@jbrowse/plugin-linear-comparative-view 3.5.1 → 3.6.0

package/dist/LinearSyntenyDisplay/components/Component.js

@@ -4,62 +4,23 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
 const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
+const BlockError_1 = __importDefault(require("./BlockError"));
+const BlockMessage_1 = __importDefault(require("./BlockMessage"));
 const LinearSyntenyRendering_1 = __importDefault(require("./LinearSyntenyRendering"));
-const useStyles = (0, mui_1.makeStyles)()(theme => {
-    const bg = theme.palette.action.disabledBackground;
-    return {
-        loading: {
-            paddingLeft: '0.6em',
-            backgroundColor: theme.palette.background.default,
-            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
-            textAlign: 'center',
-        },
-        blockMessage: {
-            background: '#f1f1f1',
-            padding: 10,
-        },
-        blockError: {
-            background: '#f1f1f1',
-            padding: 10,
-            color: 'red',
-        },
-    };
-});
-function LoadingMessage() {
-    const [shown, setShown] = (0, react_1.useState)(false);
-    const { classes } = useStyles();
-    (0, react_1.useEffect)(() => {
-        const timeout = setTimeout(() => {
-            setShown(true);
-        }, 300);
-        return () => {
-            clearTimeout(timeout);
-        };
-    });
-    return shown ? ((0, jsx_runtime_1.jsx)("div", { className: classes.loading, children: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, {}) })) : null;
-}
-function BlockMessage({ messageText }) {
-    const { classes } = useStyles();
-    return (0, jsx_runtime_1.jsx)("div", { className: classes.blockMessage, children: messageText });
-}
-function BlockError({ error }) {
-    const { classes } = useStyles();
-    return (0, jsx_runtime_1.jsx)("div", { className: classes.blockError, children: `${error}` });
-}
+const LoadingMessage_1 = __importDefault(require("./LoadingMessage"));
 const ServerSideRenderedBlockContent = (0, mobx_react_1.observer)(function ({ model, }) {
     if (model.error) {
-        return (0, jsx_runtime_1.jsx)(BlockError, { error: model.error });
+        return (0, jsx_runtime_1.jsx)(BlockError_1.default, { error: model.error });
+    }
+    else if (model.message) {
+        return (0, jsx_runtime_1.jsx)(BlockMessage_1.default, { messageText: model.message });
     }
-    if (model.message) {
-        return (0, jsx_runtime_1.jsx)(BlockMessage, { messageText: model.message });
+    else if (!model.features) {
+        return (0, jsx_runtime_1.jsx)(LoadingMessage_1.default, { message: model.loadingStatus });
     }
-    if (!model.features) {
-        return (0, jsx_runtime_1.jsx)(LoadingMessage, {});
+    else {
+        return (0, jsx_runtime_1.jsx)(LinearSyntenyRendering_1.default, { model: model });
     }
-    return (0, jsx_runtime_1.jsx)(LinearSyntenyRendering_1.default, { model: model });
 });
 exports.default = ServerSideRenderedBlockContent;

package/dist/LinearSyntenyDisplay/components/LoadingMessage.d.ts

@@ -0,0 +1,3 @@
+export default function LoadingMessage({ message }: {
+    message?: string;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/LinearSyntenyDisplay/components/LoadingMessage.js

@@ -0,0 +1,21 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LoadingMessage;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const ui_1 = require("@jbrowse/core/ui");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()(theme => {
+    const bg = theme.palette.action.disabledBackground;
+    return {
+        loading: {
+            paddingLeft: '0.6em',
+            backgroundColor: theme.palette.background.default,
+            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
+            textAlign: 'center',
+        },
+    };
+});
+function LoadingMessage({ message }) {
+    const { classes } = useStyles();
+    return ((0, jsx_runtime_1.jsx)("div", { className: classes.loading, children: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: message }) }));
+}

