react-msaview 9.0.0 → 9.1.1

package/dist/components/header/getAnnotationsMenu.js

@@ -1,73 +1,67 @@
 import { lazy } from 'react';
-import FilterAlt from '@mui/icons-material/FilterAlt';
-import FolderOpen from '@mui/icons-material/FolderOpen';
-import MenuBook from '@mui/icons-material/MenuBook';
-import Sort from '@mui/icons-material/Sort';
-import Visibility from '@mui/icons-material/Visibility';
 const FeatureFilterDialog = lazy(() => import('../dialogs/FeatureDialog.js'));
 const AnnotationFileDialog = lazy(() => import('../dialogs/AnnotationFileDialog.js'));
-const domainsTutorial = 'https://gmod.org/JBrowseMSA/tutorials/protein_family';
-export function getAnnotationsMenu({ model }) {
-    const { showDomains, actuallyShowDomains, subFeatureRows, noDomains } = model;
-    const noneLoaded = noDomains ? ' (none loaded)' : '';
-    return [
-        {
-            label: 'Open annotation file...',
-            icon: FolderOpen,
-            onClick: () => {
-                model.queueDialog(handleClose => [
-                    AnnotationFileDialog,
-                    {
-                        handleClose,
-                        model,
-                    },
-                ]);
-            },
-        },
-        // `react-msaview-cli interpro` reads InterPro's precomputed matches in
-        // seconds, and `interproscan` covers rows InterPro has not seen; this links
-        // the tutorial for both
-        {
-            label: 'How to get a domain file...',
-            icon: MenuBook,
-            onClick: () => {
-                window.open(domainsTutorial, '_blank', 'noopener,noreferrer');
-            },
+export function openAnnotationFileItem(model) {
+    return {
+        label: 'Open annotation file…',
+        onClick: () => {
+            model.queueDialog(handleClose => [
+                AnnotationFileDialog,
+                { handleClose, model },
+            ]);
         },
+    };
+}
+export function annotationsSubMenu(model) {
+    const { showDomains, actuallyShowDomains, subFeatureRows } = model;
+    return [
         {
-            label: `Show annotations${noneLoaded}`,
-            disabled: noDomains,
-            icon: Visibility,
-            checked: actuallyShowDomains,
+            label: 'Show annotations',
             type: 'checkbox',
+            checked: actuallyShowDomains,
             onClick: () => {
                 model.setShowDomains(!showDomains);
             },
         },
         {
-            label: `Use sub-row layout${noneLoaded}`,
-            disabled: noDomains,
-            checked: actuallyShowDomains ? subFeatureRows : false,
-            icon: Sort,
+            label: 'Sub-row layout',
             type: 'checkbox',
+            disabled: !actuallyShowDomains,
+            checked: actuallyShowDomains && subFeatureRows,
             onClick: () => {
                 model.setSubFeatureRows(!subFeatureRows);
             },
         },
-        {
-            label: `Filter annotations${noneLoaded}`,
-            icon: FilterAlt,
-            disabled: noDomains,
-            onClick: () => {
-                model.queueDialog(onClose => [
-                    FeatureFilterDialog,
-                    {
-                        onClose,
-                        model,
-                    },
-                ]);
-            },
-        },
+        ...typeItems(model),
     ];
 }
+// up to this many types list inline, one checkbox each; past it the filter
+// dialog, which searches and counts them, takes over
+const inlineTypes = 12;
+function typeItems(model) {
+    const types = [...model.annotationTypes.values()];
+    return types.length <= inlineTypes
+        ? [
+            { type: 'subHeader', label: 'Types' },
+            ...types.map(({ accession, name }) => ({
+                label: name || accession,
+                type: 'checkbox',
+                checked: !model.featureOff(accession),
+                onClick: () => {
+                    model.setFilter(accession, model.featureOff(accession));
+                },
+            })),
+        ]
+        : [
+            {
+                label: 'Filter annotations…',
+                onClick: () => {
+                    model.queueDialog(onClose => [
+                        FeatureFilterDialog,
+                        { onClose, model },
+                    ]);
+                },
+            },
+        ];
+}
 //# sourceMappingURL=getAnnotationsMenu.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"getAnnotationsMenu.js","sourceRoot":"","sources":["../../../src/components/header/getAnnotationsMenu.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,QAAQ,MAAM,8BAA8B,CAAA;AACnD,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,oBAAoB,GAAG,IAAI,CAC/B,GAAG,EAAE,CAAC,MAAM,CAAC,oCAAqC,CAAC,CACpD,CAAA;AAED,MAAM,eAAe,GAAG,sDAAsD,CAAA;AAE9E,MAAM,UAAU,kBAAkB,CAAC,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,WAAW,EAAE,mBAAmB,EAAE,cAAc,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC7E,MAAM,UAAU,GAAG,SAAS,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,CAAA;IACpD,OAAO;QACL;YACE,KAAK,EAAE,yBAAyB;YAChC,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,oBAAoB;oBACpB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD,uEAAuE;QACvE,4EAA4E;QAC5E,wBAAwB;QACxB;YACE,KAAK,EAAE,6BAA6B;YACpC,IAAI,EAAE,QAAQ;YACd,OAAO,EAAE,GAAG,EAAE;gBACZ,MAAM,CAAC,IAAI,CAAC,eAAe,EAAE,QAAQ,EAAE,qBAAqB,CAAC,CAAA;YAC/D,CAAC;SACF;QACD;YACE,KAAK,EAAE,mBAAmB,UAAU,EAAE;YACtC,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,mBAAmB;YAC5B,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,UAAU,EAAE;YACxC,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,qBAAqB,UAAU,EAAE;YACxC,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"}
+{"version":3,"file":"getAnnotationsMenu.js","sourceRoot":"","sources":["../../../src/components/header/getAnnotationsMenu.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAK5B,MAAM,mBAAmB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,6BAA8B,CAAC,CAAC,CAAA;AAC9E,MAAM,oBAAoB,GAAG,IAAI,CAC/B,GAAG,EAAE,CAAC,MAAM,CAAC,oCAAqC,CAAC,CACpD,CAAA;AAED,MAAM,UAAU,sBAAsB,CAAC,KAAmB;IACxD,OAAO;QACL,KAAK,EAAE,uBAAuB;QAC9B,OAAO,EAAE,GAAG,EAAE;YACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC/B,oBAAoB;gBACpB,EAAE,WAAW,EAAE,KAAK,EAAE;aACvB,CAAC,CAAA;QACJ,CAAC;KACF,CAAA;AACH,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,KAAmB;IACpD,MAAM,EAAE,WAAW,EAAE,mBAAmB,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAClE,OAAO;QACL;YACE,KAAK,EAAE,kBAAkB;YACzB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,mBAAmB;YAC5B,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;SACF;QACD;YACE,KAAK,EAAE,gBAAgB;YACvB,IAAI,EAAE,UAAU;YAChB,QAAQ,EAAE,CAAC,mBAAmB;YAC9B,OAAO,EAAE,mBAAmB,IAAI,cAAc;YAC9C,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;YAC1C,CAAC;SACF;QACD,GAAG,SAAS,CAAC,KAAK,CAAC;KACpB,CAAA;AACH,CAAC;AAED,2EAA2E;AAC3E,qDAAqD;AACrD,MAAM,WAAW,GAAG,EAAE,CAAA;AAEtB,SAAS,SAAS,CAAC,KAAmB;IACpC,MAAM,KAAK,GAAG,CAAC,GAAG,KAAK,CAAC,eAAe,CAAC,MAAM,EAAE,CAAC,CAAA;IACjD,OAAO,KAAK,CAAC,MAAM,IAAI,WAAW;QAChC,CAAC,CAAC;YACE,EAAE,IAAI,EAAE,WAAW,EAAE,KAAK,EAAE,OAAO,EAAE;YACrC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC;gBACrC,KAAK,EAAE,IAAI,IAAI,SAAS;gBACxB,IAAI,EAAE,UAAmB;gBACzB,OAAO,EAAE,CAAC,KAAK,CAAC,UAAU,CAAC,SAAS,CAAC;gBACrC,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,SAAS,CAAC,SAAS,EAAE,KAAK,CAAC,UAAU,CAAC,SAAS,CAAC,CAAC,CAAA;gBACzD,CAAC;aACF,CAAC,CAAC;SACJ;QACH,CAAC,CAAC;YACE;gBACE,KAAK,EAAE,qBAAqB;gBAC5B,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,mBAAmB;wBACnB,EAAE,OAAO,EAAE,KAAK,EAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC;aACF;SACF,CAAA;AACP,CAAC"}

