@jbrowse/plugin-linear-comparative-view 3.7.0 → 4.0.0

package/esm/util.d.ts

@@ -8,7 +8,7 @@ export interface ReducedLinearGenomeView {
     dynamicBlocks: Region[];
     displayedRegions: Region[];
     headerHeight: number;
-    scaleBarHeight: number;
+    scalebarHeight: number;
     height: number;
     features: Feature[];
     tracks: {

package/esm/util.js

@@ -1,17 +1,14 @@
-import { clamp } from '@jbrowse/core/util';
+import { clamp, sum } from '@jbrowse/core/util';
 const [, TOP, , BOTTOM] = [0, 1, 2, 3];
 export function cheight(chunk) {
     return chunk[BOTTOM] - chunk[TOP];
 }
 function heightFromSpecificLevel(views, trackConfigId, level) {
-    const heightUpUntilThisPoint = views
-        .slice(0, level)
-        .map(v => v.height + 7)
-        .reduce((a, b) => a + b, 0);
+    const heightUpUntilThisPoint = sum(views.slice(0, level).map(v => v.height + 7));
     const v = views[level];
     return (heightUpUntilThisPoint +
         v.headerHeight +
-        v.scaleBarHeight +
+        v.scalebarHeight +
         getTrackPos(v, trackConfigId) +
         1);
 }
@@ -24,8 +21,7 @@ export function getTrackPos(view, trackConfigId) {
     return accum;
 }
 export function getPxFromCoordinate(view, refName, coord) {
-    var _a;
-    return (((_a = bpToPx(view, { refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
+    return (bpToPx(view, { refName, coord })?.offsetPx || 0) - view.offsetPx;
 }
 export function overlayYPos(trackConfigId, level, views, c, cond) {
     const track = views[level].tracks.find(t => t.configuration === trackConfigId);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "3.7.0",
+  "version": "4.0.0",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -15,49 +15,43 @@
     "directory": "plugins/linear-comparative-view"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/linear-comparative-view",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@jbrowse/core": "^3.7.0",
-    "@jbrowse/plugin-alignments": "^3.7.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.7.0",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
-    "copy-to-clipboard": "^3.3.1",
-    "file-saver": "^2.0.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0",
-    "tss-react": "^4.0.0"
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "copy-to-clipboard": "^3.3.3",
+    "@types/file-saver-es": "^2.0.3",
+    "file-saver-es": "^2.0.5",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "@jbrowse/core": "^4.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.0",
+    "@jbrowse/plugin-alignments": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0",
     "react-dom": ">=18.0.0"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/linear-comparative-view",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.d.ts

@@ -1,9 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export default function LaunchSyntenyViewDialog({ session, view, feature, trackId, handleClose, }: {
-    session: AbstractSessionModel;
-    view?: LinearGenomeViewModel;
-    feature: Feature;
-    trackId: string;
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -1,53 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LaunchSyntenyViewDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const util_1 = require("./util");
-const useStyles = (0, mui_1.makeStyles)()({
-    padding: {
-        margin: 10,
-        border: '1px solid #ccc',
-    },
-});
-function LaunchSyntenyViewDialog({ session, view, feature, trackId, handleClose, }) {
-    const { classes } = useStyles();
-    const inverted = feature.get('strand') === -1;
-    const hasCIGAR = !!feature.get('CIGAR');
-    const [horizontallyFlip, setHorizontallyFlip] = (0, react_1.useState)(inverted);
-    const [windowSize, setWindowSize] = (0, react_1.useState)('1000');
-    const [useRegionOfInterest, setUseRegionOfInterest] = (0, react_1.useState)(true);
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Launch synteny view", onClose: handleClose, children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [view && hasCIGAR ? ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { className: classes.padding, control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: useRegionOfInterest, onChange: event => {
-                                setUseRegionOfInterest(event.target.checked);
-                            } }), label: "Use CIGAR string to navigate the current visible to the target" })) : null, inverted ? ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { className: classes.padding, control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: horizontallyFlip, onChange: event => {
-                                setHorizontallyFlip(event.target.checked);
-                            } }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Add window size in bp", value: windowSize, onChange: event => {
-                            setWindowSize(event.target.value);
-                        } })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                            ;
-                            (async () => {
-                                try {
-                                    await (0, util_1.navToSynteny)({
-                                        feature,
-                                        windowSize: +windowSize,
-                                        horizontallyFlip,
-                                        trackId,
-                                        session,
-                                        region: useRegionOfInterest
-                                            ? view === null || view === void 0 ? void 0 : view.dynamicBlocks.contentBlocks[0]
-                                            : undefined,
-                                    });
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    session.notifyError(`${e}`, e);
-                                }
-                            })();
-                            handleClose();
-                        }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-}

package/dist/LGVSyntenyDisplay/components/util.d.ts

@@ -1,14 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-export interface SimpleRegion {
-    refName: string;
-    start: number;
-    end: number;
-}
-export declare function navToSynteny({ feature, windowSize: ws, session, trackId, region, horizontallyFlip, }: {
-    windowSize: number;
-    trackId: string;
-    horizontallyFlip: boolean;
-    feature: Feature;
-    session: AbstractSessionModel;
-    region?: SimpleRegion;
-}): Promise<void>;