package/dist/LinearSyntenyDisplay/model.d.ts

@@ -84,6 +84,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     renderInProgress: string | undefined;
     features: Feature[] | undefined;
     message: string | undefined;
+    loadingStatus: string | undefined;
 } & {
     readonly level: number;
     readonly height: number;
@@ -166,6 +167,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             renderInProgress: string | undefined;
             features: Feature[] | undefined;
             message: string | undefined;
+            loadingStatus: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -235,12 +237,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             renderInProgress: string | undefined;
             features: Feature[] | undefined;
             message: string | undefined;
+            loadingStatus: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         highResolutionScaling: number;
     };
 } & {
     setLoading(newStopToken: string): void;
     setMessage(messageText: string): void;
+    setLoadingStatus(messageText: string): void;
     setRendered(args?: {
         features: Feature[];
     }): void;

package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.js

@@ -1,15 +1,12 @@
 "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 react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
-const Help_1 = __importDefault(require("@mui/icons-material/Help"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const getAdapter_1 = require("./getAdapter");
+const selectors_1 = require("./selectors");
 const util_1 = require("./util");
 const ImportSyntenyOpenCustomTrack = (0, mobx_react_1.observer)(function ({ model, assembly1, assembly2, selectedRow, }) {
     const [swap, setSwap] = (0, react_1.useState)(false);
@@ -64,13 +61,6 @@ const ImportSyntenyOpenCustomTrack = (0, mobx_react_1.observer)(function ({ mode
         indexFileLocation,
         radioOption,
     ]);
-    const helpStrings = {
-        '.paf': 'minimap2 target.fa query.fa',
-        '.pif.gz': 'minimap2 target.fa query.fa',
-        '.out': 'mashmap target.fa query.fa',
-        '.delta': 'mummer target.fa query.fa',
-        '.chain': 'e.g. queryToTarget.chain',
-    };
     return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 12 }, children: [error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)(material_1.Typography, { style: { textAlign: 'center' }, children: "Add a .paf (minimap2), .delta (Mummer), .chain (UCSC liftover), .anchors or .anchors.simple (MCScan), or .pif.gz (jbrowse CLI make-pif) file to view. These file types can also be gzipped." }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { value: radioOption, onChange: event => {
                     setValue(event.target.value);
                 }, children: (0, jsx_runtime_1.jsx)(material_1.Grid, { container: true, justifyContent: "center", children: [
@@ -84,46 +74,7 @@ const ImportSyntenyOpenCustomTrack = (0, mobx_react_1.observer)(function ({ mode
                     ].map(extension => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: extension, control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: extension }, extension))) }) }), (0, jsx_runtime_1.jsx)(material_1.Grid, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
                     radioOption === '.out' ||
                     radioOption === '.delta' ||
-                    radioOption === '.chain' ||
-                    radioOption === '.pif.gz' ? ((0, jsx_runtime_1.jsxs)("div", { style: {
-                        display: 'flex',
-                        flexDirection: 'column',
-                        gap: 10,
-                    }, children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${radioOption} location`, inline: true, description: "", location: fileLocation, setLocation: loc => {
-                                setFileLocation(loc);
-                            } }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Verify or click swap", (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: (0, jsx_runtime_1.jsx)("code", { children: helpStrings[radioOption] }), children: (0, jsx_runtime_1.jsx)(Help_1.default, {}) })] }), (0, jsx_runtime_1.jsxs)("div", { style: {
-                                        display: 'flex',
-                                        gap: 20,
-                                    }, children: [(0, jsx_runtime_1.jsxs)("div", { style: {
-                                                display: 'grid',
-                                                gridTemplateColumns: '1fr 1fr',
-                                                gap: 4,
-                                                alignItems: 'center',
-                                            }, children: [(0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)("i", { children: swap ? assembly2 : assembly1 }) }), (0, jsx_runtime_1.jsx)("div", { children: "query assembly" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)("i", { children: swap ? assembly1 : assembly2 }) }), (0, jsx_runtime_1.jsx)("div", { children: "target assembly" })] }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                setSwap(!swap);
-                                            }, children: "Swap?" })] })] })] })) : value === '.anchors' || value === '.anchors.simple' ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: { margin: 20 }, children: ["Open the ", value, " and .bed files for both genome assemblies from the MCScan (Python version) pipeline", ' ', (0, jsx_runtime_1.jsx)("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)", children: "(more info)" })] }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: value, location: fileLocation, setLocation: loc => {
-                                        setFileLocation(loc);
-                                    } }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => {
-                                        setBed1Location(loc);
-                                    } }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
-                                        setBed2Location(loc);
-                                    } })] }), (0, jsx_runtime_1.jsxs)("div", { style: {
-                                margin: 'auto',
-                                display: 'flex',
-                                justifyContent: 'center',
-                                gap: 20,
-                            }, children: [(0, jsx_runtime_1.jsxs)("div", { style: {
-                                        display: 'grid',
-                                        gridTemplateColumns: '1fr 1fr',
-                                        gap: 4,
-                                        alignItems: 'center',
-                                    }, children: [(0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)("i", { children: swap ? assembly2 : assembly1 }) }), (0, jsx_runtime_1.jsx)("div", { children: "bed1 assembly" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)("i", { children: swap ? assembly1 : assembly2 }) }), (0, jsx_runtime_1.jsx)("div", { children: "bed2 assembly" })] }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                        setSwap(!swap);
-                                    }, children: "Swap?" })] })] })) : value === '.pif.gz' ? ((0, jsx_runtime_1.jsxs)("div", { style: { display: 'flex' }, children: [(0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${value} location`, description: "", location: fileLocation, setLocation: loc => {
-                                    setFileLocation(loc);
-                                } }) }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${value} index location`, description: "", location: indexFileLocation, setLocation: loc => {
-                                    setIndexFileLocation(loc);
-                                } }) })] })) : ((0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
+                    radioOption === '.chain' ? ((0, jsx_runtime_1.jsx)(selectors_1.StandardFormatSelector, { assembly1: assembly1, assembly2: assembly2, swap: swap, setSwap: setSwap, fileLocation: fileLocation, setFileLocation: setFileLocation, radioOption: radioOption })) : radioOption === '.pif.gz' ? ((0, jsx_runtime_1.jsx)(selectors_1.PifGzSelector, { assembly1: assembly1, assembly2: assembly2, swap: swap, setSwap: setSwap, fileLocation: fileLocation, setFileLocation: setFileLocation, indexFileLocation: indexFileLocation, setIndexFileLocation: setIndexFileLocation, radioOption: radioOption })) : value === '.anchors' || value === '.anchors.simple' ? ((0, jsx_runtime_1.jsx)(selectors_1.AnchorsSelector, { assembly1: assembly1, assembly2: assembly2, swap: swap, setSwap: setSwap, fileLocation: fileLocation, setFileLocation: setFileLocation, bed1Location: bed1Location, setBed1Location: setBed1Location, bed2Location: bed2Location, setBed2Location: setBed2Location, radioOption: value })) : ((0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
                         setFileLocation(loc);
                     } })) })] }));
 });