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

@@ -0,0 +1,11 @@
+import type { MsaViewModel } from '../../model.ts';
+import type { MenuItem } from '@jbrowse/core/ui/Menu';
+export declare function fileMenuItems(model: MsaViewModel): MenuItem[];
+export declare function gapsSubMenu(model: MsaViewModel): MenuItem[];
+export declare function treeSubMenu(model: MsaViewModel): MenuItem[];
+export declare function viewMenuItems(model: MsaViewModel): MenuItem[];
+export declare function trackSettingsItems(model: MsaViewModel): MenuItem[];
+export declare function alignmentSettingsItems(model: MsaViewModel): MenuItem[];
+export declare function colorSettingsItems(model: MsaViewModel): MenuItem[];
+export declare function toolsMenuItems(model: MsaViewModel): MenuItem[];
+export declare function helpMenuItems(model: MsaViewModel): MenuItem[];

package/dist/components/header/menuBarItems.js

@@ -0,0 +1,277 @@
+import { lazy } from 'react';
+import { maxNeighborJoiningRows, treeOrders } from '../../constants.js';
+import { canGoTo } from '../dialogs/GoToBox.js';
+import { scrollZoomLabel } from './ScrollZoomCheckbox.js';
+import { colorSchemeMenuItems } from './colorSchemeMenuItems.js';
+import { openAnnotationFileItem } from './getAnnotationsMenu.js';
+const AboutDialog = lazy(() => import('../dialogs/AboutDialog.js'));
+const ExportSVGDialog = lazy(() => import('../dialogs/ExportSVGDialog.js'));
+const GapThresholdDialog = lazy(() => import('../dialogs/GapThresholdDialog.js'));
+const GoToDialog = lazy(() => import('../dialogs/GoToDialog.js'));
+const HelpDialog = lazy(() => import('../dialogs/HelpDialog.js'));
+const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog.js'));
+const tutorialsUrl = 'https://gmod.org/JBrowseMSA/tutorials/';
+function radio(label, checked, onClick) {
+    return { label, type: 'radio', checked, onClick };
+}
+function toggle(label, checked, set) {
+    return {
+        label,
+        type: 'checkbox',
+        checked,
+        onClick: () => {
+            set(!checked);
+        },
+    };
+}
+function action(label, onClick, disabled = false) {
+    return { label, onClick, disabled };
+}
+function subMenu(label, items, display) {
+    return { label, type: 'subMenu', subMenu: items, display };
+}
+function when(cond, items) {
+    return cond ? items : [];
+}
+export function fileMenuItems(model) {
+    return [
+        ...when(!!model.importForm, [
+            action('Open alignment…', () => {
+                model.reset();
+            }),
+        ]),
+        openAnnotationFileItem(model),
+        action('Export as SVG…', () => {
+            model.queueDialog(onClose => [ExportSVGDialog, { onClose, model }]);
+        }),
+        ...when(!model.tree.noTree, [
+            action('Export tree as Newick', () => {
+                model.exportNewick();
+            }),
+        ]),
+        action('Alignment info…', () => {
+            model.queueDialog(onClose => [MetadataDialog, { model, onClose }]);
+        }),
+    ];
+}
+function zoomSubMenu(model) {
+    return [
+        action('Zoom in', () => {
+            model.zoomIn();
+        }),
+        action('Zoom out', () => {
+            model.zoomOut();
+        }),
+        action('Fit to window', () => {
+            model.fit();
+        }),
+        action('Fit width', () => {
+            model.fitHorizontally();
+        }),
+        action('Fit height', () => {
+            model.fitVertically();
+        }),
+        action('Reset zoom', () => {
+            model.resetZoom();
+        }),
+        toggle(scrollZoomLabel, model.scrollZoom, arg => {
+            model.setScrollZoom(arg);
+        }),
+    ];
+}
+const gapPresets = [100, 90, 50];
+export function gapsSubMenu(model) {
+    const { hideGaps, allowedGappyness } = model;
+    const custom = hideGaps && !gapPresets.includes(allowedGappyness);
+    return [
+        subMenu('Gappy columns', [
+            radio('Show all columns', !hideGaps, () => {
+                model.setHideGaps(false);
+            }),
+            ...gapPresets.map(pct => radio(pct === 100 ? 'Hide columns of only gaps' : `Hide ≥${pct}% gaps`, hideGaps && allowedGappyness === pct, () => {
+                model.setHideGaps(true);
+                model.setAllowedGappyness(pct);
+            })),
+            {
+                ...radio(custom ? `Hide ≥${allowedGappyness}% gaps…` : 'Custom threshold…', custom, () => {
+                    model.setHideGaps(true);
+                    model.queueDialog(onClose => [
+                        GapThresholdDialog,
+                        { model, onClose },
+                    ]);
+                }),
+                keepMenuOpen: false,
+            },
+        ], 'select'),
+    ];
+}
+const treeOrderLabels = {
+    branchLength: 'By branch length',
+    input: 'Input order',
+    ladderize: 'Ladderize, small clades first',
+    ladderizeReverse: 'Ladderize, large clades first',
+};
+function outgroupLabel(outgroup) {
+    const [first, ...rest] = outgroup;
+    return rest.length === 0
+        ? `Outgroup ${first}`
+        : `Outgroup ${first} … ${rest.at(-1)}`;
+}
+export function treeSubMenu(model) {
+    const { drawTree, showBranchLen, labelsAlignRight, drawNodeLabels, drawLabels, treeAreaWidth, showTreeOverview, showTreeScaleBar, treeOrder, treeRoot, rotated, } = model;
+    return [
+        subMenu('Layout', [
+            radio('Phylogram', drawTree && showBranchLen, () => {
+                model.setDrawTree(true);
+                model.setShowBranchLen(true);
+            }),
+            radio('Cladogram', drawTree && !showBranchLen, () => {
+                model.setDrawTree(true);
+                model.setShowBranchLen(false);
+            }),
+            radio('Labels only', !drawTree, () => {
+                model.setDrawTree(false);
+            }),
+        ], 'segmented'),
+        toggle('Tree overview', showTreeOverview, arg => {
+            model.setShowTreeOverview(arg);
+        }),
+        toggle('Scale bar', showTreeScaleBar, arg => {
+            model.setShowTreeScaleBar(arg);
+        }),
+        subMenu('Order', [
+            ...treeOrders.map(order => radio(treeOrderLabels[order], treeOrder === order, () => {
+                model.setTreeOrder(order);
+            })),
+            ...when(rotated.length > 0, [
+                action('Undo rotations', () => {
+                    model.clearRotated();
+                }),
+            ]),
+        ], 'select'),
+        subMenu('Root', [
+            radio('Input root', treeRoot === undefined, () => {
+                model.setTreeRoot(undefined);
+            }),
+            radio('Midpoint', treeRoot === 'midpoint', () => {
+                model.setTreeRoot('midpoint');
+            }),
+            // "Reroot here" in a node's menu sets the outgroup, so this only
+            // reports it
+            ...when(typeof treeRoot === 'object', [
+                {
+                    ...radio(typeof treeRoot === 'object'
