@jbrowse/plugin-linear-comparative-view 3.1.0 → 3.3.0

package/esm/LinearSyntenyView/components/ImportForm/LinearSyntenyImportForm.js

@@ -1,38 +1,21 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
-import { AssemblySelector, ErrorMessage } from '@jbrowse/core/ui';
-import { getSession, notEmpty } from '@jbrowse/core/util';
-import ArrowForwardIosIcon from '@mui/icons-material/ArrowForwardIos';
-import CloseIcon from '@mui/icons-material/Close';
-import { Button, Container, IconButton } from '@mui/material';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
+import { Container } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import ImportSyntenyTrackSelector from './ImportSyntenyTrackSelectorArea';
+import LeftPanel from './LeftPanel';
 import { doSubmit } from './doSubmit';
 const useStyles = makeStyles()(theme => ({
     importFormContainer: {
         padding: theme.spacing(4),
     },
-    button: {
-        margin: theme.spacing(2),
-    },
-    rel: {
-        position: 'relative',
-    },
-    synbutton: {
-        position: 'absolute',
-        top: 30,
-    },
     flex: {
         display: 'flex',
         gap: 90,
     },
-    mb: {
-        marginBottom: 10,
-    },
-    bg: {
-        background: theme.palette.divider,
-    },
     rightPanel: {
         flexGrow: 11,
     },
@@ -42,7 +25,7 @@ const useStyles = makeStyles()(theme => ({
     },
 }));
 const LinearSyntenyViewImportForm = observer(function ({ model, }) {
-    const { classes, cx } = useStyles();
+    const { classes } = useStyles();
     const session = getSession(model);
     const { assemblyNames } = session;
     const defaultAssemblyName = assemblyNames[0] || '';
@@ -52,38 +35,21 @@ const LinearSyntenyViewImportForm = observer(function ({ model, }) {
         defaultAssemblyName,
     ]);
     const [error, setError] = useState();
-    return (_jsxs(Container, { className: classes.importFormContainer, children: [error ? _jsx(ErrorMessage, { error: error }) : null, _jsxs("div", { className: classes.flex, children: [_jsxs("div", { className: classes.leftPanel, children: [_jsx("div", { className: classes.mb, children: "Select assemblies for linear synteny view" }), selectedAssemblyNames.map((assemblyName, idx) => (_jsxs("div", { className: classes.rel, children: [_jsxs("span", { children: ["Row ", idx + 1, ": "] }), _jsx(IconButton, { disabled: selectedAssemblyNames.length <= 2, onClick: () => {
-                                            model.importFormRemoveRow(idx);
-                                            setSelectedAssemblyNames(selectedAssemblyNames
-                                                .map((asm, idx2) => (idx2 === idx ? undefined : asm))
-                                                .filter(notEmpty));
-                                            if (selectedRow >= selectedAssemblyNames.length - 2) {
-                                                setSelectedRow(0);
-                                            }
-                                        }, children: _jsx(CloseIcon, {}) }), _jsx(AssemblySelector, { helperText: "", selected: assemblyName, onChange: newAssembly => {
-                                            setSelectedAssemblyNames(selectedAssemblyNames.map((asm, idx2) => idx2 === idx ? newAssembly : asm));
-                                        }, session: session }), idx !== selectedAssemblyNames.length - 1 ? (_jsx(IconButton, { "data-testid": "synbutton", className: cx(classes.synbutton, idx === selectedRow ? classes.bg : undefined), onClick: () => {
-                                            setSelectedRow(idx);
-                                        }, children: _jsx(ArrowForwardIosIcon, {}) })) : null] }, `${assemblyName}-${idx}`))), _jsxs("div", { children: [_jsx(Button, { className: classes.button, variant: "contained", color: "secondary", onClick: () => {
-                                            setSelectedAssemblyNames([
-                                                ...selectedAssemblyNames,
-                                                defaultAssemblyName,
-                                            ]);
-                                        }, children: "Add row" }), _jsx(Button, { className: classes.button, onClick: () => {
-                                            ;
-                                            (async () => {
-                                                try {
-                                                    setError(undefined);
-                                                    await doSubmit({
-                                                        selectedAssemblyNames,
-                                                        model,
-                                                    });
-                                                }
-                                                catch (e) {
-                                                    console.error(e);
-                                                    setError(e);
-                                                }
-                                            })();
-                                        }, variant: "contained", color: "primary", children: "Launch" })] })] }), _jsxs("div", { className: classes.rightPanel, children: [_jsxs("div", { children: ["Synteny dataset to display between row ", selectedRow + 1, " and", ' ', selectedRow + 2] }), _jsx(ImportSyntenyTrackSelector, { model: model, selectedRow: selectedRow, assembly1: selectedAssemblyNames[selectedRow], assembly2: selectedAssemblyNames[selectedRow + 1] })] })] })] }));
+    const handleLaunch = async () => {
+        try {
+            setError(undefined);
+            await doSubmit({
+                selectedAssemblyNames,
+                model,
+            });
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    };
+    return (_jsxs(Container, { className: classes.importFormContainer, children: [error ? _jsx(ErrorMessage, { error: error }) : null, _jsxs("div", { className: classes.flex, children: [_jsx("div", { className: classes.leftPanel, children: _jsx(LeftPanel, { model: model, selectedAssemblyNames: selectedAssemblyNames, setSelectedAssemblyNames: setSelectedAssemblyNames, selectedRow: selectedRow, setSelectedRow: setSelectedRow, defaultAssemblyName: defaultAssemblyName, onLaunch: () => {
+                                handleLaunch();
+                            } }) }), _jsxs("div", { className: classes.rightPanel, children: [_jsxs("div", { children: ["Synteny dataset to display between row ", selectedRow + 1, " and", ' ', selectedRow + 2] }), _jsx(ImportSyntenyTrackSelector, { model: model, selectedRow: selectedRow, assembly1: selectedAssemblyNames[selectedRow], assembly2: selectedAssemblyNames[selectedRow + 1] })] })] })] }));
 });
 export default LinearSyntenyViewImportForm;