package/dist/LinearSyntenyView/components/ImportForm/selectors/AnchorsSelector.d.ts

@@ -0,0 +1,3 @@
+import type { SelectorProps } from './SelectorTypes';
+declare const AnchorsSelector: ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, bed1Location, setBed1Location, bed2Location, setBed2Location, radioOption, }: SelectorProps) => import("react/jsx-runtime").JSX.Element;
+export default AnchorsSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/AnchorsSelector.js

@@ -0,0 +1,13 @@
+"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 mobx_react_1 = require("mobx-react");
+const SwapAssemblies_1 = __importDefault(require("./SwapAssemblies"));
+const AnchorsSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, bed1Location = undefined, setBed1Location = () => { }, bed2Location = undefined, setBed2Location = () => { }, radioOption, }) {
+    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: { margin: 20 }, children: ["Open the ", radioOption, " and .bed files for both genome assemblies from the MCScan (Python version) pipeline", ' ', (0, jsx_runtime_1.jsx)("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)", children: "(more info)" })] }), (0, jsx_runtime_1.jsxs)("div", { style: { maxWidth: 400, margin: '0 auto' }, children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: radioOption, location: fileLocation, setLocation: setFileLocation }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: setBed1Location }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: setBed2Location }), (0, jsx_runtime_1.jsx)(SwapAssemblies_1.default, { swap: swap, radioOption: radioOption, assembly1: assembly1, assembly2: assembly2, setSwap: setSwap, text1: "bed 1 assembly", text2: "bed 2 assembly" })] })] }));
+});
+exports.default = AnchorsSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/PifGzSelector.d.ts

