npm - @jbrowse/plugin-linear-comparative-view - Versions diffs - 3.0.5 → 3.2.0 - Mend

@jbrowse/plugin-linear-comparative-view 3.0.5 → 3.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (27) hide show

package/dist/LinearComparativeView/components/Rubberband.js CHANGED Viewed

@@ -18,7 +18,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
             height: '100%',
             background: (0, material_1.alpha)(theme.palette.tertiary.main, 0.7),
             position: 'absolute',
-            zIndex: 10,
+            zIndex: 900,
             textAlign: 'center',
             overflow: 'hidden',
         },
@@ -81,13 +81,13 @@ const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberba
                     clientY,
                 });
                 (0, mobx_1.transaction)(() => {
-                    model.views.forEach(view => {
+                    for (const view of model.views) {
                         const args = computeOffsets(offsetX, view);
                         if (args) {
                             const { leftOffset, rightOffset } = args;
                             view.setOffsets(leftOffset, rightOffset);
                         }
-                    });
+                    }
                 });
                 setGuideX(undefined);
             }
@@ -125,9 +125,9 @@ const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberba
     function mouseOut() {
         setGuideX(undefined);
         (0, mobx_1.transaction)(() => {
-            model.views.forEach(view => {
+            for (const view of model.views) {
                 view.setOffsets(undefined, undefined);
-            });
+            }
         });
     }
     function handleClose() {

package/dist/LinearComparativeView/components/VerticalGuide.js CHANGED Viewed

@@ -11,19 +11,16 @@ const useStyles = (0, mui_1.makeStyles)()({
         height: '100%',
         width: 1,
         position: 'absolute',
-        zIndex: 10,
-    },
-    sm: {
-        fontSize: 10,
+        background: 'red',
+        zIndex: 1001,
     },
 });
 const VerticalGuide = (0, mobx_react_1.observer)(function ({ model, coordX, }) {
     const { classes } = useStyles();
     return ((0, jsx_runtime_1.jsx)(material_1.Tooltip, { open: true, placement: "top", title: model.views
             .map(view => view.pxToBp(coordX))
-            .map((elt, idx) => ((0, jsx_runtime_1.jsx)(material_1.Typography, { className: classes.sm, children: (0, util_1.stringify)(elt, true) }, [JSON.stringify(elt), idx].join('-')))), arrow: true, children: (0, jsx_runtime_1.jsx)("div", { className: classes.guide, style: {
+            .map((elt, idx) => ((0, jsx_runtime_1.jsx)("div", { children: (0, util_1.stringify)(elt, true) }, [JSON.stringify(elt), idx].join('-')))), arrow: true, children: (0, jsx_runtime_1.jsx)("div", { className: classes.guide, style: {
                 left: coordX,
-                background: 'red',
             } }) }));
 });
 exports.default = VerticalGuide;

package/dist/LinearComparativeView/model.d.ts CHANGED Viewed

@@ -49,6 +49,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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;
     } & {
@@ -70,10 +71,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
         rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
+        readonly pinnedTracks: any[];
+        readonly unpinnedTracks: any[];
         readonly trackLabelsSetting: any;
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
+        readonly stickyViewHeaders: boolean;
+        readonly rubberbandTop: number;
+        readonly pinnedTracksTop: number;
     } & {
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
@@ -159,6 +165,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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;
@@ -179,7 +186,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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>;
@@ -225,6 +231,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         } | 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>>;
@@ -247,7 +254,28 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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>;
 }, {
     width: number;
@@ -335,6 +363,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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;
     } & {
@@ -356,10 +385,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
         rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
+        readonly pinnedTracks: any[];
+        readonly unpinnedTracks: any[];
         readonly trackLabelsSetting: any;
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
+        readonly stickyViewHeaders: boolean;
+        readonly rubberbandTop: number;
+        readonly pinnedTracksTop: number;
     } & {
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
@@ -445,6 +479,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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;
@@ -465,7 +500,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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>;
@@ -511,6 +545,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         } | 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>>;
@@ -533,7 +568,28 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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")._NotCustomized>;
 export type LinearComparativeViewStateModel = ReturnType<typeof stateModelFactory>;