+                        ? outgroupLabel(treeRoot.outgroup)
+                        : '', true, () => { }),
+                    disabled: true,
+                },
+            ]),
+        ], 'select'),
+        subMenu('Labels', [
+            toggle('Tip labels', drawLabels, arg => {
+                model.setDrawLabels(arg);
+            }),
+            toggle('Internal node labels', drawNodeLabels, arg => {
+                model.setDrawNodeLabels(arg);
+            }),
+            toggle('Align right', labelsAlignRight, arg => {
+                model.setLabelsAlignRight(arg);
+            }),
+        ]),
+        ...when(treeAreaWidth !== undefined, [
+            action('Reset tree width', () => {
+                model.setTreeAreaWidth(undefined);
+            }),
+        ]),
+    ];
+}
+export function viewMenuItems(model) {
+    return [
+        ...when(canGoTo(model), [
+            action('Find row or column…', () => {
+                model.queueDialog(onClose => [GoToDialog, { model, onClose }]);
+            }),
+        ]),
+        subMenu('Zoom', zoomSubMenu(model)),
+    ];
+}
+export function trackSettingsItems(model) {
+    return [
+        toggle('Show track values on hover', model.showColumnStats, arg => {
+            model.setShowColumnStats(arg);
+        }),
+    ];
+}
+// the settings panel's toggles for how the alignment draws
+export function alignmentSettingsItems(model) {
+    return [
+        toggle('Show letters', model.drawMsaLetters, arg => {
+            model.setDrawMsaLetters(arg);
+        }),
+    ];
+}
+// who colors the cells comes first, since a scheme picked while the domains
+// fill them would otherwise change nothing on screen
+export function colorSettingsItems(model) {
+    const { cellFill, filteredAnnotations } = model;
+    return [
+        subMenu('Fill cells with', [
+            radio('Residues', cellFill === 'residue', () => {
+                model.setCellFill('residue');
+            }),
+            ...when(filteredAnnotations.length > 0, [
+                radio('Domains', cellFill === 'domain', () => {
+                    model.setShowDomains(true);
+                    model.setCellFill('domain');
+                }),
+            ]),
+            {
+                ...radio('Nothing', cellFill === 'none', () => {
+                    model.setCellFill('none');
+                }),
+                helpText: 'Color the letters instead',
+            },
+        ], 'segmented'),
+        {
+            type: 'subHeader',
+            label: cellFill === 'domain'
+                ? 'Residue scheme: picking one takes the cells back from the domains'
+                : 'Residue scheme',
+        },
+        ...colorSchemeMenuItems(model),
+    ];
+}
+function neighborJoiningItem(model) {
+    const rows = model.rowMap.size;
+    const tooManyRows = rows > maxNeighborJoiningRows;
+    return action(tooManyRows
+        ? `Build neighbor joining tree (over ${maxNeighborJoiningRows} rows, use FastTree)`
+        : model.noTree
+            ? 'Build neighbor joining tree'
+            : 'Replace with neighbor joining tree', () => {
+        try {
+            model.calculateNeighborJoiningTreeFromMSA();
+        }
+        catch (e) {
+            console.error('Failed to calculate NJ tree:', e);
+            model.addWarning(e instanceof Error ? e.message : String(e));
+        }
+    }, tooManyRows || rows < 2);
+}
+export function toolsMenuItems(model) {
+    return [neighborJoiningItem(model)];
+}
+export function helpMenuItems(model) {
+    return [
+        action('Mouse & keyboard…', () => {
+            model.queueDialog(onClose => [HelpDialog, { model, onClose }]);
+        }),
+        action('Tutorials', () => {
+            window.open(tutorialsUrl, '_blank', 'noopener,noreferrer');
+        }),
+        action('About & credits…', () => {
+            model.queueDialog(onClose => [AboutDialog, { onClose }]);
+        }),
+    ];
+}
+//# sourceMappingURL=menuBarItems.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"menuBarItems.js","sourceRoot":"","sources":["../../../src/components/header/menuBarItems.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,EAAE,sBAAsB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AACvE,OAAO,EAAE,OAAO,EAAE,MAAM,uBAAwB,CAAA;AAChD,OAAO,EAAE,eAAe,EAAE,MAAM,yBAA0B,CAAA;AAC1D,OAAO,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAA;AAChE,OAAO,EAAE,sBAAsB,EAAE,MAAM,yBAAyB,CAAA;AAOhE,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA4B,CAAC,CAAC,CAAA;AACpE,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,+BAAgC,CAAC,CAAC,CAAA;AAC5E,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,kCAAmC,CAAC,CAClD,CAAA;AACD,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,0BAA2B,CAAC,CAAC,CAAA;AAClE,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,0BAA2B,CAAC,CAAC,CAAA;AAClE,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA+B,CAAC,CAAC,CAAA;AAE1E,MAAM,YAAY,GAAG,wCAAwC,CAAA;AAE7D,SAAS,KAAK,CAAC,KAAa,EAAE,OAAgB,EAAE,OAAmB;IACjE,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,OAAgB,EAAE,OAAO,EAAE,OAAO,EAAE,CAAA;AAC5D,CAAC;AAED,SAAS,MAAM,CAAC,KAAa,EAAE,OAAgB,EAAE,GAA2B;IAC1E,OAAO;QACL,KAAK;QACL,IAAI,EAAE,UAAmB;QACzB,OAAO;QACP,OAAO,EAAE,GAAG,EAAE;YACZ,GAAG,CAAC,CAAC,OAAO,CAAC,CAAA;QACf,CAAC;KACF,CAAA;AACH,CAAC;AAED,SAAS,MAAM,CAAC,KAAa,EAAE,OAAmB,EAAE,QAAQ,GAAG,KAAK;IAClE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAA;AACrC,CAAC;AAED,SAAS,OAAO,CAAC,KAAa,EAAE,KAAiB,EAAE,OAAuB;IACxE,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,SAAkB,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,CAAA;AACrE,CAAC;AAED,SAAS,IAAI,CAAI,IAAa,EAAE,KAAU;IACxC,OAAO,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,KAAmB;IAC/C,OAAO;QACL,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,EAAE;YAC1B,MAAM,CAAC,iBAAiB,EAAE,GAAG,EAAE;gBAC7B,KAAK,CAAC,KAAK,EAAE,CAAA;YACf,CAAC,CAAC;SACH,CAAC;QACF,sBAAsB,CAAC,KAAK,CAAC;QAC7B,MAAM,CAAC,gBAAgB,EAAE,GAAG,EAAE;YAC5B,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,eAAe,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,CAAA;QACrE,CAAC,CAAC;QACF,GAAG,IAAI,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE;YAC1B,MAAM,CAAC,uBAAuB,EAAE,GAAG,EAAE;gBACnC,KAAK,CAAC,YAAY,EAAE,CAAA;YACtB,CAAC,CAAC;SACH,CAAC;QACF,MAAM,CAAC,iBAAiB,EAAE,GAAG,EAAE;YAC7B,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,cAAc,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;QACpE,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,KAAmB;IACtC,OAAO;QACL,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE;YACrB,KAAK,CAAC,MAAM,EAAE,CAAA;QAChB,CAAC,CAAC;QACF,MAAM,CAAC,UAAU,EAAE,GAAG,EAAE;YACtB,KAAK,CAAC,OAAO,EAAE,CAAA;QACjB,CAAC,CAAC;QACF,MAAM,CAAC,eAAe,EAAE,GAAG,EAAE;YAC3B,KAAK,CAAC,GAAG,EAAE,CAAA;QACb,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,GAAG,EAAE;YACvB,KAAK,CAAC,eAAe,EAAE,CAAA;QACzB,CAAC,CAAC;QACF,MAAM,CAAC,YAAY,EAAE,GAAG,EAAE;YACxB,KAAK,CAAC,aAAa,EAAE,CAAA;QACvB,CAAC,CAAC;QACF,MAAM,CAAC,YAAY,EAAE,GAAG,EAAE;YACxB,KAAK,CAAC,SAAS,EAAE,CAAA;QACnB,