npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.3.4 → 2.4.1 - Mend

@jbrowse/plugin-linear-genome-view 2.3.4 → 2.4.1

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 (271) hide show

package/dist/LinearGenomeView/components/TracksContainer.js CHANGED Viewed

@@ -45,18 +45,20 @@ const useStyles = (0, mui_1.makeStyles)()({
         position: 'relative',
         overflow: 'hidden',
     },
-    spacer: {
-        position: 'relative',
-        height: 3,
-    },
 });
-function TracksContainer({ children, model, }) {
+exports.default = (0, mobx_react_1.observer)(function TracksContainer({ children, model, }) {
     const { classes } = useStyles();
     const { mouseDown: mouseDown1, mouseUp } = (0, hooks_1.useSideScroll)(model);
     const ref = (0, react_1.useRef)(null);
     const { guideX, rubberbandOn, leftBpOffset, rightBpOffset, numOfBpSelected, width, left, anchorPosition, handleMenuItemClick, open, handleClose, mouseMove, mouseDown: mouseDown2, } = (0, hooks_1.useRangeSelect)(ref, model, true);
     (0, hooks_1.useWheelScroll)(ref, model);
-    return (react_1.default.createElement("div", { ref: ref, "data-testid": "trackContainer", className: classes.tracksContainer, onMouseDown: event => {
+    return (react_1.default.createElement("div", { ref: ref, "data-testid": "trackContainer", className: classes.tracksContainer, onClick: event => {
+            var _a;
+            if (event.detail === 2) {
+                const left = ((_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().left) || 0;
+                model.zoomTo(model.bpPerPx / 2, event.clientX - left, true);
+            }
+        }, onMouseDown: event => {
             mouseDown1(event);
             mouseDown2(event);
         }, onMouseMove: mouseMove, onMouseUp: mouseUp },
@@ -69,6 +71,5 @@ function TracksContainer({ children, model, }) {
             }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null,
         react_1.default.createElement(Rubberband_1.default, { model: model, ControlComponent: react_1.default.createElement(Scalebar_1.default, { model: model, style: { height: __1.SCALE_BAR_HEIGHT, boxSizing: 'border-box' } }) }),
         children));
-}
-exports.default = (0, mobx_react_1.observer)(TracksContainer);
+});
 //# sourceMappingURL=TracksContainer.js.map

package/dist/LinearGenomeView/components/TracksContainer.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"TracksContainer.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/TracksContainer.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAqC;AACrC,uCAA0C;AAC1C,2CAAqC;AACrC,yCAAuC;AAEvC,cAAc;AACd,0BAA4D;AAC5D,mCAAuE;AAEvE,mBAAmB;AACnB,8DAAqC;AACrC,0DAAiC;AACjC,4DAAmC;AACnC,8DAAqC;AACrC,oEAA2C;AAC3C,sEAA6C;AAE7C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,eAAe,EAAE;QACf,QAAQ,EAAE,UAAU;QACpB,QAAQ,EAAE,QAAQ;KACnB;CACF,CAAC,CAAA;AAIF,kBAAe,IAAA,qBAAQ,EAAC,SAAS,eAAe,CAAC,EAC/C,QAAQ,EACR,KAAK,GAIN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,IAAA,qBAAa,EAAC,KAAK,CAAC,CAAA;IAC/D,MAAM,GAAG,GAAG,IAAA,cAAM,EAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,EACJ,MAAM,EACN,YAAY,EACZ,YAAY,EACZ,aAAa,EACb,eAAe,EACf,KAAK,EACL,IAAI,EACJ,cAAc,EACd,mBAAmB,EACnB,IAAI,EACJ,WAAW,EACX,SAAS,EACT,SAAS,EAAE,UAAU,GACtB,GAAG,IAAA,sBAAc,EAAC,GAAG,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IACpC,IAAA,sBAAc,EAAC,GAAG,EAAE,KAAK,CAAC,CAAA;IAE1B,OAAO,CACL,uCACE,GAAG,EAAE,GAAG,iBACI,gBAAgB,EAC5B,SAAS,EAAE,OAAO,CAAC,eAAe,EAClC,OAAO,EAAE,KAAK,CAAC,EAAE;;YACf,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE;gBACtB,MAAM,IAAI,GAAG,CAAA,MAAA,GAAG,CAAC,OAAO,0CAAE,qBAAqB,GAAG,IAAI,KAAI,CAAC,CAAA;gBAC3D,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,GAAG,CAAC,EAAE,KAAK,CAAC,OAAO,GAAG,IAAI,EAAE,IAAI,CAAC,CAAA;aAC5D;QACH,CAAC,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,UAAU,CAAC,KAAK,CAAC,CAAA;YACjB,UAAU,CAAC,KAAK,CAAC,CAAA;QACnB,CAAC,EACD,WAAW,EAAE,SAAS,EACtB,SAAS,EAAE,OAAO;QAEjB,KAAK,CAAC,aAAa,CAAC,CAAC,CAAC,8BAAC,mBAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QACxD,KAAK,CAAC,cAAc,CAAC,CAAC,CAAC,8BAAC,oBAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC1D,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,CACtB,8BAAC,uBAAa,IAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CAChD,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CACjB,8BAAC,wBAAc,IACb,YAAY,EAAE,YAAY,EAC1B,aAAa,EAAE,aAAa,EAC5B,eAAe,EAAE,eAAe,EAChC,KAAK,EAAE,KAAK,EACZ,IAAI,EAAE,IAAI,GACV,CACH,CAAC,CAAC,CAAC,IAAI;QACP,cAAc,CAAC,CAAC,CAAC,CAChB,8BAAC,SAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;gBACd,IAAI,EAAE,cAAc,CAAC,OAAO;gBAC5B,GAAG,EAAE,cAAc,CAAC,OAAO;aAC5B,EACD,eAAe,EAAE,mBAAmB,EACpC,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,WAAW,EACpB,SAAS,EAAE,KAAK,CAAC,mBAAmB,EAAE,GACtC,CACH,CAAC,CAAC,CAAC,IAAI;QAER,8BAAC,oBAAU,IACT,KAAK,EAAE,KAAK,EACZ,gBAAgB,EACd,8BAAC,kBAAQ,IACP,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,EAAE,MAAM,EAAE,oBAAgB,EAAE,SAAS,EAAE,YAAY,EAAE,GAC5D,GAEJ;QACD,QAAQ,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA"}

