npm - @jbrowse/plugin-linear-comparative-view - Versions diffs - 3.3.0 → 3.5.0 - Mend

@jbrowse/plugin-linear-comparative-view 3.3.0 → 3.5.0

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 (39) hide show

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

@@ -19,6 +19,6 @@ const useStyles = (0, mui_1.makeStyles)()(() => ({
 const HeaderSearchBoxes = (0, mobx_react_1.observer)(function ({ view, }) {
     const { classes } = useStyles();
     const { assemblyNames, coarseTotalBp } = view;
-    return ((0, jsx_runtime_1.jsxs)("span", { className: classes.searchBox, children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SearchBox, { model: view, showHelp: false }), (0, jsx_runtime_1.jsxs)(material_1.Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: [assemblyNames.join(','), " ", (0, util_1.toLocale)(Math.round(coarseTotalBp)), " bp"] })] }));
+    return ((0, jsx_runtime_1.jsxs)("span", { className: classes.searchBox, children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SearchBox, { model: view, showHelp: false }), (0, jsx_runtime_1.jsxs)(material_1.Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: [assemblyNames.join(','), " ", (0, util_1.getBpDisplayStr)(coarseTotalBp)] })] }));
 });
 exports.default = HeaderSearchBoxes;

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

@@ -77,7 +77,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
@@ -188,13 +189,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): 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>;
+        navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
         navToSearchString({ input, assembly, }: {
             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>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+        navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): 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;
     } & {
@@ -262,9 +263,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         displayName: string | undefined;
         tracks: any[];
         minimized: boolean;
-        displayedRegions: import("@jbrowse/core/util").Region[];
         offsetPx: number;
         bpPerPx: number;
+        displayedRegions: import("@jbrowse/core/util").Region[];
         hideHeader: boolean;
         hideHeaderOverview: boolean;
         hideNoTracksActive: boolean;
@@ -392,7 +393,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
@@ -503,13 +505,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): 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>;
+        navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
         navToSearchString({ input, assembly, }: {
             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>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+        navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): 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;
     } & {
@@ -577,9 +579,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         displayName: string | undefined;
         tracks: any[];
         minimized: boolean;
-        displayedRegions: import("@jbrowse/core/util").Region[];
         offsetPx: number;
         bpPerPx: number;
+        displayedRegions: import("@jbrowse/core/util").Region[];
         hideHeader: boolean;
         hideHeaderOverview: boolean;
         hideNoTracksActive: boolean;

package/dist/LinearSyntenyDisplay/drawSynteny.js CHANGED Viewed

@@ -31,6 +31,7 @@ function drawRef(model, ctx1, ctx3) {
     const view = (0, util_1.getContainingView)(model);
     const drawCurves = view.drawCurves;
     const drawCIGAR = view.drawCIGAR;
+    const drawCIGARMatchesOnly = view.drawCIGARMatchesOnly;
     const { level, height, featPositions } = model;
     const width = view.width;
     const bpPerPxs = view.views.map(v => v.bpPerPx);
@@ -123,11 +124,19 @@ function drawRef(model, ctx1, ctx3) {
                             continuingFlag = true;
                         }
                         else {
-                            ctx1.fillStyle =
-                                colorMap[(continuingFlag && d1 > 1) || d2 > 1 ? op : 'M'];
+                            const letter = (continuingFlag && d1 > 1) || d2 > 1 ? op : 'M';
+                            ctx1.fillStyle = colorMap[letter];
                             continuingFlag = false;
-                            (0, util_2.draw)(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
-                            ctx1.fill();
+                            if (drawCIGARMatchesOnly) {
+                                if (letter === 'M') {
+                                    (0, util_2.draw)(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
+                                    ctx1.fill();
+                                }
+                            }
+                            else {
+                                (0, util_2.draw)(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
+                                ctx1.fill();
+                            }
                             if (ctx3) {
                                 ctx3.fillStyle = makeColor(idx);
                                 (0, util_2.draw)(ctx3, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);