package/dist/LinearComparativeView/model.js CHANGED Viewed

@@ -102,18 +102,23 @@ function stateModelFactory(pluginManager) {
             }
         },
         onSubviewAction(actionName, path, args) {
-            self.views.forEach(view => {
+            for (const view of self.views) {
                 const ret = (0, mobx_state_tree_1.getPath)(view);
                 if (!ret.endsWith(path)) {
                     view[actionName](args === null || args === void 0 ? void 0 : args[0]);
                 }
-            });
+            }
         },
         setWidth(newWidth) {
             self.width = newWidth;
         },
         setViews(views) {
             self.views = (0, mobx_state_tree_1.cast)(views);
+            const levels = [];
+            for (let i = 0; i < views.length - 1; i++) {
+                levels.push({ level: i });
+            }
+            self.levels = (0, mobx_state_tree_1.cast)(levels);
         },
         removeView(view) {
             self.views.remove(view);

package/dist/LinearReadVsRef/LinearReadVsRef.js CHANGED Viewed

@@ -101,12 +101,12 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
             };
             const totalLength = flags & 2048 ? getLength(suppAlns[0].CIGAR) : getLength(cigar);
             const features = [feat, ...suppAlns];
-            features.forEach((f, idx) => {
+            for (const [idx, f] of features.entries()) {
                 f.refName = assembly.getCanonicalRefName(f.refName) || f.refName;
                 f.syntenyId = idx;
                 f.mate.syntenyId = idx;
                 f.mate.uniqueId = `${f.uniqueId}_mate`;
-            });
+            }
             features.sort((a, b) => a.clipPos - b.clipPos);
             const featSeq = feature.get('seq');
             const configFeatureStore = [...features, ...features.map(f => f.mate)];

package/dist/LinearSyntenyView/components/ImportForm/LeftPanel.d.ts ADDED Viewed

@@ -0,0 +1,11 @@
+import type { LinearSyntenyViewModel } from '../../model';
+declare const LeftPanel: ({ model, selectedAssemblyNames, setSelectedAssemblyNames, selectedRow, setSelectedRow, defaultAssemblyName, onLaunch, }: {
+    model: LinearSyntenyViewModel;
+    selectedAssemblyNames: string[];
+    setSelectedAssemblyNames: (names: string[]) => void;
+    selectedRow: number;
+    setSelectedRow: (row: number) => void;
+    defaultAssemblyName: string;
+    onLaunch: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default LeftPanel;

package/dist/LinearSyntenyView/components/ImportForm/LeftPanel.js ADDED Viewed

@@ -0,0 +1,58 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const ArrowForwardIos_1 = __importDefault(require("@mui/icons-material/ArrowForwardIos"));
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    mb: {
+        marginBottom: 10,
+    },
+    button: {
+        margin: theme.spacing(2),
+    },
+    rel: {
+        position: 'relative',
+    },
+    synbutton: {
+        position: 'absolute',
+        top: 30,
+    },
+    bg: {
+        background: theme.palette.divider,
+    },
+}));
+const AssemblyRows = (0, mobx_react_1.observer)(function ({ selectedRow, selectedAssemblyNames, setSelectedRow, setSelectedAssemblyNames, model, }) {
+    const { classes, cx } = useStyles();
+    const session = (0, util_1.getSession)(model);
+    return selectedAssemblyNames.map((assemblyName, idx) => ((0, jsx_runtime_1.jsxs)("div", { className: classes.rel, children: [(0, jsx_runtime_1.jsxs)("span", { children: ["Row ", idx + 1, ": "] }), (0, jsx_runtime_1.jsx)(material_1.IconButton, { disabled: selectedAssemblyNames.length <= 2, onClick: () => {
+                    model.importFormRemoveRow(idx);
+                    setSelectedAssemblyNames(selectedAssemblyNames
+                        .map((asm, idx2) => (idx2 === idx ? undefined : asm))
+                        .filter(util_1.notEmpty));
+                    if (selectedRow >= selectedAssemblyNames.length - 2) {
+                        setSelectedRow(0);
+                    }
+                }, children: (0, jsx_runtime_1.jsx)(Close_1.default, {}) }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "", selected: assemblyName, onChange: newAssembly => {
+                    setSelectedAssemblyNames(selectedAssemblyNames.map((asm, idx2) => idx2 === idx ? newAssembly : asm));
+                }, session: session }), idx !== selectedAssemblyNames.length - 1 ? ((0, jsx_runtime_1.jsx)(material_1.IconButton, { "data-testid": "synbutton", className: cx(classes.synbutton, idx === selectedRow ? classes.bg : undefined), onClick: () => {
+                    setSelectedRow(idx);
+                }, children: (0, jsx_runtime_1.jsx)(ArrowForwardIos_1.default, {}) })) : null] }, `${assemblyName}-${idx}`)));
+});
+const LeftPanel = (0, mobx_react_1.observer)(function ({ model, selectedAssemblyNames, setSelectedAssemblyNames, selectedRow, setSelectedRow, defaultAssemblyName, onLaunch, }) {
+    const { classes } = useStyles();
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", { className: classes.mb, children: "Select assemblies for linear synteny view" }), (0, jsx_runtime_1.jsx)(AssemblyRows, { model: model, selectedAssemblyNames: selectedAssemblyNames, setSelectedAssemblyNames: setSelectedAssemblyNames, selectedRow: selectedRow, setSelectedRow: setSelectedRow }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { className: classes.button, variant: "contained", color: "secondary", onClick: () => {
+                            setSelectedAssemblyNames([
+                                ...selectedAssemblyNames,
+                                defaultAssemblyName,
+                            ]);
+                        }, children: "Add row" }), (0, jsx_runtime_1.jsx)(material_1.Button, { className: classes.button, onClick: onLaunch, variant: "contained", color: "primary", children: "Launch" })] })] }));
+});
+exports.default = LeftPanel;

