react-msaview 5.0.7 → 5.0.16

package/dist/components/header/HeaderMenu.js

@@ -1,57 +1,11 @@
-import React, { lazy } from 'react';
+import React from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import AccountTree from '@mui/icons-material/AccountTree';
-import Assignment from '@mui/icons-material/Assignment';
-import FilterAlt from '@mui/icons-material/FilterAlt';
-import FolderOpen from '@mui/icons-material/FolderOpen';
 import MoreVert from '@mui/icons-material/Menu';
-import PhotoCamera from '@mui/icons-material/PhotoCamera';
-import Search from '@mui/icons-material/Search';
-import Sort from '@mui/icons-material/Sort';
 import Visibility from '@mui/icons-material/Visibility';
 import { observer } from 'mobx-react';
-// lazies
-const MetadataDialog = lazy(() => import("../dialogs/MetadataDialog.js"));
-const ExportSVGDialog = lazy(() => import("../dialogs/ExportSVGDialog.js"));
-const FeatureFilterDialog = lazy(() => import("../dialogs/FeatureDialog.js"));
-const SettingsDialog = lazy(() => import("../dialogs/SettingsDialog.js"));
-const UserProvidedDomainsDialog = lazy(() => import("../dialogs/UserProvidedDomainsDialog.js"));
-const InterProScanDialog = lazy(() => import("../dialogs/InterProScanDialog.js"));
 const HeaderMenu = observer(({ model }) => {
-    const { showDomains, actuallyShowDomains, subFeatureRows, noDomains, tracks, turnedOffTracks, } = model;
+    const { tracks, turnedOffTracks } = model;
     return (React.createElement(CascadingMenuButton, { menuItems: [
-            {
-                label: 'Return to import form',
-                icon: FolderOpen,
-                onClick: () => {
-                    model.reset();
-                },
-            },
-            {
-                label: 'Metadata',
-                icon: Assignment,
-                onClick: () => {
-                    model.queueDialog(onClose => [
-                        MetadataDialog,
-                        {
-                            model,
-                            onClose,
-                        },
-                    ]);
-                },
-            },
-            {
-                label: 'More settings',
-                onClick: () => {
-                    model.queueDialog(onClose => [
-                        SettingsDialog,
-                        {
-                            model,
-                            onClose,
-                        },
-                    ]);
-                },
-            },
             {
                 label: 'Tracks',
                 icon: Visibility,
@@ -65,104 +19,8 @@ const HeaderMenu = observer(({ model }) => {
                     },
                 })),
             },
-            {
-                label: 'Export SVG',
-                icon: PhotoCamera,
-                onClick: () => {
-                    model.queueDialog(onClose => [
-                        ExportSVGDialog,
-                        {
-                            onClose,
-                            model,
-                        },
-                    ]);
-                },
-            },
-            ...(model.rows.length >= 2
-                ? [
-                    {
-                        label: 'Calculate neighbor joining tree (BLOSUM62)',
-                        icon: AccountTree,
-                        onClick: () => {
-                            try {
-                                model.calculateNeighborJoiningTreeFromMSA();
-                            }
-                            catch (e) {
-                                console.error('Failed to calculate NJ tree:', e);
-                                model.setError(e);
-                            }
-                        },
-                    },
-                ]
-                : []),
-            {
-                label: 'Features/protein domains',
-                type: 'subMenu',
-                subMenu: [
-                    {
-                        label: 'Open domains...',
-                        icon: FolderOpen,
-                        onClick: () => {
-                            model.queueDialog(handleClose => [
-                                UserProvidedDomainsDialog,
-                                {
-                                    handleClose,
-                                    model,
-                                },
-                            ]);
-                        },
-                    },
-                    {
-                        label: 'Query InterProScan for domains...',
-                        icon: Search,
-                        onClick: () => {
-                            model.queueDialog(handleClose => [
-                                InterProScanDialog,
-                                {
-                                    handleClose,
-                                    model,
-                                },
-                            ]);
-                        },
-                    },
-                    {
-                        label: `Show domains${noDomains ? ' (no domains loaded)' : ''}`,
-                        disabled: noDomains,
-                        icon: Visibility,
-                        checked: actuallyShowDomains ? showDomains : false,
-                        type: 'checkbox',
-                        onClick: () => {
-                            model.setShowDomains(!showDomains);
-                        },
-                    },
-                    {
-                        label: `Use sub-row layout${noDomains ? ' (no domains loaded)' : ''}`,
-                        disabled: noDomains,
-                        checked: actuallyShowDomains ? subFeatureRows : false,
-                        icon: Sort,
-                        type: 'checkbox',
-                        onClick: () => {
-                            model.setSubFeatureRows(!subFeatureRows);
-                        },
-                    },
-                    {
-                        label: `Filter domains${noDomains ? ' (no domains loaded)' : ''}`,
-                        icon: FilterAlt,
-                        disabled: noDomains,
-                        onClick: () => {
-                            model.queueDialog(onClose => [
-                                FeatureFilterDialog,
-                                {
-                                    onClose,
-                                    model,
-                                },
-                            ]);
-                        },
-                    },
-                ],
-            },
             ...model.extraViewMenuItems(),
-        ] },
+        ], anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' } },
         React.createElement(MoreVert, null)));
 });
 export default HeaderMenu;