CAAC,CAAC;QACF,MAAM,CAAC,eAAe,EAAE,KAAK,CAAC,UAAU,EAAE,GAAG,CAAC,EAAE;YAC9C,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC1B,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,GAAG,EAAE,EAAE,EAAE,EAAE,CAAC,CAAA;AAEhC,MAAM,UAAU,WAAW,CAAC,KAAmB;IAC7C,MAAM,EAAE,QAAQ,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,MAAM,GAAG,QAAQ,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,gBAAgB,CAAC,CAAA;IACjE,OAAO;QACL,OAAO,CACL,eAAe,EACf;YACE,KAAK,CAAC,kBAAkB,EAAE,CAAC,QAAQ,EAAE,GAAG,EAAE;gBACxC,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;YAC1B,CAAC,CAAC;YACF,GAAG,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CACtB,KAAK,CACH,GAAG,KAAK,GAAG,CAAC,CAAC,CAAC,2BAA2B,CAAC,CAAC,CAAC,SAAS,GAAG,QAAQ,EAChE,QAAQ,IAAI,gBAAgB,KAAK,GAAG,EACpC,GAAG,EAAE;gBACH,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACvB,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;YAChC,CAAC,CACF,CACF;YACD;gBACE,GAAG,KAAK,CACN,MAAM,CAAC,CAAC,CAAC,SAAS,gBAAgB,SAAS,CAAC,CAAC,CAAC,mBAAmB,EACjE,MAAM,EACN,GAAG,EAAE;oBACH,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;oBACvB,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,kBAAkB;wBAClB,EAAE,KAAK,EAAE,OAAO,EAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC,CACF;gBACD,YAAY,EAAE,KAAK;aACpB;SACF,EACD,QAAQ,CACT;KACF,CAAA;AACH,CAAC;AAED,MAAM,eAAe,GAA8B;IACjD,YAAY,EAAE,kBAAkB;IAChC,KAAK,EAAE,aAAa;IACpB,SAAS,EAAE,+BAA+B;IAC1C,gBAAgB,EAAE,+BAA+B;CAClD,CAAA;AAED,SAAS,aAAa,CAAC,QAAkB;IACvC,MAAM,CAAC,KAAK,EAAE,GAAG,IAAI,CAAC,GAAG,QAAQ,CAAA;IACjC,OAAO,IAAI,CAAC,MAAM,KAAK,CAAC;QACtB,CAAC,CAAC,YAAY,KAAK,EAAE;QACrB,CAAC,CAAC,YAAY,KAAK,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAmB;IAC7C,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,cAAc,EACd,UAAU,EACV,aAAa,EACb,gBAAgB,EAChB,gBAAgB,EAChB,SAAS,EACT,QAAQ,EACR,OAAO,GACR,GAAG,KAAK,CAAA;IACT,OAAO;QACL,OAAO,CACL,QAAQ,EACR;YACE,KAAK,CAAC,WAAW,EAAE,QAAQ,IAAI,aAAa,EAAE,GAAG,EAAE;gBACjD,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACvB,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;YAC9B,CAAC,CAAC;YACF,KAAK,CAAC,WAAW,EAAE,QAAQ,IAAI,CAAC,aAAa,EAAE,GAAG,EAAE;gBAClD,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACvB,KAAK,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;YAC/B,CAAC,CAAC;YACF,KAAK,CAAC,aAAa,EAAE,CAAC,QAAQ,EAAE,GAAG,EAAE;gBACnC,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;YAC1B,CAAC,CAAC;SACH,EACD,WAAW,CACZ;QACD,MAAM,CAAC,eAAe,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YAC9C,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YAC1C,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,OAAO,CACL,OAAO,EACP;YACE,GAAG,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CACxB,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,SAAS,KAAK,KAAK,EAAE,GAAG,EAAE;gBACtD,KAAK,CAAC,YAAY,CAAC,KAAK,CAAC,CAAA;YAC3B,CAAC,CAAC,CACH;YACD,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;gBAC1B,MAAM,CAAC,gBAAgB,EAAE,GAAG,EAAE;oBAC5B,KAAK,CAAC,YAAY,EAAE,CAAA;gBACtB,CAAC,CAAC;aACH,CAAC;SACH,EACD,QAAQ,CACT;QACD,OAAO,CACL,MAAM,EACN;YACE,KAAK,CAAC,YAAY,EAAE,QAAQ,KAAK,SAAS,EAAE,GAAG,EAAE;gBAC/C,KAAK,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;YAC9B,CAAC,CAAC;YACF,KAAK,CAAC,UAAU,EAAE,QAAQ,KAAK,UAAU,EAAE,GAAG,EAAE;gBAC9C,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC/B,CAAC,CAAC;YACF,iEAAiE;YACjE,aAAa;YACb,GAAG,IAAI,CAAC,OAAO,QAAQ,KAAK,QAAQ,EAAE;gBACpC;oBACE,GAAG,KAAK,CACN,OAAO,QAAQ,KAAK,QAAQ;wBAC1B,CAAC,CAAC,aAAa,CAAC,QAAQ,CAAC,QAAQ,CAAC;wBAClC,CAAC,CAAC,EAAE,EACN,IAAI,EACJ,GAAG,EAAE,GAAE,CAAC,CACT;oBACD,QAAQ,EAAE,IAAI;iBACf;aACF,CAAC;SACH,EACD,QAAQ,CACT;QACD,OAAO,CAAC,QAAQ,EAAE;YAChB,MAAM,CAAC,YAAY,EAAE,UAAU,EAAE,GAAG,CAAC,EAAE;gBACrC,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;YAC1B,CAAC,CAAC;YACF,MAAM,CAAC,sBAAsB,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;gBACnD,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;YAC9B,CAAC,CAAC;YACF,MAAM,CAAC,aAAa,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;gBAC5C,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;YAChC,CAAC,CAAC;SACH,CAAC;QACF,GAAG,IAAI,CAAC,aAAa,KAAK,SAAS,EAAE;YACnC,MAAM,CAAC,kBAAkB,EAAE,GAAG,EAAE;gBAC9B,KAAK,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC;SACH,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,KAAmB;IAC/C,OAAO;QACL,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;YACtB,MAAM,CAAC,qBAAqB,EAAE,GAAG,EAAE;gBACjC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,UAAU,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;YAChE,CAAC,CAAC;SACH,CAAC;QACF,OAAO,CAAC,MAAM,EAAE,WAAW,CAAC,KAAK,CAAC,CAAC;KACpC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,KAAmB;IACpD,OAAO;QACL,MAAM,CAAC,4BAA4B,EAAE,KAAK,CAAC,eAAe,EAAE,GAAG,CAAC,EAAE;YAChE,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,2DAA2D;AAC3D,MAAM,UAAU,sBAAsB,CAAC,KAAmB;IACxD,OAAO;QACL,MAAM,CAAC,cAAc,EAAE,KAAK,CAAC,cAAc,EAAE,GAAG,CAAC,EAAE;YACjD,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,4EAA4E;AAC5E,qDAAqD;AACrD,MAAM,UAAU,kBAAkB,CAAC,KAAmB;IACpD,MAAM,EAAE,QAAQ,EAAE,mBAAmB,EAAE,GAAG,KAAK,CAAA;IAC/C,OAAO;QACL,OAAO,CACL,iBAAiB,EACjB;YACE,KAAK,CAAC,UAAU,EAAE,QAAQ,KAAK,SAAS,EAAE,GAAG,EAAE;gBAC7C,KAAK,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;YAC9B,CAAC,CAAC;YACF,GAAG,IAAI,CAAC,mBAAmB,CAAC,MAAM,GAAG,CAAC,EAAE;gBACtC,KAAK,CAAC,SAAS,EAAE,QAAQ,KAAK,QAAQ,EAAE,GAAG,EAAE;oBAC3C,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;oBAC1B,KAAK,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAA;gBAC7B,CAAC,CAAC;aACH,CAAC;YACF;gBACE,GAAG,KAAK,CAAC,SAAS,EAAE,QAAQ,KAAK,MAAM,EAAE,GAAG,EAAE;oBAC5C,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;gBAC3B,CAAC,CAAC;gBACF,QAAQ,EAAE,2BAA2B;aACtC;SACF,EACD,WAAW,CACZ;QACD;YACE,IAAI,EAAE,WAAW;YACjB,KAAK,EACH,QAAQ,KAAK,QAAQ;gBACnB,CAAC,CAAC,mEAAmE;gBACrE,CAAC,CAAC,gBAAgB;SACvB;QACD,GAAG,oBAAoB,CAAC,KAAK,CAAC;KAC/B,CAAA;AACH,CAAC;AAED,SAAS,mBAAmB,CAAC,KAAmB;IAC9C,MAAM,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,IAAI,CAAA;IAC9B,MAAM,WAAW,GAAG,IAAI,GAAG,sBAAsB,CAAA;IACjD,OAAO,MAAM,CACX,WAAW;QACT,CAAC,CAAC,qCAAqC,sBAAsB,sBAAsB;QACnF,CAAC,CAAC,KAAK,CAAC,MAAM;YACZ,CAAC,CAAC,6BAA6B;YAC/B,CAAC,CAAC,oCAAoC,EAC1C,GAAG,EAAE;QACH,IAAI,CAAC;YACH,KAAK,CAAC,mCAAmC,EAAE,CAAA;QAC7C,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,OAAO,CAAC,KAAK,CAAC,8BAA8B,EAAE,CAAC,CAAC,CAAA;YAChD,KAAK,CAAC,UAAU,CAAC,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;QAC9D,CAAC;IACH,CAAC,EACD,WAAW,IAAI,IAAI,GAAG,CAAC,CACxB,CAAA;AACH,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,KAAmB;IAChD,OAAO,CAAC,mBAAmB,CAAC,KAAK,CAAC,CAAC,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,KAAmB;IAC/C,OAAO;QACL,MAAM,CAAC,mBAAmB,EAAE,GAAG,EAAE;YAC/B,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,UAAU,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;QAChE,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,GAAG,EAAE;YACvB,MAAM,CAAC,IAAI,CAAC,YAAY,EAAE,QAAQ,EAAE,qBAAqB,CAAC,CAAA;QAC5D,CAAC,CAAC;QACF,MAAM,CAAC,kBAAkB,EAAE,GAAG,EAAE;YAC9B,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;QAC1D,CAAC,CAAC;KACH,CAAA;AACH,CAAC"}