package/dist/LinearSyntenyView/components/ImportForm/LinearSyntenyImportForm.js CHANGED Viewed

@@ -7,37 +7,20 @@ const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
-const ArrowForwardIos_1 = __importDefault(require("@mui/icons-material/ArrowForwardIos"));
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
 const ImportSyntenyTrackSelectorArea_1 = __importDefault(require("./ImportSyntenyTrackSelectorArea"));
+const LeftPanel_1 = __importDefault(require("./LeftPanel"));
 const doSubmit_1 = require("./doSubmit");
 const useStyles = (0, mui_1.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,
     },
@@ -47,7 +30,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
     },
 }));
 const LinearSyntenyViewImportForm = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes, cx } = useStyles();
+    const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const { assemblyNames } = session;
     const defaultAssemblyName = assemblyNames[0] || '';
@@ -57,38 +40,21 @@ const LinearSyntenyViewImportForm = (0, mobx_react_1.observer)(function ({ model
         defaultAssemblyName,
     ]);
     const [error, setError] = (0, react_1.useState)();
-    return ((0, jsx_runtime_1.jsxs)(material_1.Container, { className: classes.importFormContainer, children: [error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsxs)("div", { className: classes.flex, children: [(0, jsx_runtime_1.jsxs)("div", { className: classes.leftPanel, children: [(0, jsx_runtime_1.jsx)("div", { className: classes.mb, children: "Select assemblies for linear synteny view" }), selectedAssemblyNames.map((assemblyName, idx) => ((0, jsx_runtime_1.jsxs)("div", { className: classes.rel, children: [(0, jsx_runtime_1.jsxs)("span", { children: ["Row ", idx + 1, ": "] }), (0, jsx_runtime_1.jsx)(material_1.IconButton, { disabled: selectedAssemblyNames.length <= 2, onClick: () => {
-                                            model.importFormRemoveRow(idx);
-                                            setSelectedAssemblyNames(selectedAssemblyNames
-                                                .map((asm, idx2) => (idx2 === idx ? undefined : asm))
-                                                .filter(util_1.notEmpty));
-                                            if (selectedRow >= selectedAssemblyNames.length - 2) {
-                                                setSelectedRow(0);
-                                            }
-                                        }, children: (0, jsx_runtime_1.jsx)(Close_1.default, {}) }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "", selected: assemblyName, onChange: newAssembly => {
-                                            setSelectedAssemblyNames(selectedAssemblyNames.map((asm, idx2) => idx2 === idx ? newAssembly : asm));
-                                        }, session: session }), idx !== selectedAssemblyNames.length - 1 ? ((0, jsx_runtime_1.jsx)(material_1.IconButton, { "data-testid": "synbutton", className: cx(classes.synbutton, idx === selectedRow ? classes.bg : undefined), onClick: () => {
-                                            setSelectedRow(idx);
-                                        }, children: (0, jsx_runtime_1.jsx)(ArrowForwardIos_1.default, {}) })) : null] }, `${assemblyName}-${idx}`))), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { className: classes.button, variant: "contained", color: "secondary", onClick: () => {
-                                            setSelectedAssemblyNames([
-                                                ...selectedAssemblyNames,
-                                                defaultAssemblyName,
-                                            ]);
-                                        }, children: "Add row" }), (0, jsx_runtime_1.jsx)(material_1.Button, { className: classes.button, onClick: () => {
-                                            ;
-                                            (async () => {
-                                                try {
-                                                    setError(undefined);
-                                                    await (0, doSubmit_1.doSubmit)({
-                                                        selectedAssemblyNames,
-                                                        model,
-                                                    });
-                                                }
-                                                catch (e) {
-                                                    console.error(e);
-                                                    setError(e);
-                                                }
-                                            })();
-                                        }, variant: "contained", color: "primary", children: "Launch" })] })] }), (0, jsx_runtime_1.jsxs)("div", { className: classes.rightPanel, children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Synteny dataset to display between row ", selectedRow + 1, " and", ' ', selectedRow + 2] }), (0, jsx_runtime_1.jsx)(ImportSyntenyTrackSelectorArea_1.default, { model: model, selectedRow: selectedRow, assembly1: selectedAssemblyNames[selectedRow], assembly2: selectedAssemblyNames[selectedRow + 1] })] })] })] }));
+    const handleLaunch = async () => {
+        try {
+            setError(undefined);
+            await (0, doSubmit_1.doSubmit)({
+                selectedAssemblyNames,
+                model,
+            });
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    };
+    return ((0, jsx_runtime_1.jsxs)(material_1.Container, { className: classes.importFormContainer, children: [error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsxs)("div", { className: classes.flex, children: [(0, jsx_runtime_1.jsx)("div", { className: classes.leftPanel, children: (0, jsx_runtime_1.jsx)(LeftPanel_1.default, { model: model, selectedAssemblyNames: selectedAssemblyNames, setSelectedAssemblyNames: setSelectedAssemblyNames, selectedRow: selectedRow, setSelectedRow: setSelectedRow, defaultAssemblyName: defaultAssemblyName, onLaunch: () => {
+                                handleLaunch();
+                            } }) }), (0, jsx_runtime_1.jsxs)("div", { className: classes.rightPanel, children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Synteny dataset to display between row ", selectedRow + 1, " and", ' ', selectedRow + 2] }), (0, jsx_runtime_1.jsx)(ImportSyntenyTrackSelectorArea_1.default, { model: model, selectedRow: selectedRow, assembly1: selectedAssemblyNames[selectedRow], assembly2: selectedAssemblyNames[selectedRow + 1] })] })] })] }));
 });
 exports.default = LinearSyntenyViewImportForm;