package/dist/components/header/HeaderMenu.js.map

@@ -1 +1 @@
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+{"version":3,"file":"HeaderMenu.js","sourceRoot":"","sources":["../../../src/components/header/HeaderMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,QAAQ,MAAM,0BAA0B,CAAA;AAC/C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,UAAU,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACjE,MAAM,EAAE,MAAM,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACzC,OAAO,CACL,oBAAC,mBAAmB,IAClB,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,QAAQ;gBACf,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;oBAC5B,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI;oBACvB,IAAI,EAAE,UAAmB;oBACzB,OAAO,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;oBAC7C,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;oBACnC,CAAC;iBACF,CAAC,CAAC;aACJ;YACD,GAAG,KAAK,CAAC,kBAAkB,EAAE;SAC9B,EACD,YAAY,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,eAAe,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE;QAExD,oBAAC,QAAQ,OAAG,CACQ,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/header/MSASettingsMenu.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+declare const MSASettingsMenu: ({ model }: {
+    model: MsaViewModel;
+}) => React.JSX.Element;
+export default MSASettingsMenu;

package/dist/components/header/MSASettingsMenu.js

@@ -0,0 +1,36 @@
+import React from 'react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import Tune from '@mui/icons-material/Tune';
+import { observer } from 'mobx-react';
+const MSASettingsMenu = observer(function ({ model }) {
+    const { drawMsaLetters, hideGaps, bgColor } = model;
+    return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: [
+            {
+                label: 'Draw letters',
+                type: 'checkbox',
+                checked: drawMsaLetters,
+                onClick: () => {
+                    model.setDrawMsaLetters(!drawMsaLetters);
+                },
+            },
+            {
+                label: 'Color letters instead of background of tiles',
+                type: 'checkbox',
+                checked: !bgColor,
+                onClick: () => {
+                    model.setBgColor(!bgColor);
+                },
+            },
+            {
+                label: 'Enable hiding gappy columns?',
+                type: 'checkbox',
+                checked: hideGaps,
+                onClick: () => {
+                    model.setHideGaps(!hideGaps);
+                },
+            },
+        ] },
+        React.createElement(Tune, null)));
+});
+export default MSASettingsMenu;
+//# sourceMappingURL=MSASettingsMenu.js.map

package/dist/components/header/MSASettingsMenu.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"MSASettingsMenu.js","sourceRoot":"","sources":["../../../src/components/header/MSASettingsMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC3E,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACnD,OAAO,CACL,oBAAC,mBAAmB,IAClB,mBAAmB,EAAE,KAAK,EAC1B,YAAY,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,eAAe,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,cAAc;gBACrB,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,cAAc;gBACvB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;gBAC1C,CAAC;aACF;YACD;gBACE,KAAK,EAAE,8CAA8C;gBACrD,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,CAAC,OAAO;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,UAAU,CAAC,CAAC,OAAO,CAAC,CAAA;gBAC5B,CAAC;aACF;YACD;gBACE,KAAK,EAAE,8BAA8B;gBACrC,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,QAAQ;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;gBAC9B,CAAC;aACF;SACF;QAED,oBAAC,IAAI,OAAG,CACY,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/header/SettingsMenu.js