package/dist/components/import/ImportForm.js

@@ -10,8 +10,8 @@ const ImportForm = observer(function ({ model }) {
     const [treeFile, setTreeFile] = useState();
     const [gffFile, setGffFile] = useState();
     const { error } = model;
-    return (React.createElement(Container, null,
-        React.createElement(Box, { sx: { width: '50%', [phone]: { width: '100%' } } },
+    return (React.createElement(Container, { sx: { pt: 2, pb: 3 } },
+        React.createElement(Box, { sx: { width: '50%', mb: 2, [phone]: { width: '100%' } } },
             error ? React.createElement(ErrorMessage, { error: error }) : null,
             React.createElement(Typography, null, "Open an MSA file (FASTA, Stockholm, Clustal, A3M or EMF format) and/or a tree file (Newick format)."),
             React.createElement(Typography, { color: "text.secondary" }, "An MSA alone or a tree alone is enough, and a Stockholm file with an embedded tree needs no separate tree file.")),
@@ -26,16 +26,22 @@ const ImportForm = observer(function ({ model }) {
                     gap: '16px',
                 },
             } },
-            React.createElement("div", null,
+            React.createElement(Box, { sx: {
+                    width: 400,
+                    display: 'flex',
+                    flexDirection: 'column',
+                    gap: 1.5,
+                    [phone]: { width: 'auto' },
+                } },
                 React.createElement("div", null,
                     React.createElement(Typography, null, "MSA file or URL"),
-                    React.createElement(FileSelector, { location: msaFile, setLocation: setMsaFile })),
+                    React.createElement(FileSelector, { inline: true, location: msaFile, setLocation: setMsaFile })),
                 React.createElement("div", null,
                     React.createElement(Typography, null, "Tree file or URL"),
-                    React.createElement(FileSelector, { location: treeFile, setLocation: setTreeFile })),
+                    React.createElement(FileSelector, { inline: true, location: treeFile, setLocation: setTreeFile })),
                 React.createElement("div", null,
                     React.createElement(Typography, null, "Annotation GFF file or URL (optional)"),
-                    React.createElement(FileSelector, { location: gffFile, setLocation: setGffFile }))),
+                    React.createElement(FileSelector, { inline: true, location: gffFile, setLocation: setGffFile }))),
             React.createElement("div", null,
                 React.createElement(Button, { onClick: () => {
                         try {