@@ -0,0 +1,3 @@
+import type { SelectorProps } from './SelectorTypes';
+declare const PifGzSelector: ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, indexFileLocation, setIndexFileLocation, radioOption, }: SelectorProps) => import("react/jsx-runtime").JSX.Element;
+export default PifGzSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/PifGzSelector.js

@@ -0,0 +1,13 @@
+"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 mobx_react_1 = require("mobx-react");
+const SwapAssemblies_1 = __importDefault(require("./SwapAssemblies"));
+const PifGzSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, indexFileLocation = undefined, setIndexFileLocation = () => { }, radioOption, }) {
+    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: { margin: 20 }, children: ["Open the ", radioOption, " and .pif.gz and index file (.pif.gz.tbi or .pif.gz.csi) files for created by `jbrowse make-pif`"] }), (0, jsx_runtime_1.jsxs)("div", { style: { maxWidth: 400, margin: '0 auto' }, children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${radioOption} location`, inline: true, description: "", location: fileLocation, setLocation: setFileLocation }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${radioOption} index location`, inline: true, description: "", location: indexFileLocation, setLocation: setIndexFileLocation }), (0, jsx_runtime_1.jsx)(SwapAssemblies_1.default, { swap: swap, radioOption: radioOption, assembly1: assembly1, assembly2: assembly2, setSwap: setSwap, text1: "query assembly", text2: "target assembly" })] })] }));
+});
+exports.default = PifGzSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/SelectorTypes.d.ts

@@ -0,0 +1,19 @@
+import type { FileLocation } from '@jbrowse/core/util/types';
+export interface SelectorProps {
+    assembly1: string;
+    assembly2: string;
+    swap: boolean;
+    setSwap?: (swap: boolean) => void;
+    fileLocation: FileLocation | undefined;
+    setFileLocation: (location: FileLocation | undefined) => void;
+    indexFileLocation?: FileLocation | undefined;
+    setIndexFileLocation?: (location: FileLocation | undefined) => void;
+    bed1Location?: FileLocation | undefined;
+    setBed1Location?: (location: FileLocation | undefined) => void;
+    bed2Location?: FileLocation | undefined;
+    setBed2Location?: (location: FileLocation | undefined) => void;
+    radioOption: string;
+}
+export type SetLocationFunction = (location: FileLocation | undefined) => void;
+export type HelpStrings = Record<string, string>;
+export declare const helpStrings: HelpStrings;

package/dist/LinearSyntenyView/components/ImportForm/selectors/SelectorTypes.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.helpStrings = void 0;
+exports.helpStrings = {
+    '.paf': 'minimap2 target.fa query.fa',
+    '.pif.gz': 'minimap2 target.fa query.fa',
+    '.out': 'mashmap target.fa query.fa',
+    '.delta': 'mummer target.fa query.fa',
+    '.chain': 'e.g. queryToTarget.chain',
+};

package/dist/LinearSyntenyView/components/ImportForm/selectors/StandardFormatSelector.d.ts

@@ -0,0 +1,3 @@
+import type { SelectorProps } from './SelectorTypes';
+declare const StandardFormatSelector: ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, radioOption, }: SelectorProps) => import("react/jsx-runtime").JSX.Element;
+export default StandardFormatSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/StandardFormatSelector.js

@@ -0,0 +1,20 @@
+"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 Help_1 = __importDefault(require("@mui/icons-material/Help"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const SelectorTypes_1 = require("./SelectorTypes");
+const SwapAssemblies_1 = __importDefault(require("./SwapAssemblies"));
+const StandardFormatSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, radioOption, }) {
+    return ((0, jsx_runtime_1.jsxs)("div", { style: {
+            display: 'flex',
+            flexDirection: 'column',
+            gap: 10,
+        }, children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${radioOption} location`, inline: true, description: "", location: fileLocation, setLocation: setFileLocation }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Verify or click swap", (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: (0, jsx_runtime_1.jsx)("code", { children: SelectorTypes_1.helpStrings[radioOption] }), children: (0, jsx_runtime_1.jsx)(Help_1.default, {}) })] }), (0, jsx_runtime_1.jsx)(SwapAssemblies_1.default, { swap: swap, radioOption: radioOption, assembly1: assembly1, assembly2: assembly2, setSwap: setSwap, text1: "query assembly", text2: "target assembly" })] })] }));
+});
+exports.default = StandardFormatSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/SwapAssemblies.d.ts