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

@@ -1,4 +1,4 @@
-import type { ExportSvgOptions } from '../model';
+import type { ExportSvgOptions } from '../types';
 export default function ExportSvgDialog({ model, handleClose, }: {
     model: {
         exportSvg(opts: ExportSvgOptions): Promise<void>;

package/dist/LinearSyntenyView/components/ExportSvgDialog.js CHANGED Viewed

@@ -1,4 +1,7 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = ExportSvgDialog;
 const jsx_runtime_1 = require("react/jsx-runtime");
@@ -6,15 +9,13 @@ const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
+const TextField2_1 = __importDefault(require("./TextField2"));
 function LoadingMessage() {
     return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.CircularProgress, { size: 20, style: { marginRight: 20 } }), (0, jsx_runtime_1.jsx)(material_1.Typography, { display: "inline", children: "Creating SVG" })] }));
 }
 function useSvgLocal(key, val) {
     return (0, util_1.useLocalStorage)(`svg-${key}`, val);
 }
-function TextField2({ children, ...rest }) {
-    return ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { ...rest, children: children }) }));
-}
 function ExportSvgDialog({ model, handleClose, }) {
     const session = (0, util_1.getSession)(model);
     const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
@@ -24,11 +25,11 @@ function ExportSvgDialog({ model, handleClose, }) {
     const [trackLabels, setTrackLabels] = useSvgLocal('tracklabels', 'offset');
     const [themeName, setThemeName] = useSvgLocal('theme', session.themeName || 'default');
     const [error, setError] = (0, react_1.useState)();
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : loading ? ((0, jsx_runtime_1.jsx)(LoadingMessage, {})) : null, (0, jsx_runtime_1.jsx)(TextField2, { helperText: "filename", value: filename, onChange: event => {
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : loading ? ((0, jsx_runtime_1.jsx)(LoadingMessage, {})) : null, (0, jsx_runtime_1.jsx)(TextField2_1.default, { helperText: "filename", value: filename, onChange: event => {
                             setFilename(event.target.value);
-                        } }), (0, jsx_runtime_1.jsxs)(TextField2, { select: true, label: "Track label positioning", variant: "outlined", value: trackLabels, style: { width: 150 }, onChange: event => {
+                        } }), (0, jsx_runtime_1.jsxs)(TextField2_1.default, { select: true, label: "Track label positioning", variant: "outlined", value: trackLabels, style: { width: 150 }, onChange: event => {
                             setTrackLabels(event.target.value);
-                        }, children: [(0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "offset", children: "Offset" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "overlay", children: "Overlay" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "left", children: "Left" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "none", children: "None" })] }), (0, jsx_runtime_1.jsx)("br", {}), session.allThemes ? ((0, jsx_runtime_1.jsx)(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => {
+                        }, children: [(0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "offset", children: "Offset" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "overlay", children: "Overlay" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "left", children: "Left" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "none", children: "None" })] }), (0, jsx_runtime_1.jsx)("br", {}), session.allThemes ? ((0, jsx_runtime_1.jsx)(TextField2_1.default, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => {
                             setThemeName(event.target.value);
                         }, children: Object.entries(session.allThemes()).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) })) : null, offscreenCanvas ? ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => {
                                 setRasterizeLayers(val => !val);

package/dist/LinearSyntenyView/components/TextField2.d.ts ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import type { TextFieldProps } from '@mui/material';
2	+ export default function TextField2({ children, ...rest }: TextFieldProps): import("react/jsx-runtime").JSX.Element;

package/dist/LinearSyntenyView/components/TextField2.js ADDED Viewed

@@ -0,0 +1,8 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = TextField2;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const material_1 = require("@mui/material");
+function TextField2({ children, ...rest }) {
+    return ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { ...rest, children: children }) }));
+}