package/dist/LinearGenomeView/components/ZoomControls.js CHANGED Viewed

@@ -32,7 +32,7 @@ const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 const ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
 const ZoomOut_1 = __importDefault(require("@mui/icons-material/ZoomOut"));
-const useStyles = (0, mui_1.makeStyles)()({
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     container: {
         display: 'flex',
         flexDirection: 'row',
@@ -40,8 +40,9 @@ const useStyles = (0, mui_1.makeStyles)()({
     },
     slider: {
         width: 70,
+        color: theme.palette.text.secondary,
     },
-});
+}));
 function ZoomControls({ model }) {
     const { classes } = useStyles();
     const { maxBpPerPx, minBpPerPx, bpPerPx, scaleFactor } = model;
@@ -50,10 +51,10 @@ function ZoomControls({ model }) {
         setValue(-Math.log2(bpPerPx) * 100);
     }, [setValue, bpPerPx]);
     return (react_1.default.createElement("div", { className: classes.container },
-        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1, color: "secondary", size: "large" },
+        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1, size: "large" },
             react_1.default.createElement(ZoomOut_1.default, null)),
         react_1.default.createElement(material_1.Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChange: (_, val) => setValue(val), onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), disabled: scaleFactor !== 1 }),
-        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, color: "secondary", size: "large" },
+        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, size: "large" },
             react_1.default.createElement(ZoomIn_1.default, null))));
 }
 exports.default = (0, mobx_react_1.observer)(ZoomControls);