@@ -6,7 +6,7 @@ import Settings from '@mui/icons-material/Settings';
 import { observer } from 'mobx-react';
 import colorSchemes from "../../colorSchemes.js";
 const SettingsMenu = observer(function ({ model }) {
-    const { colorSchemeName, drawMsaLetters, contrastLettering, hideGaps, bgColor, drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawLabels, treeWidthMatchesArea, noTree, } = model;
+    const { colorSchemeName, drawMsaLetters, hideGaps, bgColor, drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawLabels, } = model;
     return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, menuItems: [
             {
                 label: 'Color scheme',
@@ -41,14 +41,6 @@ const SettingsMenu = observer(function ({ model }) {
                             model.setBgColor(!bgColor);
                         },
                     },
-                    {
-                        label: 'Use contrast lettering',
-                        type: 'checkbox',
-                        checked: contrastLettering,
-                        onClick: () => {
-                            model.setContrastLettering(!contrastLettering);
-                        },
-                    },
                     {
                         label: 'Enable hiding gappy columns?',
                         type: 'checkbox',
@@ -104,18 +96,6 @@ const SettingsMenu = observer(function ({ model }) {
                             model.setDrawLabels(!drawLabels);
                         },
                     },
-                    ...(noTree
-                        ? []
-                        : [
-                            {
-                                label: 'Make tree width fit to tree area',
-                                type: 'checkbox',
-                                checked: treeWidthMatchesArea,
-                                onClick: () => {
-                                    model.setTreeWidthMatchesArea(!treeWidthMatchesArea);
-                                },
-                            },
-                        ]),
                 ],
             },
         ] },

package/dist/components/header/SettingsMenu.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SettingsMenu.js","sourceRoot":"","sources":["../../../src/components/header/SettingsMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,OAAO,MAAM,6BAA6B,CAAA;AACjD,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,YAAY,MAAM,uBAAuB,CAAA;AAIhD,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACxE,MAAM,EACJ,eAAe,EACf,cAAc,EACd,QAAQ,EACR,OAAO,EACP,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,UAAU,GACX,GAAG,KAAK,CAAA;IACT,OAAO,CACL,oBAAC,mBAAmB,IAClB,mBAAmB,EAAE,KAAK,EAC1B,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,cAAc;gBACrB,IAAI,EAAE,OAAO;gBACb,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CACpC,MAAM,CAAC,EAAE,CACP,CAAC;oBACC,KAAK,EAAE,MAAM;oBACb,IAAI,EAAE,OAAO;oBACb,OAAO,EAAE,eAAe,KAAK,MAAM;oBACnC,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;oBAClC,CAAC;iBACF,CAAU,CACd;aACF;YACD;gBACE,KAAK,EAAE,cAAc;gBACrB,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE;oBACP;wBACE,KAAK,EAAE,cAAc;wBACrB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,cAAc;wBACvB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;wBAC1C,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,8CAA8C;wBACrD,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,CAAC,OAAO;wBACjB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,UAAU,CAAC,CAAC,OAAO,CAAC,CAAA;wBAC5B,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,8BAA8B;wBACrC,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,QAAQ;wBACjB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;wBAC9B,CAAC;qBACF;iBACF;aACF;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,SAAS;gBACf,IAAI,EAAE,WAAW;gBACjB,OAAO,EAAE;oBACP;wBACE,KAAK,EAAE,oBAAoB;wBAC3B,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,aAAa;wBACtB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;wBACxC,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,WAAW;wBAClB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,QAAQ;wBACjB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;wBAC9B,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,yCAAyC;wBAChD,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,eAAe;wBACxB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC,CAAA;wBAC5C,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,yBAAyB;wBAChC,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,gBAAgB;wBACzB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,mBAAmB,CAAC,CAAC,gBAAgB,CAAC,CAAA;wBAC9C,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,aAAa;wBACpB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,UAAU;wBACnB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,aAAa,CAAC,CAAC,UAAU,CAAC,CAAA;wBAClC,CAAC;qBACF;iBACF;aACF;SACF;QAED,oBAAC,QAAQ,OAAG,CACQ,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