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

@@ -1,24 +1,7 @@
-import type React from 'react';
 import { Curves } from './components/Icons';
-import type { ImportFormSyntenyTrack } from './types';
+import type { ExportSvgOptions, ImportFormSyntenyTrack } from './types';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { Instance } from 'mobx-state-tree';
-export interface ExportSvgOptions {
-    rasterizeLayers?: boolean;
-    scale?: number;
-    filename?: string;
-    Wrapper?: React.FC<{
-        children: React.ReactNode;
-    }>;
-    fontSize?: number;
-    rulerHeight?: number;
-    textHeight?: number;
-    paddingHeight?: number;
-    headerHeight?: number;
-    cytobandHeight?: number;
-    themeName?: string;
-    trackLabels?: string;
-}
 export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     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>>;
@@ -94,7 +77,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
@@ -205,13 +189,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): 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>;
+        navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
         navToSearchString({ input, assembly, }: {
             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>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+        navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): 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;
     } & {
@@ -279,9 +263,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         displayName: string | undefined;
         tracks: any[];
         minimized: boolean;
-        displayedRegions: import("@jbrowse/core/util").Region[];
         offsetPx: number;
         bpPerPx: number;
+        displayedRegions: import("@jbrowse/core/util").Region[];
         hideHeader: boolean;
         hideHeaderOverview: boolean;
         hideNoTracksActive: boolean;
@@ -298,6 +282,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearSyntenyView">;
     drawCIGAR: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawCIGARMatchesOnly: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawCurves: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     width: number;
@@ -346,6 +331,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     setImportFormSyntenyTrack(arg: number, val: ImportFormSyntenyTrack): void;
     setDrawCurves(arg: boolean): void;
     setDrawCIGAR(arg: boolean): void;
+    setDrawCIGARMatchesOnly(arg: boolean): void;
     showAllRegions(): void;
 } & {
     exportSvg(opts: ExportSvgOptions): Promise<void>;
@@ -476,7 +462,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
@@ -587,13 +574,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): 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>;
+        navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
         navToSearchString({ input, assembly, }: {
             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>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+        navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): 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;
     } & {
@@ -661,9 +648,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         displayName: string | undefined;
         tracks: any[];
         minimized: boolean;
-        displayedRegions: import("@jbrowse/core/util").Region[];
         offsetPx: number;
         bpPerPx: number;
+        displayedRegions: import("@jbrowse/core/util").Region[];
         hideHeader: boolean;
         hideHeaderOverview: boolean;
         hideNoTracksActive: boolean;

package/dist/LinearSyntenyView/model.js CHANGED Viewed

@@ -54,6 +54,7 @@ function stateModelFactory(pluginManager) {
         .compose('LinearSyntenyView', (0, model_1.default)(pluginManager), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('LinearSyntenyView'),
         drawCIGAR: true,
+        drawCIGARMatchesOnly: false,
         drawCurves: false,
     }))
         .volatile(() => ({
@@ -75,6 +76,9 @@ function stateModelFactory(pluginManager) {
         setDrawCIGAR(arg) {
             self.drawCIGAR = arg;
         },
+        setDrawCIGARMatchesOnly(arg) {
+            self.drawCIGARMatchesOnly = arg;
+        },
         showAllRegions() {
             (0, mobx_1.transaction)(() => {
                 for (const view of self.views) {
@@ -114,11 +118,20 @@ function stateModelFactory(pluginManager) {
                         label: 'Draw CIGAR',
                         checked: self.drawCIGAR,
                         type: 'checkbox',
-                        description: 'Draws per-base CIGAR level alignments',
+                        description: 'If disabled, only draws the broad scale CIGAR match',
                         onClick: () => {
                             self.setDrawCIGAR(!self.drawCIGAR);
                         },
                     },
+                    {
+                        label: 'Draw only CIGAR matches',
+                        checked: self.drawCIGARMatchesOnly,
+                        type: 'checkbox',
+                        description: 'If enabled, it hides the insertions and deletions in the CIGAR strings, helps with divergent',
+                        onClick: () => {
+                            self.setDrawCIGARMatchesOnly(!self.drawCIGARMatchesOnly);
+                        },
+                    },
                     {
                         label: 'Link views',
                         type: 'checkbox',

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.d.ts CHANGED Viewed

@@ -1,2 +1,3 @@
-import type { ExportSvgOptions, LinearSyntenyViewModel } from '../model';
+import type { LinearSyntenyViewModel } from '../model';
+import type { ExportSvgOptions } from '../types';
 export declare function renderToSvg(model: LinearSyntenyViewModel, opts: ExportSvgOptions): Promise<string>;

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js CHANGED Viewed

@@ -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/dist/LinearSyntenyView/types.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+import type React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { SnapshotIn } from 'mobx-state-tree';
 export type Conf = SnapshotIn<AnyConfigurationModel>;
@@ -10,3 +11,19 @@ export type ImportFormSyntenyTrack = {
 } | {
     type: 'none';
 };
+export interface ExportSvgOptions {
+    rasterizeLayers?: boolean;
+    scale?: number;
+    filename?: string;
+    Wrapper?: React.FC<{
+        children: React.ReactNode;
+    }>;
+    fontSize?: number;
+    rulerHeight?: number;
+    textHeight?: number;
+    paddingHeight?: number;
+    headerHeight?: number;
+    cytobandHeight?: number;
+    themeName?: string;
+    trackLabels?: string;
+}

package/dist/SyntenyFeatureDetail/Formatter.d.ts ADDED Viewed

@@ -0,0 +1,3 @@
+export default function Formatter({ value }: {
+    value: unknown;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/SyntenyFeatureDetail/Formatter.js ADDED Viewed