package/dist/LinearGenomeView/components/ZoomControls.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"ZoomControls.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/ZoomControls.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAkD;AAClD,2CAAqC;AACrC,4CAAkD;AAClD,uCAA0C;AAC1C,wEAA+C;AAC/C,0EAAiD;AAGjD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;~~IAC7B~~,SAAS,EAAE;QACT,OAAO,EAAE,MAAM;QACf,aAAa,EAAE,KAAK;QACpB,UAAU,EAAE,QAAQ;KACrB;IACD,MAAM,EAAE;QACN,KAAK,EAAE,EAAE;~~KACV~~;CACF,CAAC,CAAA;~~AAEF~~,SAAS,YAAY,CAAC,EAAE,KAAK,EAAoC;IAC/D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC9D,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAA;IAC7D,IAAA,iBAAS,EAAC,GAAG,EAAE;QACb,QAAQ,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAA;IACrC,CAAC,EAAE,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAA;IAEvB,OAAO,CACL,uCAAK,SAAS,EAAE,OAAO,CAAC,SAAS;QAC/B,8BAAC,qBAAU,mBACG,UAAU,EACtB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,GAAG,CAAC,CAAC,EACtC,QAAQ,EAAE,OAAO,IAAI,UAAU,GAAG,MAAM,IAAI,WAAW,KAAK,CAAC,EAC7D,~~KAAK,EAAC,WAAW,EACjB,~~IAAI,EAAC,OAAO;YAEZ,8BAAC,iBAAO,OAAG,CACA;QAEb,8BAAC,iBAAM,IACL,IAAI,EAAC,OAAO,EACZ,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE,KAAK,EACZ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,GAAG,EACjC,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,GAAG,EACjC,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,QAAQ,CAAC,GAAa,CAAC,EAC7C,iBAAiB,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,CAAC,EAC1D,QAAQ,EAAE,WAAW,KAAK,CAAC,GAC3B;QACF,8BAAC,qBAAU,mBACG,SAAS,EACrB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,CAAC,CAAC,EAC5C,QAAQ,EAAE,OAAO,IAAI,UAAU,GAAG,MAAM,IAAI,WAAW,KAAK,CAAC,EAC7D,~~KAAK,EAAC,WAAW,EACjB,~~IAAI,EAAC,OAAO;YAEZ,8BAAC,gBAAM,OAAG,CACC,CACT,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,YAAY,CAAC,CAAA"}
1	+ {"version":3,"file":"ZoomControls.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/ZoomControls.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAkD;AAClD,2CAAqC;AACrC,4CAAkD;AAClD,uCAA0C;AAC1C,wEAA+C;AAC/C,0EAAiD;AAGjD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,SAAS,EAAE;QACT,OAAO,EAAE,MAAM;QACf,aAAa,EAAE,KAAK;QACpB,UAAU,EAAE,QAAQ;KACrB;IACD,MAAM,EAAE;QACN,KAAK,EAAE,EAAE;QACT,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS;KACpC;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,YAAY,CAAC,EAAE,KAAK,EAAoC;IAC/D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC9D,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAA;IAC7D,IAAA,iBAAS,EAAC,GAAG,EAAE;QACb,QAAQ,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAA;IACrC,CAAC,EAAE,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAA;IAEvB,OAAO,CACL,uCAAK,SAAS,EAAE,OAAO,CAAC,SAAS;QAC/B,8BAAC,qBAAU,mBACG,UAAU,EACtB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,GAAG,CAAC,CAAC,EACtC,QAAQ,EAAE,OAAO,IAAI,UAAU,GAAG,MAAM,IAAI,WAAW,KAAK,CAAC,EAC7D,IAAI,EAAC,OAAO;YAEZ,8BAAC,iBAAO,OAAG,CACA;QAEb,8BAAC,iBAAM,IACL,IAAI,EAAC,OAAO,EACZ,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE,KAAK,EACZ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,GAAG,EACjC,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,GAAG,EACjC,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,QAAQ,CAAC,GAAa,CAAC,EAC7C,iBAAiB,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,CAAC,EAC1D,QAAQ,EAAE,WAAW,KAAK,CAAC,GAC3B;QACF,8BAAC,qBAAU,mBACG,SAAS,EACrB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,CAAC,CAAC,EAC5C,QAAQ,EAAE,OAAO,IAAI,UAAU,GAAG,MAAM,IAAI,WAAW,KAAK,CAAC,EAC7D,IAAI,EAAC,OAAO;YAEZ,8BAAC,gBAAM,OAAG,CACC,CACT,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,YAAY,CAAC,CAAA"}

package/dist/LinearGenomeView/components/hooks.d.ts CHANGED Viewed

@@ -61,5 +61,10 @@ export declare function useRangeSelect(ref: React.RefObject<HTMLDivElement>, mod
     left: number;
     guideX?: undefined;
 };
-export declare function useWheelScroll(ref: React.RefObject<HTMLDivElement>, model: LGV): void;
+export declare function useWheelScroll(ref: React.RefObject<HTMLDivElement>, model: {
+    bpPerPx: number;
+    zoomTo: (arg: number, arg2?: number) => void;
+    setScaleFactor: (arg: number) => void;
+    horizontalScroll: (arg: number) => void;
+}): void;
 export {};

package/dist/LinearGenomeView/components/hooks.js CHANGED Viewed

@@ -227,7 +227,7 @@ function useWheelScroll(ref, model) {
                     model.setScaleFactor(1);
                     model.zoomTo(delta.current > 0
                         ? model.bpPerPx * (1 + delta.current)
-                        : model.bpPerPx / (1 - delta.current));
+                        : model.bpPerPx / (1 - delta.current), origEvent.clientX - ((curr === null || curr === void 0 ? void 0 : curr.getBoundingClientRect().left) || 0));
                     delta.current = 0;
                 }, 300);
             }

package/dist/LinearGenomeView/components/hooks.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/LinearGenomeView/components/util.d.ts CHANGED Viewed