package/esm/LinearSyntenyView/components/LinearSyntenyView.d.ts

@@ -1,6 +1,5 @@
 import type { LinearSyntenyViewModel } from '../model';
-type LSV = LinearSyntenyViewModel;
-declare const LinearSyntenyView: ({ model }: {
-    model: LSV;
+declare const LinearSyntenyView: ({ model, }: {
+    model: LinearSyntenyViewModel;
 }) => import("react/jsx-runtime").JSX.Element;
 export default LinearSyntenyView;

package/esm/LinearSyntenyView/components/LinearSyntenyView.js

@@ -3,7 +3,7 @@ import { lazy } from 'react';
 import { observer } from 'mobx-react';
 import LinearComparativeViewComponent from '../../LinearComparativeView/components/LinearComparativeView';
 const LinearSyntenyImportForm = lazy(() => import('./ImportForm/LinearSyntenyImportForm'));
-const LinearSyntenyView = observer(function ({ model }) {
+const LinearSyntenyView = observer(function ({ model, }) {
     return !model.initialized ? (_jsx(LinearSyntenyImportForm, { model: model })) : (_jsx(LinearComparativeViewComponent, { model: model }));
 });
 export default LinearSyntenyView;

package/esm/LinearSyntenyView/model.d.ts

@@ -66,6 +66,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        init: import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
     }, {
         width: number;
     } & {
@@ -94,6 +95,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
         readonly stickyViewHeaders: boolean;
+        readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
         scaleBarDisplayPrefix(): string | undefined;
@@ -180,6 +182,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
+        setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
         exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
@@ -200,7 +203,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly coarseVisibleLocStrings: string;
     } & {
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
-        afterAttach(): void;
     } & {
         moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         navToLocString(input: string, optAssemblyName?: string): Promise<void>;
@@ -208,6 +210,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             input: string;
             assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
         navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
         navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
@@ -246,6 +249,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         } | undefined;
     } & {
         afterCreate(): void;
+        afterAttach(): void;
     }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -268,7 +272,28 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    }>>, import("mobx-state-tree")._NotCustomized>>;
+        init: import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
+    }>>, {
+        id: string;
+        type: string;
+        displayName: string | undefined;
+        tracks: any[];
+        minimized: boolean;
+        displayedRegions: import("@jbrowse/core/util").Region[];
+        offsetPx: number;
+        bpPerPx: number;
+        hideHeader: boolean;
+        hideHeaderOverview: boolean;
+        hideNoTracksActive: boolean;
+        trackSelectorType: string;
+        showCenterLine: boolean;
+        showCytobandsSetting: boolean;
+        trackLabels: string;
+        showGridlines: boolean;
+        highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
+        colorByCDS: boolean;
+        showTrackOutlines: boolean;
+    }>>;
     viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearSyntenyView">;
@@ -336,10 +361,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         type?: undefined;
     } | {
         label: string;
-        onClick: () => void;
         checked: boolean;
         type: string;
         description: string;
+        onClick: () => void;
         icon?: undefined;
     } | {
         label: string;
@@ -423,6 +448,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        init: import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
     }, {
         width: number;
     } & {
@@ -451,6 +477,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
         readonly stickyViewHeaders: boolean;
+        readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