@@ -0,0 +1,23 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = Formatter;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+function Formatter({ value }) {
+    const [show, setShow] = (0, react_1.useState)(false);
+    const [copied, setCopied] = (0, react_1.useState)(false);
+    const display = String(value);
+    return display.length > 100 ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
+                    (0, copy_to_clipboard_1.default)(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                }, children: copied ? 'Copied to clipboard' : 'Copy' }), (0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
+                    setShow(val => !val);
+                }, children: show ? 'Show less' : 'Show more' }), (0, jsx_runtime_1.jsx)("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : ((0, jsx_runtime_1.jsx)("div", { children: display }));
+}

package/dist/SyntenyFeatureDetail/LinkToSyntenyView.d.ts CHANGED Viewed

@@ -1,5 +1,7 @@
 import type { SyntenyFeatureDetailModel } from './types';
-declare const LinkToSyntenyView: ({ model, }: {
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+declare const LinkToSyntenyView: ({ model, feat, }: {
     model: SyntenyFeatureDetailModel;
+    feat: SimpleFeatureSerialized;
 }) => import("react/jsx-runtime").JSX.Element;
 export default LinkToSyntenyView;

package/dist/SyntenyFeatureDetail/LinkToSyntenyView.js CHANGED Viewed

@@ -39,19 +39,19 @@ const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const LaunchSyntenyViewDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'))));
-const LinkToSyntenyView = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { featureData, view, level, trackId } = model;
+const LinkToSyntenyView = (0, mobx_react_1.observer)(function ({ model, feat, }) {
+    const { view, level, trackId } = model;
     return ((0, jsx_runtime_1.jsxs)("ul", { children: [view.type === 'LinearSyntenyView' ? ((0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
                         var _a, _b;
                         event.preventDefault();
                         const { views } = view;
                         if (level !== undefined) {
-                            (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(featureData);
-                            (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(featureData.mate);
+                            (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(feat);
+                            (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(feat.mate);
                         }
                         else {
-                            const f1 = featureData;
-                            const f2 = featureData.mate;
+                            const f1 = feat;
+                            const f2 = feat.mate;
                             const r1 = f1.assemblyName;
                             const r2 = f2.assemblyName;
                             const v1 = views.find(view => view.assemblyNames[0] === r1);
@@ -71,7 +71,7 @@ const LinkToSyntenyView = (0, mobx_react_1.observer)(function ({ model, }) {
                         }
                     }, children: "Center view on this feature" }) })) : null, (0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
                         event.preventDefault();
-                        const feature = new util_1.SimpleFeature(featureData);
+                        const feature = new util_1.SimpleFeature(feat);
                         const session = (0, util_1.getSession)(model);
                         session.queueDialog(handleClose => [
                             LaunchSyntenyViewDialog,

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 import type { SyntenyFeatureDetailModel } from './types';
-declare const SyntenyFeatureDetail: ({ model, }: {
+declare const SyntenyFeatureDetail: (props: {
     model: SyntenyFeatureDetailModel;
 }) => import("react/jsx-runtime").JSX.Element;
 export default SyntenyFeatureDetail;

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js CHANGED Viewed

@@ -4,12 +4,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
-const BaseFeatureDetail_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail"));
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
+const Formatter_1 = __importDefault(require("./Formatter"));
 const LinkToSyntenyView_1 = __importDefault(require("./LinkToSyntenyView"));
-const SyntenyFeatureDetail = (0, mobx_react_1.observer)(function ({ model, }) {
-    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { children: [(0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.default, { title: "Feature", model: model }), (0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "Link to view", children: (0, jsx_runtime_1.jsx)(LinkToSyntenyView_1.default, { model: model }) })] }));
+const SyntenyFeatureDetail = (0, mobx_react_1.observer)(function (props) {
+    const { model } = props;
+    const { featureData } = model;
+    const feat = structuredClone(featureData);
+    return feat ? ((0, jsx_runtime_1.jsxs)(material_1.Paper, { children: [(0, jsx_runtime_1.jsx)(FeatureDetails_1.default, { ...props, feature: feat, formatter: value => (0, jsx_runtime_1.jsx)(Formatter_1.default, { value: value }) }), (0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "Link to view", children: (0, jsx_runtime_1.jsx)(LinkToSyntenyView_1.default, { model: model, feat: feat }) })] })) : ((0, jsx_runtime_1.jsx)("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
 });
 exports.default = SyntenyFeatureDetail;