@@ -16,3 +16,9 @@ export declare function getRelativeX<T extends {
     clientX: number;
     target: EventTarget | null;
 }>(event: T, element: HTMLElement | null): number;
+export declare function getCytobands(assembly: Assembly | undefined, refName: string): {
+    refName: string;
+    start: number;
+    end: number;
+    type: any;
+}[];

package/dist/LinearGenomeView/components/util.js CHANGED Viewed

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getRelativeX = exports.splitLast = exports.fetchResults = void 0;
+exports.getCytobands = exports.getRelativeX = exports.splitLast = exports.fetchResults = void 0;
 const util_1 = require("@jbrowse/core/util");
 const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
 async function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }) {
@@ -36,4 +36,14 @@ function getRelativeX(event, element) {
     return event.clientX - ((element === null || element === void 0 ? void 0 : element.getBoundingClientRect().left) || 0);
 }
 exports.getRelativeX = getRelativeX;
+function getCytobands(assembly, refName) {
+    var _a;
+    return (((_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.map(f => ({
+        refName: assembly.getCanonicalRefName(f.get('refName')),
+        start: f.get('start'),
+        end: f.get('end'),
+        type: f.get('type'),
+    })).filter(f => f.refName === refName)) || []);
+}
+exports.getCytobands = getCytobands;
 //# sourceMappingURL=util.js.map

package/dist/LinearGenomeView/components/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearGenomeView/index.js CHANGED Viewed

@@ -30,12 +30,14 @@ const react_1 = require("react");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const model_1 = require("./model");
 exports.default = (pluginManager) => {
-    pluginManager.addViewType(() => new pluggableElementTypes_1.ViewType({
-        name: 'LinearGenomeView',
-        displayName: 'Linear genome view',
-        stateModel: (0, model_1.stateModelFactory)(pluginManager),
-        ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/LinearGenomeView')))),
-    }));
+    pluginManager.addViewType(() => {
+        return new pluggableElementTypes_1.ViewType({
+            name: 'LinearGenomeView',
+            displayName: 'Linear genome view',
+            stateModel: (0, model_1.stateModelFactory)(pluginManager),
+            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/LinearGenomeView')))),
+        });
+    });
 };
 __exportStar(require("./model"), exports);
 //# sourceMappingURL=index.js.map

package/dist/LinearGenomeView/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearGenomeView/model.d.ts CHANGED Viewed

@@ -5,11 +5,6 @@ import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes';
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { renderToSvg } from './components/LinearGenomeViewSvg';
-import RefNameAutocomplete from './components/RefNameAutocomplete';
-import SearchBox from './components/SearchBox';
-import ZoomControls from './components/ZoomControls';
-import LinearGenomeView from './components/LinearGenomeView';
 export interface BpOffset {
     refName?: string;
     index: number;
@@ -25,6 +20,14 @@ export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     filename?: string;
     Wrapper?: React.FC<any>;
+    fontSize?: number;
+    rulerHeight?: number;
+    textHeight?: number;
+    paddingHeight?: number;
+    headerHeight?: number;
+    cytobandHeight?: number;
+    trackLabels?: string;
+    themeName?: string;
 }
 export interface NavLocation {
     refName: string;
@@ -148,15 +151,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly trackHeights: any;
+    readonly trackHeights: number;
     /**
      * #getter
      */
-    readonly trackHeightsWithResizeHandles: any;
+    readonly trackHeightsWithResizeHandles: number;
     /**
      * #getter
      */
-    readonly height: any;
+    readonly height: number;
     /**
      * #getter
      */
@@ -250,7 +253,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    zoomTo(bpPerPx: number): number;
+    zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
     /**
      * #action
      * sets offsets used in the get sequence dialog
@@ -366,7 +369,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     clearView(): void;
     /**
-     * #action
+     * #method
      * creates an svg export and save using FileSaver
      */
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
@@ -529,7 +532,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         reversed: boolean;
     } | undefined;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export { renderToSvg, RefNameAutocomplete, SearchBox, ZoomControls, LinearGenomeView, };
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
-export { default as ReactComponent } from './components/LinearGenomeView';
+export { default as ReactComponent, default as LinearGenomeView, } from './components/LinearGenomeView';
+export { default as RefNameAutocomplete } from './components/RefNameAutocomplete';
+export { default as SearchBox } from './components/SearchBox';
+export { default as ZoomControls } from './components/ZoomControls';
+export { renderToSvg } from './svgcomponents/SVGLinearGenomeView';