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

@@ -1 +1 @@
-{"version":3,"file":"ImportForm.js","sourceRoot":"","sources":["../../../src/components/import/ImportForm.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,GAAG,EAAE,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClE,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,kBAAkB,MAAM,yBAA0B,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAA;AAKhC,MAAM,KAAK,GAAG,2BAA2B,CAAA;AAEzC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAEvB,OAAO,CACL,oBAAC,SAAS;QACR,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE;YAClD,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,UAAU,8GAGE;YACb,oBAAC,UAAU,IAAC,KAAK,EAAC,gBAAgB,sHAGrB,CACT;QAEN,oBAAC,GAAG,IACF,EAAE,EAAE;gBACF,OAAO,EAAE,MAAM;gBACf,cAAc,EAAE,QAAQ;gBACxB,UAAU,EAAE,QAAQ;gBACpB,GAAG,EAAE,MAAM;gBACX,CAAC,KAAK,CAAC,EAAE;oBACP,aAAa,EAAE,QAAQ;oBACvB,UAAU,EAAE,SAAS;oBACrB,GAAG,EAAE,MAAM;iBACZ;aACF;YAED;gBACE;oBACE,oBAAC,UAAU,0BAA6B;oBACxC,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD;gBACN;oBACE,oBAAC,UAAU,2BAA8B;oBACzC,oBAAC,YAAY,IAAC,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,GAAI,CAC1D;gBACN;oBACE,oBAAC,UAAU,gDAAmD;oBAC9D,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD,CACF;YACN;gBACE,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC;4BACH,IAAI,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAA;wBACzC,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACnB,CAAC;oBACH,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,OAAO,IAAI,CAAC,QAAQ,WAGxB,CACL;YAEN;gBACE,oBAAC,UAAU,mBAAsB;gBACjC,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI,CAChC,CACF,CACI,CACb,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}
+{"version":3,"file":"ImportForm.js","sourceRoot":"","sources":["../../../src/components/import/ImportForm.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,GAAG,EAAE,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClE,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,kBAAkB,MAAM,yBAA0B,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAA;AAKhC,MAAM,KAAK,GAAG,2BAA2B,CAAA;AAEzC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAEvB,OAAO,CACL,oBAAC,SAAS,IAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE;QAC7B,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE;YACzD,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,UAAU,8GAGE;YACb,oBAAC,UAAU,IAAC,KAAK,EAAC,gBAAgB,sHAGrB,CACT;QAEN,oBAAC,GAAG,IACF,EAAE,EAAE;gBACF,OAAO,EAAE,MAAM;gBACf,cAAc,EAAE,QAAQ;gBACxB,UAAU,EAAE,QAAQ;gBACpB,GAAG,EAAE,MAAM;gBACX,CAAC,KAAK,CAAC,EAAE;oBACP,aAAa,EAAE,QAAQ;oBACvB,UAAU,EAAE,SAAS;oBACrB,GAAG,EAAE,MAAM;iBACZ;aACF;YAED,oBAAC,GAAG,IACF,EAAE,EAAE;oBACF,KAAK,EAAE,GAAG;oBACV,OAAO,EAAE,MAAM;oBACf,aAAa,EAAE,QAAQ;oBACvB,GAAG,EAAE,GAAG;oBACR,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE;iBAC3B;gBAED;oBACE,oBAAC,UAAU,0BAA6B;oBACxC,oBAAC,YAAY,IAAC,MAAM,QAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CAC/D;gBACN;oBACE,oBAAC,UAAU,2BAA8B;oBACzC,oBAAC,YAAY,IACX,MAAM,QACN,QAAQ,EAAE,QAAQ,EAClB,WAAW,EAAE,WAAW,GACxB,CACE;gBACN;oBACE,oBAAC,UAAU,gDAAmD;oBAC9D,oBAAC,YAAY,IAAC,MAAM,QAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CAC/D,CACF;YACN;gBACE,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC;4BACH,IAAI,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAA;wBACzC,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACnB,CAAC;oBACH,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,OAAO,IAAI,CAAC,QAAQ,WAGxB,CACL;YAEN;gBACE,oBAAC,UAAU,mBAAsB;gBACjC,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI,CAChC,CACF,CACI,CACb,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/import/data/seq2.d.ts

@@ -1,3 +1,2 @@
 export declare const smallMSA = "CLUSTAL O(1.2.3) multiple sequence alignment\nUniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM\nUniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI\nUniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM\nUniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM\nUniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM\nUniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------\nUniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS\nUniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV\nUniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP\nUniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------\nUniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST\nUniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------\n";
-export declare const smallMSAOnly = "CLUSTAL O(1.2.4) multiple sequence alignment\n\n\nsp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\t60\nsp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG\t60\nsp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG\t60\n                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**\n\nsp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\t120\nsp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP\t120\nsp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA\t120\n                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**\n\nsp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR\t142\n                           .**: ****: ** ***.***";
 export declare const smallTree = "(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)";

package/dist/components/import/data/seq2.js

@@ -12,22 +12,5 @@ UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP-------------
 UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
 UniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------
 `;
-export const smallMSAOnly = `CLUSTAL O(1.2.4) multiple sequence alignment
-
-
-sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
-sp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG	60
-sp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG	60
-                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**
-
-sp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP	120
-sp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP	120
-sp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA	120
-                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**
-
-sp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR	142
-sp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR	142
-sp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR	142
-                           .**: ****: ** ***.***`;
 export const smallTree = '(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)';
 //# sourceMappingURL=seq2.js.map

package/dist/components/import/data/seq2.js.map

@@ -1 +1 @@
-{"version":3,"file":"seq2.js","sourceRoot":"","sources":["../../../../src/components/import/data/seq2.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,QAAQ,GAAG;;;;;;;;;;;;;CAavB,CAAA;AAED,MAAM,CAAC,MAAM,YAAY,GAAG;;;;;;;;;;;;;;;;iDAgBqB,CAAA;AAEjD,MAAM,CAAC,MAAM,SAAS,GACpB,+nBAA+nB,CAAA"}
+{"version":3,"file":"seq2.js","sourceRoot":"","sources":["../../../../src/components/import/data/seq2.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,QAAQ,GAAG;;;;;;;;;;;;;CAavB,CAAA;AAED,MAAM,CAAC,MAAM,SAAS,GACpB,+nBAA+nB,CAAA"}