package/dist/SyntenyFeatureDetail/types.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export interface SyntenyFeatureDetailModel {
     trackId: string;
-    featureData: SimpleFeatureSerialized;
+    featureData?: SimpleFeatureSerialized;
     level?: number;
     view: {
         type: string;

package/esm/LinearComparativeView/components/HeaderSearchBoxes.js CHANGED Viewed

@@ -1,5 +1,5 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { toLocale } from '@jbrowse/core/util';
+import { getBpDisplayStr } from '@jbrowse/core/util';
 import { SearchBox } from '@jbrowse/plugin-linear-genome-view';
 import { Typography } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -17,6 +17,6 @@ const useStyles = makeStyles()(() => ({
 const HeaderSearchBoxes = observer(function ({ view, }) {
     const { classes } = useStyles();
     const { assemblyNames, coarseTotalBp } = view;
-    return (_jsxs("span", { className: classes.searchBox, children: [_jsx(SearchBox, { model: view, showHelp: false }), _jsxs(Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: [assemblyNames.join(','), " ", toLocale(Math.round(coarseTotalBp)), " bp"] })] }));
+    return (_jsxs("span", { className: classes.searchBox, children: [_jsx(SearchBox, { model: view, showHelp: false }), _jsxs(Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: [assemblyNames.join(','), " ", getBpDisplayStr(coarseTotalBp)] })] }));
 });
 export default HeaderSearchBoxes;

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

@@ -77,7 +77,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
@@ -188,13 +189,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): 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>;
+        navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
         navToSearchString({ input, assembly, }: {
             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>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+        navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): 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;
     } & {
@@ -262,9 +263,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         displayName: string | undefined;
         tracks: any[];
         minimized: boolean;
-        displayedRegions: import("@jbrowse/core/util").Region[];
         offsetPx: number;
         bpPerPx: number;
+        displayedRegions: import("@jbrowse/core/util").Region[];
         hideHeader: boolean;
         hideHeaderOverview: boolean;
         hideNoTracksActive: boolean;
@@ -392,7 +393,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
@@ -503,13 +505,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): 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>;
+        navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
         navToSearchString({ input, assembly, }: {
             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>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+        navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): 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;
     } & {
@@ -577,9 +579,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         displayName: string | undefined;
         tracks: any[];
         minimized: boolean;
-        displayedRegions: import("@jbrowse/core/util").Region[];
         offsetPx: number;
         bpPerPx: number;
+        displayedRegions: import("@jbrowse/core/util").Region[];
         hideHeader: boolean;
         hideHeaderOverview: boolean;
         hideNoTracksActive: boolean;

package/esm/LinearSyntenyDisplay/drawSynteny.js CHANGED Viewed

@@ -25,6 +25,7 @@ export function drawRef(model, ctx1, ctx3) {
     const view = getContainingView(model);
     const drawCurves = view.drawCurves;
     const drawCIGAR = view.drawCIGAR;
+    const drawCIGARMatchesOnly = view.drawCIGARMatchesOnly;
     const { level, height, featPositions } = model;
     const width = view.width;
     const bpPerPxs = view.views.map(v => v.bpPerPx);
@@ -117,11 +118,19 @@ export function drawRef(model, ctx1, ctx3) {
                             continuingFlag = true;
                         }
                         else {
-                            ctx1.fillStyle =
-                                colorMap[(continuingFlag && d1 > 1) || d2 > 1 ? op : 'M'];
+                            const letter = (continuingFlag && d1 > 1) || d2 > 1 ? op : 'M';
+                            ctx1.fillStyle = colorMap[letter];
                             continuingFlag = false;
-                            draw(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
-                            ctx1.fill();
+                            if (drawCIGARMatchesOnly) {
+                                if (letter === 'M') {
+                                    draw(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
+                                    ctx1.fill();
+                                }
+                            }
+                            else {
+                                draw(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);
+                                ctx1.fill();
+                            }
                             if (ctx3) {
                                 ctx3.fillStyle = makeColor(idx);
                                 draw(ctx3, px1, cx1, y1, cx2, px2, y2, mid, drawCurves);

package/esm/LinearSyntenyView/components/ExportSvgDialog.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import type { ExportSvgOptions } from '../model';
+import type { ExportSvgOptions } from '../types';
 export default function ExportSvgDialog({ model, handleClose, }: {
     model: {
         exportSvg(opts: ExportSvgOptions): Promise<void>;