package/dist/components/header/TreeSettingsMenu.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+declare const TreeSettingsMenu: ({ model, }: {
+    model: MsaViewModel;
+}) => React.JSX.Element;
+export default TreeSettingsMenu;

package/dist/components/header/TreeSettingsMenu.js

@@ -0,0 +1,74 @@
+import React from 'react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import AccountTree from '@mui/icons-material/AccountTree';
+import { observer } from 'mobx-react';
+const TreeSettingsMenu = observer(function ({ model, }) {
+    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawLabels, rows, } = model;
+    return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: [
+            {
+                label: 'Show branch length',
+                type: 'checkbox',
+                checked: showBranchLen,
+                onClick: () => {
+                    model.setShowBranchLen(!showBranchLen);
+                },
+            },
+            {
+                label: 'Show tree',
+                type: 'checkbox',
+                checked: drawTree,
+                onClick: () => {
+                    model.setDrawTree(!drawTree);
+                },
+            },
+            {
+                label: 'Draw clickable bubbles on tree branches',
+                type: 'checkbox',
+                checked: drawNodeBubbles,
+                onClick: () => {
+                    model.setDrawNodeBubbles(!drawNodeBubbles);
+                },
+            },
+            {
+                label: 'Tree labels align right',
+                type: 'checkbox',
+                checked: labelsAlignRight,
+                onClick: () => {
+                    model.setLabelsAlignRight(!labelsAlignRight);
+                },
+            },
+            {
+                label: 'Draw labels',
+                type: 'checkbox',
+                checked: drawLabels,
+                onClick: () => {
+                    model.setDrawLabels(!drawLabels);
+                },
+            },
+            ...(rows.length >= 2
+                ? [
+                    {
+                        label: 'Advanced',
+                        type: 'subMenu',
+                        subMenu: [
+                            {
+                                label: 'Calculate neighbor joining tree (BLOSUM62)',
+                                onClick: () => {
+                                    try {
+                                        model.calculateNeighborJoiningTreeFromMSA();
+                                    }
+                                    catch (e) {
+                                        console.error('Failed to calculate NJ tree:', e);
+                                        model.setError(e);
+                                    }
+                                },
+                            },
+                        ],
+                    },
+                ]
+                : []),
+        ] },
+        React.createElement(AccountTree, null)));
+});
+export default TreeSettingsMenu;
+//# sourceMappingURL=TreeSettingsMenu.js.map