@@ -0,0 +1,13 @@
+import type { ReactNode } from 'react';
+export interface SwapAssembliesProps {
+    assembly1?: string;
+    assembly2?: string;
+    swap?: boolean;
+    setSwap?: (arg: boolean) => void;
+    radioOption: string;
+    helpContent?: ReactNode;
+    text1: string;
+    text2: string;
+}
+declare const SwapAssemblies: ({ assembly1, assembly2, swap, setSwap, radioOption, helpContent, text1, text2, }: SwapAssembliesProps) => import("react/jsx-runtime").JSX.Element;
+export default SwapAssemblies;

package/dist/LinearSyntenyView/components/ImportForm/selectors/SwapAssemblies.js

@@ -0,0 +1,32 @@
+"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 Help_1 = __importDefault(require("@mui/icons-material/Help"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const SelectorTypes_1 = require("./SelectorTypes");
+const useStyles = (0, mui_1.makeStyles)()({
+    row: {
+        display: 'flex',
+        gap: 20,
+    },
+    swap: {
+        display: 'grid',
+        gridTemplateColumns: '1fr 1fr',
+        gap: 4,
+        alignItems: 'center',
+    },
+});
+const SwapAssemblies = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, radioOption, helpContent, text1, text2, }) {
+    const { classes } = useStyles();
+    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Verify or click swap", (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: helpContent || (0, jsx_runtime_1.jsx)("code", { children: SelectorTypes_1.helpStrings[radioOption] }), children: (0, jsx_runtime_1.jsx)(Help_1.default, {}) })] }), (0, jsx_runtime_1.jsxs)("div", { className: classes.row, children: [(0, jsx_runtime_1.jsxs)("div", { className: classes.swap, children: [(0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)("i", { children: swap ? assembly2 : assembly1 }) }), (0, jsx_runtime_1.jsx)("div", { children: text1 }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)("i", { children: swap ? assembly1 : assembly2 }) }), (0, jsx_runtime_1.jsx)("div", { children: text2 })] }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                            if (setSwap) {
+                                setSwap(!swap);
+                            }
+                        }, children: "Swap?" })] })] }));
+});
+exports.default = SwapAssemblies;

package/dist/LinearSyntenyView/components/ImportForm/selectors/index.d.ts

@@ -0,0 +1,4 @@
+export { default as StandardFormatSelector } from './StandardFormatSelector';
+export { default as PifGzSelector } from './PifGzSelector';
+export { default as AnchorsSelector } from './AnchorsSelector';
+export * from './SelectorTypes';

package/dist/LinearSyntenyView/components/ImportForm/selectors/index.js

@@ -0,0 +1,27 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AnchorsSelector = exports.PifGzSelector = exports.StandardFormatSelector = void 0;
+var StandardFormatSelector_1 = require("./StandardFormatSelector");
+Object.defineProperty(exports, "StandardFormatSelector", { enumerable: true, get: function () { return __importDefault(StandardFormatSelector_1).default; } });
+var PifGzSelector_1 = require("./PifGzSelector");
+Object.defineProperty(exports, "PifGzSelector", { enumerable: true, get: function () { return __importDefault(PifGzSelector_1).default; } });
+var AnchorsSelector_1 = require("./AnchorsSelector");
+Object.defineProperty(exports, "AnchorsSelector", { enumerable: true, get: function () { return __importDefault(AnchorsSelector_1).default; } });
+__exportStar(require("./SelectorTypes"), exports);