package/esm/LinearSyntenyView/components/ExportSvgDialog.js CHANGED Viewed

@@ -2,16 +2,14 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
 import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
 import { getSession, useLocalStorage } from '@jbrowse/core/util';
-import { Button, Checkbox, CircularProgress, DialogActions, DialogContent, FormControlLabel, MenuItem, TextField, Typography, } from '@mui/material';
+import { Button, Checkbox, CircularProgress, DialogActions, DialogContent, FormControlLabel, MenuItem, Typography, } from '@mui/material';
+import TextField2 from './TextField2';
 function LoadingMessage() {
     return (_jsxs("div", { children: [_jsx(CircularProgress, { size: 20, style: { marginRight: 20 } }), _jsx(Typography, { display: "inline", children: "Creating SVG" })] }));
 }
 function useSvgLocal(key, val) {
     return useLocalStorage(`svg-${key}`, val);
 }
-function TextField2({ children, ...rest }) {
-    return (_jsx("div", { children: _jsx(TextField, { ...rest, children: children }) }));
-}
 export default function ExportSvgDialog({ model, handleClose, }) {
     const session = getSession(model);
     const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';

package/esm/LinearSyntenyView/components/TextField2.d.ts ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import type { TextFieldProps } from '@mui/material';
2	+ export default function TextField2({ children, ...rest }: TextFieldProps): import("react/jsx-runtime").JSX.Element;

package/esm/LinearSyntenyView/components/TextField2.js ADDED Viewed

@@ -0,0 +1,5 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { TextField } from '@mui/material';
+export default function TextField2({ children, ...rest }) {
+    return (_jsx("div", { children: _jsx(TextField, { ...rest, children: children }) }));
+}

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

@@ -1,24 +1,7 @@
-import type React from 'react';
 import { Curves } from './components/Icons';
-import type { ImportFormSyntenyTrack } from './types';
+import type { ExportSvgOptions, ImportFormSyntenyTrack } from './types';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { Instance } from 'mobx-state-tree';
-export interface ExportSvgOptions {
-    rasterizeLayers?: boolean;
-    scale?: number;
-    filename?: string;
-    Wrapper?: React.FC<{
-        children: React.ReactNode;
-    }>;
-    fontSize?: number;
-    rulerHeight?: number;
-    textHeight?: number;
-    paddingHeight?: number;
-    headerHeight?: number;
-    cytobandHeight?: number;
-    themeName?: string;
-    trackLabels?: string;
-}
 export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     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>>;
@@ -94,7 +77,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
@@ -205,13 +189,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): 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>;
+        navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
         navToSearchString({ input, assembly, }: {
             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>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+        navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): 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;
     } & {
@@ -279,9 +263,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         displayName: string | undefined;
         tracks: any[];
         minimized: boolean;
-        displayedRegions: import("@jbrowse/core/util").Region[];
         offsetPx: number;
         bpPerPx: number;
+        displayedRegions: import("@jbrowse/core/util").Region[];
         hideHeader: boolean;
         hideHeaderOverview: boolean;
         hideNoTracksActive: boolean;
@@ -298,6 +282,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearSyntenyView">;
     drawCIGAR: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawCIGARMatchesOnly: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawCurves: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     width: number;
@@ -346,6 +331,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     setImportFormSyntenyTrack(arg: number, val: ImportFormSyntenyTrack): void;
     setDrawCurves(arg: boolean): void;
     setDrawCIGAR(arg: boolean): void;
+    setDrawCIGARMatchesOnly(arg: boolean): void;
     showAllRegions(): void;
 } & {
     exportSvg(opts: ExportSvgOptions): Promise<void>;
@@ -476,7 +462,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {
@@ -587,13 +574,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): 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>;
+        navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
         navToSearchString({ input, assembly, }: {
             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>;
+        navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+        navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): 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;
     } & {
@@ -661,9 +648,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         displayName: string | undefined;
         tracks: any[];
         minimized: boolean;
-        displayedRegions: import("@jbrowse/core/util").Region[];
         offsetPx: number;
         bpPerPx: number;
+        displayedRegions: import("@jbrowse/core/util").Region[];
         hideHeader: boolean;
         hideHeaderOverview: boolean;
         hideNoTracksActive: boolean;