package/dist/components/header/TreeSettingsMenu.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"TreeSettingsMenu.js","sourceRoot":"","sources":["../../../src/components/header/TreeSettingsMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,EAC1C,KAAK,GAGN;IACC,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,UAAU,EACV,IAAI,GACL,GAAG,KAAK,CAAA;IACT,OAAO,CACL,oBAAC,mBAAmB,IAClB,mBAAmB,EAAE,KAAK,EAC1B,YAAY,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,eAAe,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,oBAAoB;gBAC3B,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,aAAa;gBACtB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;gBACxC,CAAC;aACF;YACD;gBACE,KAAK,EAAE,WAAW;gBAClB,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,QAAQ;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;gBAC9B,CAAC;aACF;YACD;gBACE,KAAK,EAAE,yCAAyC;gBAChD,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,eAAe;gBACxB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC,CAAA;gBAC5C,CAAC;aACF;YACD;gBACE,KAAK,EAAE,yBAAyB;gBAChC,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,gBAAgB;gBACzB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,mBAAmB,CAAC,CAAC,gBAAgB,CAAC,CAAA;gBAC9C,CAAC;aACF;YACD;gBACE,KAAK,EAAE,aAAa;gBACpB,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,UAAU;gBACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,aAAa,CAAC,CAAC,UAAU,CAAC,CAAA;gBAClC,CAAC;aACF;YACD,GAAG,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC;gBAClB,CAAC,CAAC;oBACE;wBACE,KAAK,EAAE,UAAU;wBACjB,IAAI,EAAE,SAAkB;wBACxB,OAAO,EAAE;4BACP;gCACE,KAAK,EAAE,4CAA4C;gCACnD,OAAO,EAAE,GAAG,EAAE;oCACZ,IAAI,CAAC;wCACH,KAAK,CAAC,mCAAmC,EAAE,CAAA;oCAC7C,CAAC;oCAAC,OAAO,CAAC,EAAE,CAAC;wCACX,OAAO,CAAC,KAAK,CAAC,8BAA8B,EAAE,CAAC,CAAC,CAAA;wCAChD,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;oCACnB,CAAC;gCACH,CAAC;6BACF;yBACF;qBACF;iBACF;gBACH,CAAC,CAAC,EAAE,CAAC;SACR;QAED,oBAAC,WAAW,OAAG,CACK,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/components/header/ZoomMenu.js

@@ -30,14 +30,6 @@ const ZoomMenu = observer(function ({ model }) {
                     model.resetZoom();
                 },
             },
-            {
-                label: 'Show extra zoom options',
-                checked: model.showZoomStar,
-                type: 'checkbox',
-                onClick: () => {
-                    model.setShowZoomStar(!model.showZoomStar);
-                },
-            },
         ] },
         React.createElement(MoreVert, null)));
 });

package/dist/components/header/ZoomMenu.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ZoomMenu.js","sourceRoot":"","sources":["../../../src/components/header/ZoomMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACpE,OAAO,CACL,oBAAC,mBAAmB,IAClB,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,kCAAkC;gBACzC,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,GAAG,EAAE,CAAA;gBACb,CAAC;aACF;YACD;gBACE,KAAK,EAAE,gBAAgB;gBACvB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,aAAa,EAAE,CAAA;gBACvB,CAAC;aACF;YACD;gBACE,KAAK,EAAE,kBAAkB;gBACzB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,eAAe,EAAE,CAAA;gBACzB,CAAC;aACF;YAED;gBACE,KAAK,EAAE,uBAAuB;gBAC9B,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,SAAS,EAAE,CAAA;gBACnB,CAAC;aACF;SACF;QAED,oBAAC,QAAQ,OAAG,CACQ,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/header/getDomainsMenu.d.ts

@@ -0,0 +1,31 @@
+import type { MsaViewModel } from '../../model.ts';
+export declare function getDomainMenu({ model }: {
+    model: MsaViewModel;
+}): ({
+    label: string;
+    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+        muiName: string;
+    };
+    onClick: () => void;
+    disabled?: undefined;
+    checked?: undefined;
+    type?: undefined;
+} | {
+    label: string;
+    disabled: boolean;
+    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+        muiName: string;
+    };
+    checked: boolean;
+    type: "checkbox";
+    onClick: () => void;
+} | {
+    label: string;
+    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+        muiName: string;
+    };
+    disabled: boolean;
+    onClick: () => void;
+    checked?: undefined;
+    type?: undefined;
+})[];