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -73,7 +73,7 @@ async function renderToSvg(model, opts) {
         const rendering = renderings[i - 1];
         const height = heights[i];
         const levelHeight = level.height || 0;
-        RenderList.push((0, jsx_runtime_1.jsxs)("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? ((0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: `synclip-${i}`, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, (0, jsx_runtime_1.jsx)("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (0, jsx_runtime_1.jsx)(util_1.ReactRendering, { rendering: r }, i)) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${levelHeight})`, children: (0, jsx_runtime_1.jsx)(SVGLinearGenomeView_1.default, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
+        RenderList.push((0, jsx_runtime_1.jsxs)("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? ((0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: `synclip-${i}`, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, (0, jsx_runtime_1.jsx)("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => ((0, jsx_runtime_1.jsx)(util_1.ReactRendering, { rendering: r }, i))) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${levelHeight})`, children: (0, jsx_runtime_1.jsx)(SVGLinearGenomeView_1.default, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
         currOffset += height + fontSize + rulerHeight + levelHeight;
     }
     return (0, util_1.renderToStaticMarkup)((0, jsx_runtime_1.jsx)(material_1.ThemeProvider, { theme: theme, children: (0, jsx_runtime_1.jsx)(Wrapper, { children: (0, jsx_runtime_1.jsxs)("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString(), children: [(0, jsx_runtime_1.jsx)(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }), RenderList] }) }) }));

package/esm/LinearComparativeDisplay/stateModelFactory.d.ts

@@ -70,6 +70,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     renderInProgress: string | undefined;
     features: Feature[] | undefined;
     message: string | undefined;
+    loadingStatus: string | undefined;
 } & {
     readonly level: number;
     readonly height: number;
@@ -152,6 +153,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             renderInProgress: string | undefined;
             features: Feature[] | undefined;
             message: string | undefined;
+            loadingStatus: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -221,12 +223,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             renderInProgress: string | undefined;
             features: Feature[] | undefined;
             message: string | undefined;
+            loadingStatus: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         highResolutionScaling: number;
     };
 } & {
     setLoading(newStopToken: string): void;
     setMessage(messageText: string): void;
+    setLoadingStatus(messageText: string): void;
     setRendered(args?: {
         features: Feature[];
     }): void;

package/esm/LinearComparativeDisplay/stateModelFactory.js

@@ -14,6 +14,7 @@ function stateModelFactory(configSchema) {
         renderInProgress: undefined,
         features: undefined,
         message: undefined,
+        loadingStatus: undefined,
     }))
         .views(self => ({
         get level() {
@@ -43,6 +44,9 @@ function stateModelFactory(configSchema) {
                 self.error = undefined;
                 stopToken = undefined;
             },
+            setLoadingStatus(messageText) {
+                self.loadingStatus = messageText;
+            },
             setRendered(args) {
                 if (!args) {
                     return;
@@ -108,6 +112,7 @@ function renderBlockData(self) {
             rpcManager,
             renderProps: {
                 ...display.renderProps(),
+                model: display,
                 level,
                 view: parent,
                 adapterConfig,
@@ -123,15 +128,17 @@ async function renderBlockEffect(props) {
         return;
     }
     const { rpcManager, renderProps } = props;
-    const { sessionId, adapterConfig, level } = renderProps;
+    const { model, sessionId, adapterConfig, level } = renderProps;
     const view = renderProps.view.views[level];
-    const features = (await rpcManager.call('getFeats', 'CoreGetFeatures', {
-        regions: view.staticBlocks.contentBlocks,
-        sessionId,
-        adapterConfig,
-    }));
     return {
-        features: dedupe(features, f => f.id()),
+        features: dedupe((await rpcManager.call('getFeats', 'CoreGetFeatures', {
+            regions: view.staticBlocks.contentBlocks,
+            sessionId,
+            adapterConfig,
+            statusCallback: (arg) => {
+                model.setLoadingStatus(arg);
+            },
+        })), f => f.id()),
     };
 }
 export default stateModelFactory;

package/esm/LinearComparativeView/components/Rubberband.d.ts

@@ -1,7 +1,7 @@
 import type { LinearComparativeViewModel } from '../model';
 type LCV = LinearComparativeViewModel;
-declare const LinearComparativeRubberband: ({ model, ControlComponent, }: {
+declare const Rubberband: ({ model, ControlComponent, }: {
     model: LCV;
     ControlComponent?: React.ReactElement;
 }) => import("react/jsx-runtime").JSX.Element;
-export default LinearComparativeRubberband;
+export default Rubberband;