package/esm/LinearSyntenyView/model.js CHANGED Viewed

@@ -15,6 +15,7 @@ export default function stateModelFactory(pluginManager) {
         .compose('LinearSyntenyView', baseModel(pluginManager), types.model({
         type: types.literal('LinearSyntenyView'),
         drawCIGAR: true,
+        drawCIGARMatchesOnly: false,
         drawCurves: false,
     }))
         .volatile(() => ({
@@ -36,6 +37,9 @@ export default function stateModelFactory(pluginManager) {
         setDrawCIGAR(arg) {
             self.drawCIGAR = arg;
         },
+        setDrawCIGARMatchesOnly(arg) {
+            self.drawCIGARMatchesOnly = arg;
+        },
         showAllRegions() {
             transaction(() => {
                 for (const view of self.views) {
@@ -75,11 +79,20 @@ export default function stateModelFactory(pluginManager) {
                         label: 'Draw CIGAR',
                         checked: self.drawCIGAR,
                         type: 'checkbox',
-                        description: 'Draws per-base CIGAR level alignments',
+                        description: 'If disabled, only draws the broad scale CIGAR match',
                         onClick: () => {
                             self.setDrawCIGAR(!self.drawCIGAR);
                         },
                     },
+                    {
+                        label: 'Draw only CIGAR matches',
+                        checked: self.drawCIGARMatchesOnly,
+                        type: 'checkbox',
+                        description: 'If enabled, it hides the insertions and deletions in the CIGAR strings, helps with divergent',
+                        onClick: () => {
+                            self.setDrawCIGARMatchesOnly(!self.drawCIGARMatchesOnly);
+                        },
+                    },
                     {
                         label: 'Link views',
                         type: 'checkbox',

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.d.ts CHANGED Viewed

@@ -1,2 +1,3 @@
-import type { ExportSvgOptions, LinearSyntenyViewModel } from '../model';
+import type { LinearSyntenyViewModel } from '../model';
+import type { ExportSvgOptions } from '../types';
 export declare function renderToSvg(model: LinearSyntenyViewModel, opts: ExportSvgOptions): Promise<string>;

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js CHANGED Viewed

@@ -67,7 +67,7 @@ export async function renderToSvg(model, opts) {
         const rendering = renderings[i - 1];
         const height = heights[i];
         const levelHeight = level.height || 0;
-        RenderList.push(_jsxs("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? (_jsx("defs", { children: _jsx("clipPath", { id: `synclip-${i}`, children: _jsx("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, _jsx("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (_jsx(ReactRendering, { rendering: r }, i))) }), _jsx("g", { transform: `translate(0 ${levelHeight})`, children: _jsx(SVGLinearGenomeView, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
+        RenderList.push(_jsxs("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? (_jsx("defs", { children: _jsx("clipPath", { id: `synclip-${i}`, children: _jsx("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, _jsx("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => _jsx(ReactRendering, { rendering: r }, i)) }), _jsx("g", { transform: `translate(0 ${levelHeight})`, children: _jsx(SVGLinearGenomeView, { 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 renderToStaticMarkup(_jsx(ThemeProvider, { theme: theme, children: _jsx(Wrapper, { children: _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: [_jsx(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }), RenderList] }) }) }));

package/esm/LinearSyntenyView/types.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+import type React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { SnapshotIn } from 'mobx-state-tree';
 export type Conf = SnapshotIn<AnyConfigurationModel>;
@@ -10,3 +11,19 @@ export type ImportFormSyntenyTrack = {
 } | {
     type: 'none';
 };
+export interface ExportSvgOptions {
+    rasterizeLayers?: boolean;
+    scale?: number;
+    filename?: string;
+    Wrapper?: React.FC<{
+        children: React.ReactNode;
+    }>;
+    fontSize?: number;
+    rulerHeight?: number;
+    textHeight?: number;
+    paddingHeight?: number;
+    headerHeight?: number;
+    cytobandHeight?: number;
+    themeName?: string;
+    trackLabels?: string;
+}

package/esm/SyntenyFeatureDetail/Formatter.d.ts ADDED Viewed

@@ -0,0 +1,3 @@
+export default function Formatter({ value }: {
+    value: unknown;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/SyntenyFeatureDetail/Formatter.js ADDED Viewed