package/dist/components/header/getDomainsMenu.js

@@ -0,0 +1,75 @@
+import { lazy } from 'react';
+import FilterAlt from '@mui/icons-material/FilterAlt';
+import FolderOpen from '@mui/icons-material/FolderOpen';
+import Search from '@mui/icons-material/Search';
+import Sort from '@mui/icons-material/Sort';
+import Visibility from '@mui/icons-material/Visibility';
+const FeatureFilterDialog = lazy(() => import("../dialogs/FeatureDialog.js"));
+const UserProvidedDomainsDialog = lazy(() => import("../dialogs/UserProvidedDomainsDialog.js"));
+const InterProScanDialog = lazy(() => import("../dialogs/InterProScanDialog.js"));
+export function getDomainMenu({ model }) {
+    const { showDomains, actuallyShowDomains, subFeatureRows, noDomains } = model;
+    return [
+        {
+            label: 'Open domains...',
+            icon: FolderOpen,
+            onClick: () => {
+                model.queueDialog(handleClose => [
+                    UserProvidedDomainsDialog,
+                    {
+                        handleClose,
+                        model,
+                    },
+                ]);
+            },
+        },
+        {
+            label: 'Query InterProScan for domains...',
+            icon: Search,
+            onClick: () => {
+                model.queueDialog(handleClose => [
+                    InterProScanDialog,
+                    {
+                        handleClose,
+                        model,
+                    },
+                ]);
+            },
+        },
+        {
+            label: `Show domains${noDomains ? ' (no domains loaded)' : ''}`,
+            disabled: noDomains,
+            icon: Visibility,
+            checked: actuallyShowDomains ? showDomains : false,
+            type: 'checkbox',
+            onClick: () => {
+                model.setShowDomains(!showDomains);
+            },
+        },
+        {
+            label: `Use sub-row layout${noDomains ? ' (no domains loaded)' : ''}`,
+            disabled: noDomains,
+            checked: actuallyShowDomains ? subFeatureRows : false,
+            icon: Sort,
+            type: 'checkbox',
+            onClick: () => {
+                model.setSubFeatureRows(!subFeatureRows);
+            },
+        },
+        {
+            label: `Filter domains${noDomains ? ' (no domains loaded)' : ''}`,
+            icon: FilterAlt,
+            disabled: noDomains,
+            onClick: () => {
+                model.queueDialog(onClose => [
+                    FeatureFilterDialog,
+                    {
+                        onClose,
+                        model,
+                    },
+                ]);
+            },
+        },
+    ];
+}
+//# sourceMappingURL=getDomainsMenu.js.map

package/dist/components/header/getDomainsMenu.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"getDomainsMenu.js","sourceRoot":"","sources":["../../../src/components/header/getDomainsMenu.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,SAAS,MAAM,+BAA+B,CAAA;AACrD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,MAAM,mBAAmB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,6BAA8B,CAAC,CAAC,CAAA;AAC9E,MAAM,yBAAyB,GAAG,IAAI,CACpC,GAAG,EAAE,CAAC,MAAM,CAAC,yCAA0C,CAAC,CACzD,CAAA;AACD,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,kCAAmC,CAAC,CAClD,CAAA;AAED,MAAM,UAAU,aAAa,CAAC,EAAE,KAAK,EAA2B;IAC9D,MAAM,EAAE,WAAW,EAAE,mBAAmB,EAAE,cAAc,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC7E,OAAO;QACL;YACE,KAAK,EAAE,iBAAiB;YACxB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,yBAAyB;oBACzB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD;YACE,KAAK,EAAE,mCAAmC;YAC1C,IAAI,EAAE,MAAM;YACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,kBAAkB;oBAClB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD;YACE,KAAK,EAAE,eAAe,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;YAC/D,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK;YAClD,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;SACF;QACD;YACE,KAAK,EAAE,qBAAqB,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;YACrE,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK;YACrD,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;YAC1C,CAAC;SACF;QACD;YACE,KAAK,EAAE,iBAAiB,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;YACjE,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,mBAAmB;oBACnB;wBACE,OAAO;wBACP,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;KACF,CAAA;AACH,CAAC"}