         scaleBarDisplayPrefix(): string | undefined;
@@ -537,6 +564,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
+        setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
         exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
@@ -557,7 +585,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly coarseVisibleLocStrings: string;
     } & {
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
-        afterAttach(): void;
     } & {
         moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         navToLocString(input: string, optAssemblyName?: string): Promise<void>;
@@ -565,6 +592,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             input: string;
             assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
         navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
         navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
@@ -603,6 +631,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         } | undefined;
     } & {
         afterCreate(): void;
+        afterAttach(): void;
     }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -625,7 +654,28 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    }>>, import("mobx-state-tree")._NotCustomized>>;
+        init: import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
+    }>>, {
+        id: string;
+        type: string;
+        displayName: string | undefined;
+        tracks: any[];
+        minimized: boolean;
+        displayedRegions: import("@jbrowse/core/util").Region[];
+        offsetPx: number;
+        bpPerPx: number;
+        hideHeader: boolean;
+        hideHeaderOverview: boolean;
+        hideNoTracksActive: boolean;
+        trackSelectorType: string;
+        showCenterLine: boolean;
+        showCytobandsSetting: boolean;
+        trackLabels: string;
+        showGridlines: boolean;
+        highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
+        colorByCDS: boolean;
+        showTrackOutlines: boolean;
+    }>>;
     viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type LinearSyntenyViewStateModel = ReturnType<typeof stateModelFactory>;

package/esm/LinearSyntenyView/model.js

@@ -73,12 +73,12 @@ export default function stateModelFactory(pluginManager) {
                     },
                     {
                         label: 'Draw CIGAR',
-                        onClick: () => {
-                            self.setDrawCIGAR(!self.drawCIGAR);
-                        },
                         checked: self.drawCIGAR,
                         type: 'checkbox',
                         description: 'Draws per-base CIGAR level alignments',
+                        onClick: () => {
+                            self.setDrawCIGAR(!self.drawCIGAR);
+                        },
                     },
                     {
                         label: 'Link views',

package/esm/LinearSyntenyViewHelper/stateModelFactory.js

@@ -48,9 +48,9 @@ export function linearSyntenyViewHelperModelFactory(pluginManager) {
             const config = resolveIdentifier(schema, getRoot(self), trackId);
             const shownTracks = self.tracks.filter(t => t.configuration === config);
             transaction(() => {
-                shownTracks.forEach(t => {
+                for (const t of shownTracks) {
                     self.tracks.remove(t);
-                });
+                }
             });
             return shownTracks.length;
         },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "3.1.0",
+  "version": "3.3.0",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -36,11 +36,11 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.1.0",
-    "@jbrowse/plugin-alignments": "^3.1.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.1.0",
-    "@mui/icons-material": "^6.0.0",
-    "@mui/material": "^6.0.0",
+    "@jbrowse/core": "^3.3.0",
+    "@jbrowse/plugin-alignments": "^3.3.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.3.0",
+    "@mui/icons-material": "^7.0.0",
+    "@mui/material": "^7.0.0",
     "copy-to-clipboard": "^3.3.1",
     "file-saver": "^2.0.0",
     "mobx": "^6.0.0",
@@ -59,5 +59,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
+  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
 }