@@ -0,0 +1,17 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import copy from 'copy-to-clipboard';
+export default function Formatter({ value }) {
+    const [show, setShow] = useState(false);
+    const [copied, setCopied] = useState(false);
+    const display = String(value);
+    return display.length > 100 ? (_jsxs(_Fragment, { children: [_jsx("button", { type: "button", onClick: () => {
+                    copy(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                }, children: copied ? 'Copied to clipboard' : 'Copy' }), _jsx("button", { type: "button", onClick: () => {
+                    setShow(val => !val);
+                }, children: show ? 'Show less' : 'Show more' }), _jsx("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : (_jsx("div", { children: display }));
+}

package/esm/SyntenyFeatureDetail/LinkToSyntenyView.d.ts CHANGED Viewed

@@ -1,5 +1,7 @@
 import type { SyntenyFeatureDetailModel } from './types';
-declare const LinkToSyntenyView: ({ model, }: {
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+declare const LinkToSyntenyView: ({ model, feat, }: {
     model: SyntenyFeatureDetailModel;
+    feat: SimpleFeatureSerialized;
 }) => import("react/jsx-runtime").JSX.Element;
 export default LinkToSyntenyView;

package/esm/SyntenyFeatureDetail/LinkToSyntenyView.js CHANGED Viewed

@@ -4,19 +4,19 @@ import { SimpleFeature, assembleLocString, getSession, } from '@jbrowse/core/uti
 import { Link } from '@mui/material';
 import { observer } from 'mobx-react';
 const LaunchSyntenyViewDialog = lazy(() => import('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'));
-const LinkToSyntenyView = observer(function ({ model, }) {
-    const { featureData, view, level, trackId } = model;
+const LinkToSyntenyView = observer(function ({ model, feat, }) {
+    const { view, level, trackId } = model;
     return (_jsxs("ul", { children: [view.type === 'LinearSyntenyView' ? (_jsx("li", { children: _jsx(Link, { href: "#", onClick: event => {
                         var _a, _b;
                         event.preventDefault();
                         const { views } = view;
                         if (level !== undefined) {
-                            (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(featureData);
-                            (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(featureData.mate);
+                            (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(feat);
+                            (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(feat.mate);
                         }
                         else {
-                            const f1 = featureData;
-                            const f2 = featureData.mate;
+                            const f1 = feat;
+                            const f2 = feat.mate;
                             const r1 = f1.assemblyName;
                             const r2 = f2.assemblyName;
                             const v1 = views.find(view => view.assemblyNames[0] === r1);
@@ -36,7 +36,7 @@ const LinkToSyntenyView = observer(function ({ model, }) {
                         }
                     }, children: "Center view on this feature" }) })) : null, _jsx("li", { children: _jsx(Link, { href: "#", onClick: event => {
                         event.preventDefault();
-                        const feature = new SimpleFeature(featureData);
+                        const feature = new SimpleFeature(feat);
                         const session = getSession(model);
                         session.queueDialog(handleClose => [
                             LaunchSyntenyViewDialog,

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 import type { SyntenyFeatureDetailModel } from './types';
-declare const SyntenyFeatureDetail: ({ model, }: {
+declare const SyntenyFeatureDetail: (props: {
     model: SyntenyFeatureDetailModel;
 }) => import("react/jsx-runtime").JSX.Element;
 export default SyntenyFeatureDetail;

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js CHANGED Viewed

@@ -1,10 +1,14 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import BaseFeatureDetail from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
+import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
+import Formatter from './Formatter';
 import LinkToSyntenyView from './LinkToSyntenyView';
-const SyntenyFeatureDetail = observer(function ({ model, }) {
-    return (_jsxs(Paper, { children: [_jsx(BaseFeatureDetail, { title: "Feature", model: model }), _jsx(BaseCard, { title: "Link to view", children: _jsx(LinkToSyntenyView, { model: model }) })] }));
+const SyntenyFeatureDetail = observer(function (props) {
+    const { model } = props;
+    const { featureData } = model;
+    const feat = structuredClone(featureData);
+    return feat ? (_jsxs(Paper, { children: [_jsx(FeatureDetails, { ...props, feature: feat, formatter: value => _jsx(Formatter, { value: value }) }), _jsx(BaseCard, { title: "Link to view", children: _jsx(LinkToSyntenyView, { model: model, feat: feat }) })] })) : (_jsx("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
 });
 export default SyntenyFeatureDetail;

package/esm/SyntenyFeatureDetail/types.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export interface SyntenyFeatureDetailModel {
     trackId: string;
-    featureData: SimpleFeatureSerialized;
+    featureData?: SimpleFeatureSerialized;
     level?: number;
     view: {
         type: string;

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "3.3.0",
+  "version": "3.5.0",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -36,9 +36,9 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.3.0",
-    "@jbrowse/plugin-alignments": "^3.3.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.3.0",
+    "@jbrowse/core": "^3.5.0",
+    "@jbrowse/plugin-alignments": "^3.5.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.5.0",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "copy-to-clipboard": "^3.3.1",
@@ -59,5 +59,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
+  "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
 }