package/dist/components/minimap/Minimap.js

@@ -1,13 +1,13 @@
 import React, { useCallback } from 'react';
-import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { useCanvasTheme } from '../../darkReader.js';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import DragHandle, { scrollbarThumbFill } from '../DragHandle.js';
 import { msaThumbnail } from '../msa/msaRaster.js';
-import { MINIMAP_BAR_HEIGHT, getMinimapLayout } from './minimapLayout.js';
+import { MINIMAP_BAR_HEIGHT, getMinimapLayout, minimapDomainRects, } from './minimapLayout.js';
 const Minimap = observer(function ({ model }) {
     const { minimapHeight, msaCanvasWidth, highResScaleFactor } = model;
-    const theme = useTheme();
+    const theme = useCanvasTheme();
     const { unit, s, w, polygonHeight, polygonPoints } = getMinimapLayout(model);
     // the whole alignment, sampled down to the bar
     const barWidth = Math.round(msaCanvasWidth * highResScaleFactor);
@@ -25,6 +25,10 @@ const Minimap = observer(function ({ model }) {
                 ctx.imageSmoothingEnabled = true;
                 ctx.drawImage(thumbnail, 0, 0, thumbnail.width, thumbnail.height, 0, 0, barWidth, barHeight);
             }
+            for (const r of minimapDomainRects(model, barWidth, barHeight)) {
+                ctx.fillStyle = r.fill;
+                ctx.fillRect(r.x, r.y, r.w, r.h);
+            }
         },
         width: barWidth,
         height: barHeight,

package/dist/components/minimap/Minimap.js.map

@@ -1 +1 @@
-{"version":3,"file":"Minimap.js","sourceRoot":"","sources":["../../../src/components/minimap/Minimap.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,OAAO,CAAA;AAE1C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,UAAU,EAAE,EAAE,kBAAkB,EAAE,MAAM,kBAAmB,CAAA;AAClE,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAClD,OAAO,EAAE,kBAAkB,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAIzE,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,aAAa,EAAE,cAAc,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC,EAAE,aAAa,EAAE,aAAa,EAAE,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAA;IAE5E,+CAA+C;IAC/C,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,kBAAkB,CAAC,CAAA;IAChE,MAAM,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,GAAG,kBAAkB,CAAC,CAAA;IACrE,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;YACxC,MAAM,SAAS,GAAG,YAAY,CAAC;gBAC7B,KAAK;gBACL,KAAK;gBACL,MAAM,EAAE,kBAAkB;aAC3B,CAAC,CAAA;YACF,IAAI,SAAS,EAAE,CAAC;gBACd,GAAG,CAAC,qBAAqB,GAAG,IAAI,CAAA;gBAChC,GAAG,CAAC,SAAS,CACX,SAAS,EACT,CAAC,EACD,CAAC,EACD,SAAS,CAAC,KAAK,EACf,SAAS,CAAC,MAAM,EAChB,CAAC,EACD,CAAC,EACD,QAAQ,EACR,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,KAAK,EAAE,QAAQ;QACf,MAAM,EAAE,SAAS;QACjB,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC;KACrB,CAAC,CAAA;IAEF,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,UAAU,CAAC,WAAW,GAAG,KAAK,GAAG,IAAI,CAAC,CAAA;IAC9C,CAAC,EACD,CAAC,KAAK,EAAE,IAAI,CAAC,CACd,CAAA;IAED,OAAO,CAIL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,aAAa;YACrB,KAAK,EAAE,cAAc;YACrB,UAAU,EAAE,CAAC;SACd;QAED,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,QAAQ,EACf,MAAM,EAAE,SAAS,EACjB,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,IAAI,GAAG,CAAC,EAAE,CAAC;oBACnC,MAAM,CAAC,GACL,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,aAAa,CAAC,qBAAqB,EAAE,CAAC,IAAI,CAAA;oBAClE,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,cAAc,GAAG,CAAC,CAAC,CAAA;gBAClD,CAAC;YACH,CAAC,EACD,KAAK,EAAE;gBACL,OAAO,EAAE,OAAO;gBAChB,KAAK,EAAE,cAAc;gBACrB,MAAM,EAAE,kBAAkB;gBAC1B,SAAS,EAAE,YAAY;gBACvB,MAAM,EAAE,aAAa,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,EAAE;aACpD,GACD;QACF,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,OAAO,EACf,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,OAAO,EAC7B,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;gBACL,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACpB,MAAM,EAAE,kBAAkB;gBAC1B,KAAK,EAAE,CAAC;aACT,GACD;QAEF,6BAAK,MAAM,EAAE,aAAa,EAAE,KAAK,EAAE,cAAc;YAC/C,iCAAS,IAAI,EAAE,kBAAkB,EAAE,MAAM,EAAE,aAAa,GAAI,CACxD,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}
+{"version":3,"file":"Minimap.js","sourceRoot":"","sources":["../../../src/components/minimap/Minimap.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,OAAO,CAAA;AAE1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,UAAU,EAAE,EAAE,kBAAkB,EAAE,MAAM,kBAAmB,CAAA;AAClE,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAClD,OAAO,EACL,kBAAkB,EAClB,gBAAgB,EAChB,kBAAkB,GACnB,MAAM,oBAAoB,CAAA;AAI3B,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,aAAa,EAAE,cAAc,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,KAAK,GAAG,cAAc,EAAE,CAAA;IAC9B,MAAM,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC,EAAE,aAAa,EAAE,aAAa,EAAE,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAA;IAE5E,+CAA+C;IAC/C,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,kBAAkB,CAAC,CAAA;IAChE,MAAM,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,GAAG,kBAAkB,CAAC,CAAA;IACrE,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;YACxC,MAAM,SAAS,GAAG,YAAY,CAAC;gBAC7B,KAAK;gBACL,KAAK;gBACL,MAAM,EAAE,kBAAkB;aAC3B,CAAC,CAAA;YACF,IAAI,SAAS,EAAE,CAAC;gBACd,GAAG,CAAC,qBAAqB,GAAG,IAAI,CAAA;gBAChC,GAAG,CAAC,SAAS,CACX,SAAS,EACT,CAAC,EACD,CAAC,EACD,SAAS,CAAC,KAAK,EACf,SAAS,CAAC,MAAM,EAChB,CAAC,EACD,CAAC,EACD,QAAQ,EACR,SAAS,CACV,CAAA;YACH,CAAC;YACD,KAAK,MAAM,CAAC,IAAI,kBAAkB,CAAC,KAAK,EAAE,QAAQ,EAAE,SAAS,CAAC,EAAE,CAAC;gBAC/D,GAAG,CAAC,SAAS,GAAG,CAAC,CAAC,IAAI,CAAA;gBACtB,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;QACD,KAAK,EAAE,QAAQ;QACf,MAAM,EAAE,SAAS;QACjB,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC;KACrB,CAAC,CAAA;IAEF,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,UAAU,CAAC,WAAW,GAAG,KAAK,GAAG,IAAI,CAAC,CAAA;IAC9C,CAAC,EACD,CAAC,KAAK,EAAE,IAAI,CAAC,CACd,CAAA;IAED,OAAO,CAIL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,aAAa;YACrB,KAAK,EAAE,cAAc;YACrB,UAAU,EAAE,CAAC;SACd;QAED,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,QAAQ,EACf,MAAM,EAAE,SAAS,EACjB,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,IAAI,GAAG,CAAC,EAAE,CAAC;oBACnC,MAAM,CAAC,GACL,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,aAAa,CAAC,qBAAqB,EAAE,CAAC,IAAI,CAAA;oBAClE,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,cAAc,GAAG,CAAC,CAAC,CAAA;gBAClD,CAAC;YACH,CAAC,EACD,KAAK,EAAE;gBACL,OAAO,EAAE,OAAO;gBAChB,KAAK,EAAE,cAAc;gBACrB,MAAM,EAAE,kBAAkB;gBAC1B,SAAS,EAAE,YAAY;gBACvB,MAAM,EAAE,aAAa,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,EAAE;aACpD,GACD;QACF,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,OAAO,EACf,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,OAAO,EAC7B,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;gBACL,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACpB,MAAM,EAAE,kBAAkB;gBAC1B,KAAK,EAAE,CAAC;aACT,GACD;QAEF,6BAAK,MAAM,EAAE,aAAa,EAAE,KAAK,EAAE,cAAc;YAC/C,iCAAS,IAAI,EAAE,kBAAkB,EAAE,MAAM,EAAE,aAAa,GAAI,CACxD,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/minimap/MinimapSVG.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import { scrollbarThumbFill } from '../DragHandle.js';
 import { canvasHref, msaThumbnail } from '../msa/msaRaster.js';
-import { MINIMAP_BAR_HEIGHT, getMinimapLayout } from './minimapLayout.js';
+import { MINIMAP_BAR_HEIGHT, getMinimapLayout, minimapDomainRects, } from './minimapLayout.js';
 // The static counterpart to Minimap, for the SVG export. renderToSvg drives it
 // through renderToStaticMarkup, so it reads the model once and never re-renders
 // -- no observer wrapper.
@@ -13,6 +13,7 @@ export default function MinimapSVG({ model, theme, }) {
     const href = canvasHref(msaThumbnail({ model, theme, height: MINIMAP_BAR_HEIGHT }));
     return (React.createElement(React.Fragment, null,
         href ? (React.createElement("image", { href: href, x: 0, y: 0, width: msaCanvasWidth, height: MINIMAP_BAR_HEIGHT, preserveAspectRatio: "none" })) : null,
+        minimapDomainRects(model, msaCanvasWidth, MINIMAP_BAR_HEIGHT).map(({ x, y, w, h, fill }) => (React.createElement("rect", { key: `${x},${y},${w},${fill}`, x: x, y: y, width: w, height: h, fill: fill }))),
         React.createElement("rect", { x: 0, y: 0, width: msaCanvasWidth, height: MINIMAP_BAR_HEIGHT, stroke: theme.palette.text.secondary, fill: "none" }),
         React.createElement("rect", { x: Math.max(0, s), y: 0, width: w, height: MINIMAP_BAR_HEIGHT, fill: scrollbarThumbFill, stroke: theme.palette.text.secondary }),
         React.createElement("g", { transform: `translate(0 ${MINIMAP_BAR_HEIGHT})` },