package/dist/LinearGenomeView/model.js CHANGED Viewed

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ReactComponent = exports.LinearGenomeView = exports.ZoomControls = exports.SearchBox = exports.RefNameAutocomplete = exports.renderToSvg = exports.stateModelFactory = exports.WIDGET_HEIGHT = exports.SPACING = exports.INTER_REGION_PADDING_WIDTH = exports.RESIZE_HANDLE_HEIGHT = exports.SCALE_BAR_HEIGHT = exports.HEADER_OVERVIEW_HEIGHT = exports.HEADER_BAR_HEIGHT = void 0;
+exports.renderToSvg = exports.ZoomControls = exports.SearchBox = exports.RefNameAutocomplete = exports.LinearGenomeView = exports.ReactComponent = exports.stateModelFactory = exports.WIDGET_HEIGHT = exports.SPACING = exports.INTER_REGION_PADDING_WIDTH = exports.RESIZE_HANDLE_HEIGHT = exports.SCALE_BAR_HEIGHT = exports.HEADER_OVERVIEW_HEIGHT = exports.HEADER_BAR_HEIGHT = void 0;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
@@ -52,19 +52,10 @@ const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera")
 const ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
 const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
 // locals
-const LinearGenomeViewSvg_1 = require("./components/LinearGenomeViewSvg");
-Object.defineProperty(exports, "renderToSvg", { enumerable: true, get: function () { return LinearGenomeViewSvg_1.renderToSvg; } });
-const RefNameAutocomplete_1 = __importDefault(require("./components/RefNameAutocomplete"));
-exports.RefNameAutocomplete = RefNameAutocomplete_1.default;
-const SearchBox_1 = __importDefault(require("./components/SearchBox"));
-exports.SearchBox = SearchBox_1.default;
+const SVGLinearGenomeView_1 = require("./svgcomponents/SVGLinearGenomeView");
 const ExportSvgDialog_1 = __importDefault(require("./components/ExportSvgDialog"));
 const MiniControls_1 = __importDefault(require("./components/MiniControls"));
 const Header_1 = __importDefault(require("./components/Header"));
-const ZoomControls_1 = __importDefault(require("./components/ZoomControls"));
-exports.ZoomControls = ZoomControls_1.default;
-const LinearGenomeView_1 = __importDefault(require("./components/LinearGenomeView"));
-exports.LinearGenomeView = LinearGenomeView_1.default;
 // lazies
 const SequenceSearchDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SequenceSearchDialog'))));
 function calculateVisibleLocStrings(contentBlocks) {
@@ -283,9 +274,7 @@ function stateModelFactory(pluginManager) {
          * #getter
          */
         get trackHeights() {
-            return self.tracks
-                .map(t => t.displays[0].height)
-                .reduce((a, b) => a + b, 0);
+            return (0, util_1.sum)(self.tracks.map(t => t.displays[0].height));
         },
         /**
          * #getter
@@ -378,12 +367,12 @@ function stateModelFactory(pluginManager) {
          */
         rankSearchResults(results) {
             // order of rank
-            const openTrackIds = self.tracks.map(track => track.configuration.trackId);
-            results.forEach(result => {
-                if (openTrackIds.includes(result.trackId)) {
+            const openTrackIds = new Set(self.tracks.map(track => track.configuration.trackId));
+            for (const result of results) {
+                if (openTrackIds.has(result.trackId)) {
                     result.updateScore(result.getScore() + 1);
                 }
-            });
+            }
             return results;
         },
         /**
@@ -478,21 +467,21 @@ function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        zoomTo(bpPerPx) {
+        zoomTo(bpPerPx, offset = self.width / 2, centerAtOffset = false) {
             const newBpPerPx = (0, util_1.clamp)(bpPerPx, self.minBpPerPx, self.maxBpPerPx);
             if (newBpPerPx === self.bpPerPx) {
                 return newBpPerPx;
             }
             const oldBpPerPx = self.bpPerPx;
-            self.bpPerPx = newBpPerPx;
             if (Math.abs(oldBpPerPx - newBpPerPx) < 0.000001) {
                 console.warn('zoomTo bpPerPx rounding error');
                 return oldBpPerPx;
             }
-            // tweak the offset so that the center of the view remains at the same coordinate
-            const viewWidth = self.width;
-            this.scrollTo(Math.round(((self.offsetPx + viewWidth / 2) * oldBpPerPx) / newBpPerPx -
-                viewWidth / 2));
+            self.bpPerPx = newBpPerPx;