package/dist/LinearSyntenyView/components/LinearSyntenyView.d.ts CHANGED Viewed

@@ -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/dist/LinearSyntenyView/components/LinearSyntenyView.js CHANGED Viewed

@@ -41,7 +41,7 @@ const react_1 = require("react");
 const mobx_react_1 = require("mobx-react");
 const LinearComparativeView_1 = __importDefault(require("../../LinearComparativeView/components/LinearComparativeView"));
 const LinearSyntenyImportForm = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ImportForm/LinearSyntenyImportForm'))));
-const LinearSyntenyView = (0, mobx_react_1.observer)(function ({ model }) {
+const LinearSyntenyView = (0, mobx_react_1.observer)(function ({ model, }) {
     return !model.initialized ? ((0, jsx_runtime_1.jsx)(LinearSyntenyImportForm, { model: model })) : ((0, jsx_runtime_1.jsx)(LinearComparativeView_1.default, { model: model }));
 });
 exports.default = LinearSyntenyView;

package/dist/LinearSyntenyView/model.d.ts CHANGED Viewed

@@ -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;
     } & {
@@ -87,10 +88,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
         rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
+        readonly pinnedTracks: any[];
+        readonly unpinnedTracks: any[];
         readonly trackLabelsSetting: any;
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
+        readonly stickyViewHeaders: boolean;
+        readonly rubberbandTop: number;
+        readonly pinnedTracksTop: number;
     } & {
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
@@ -176,6 +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;
@@ -196,7 +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>;
@@ -242,6 +248,7 @@ 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>>;
@@ -264,7 +271,28 @@ 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">;
@@ -332,10 +360,10 @@ 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;
@@ -419,6 +447,7 @@ 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;
     } & {
@@ -440,10 +469,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
         rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
+        readonly pinnedTracks: any[];
+        readonly unpinnedTracks: any[];
         readonly trackLabelsSetting: any;
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
+        readonly stickyViewHeaders: boolean;
+        readonly rubberbandTop: number;
+        readonly pinnedTracksTop: number;
     } & {
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
@@ -529,6 +563,7 @@ 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;
@@ -549,7 +584,6 @@ 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>;
@@ -595,6 +629,7 @@ 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>>;
@@ -617,7 +652,28 @@ 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>;