package/dist/components/import/ImportFormExamples.js

@@ -10,25 +10,16 @@ function ListItem({ onClick, model, children, }) {
                 event.preventDefault();
                 onClick();
             }, href: "#" },
-            React.createElement(Typography, { display: "inline" }, children))));
+            React.createElement(Typography, { component: "span" }, children))));
 }
+const BASE = 'https://jbrowse.org/genomes/multiple_sequence_alignments';
 const ImportFormExamples = observer(function ({ model, }) {
-    function l2(uri1, uri2) {
+    function loadUris({ msa, tree, gff, }) {
         // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
-                await load(model, uri1
-                    ? {
-                        uri: uri1,
-                        locationType: 'UriLocation',
-                    }
-                    : undefined, uri2
-                    ? {
-                        uri: uri2,
-                        locationType: 'UriLocation',
-                    }
-                    : undefined);
+                await load(model, msa ? { uri: msa, locationType: 'UriLocation' } : undefined, tree ? { uri: tree, locationType: 'UriLocation' } : undefined, gff ? { uri: gff, locationType: 'UriLocation' } : undefined);
             }
             catch (e) {
                 console.error(e);
@@ -38,7 +29,9 @@ const ImportFormExamples = observer(function ({ model, }) {
     }
     return (React.createElement("ul", null,
         React.createElement(ListItem, { model: model, onClick: () => {
-                l2(undefined, 'https://jbrowse.org/genomes/newicktrees/sarscov2phylo.pub.ft.nh');
+                loadUris({
+                    tree: 'https://jbrowse.org/genomes/newicktrees/sarscov2phylo.pub.ft.nh',
+                });
             } }, "230k COVID-19 samples (tree only)"),
         React.createElement(ListItem, { model: model, onClick: () => {
                 model.setData({ msa: smallMSA, tree: smallTree });
@@ -47,22 +40,31 @@ const ImportFormExamples = observer(function ({ model, }) {
                 model.setData({ msa: smallMSAOnly });
             } }, "Small MSA only"),
         React.createElement(ListItem, { model: model, onClick: () => {
-                l2('https://jbrowse.org/genomes/multiple_sequence_alignments/pfam-cov2.stock');
+                loadUris({ msa: `${BASE}/pfam-cov2.stock` });
             } }, "PFAM SARS-CoV2 multi-stockholm"),
         React.createElement(ListItem, { model: model, onClick: () => {
-                l2('https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock');
+                loadUris({
+                    msa: `${BASE}/pfam-cov2.stock`,
+                    gff: `${BASE}/pfam-cov2-domains.gff`,
+                });
+            } }, "PFAM SARS-CoV2 multi-stockholm w/ domains loaded"),
+        React.createElement(ListItem, { model: model, onClick: () => {
+                loadUris({ msa: `${BASE}/Lysine.stock` });
             } }, "Lysine stockholm file"),
         React.createElement(ListItem, { model: model, onClick: () => {
-                l2('https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt');
+                loadUris({ msa: `${BASE}/PF01601_full.txt` });
             } }, "PF01601 stockholm file (SARS-CoV2 spike protein)"),
         React.createElement(ListItem, { model: model, onClick: () => {
-                l2('https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa');
+                loadUris({ msa: `${BASE}/europe_covid.fa` });
             } }, "Europe COVID full genomes (LR883044.1 and 199 other sequences)"),
         React.createElement(ListItem, { model: model, onClick: () => {
-                l2('https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.fa', 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.nh');
+                loadUris({
+                    msa: `${BASE}/rhv_test-only.aligned_with_mafft_auto.fa`,
+                    tree: `${BASE}/rhv_test-only.aligned_with_mafft_auto.nh`,
+                });
             } }, "MAFFT+VeryFastTree(17.9k samples)"),
         React.createElement(ListItem, { model: model, onClick: () => {
-                l2('https://jbrowse.org/demos/ttc39a.mfa');
+                loadUris({ msa: 'https://jbrowse.org/demos/ttc39a.mfa' });
             } }, "Human BLAST results mfa")));
 });
 export default ImportFormExamples;

package/dist/components/import/ImportFormExamples.js.map

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