package/dist/LGVSyntenyDisplay/components/util.js

@@ -1,100 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.navToSynteny = navToSynteny;
-const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-const { parseCigar } = plugin_alignments_1.MismatchParser;
-function findPosInCigar(cigar, startX) {
-    let featX = 0;
-    let mateX = 0;
-    for (let i = 0; i < cigar.length; i++) {
-        const len = +cigar[i];
-        const op = cigar[i + 1];
-        const min = Math.min(len, startX - featX);
-        if (featX >= startX) {
-            break;
-        }
-        if (op === 'I') {
-            mateX += len;
-        }
-        else if (op === 'D') {
-            featX += min;
-        }
-        else if (op === 'M' || op === '=' || op === 'X') {
-            mateX += min;
-            featX += min;
-        }
-    }
-    return [featX, mateX];
-}
-async function navToSynteny({ feature, windowSize: ws, session, trackId, region, horizontallyFlip, }) {
-    const cigar = feature.get('CIGAR');
-    const strand = feature.get('strand');
-    const featRef = feature.get('refName');
-    const featAsm = feature.get('assemblyName');
-    const featStart = feature.get('start');
-    const featEnd = feature.get('end');
-    const mate = feature.get('mate');
-    const mateStart = mate.start;
-    const mateEnd = mate.end;
-    const mateAsm = mate.assemblyName;
-    const mateRef = mate.refName;
-    let rMateStart;
-    let rMateEnd;
-    let rFeatStart;
-    let rFeatEnd;
-    if (region && cigar) {
-        const regStart = region.start;
-        const regEnd = region.end;
-        const p = parseCigar(cigar);
-        const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
-        const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
-        const flipper = strand === -1 ? -1 : 1;
-        rFeatStart = featStart + fStartX;
-        rFeatEnd = featStart + fEndX;
-        rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper;
-        rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper;
-    }
-    else {
-        rFeatStart = featStart;
-        rFeatEnd = featEnd;
-        rMateStart = mateStart;
-        rMateEnd = mateEnd;
-    }
-    const l1 = `${featRef}:${Math.floor(rFeatStart - ws)}-${Math.floor(rFeatEnd + ws)}`;
-    const m1 = Math.min(rMateStart, rMateEnd);
-    const m2 = Math.max(rMateStart, rMateEnd);
-    const l2 = `${mateRef}:${Math.floor(m1 - ws)}-${Math.floor(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
-    session.addView('LinearSyntenyView', {
-        type: 'LinearSyntenyView',
-        views: [
-            {
-                type: 'LinearGenomeView',
-                hideHeader: true,
-                init: {
-                    assembly: featAsm,
-                    loc: l1,
-                },
-            },
-            {
-                type: 'LinearGenomeView',
-                hideHeader: true,
-                init: {
-                    assembly: mateAsm,
-                    loc: l2,
-                },
-            },
-        ],
-        tracks: [
-            {
-                configuration: trackId,
-                type: 'SyntenyTrack',
-                displays: [
-                    {
-                        type: 'LinearSyntenyDisplay',
-                        configuration: `${trackId}-LinearSyntenyDisplay`,
-                    },
-                ],
-            },
-        ],
-    });
-}

package/dist/LGVSyntenyDisplay/configSchemaF.d.ts

@@ -1,66 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    mouseover: {
-        type: string;
-        defaultValue: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    defaultRendering: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        defaultValue: string;
-    };
-    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        PileupRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    colorBy: {
-        type: string;
-        description: string;
-        defaultValue: {
-            type: string;
-        };
-    };
-    filterBy: {
-        type: string;
-        description: string;
-        defaultValue: {
-            flagInclude: number;
-            flagExclude: number;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("mobx-state-tree").IAnyModelType;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>, undefined>>;
-export default configSchemaF;

package/dist/LGVSyntenyDisplay/configSchemaF.js

@@ -1,38 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-function configSchemaF(pluginManager) {
-    pluginManager.jexl.addFunction('lgvSyntenyTooltip', (f) => {
-        const mate = f.get('mate');
-        const l1name = f.get('name') || f.get('id');
-        const l2name = (mate === null || mate === void 0 ? void 0 : mate.name) || (mate === null || mate === void 0 ? void 0 : mate.id);
-        return [
-            l1name ? `Name1: ${l1name}` : '',
-            l2name ? `Name2: ${l2name}` : '',
-            `Loc1: ${(0, util_1.assembleLocString)({
-                refName: f.get('refName'),
-                start: f.get('start'),
-                end: f.get('end'),
-            })} (${(0, util_1.toLocale)(f.get('end') - f.get('start'))}bp)`,
-            `Loc2: ${(0, util_1.assembleLocString)({
-                refName: mate.refName,
-                start: mate.start,
-                end: mate.end,
-            })} (${(0, util_1.toLocale)(mate.end - mate.start)}bp)`,
-        ]
-            .filter(f => !!f)
-            .join('<br/>');
-    });
-    return (0, configuration_1.ConfigurationSchema)('LGVSyntenyDisplay', {
-        mouseover: {
-            type: 'string',
-            defaultValue: 'jexl:lgvSyntenyTooltip(feature)',
-        },
-    }, {
-        baseConfiguration: (0, plugin_alignments_1.linearPileupDisplayConfigSchemaFactory)(pluginManager),
-        explicitlyTyped: true,
-    });
-}
-exports.default = configSchemaF;

package/dist/LGVSyntenyDisplay/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function LGVSyntenyDisplayF(pluginManager: PluginManager): void;

package/dist/LGVSyntenyDisplay/index.js

@@ -1,24 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LGVSyntenyDisplayF;
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const configSchemaF_1 = __importDefault(require("./configSchemaF"));
-const model_1 = __importDefault(require("./model"));
-function LGVSyntenyDisplayF(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchemaF_1.default)(pluginManager);
-        const stateModel = (0, model_1.default)(configSchema);
-        return new DisplayType_1.default({
-            name: 'LGVSyntenyDisplay',
-            configSchema,
-            stateModel,
-            trackType: 'SyntenyTrack',
-            viewType: 'LinearGenomeView',
-            ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
-        });
-    });
-}