package/dist/components/minimap/MinimapSVG.js.map

@@ -1 +1 @@
-{"version":3,"file":"MinimapSVG.js","sourceRoot":"","sources":["../../../src/components/minimap/MinimapSVG.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAmB,CAAA;AACtD,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAC9D,OAAO,EAAE,kBAAkB,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAKzE,+EAA+E;AAC/E,gFAAgF;AAChF,0BAA0B;AAC1B,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,KAAK,EACL,KAAK,GAIN;IACC,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,aAAa,EAAE,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAA;IACvD,0EAA0E;IAC1E,0EAA0E;IAC1E,MAAM,IAAI,GAAG,UAAU,CACrB,YAAY,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,kBAAkB,EAAE,CAAC,CAC3D,CAAA;IAED,OAAO,CACL;QACG,IAAI,CAAC,CAAC,CAAC,CACN,+BACE,IAAI,EAAE,IAAI,EACV,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,cAAc,EACrB,MAAM,EAAE,kBAAkB,EAC1B,mBAAmB,EAAC,MAAM,GAC1B,CACH,CAAC,CAAC,CAAC,IAAI;QACR,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,cAAc,EACrB,MAAM,EAAE,kBAAkB,EAC1B,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,EACpC,IAAI,EAAC,MAAM,GACX;QACF,8BACE,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EACjB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,CAAC,EACR,MAAM,EAAE,kBAAkB,EAC1B,IAAI,EAAE,kBAAkB,EACxB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC;QACF,2BAAG,SAAS,EAAE,eAAe,kBAAkB,GAAG;YAChD,iCAAS,IAAI,EAAE,kBAAkB,EAAE,MAAM,EAAE,aAAa,GAAI,CAC1D,CACH,CACJ,CAAA;AACH,CAAC"}
+{"version":3,"file":"MinimapSVG.js","sourceRoot":"","sources":["../../../src/components/minimap/MinimapSVG.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAmB,CAAA;AACtD,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAC9D,OAAO,EACL,kBAAkB,EAClB,gBAAgB,EAChB,kBAAkB,GACnB,MAAM,oBAAoB,CAAA;AAK3B,+EAA+E;AAC/E,gFAAgF;AAChF,0BAA0B;AAC1B,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,KAAK,EACL,KAAK,GAIN;IACC,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,aAAa,EAAE,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAA;IACvD,0EAA0E;IAC1E,0EAA0E;IAC1E,MAAM,IAAI,GAAG,UAAU,CACrB,YAAY,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,kBAAkB,EAAE,CAAC,CAC3D,CAAA;IAED,OAAO,CACL;QACG,IAAI,CAAC,CAAC,CAAC,CACN,+BACE,IAAI,EAAE,IAAI,EACV,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,cAAc,EACrB,MAAM,EAAE,kBAAkB,EAC1B,mBAAmB,EAAC,MAAM,GAC1B,CACH,CAAC,CAAC,CAAC,IAAI;QACP,kBAAkB,CAAC,KAAK,EAAE,cAAc,EAAE,kBAAkB,CAAC,CAAC,GAAG,CAChE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CACxB,8BACE,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,IAAI,EAAE,EAC7B,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,CAAC,EACR,MAAM,EAAE,CAAC,EACT,IAAI,EAAE,IAAI,GACV,CACH,CACF;QACD,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,cAAc,EACrB,MAAM,EAAE,kBAAkB,EAC1B,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,EACpC,IAAI,EAAC,MAAM,GACX;QACF,8BACE,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EACjB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,CAAC,EACR,MAAM,EAAE,kBAAkB,EAC1B,IAAI,EAAE,kBAAkB,EACxB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC;QACF,2BAAG,SAAS,EAAE,eAAe,kBAAkB,GAAG;YAChD,iCAAS,IAAI,EAAE,kBAAkB,EAAE,MAAM,EAAE,aAAa,GAAI,CAC1D,CACH,CACJ,CAAA;AACH,CAAC"}

package/dist/components/minimap/minimapLayout.d.ts

@@ -13,3 +13,15 @@ export declare function getMinimapLayout(model: MsaViewModel): {
     polygonHeight: number;
     polygonPoints: string;
 };
+/**
+ * The domain overlay's boxes scaled onto the minimap bar, one per row's band,
+ * in the colors the alignment draws them, so the overview shows the domains
+ * the alignment does. Empty unless the domains fill the cells.
+ */
+export declare function minimapDomainRects(model: MsaViewModel, width: number, height: number): {
+    x: number;
+    y: number;
+    w: number;
+    h: number;
+    fill: string;
+}[];