+            // tweak the offset so that the center of the view remains at the same
+            // coordinate
+            this.scrollTo(Math.round(((self.offsetPx + offset) * oldBpPerPx) / newBpPerPx -
+                (centerAtOffset ? self.width / 2 : offset)));
             return newBpPerPx;
         },
         /**
@@ -527,8 +516,7 @@ function stateModelFactory(pluginManager) {
          * #action
          */
         horizontallyFlip() {
-            self.displayedRegions = (0, mobx_state_tree_1.cast)(self.displayedRegions
-                .slice()
+            self.displayedRegions = (0, mobx_state_tree_1.cast)([...self.displayedRegions]
                 .reverse()
                 .map(region => ({ ...region, reversed: !region.reversed })));
             this.scrollTo(self.totalBp / self.bpPerPx - self.offsetPx - self.width);
@@ -547,8 +535,8 @@ function stateModelFactory(pluginManager) {
                 throw new Error(`Unknown track type ${conf.type}`);
             }
             const viewType = pluginManager.getViewType(self.type);
-            const supportedDisplays = viewType.displayTypes.map(d => d.name);
-            const displayConf = conf.displays.find((d) => supportedDisplays.includes(d.type));
+            const supportedDisplays = new Set(viewType.displayTypes.map(d => d.name));
+            const displayConf = conf.displays.find((d) => supportedDisplays.has(d.type));
             if (!displayConf) {
                 throw new Error(`Could not find a compatible display for view type ${self.type}`);
             }
@@ -764,12 +752,12 @@ function stateModelFactory(pluginManager) {
             self.zoomTo(10);
         },
         /**
-         * #action
+         * #method
          * creates an svg export and save using FileSaver
          */
         async exportSvg(opts = {}) {
             // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            const html = await (0, LinearGenomeViewSvg_1.renderToSvg)(self, opts);
+            const html = await (0, SVGLinearGenomeView_1.renderToSvg)(self, opts);
             const blob = new Blob([html], { type: 'image/svg+xml' });
             (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
         },
@@ -1163,7 +1151,7 @@ function stateModelFactory(pluginManager) {
             }
             else {
                 self.setDisplayedRegions(
-                // @ts-ignore
+                // @ts-expect-error
                 locations.map(r => (r.start === undefined ? r.parentRegion : r)));
                 self.showAllRegions();
             }
@@ -1341,13 +1329,22 @@ function stateModelFactory(pluginManager) {
          * #getter
          */
         get centerLineInfo() {
-            return self.displayedRegions.length
+            return self.displayedRegions.length > 0
                 ? this.pxToBp(self.width / 2)
                 : undefined;
         },
     }));
 }
 exports.stateModelFactory = stateModelFactory;
-var LinearGenomeView_2 = require("./components/LinearGenomeView");
-Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_2).default; } });
+var LinearGenomeView_1 = require("./components/LinearGenomeView");
+Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_1).default; } });
+Object.defineProperty(exports, "LinearGenomeView", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_1).default; } });
+var RefNameAutocomplete_1 = require("./components/RefNameAutocomplete");
+Object.defineProperty(exports, "RefNameAutocomplete", { enumerable: true, get: function () { return __importDefault(RefNameAutocomplete_1).default; } });
+var SearchBox_1 = require("./components/SearchBox");
+Object.defineProperty(exports, "SearchBox", { enumerable: true, get: function () { return __importDefault(SearchBox_1).default; } });
+var ZoomControls_1 = require("./components/ZoomControls");
+Object.defineProperty(exports, "ZoomControls", { enumerable: true, get: function () { return __importDefault(ZoomControls_1).default; } });
+var SVGLinearGenomeView_2 = require("./svgcomponents/SVGLinearGenomeView");
+Object.defineProperty(exports, "renderToSvg", { enumerable: true, get: function () { return SVGLinearGenomeView_2.renderToSvg; } });
 //# sourceMappingURL=model.js.map

package/dist/LinearGenomeView/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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