dist/index.js

@@ -8,6 +8,7 @@ import BgzipFastaMsaAdapterF from './BgzipFastaMsaAdapter';
 import LaunchMsaViewF from './LaunchMsaView';
 import LaunchMsaViewExtensionPointF from './LaunchMsaViewExtensionPoint';
 import MsaViewF from './MsaViewPanel';
+import { launchMsaView } from './utils/launchMsaView';
 import { version } from './version';
 export default class MsaViewPlugin extends Plugin {
     constructor() {
@@ -49,7 +50,9 @@ export default class MsaViewPlugin extends Plugin {
                 label: 'Multiple sequence alignment view',
                 icon: GridOn,
                 onClick: (session) => {
-                    session.addView('MsaView', {});
+                    // stacked, by default: nothing was launched from, so there is no
+                    // connected view for it to sit beside
+                    launchMsaView(session, {});
                 },
             });
         }