@jbrowse/plugin-circular-view 2.0.0 → 2.1.2

package/dist/CircularView/components/Ruler.js.map

@@ -1 +1 @@
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package/dist/CircularView/models/CircularView.js

@@ -1,39 +1,17 @@
 "use strict";
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
-var __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
-        }
-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var mobx_state_tree_1 = require("mobx-state-tree");
-var mst_1 = require("@jbrowse/core/util/types/mst");
-var mobx_1 = require("mobx");
-var configuration_1 = require("@jbrowse/core/configuration");
-var util_1 = require("@jbrowse/core/util");
-var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-var slices_1 = require("./slices");
-var viewportVisibleRegion_1 = require("./viewportVisibleRegion");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mst_1 = require("@jbrowse/core/util/types/mst");
+const mobx_1 = require("mobx");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+const slices_1 = require("./slices");
+const viewportVisibleRegion_1 = require("./viewportVisibleRegion");
 function CircularView(pluginManager) {
-    var minHeight = 40;
-    var minWidth = 100;
-    var defaultHeight = 400;
+    const minHeight = 40;
+    const minWidth = 100;
+    const defaultHeight = 400;
     return mobx_state_tree_1.types.compose(models_1.BaseViewModel, mobx_state_tree_1.types
         .model('CircularView', {
         type: mobx_state_tree_1.types.literal('CircularView'),
@@ -44,7 +22,7 @@ function CircularView(pluginManager) {
         hideTrackSelectorButton: false,
         lockedFitToWindow: true,
         disableImportForm: false,
-        height: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.refinement('trackHeight', mobx_state_tree_1.types.number, function (n) { return n >= minHeight; }), defaultHeight),
+        height: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.refinement('trackHeight', mobx_state_tree_1.types.number, n => n >= minHeight), defaultHeight),
         minimumRadiusPx: 25,
         spacingPx: 10,
         paddingPx: 80,
@@ -56,10 +34,10 @@ function CircularView(pluginManager) {
         scrollY: 0,
         trackSelectorType: 'hierarchical',
     })
-        .volatile(function () { return ({
+        .volatile(() => ({
         width: 0,
-    }); })
-        .views(function (self) { return ({
+    }))
+        .views(self => ({
         get staticSlices() {
             return (0, slices_1.calculateStaticSlices)(self);
         },
@@ -75,20 +53,9 @@ function CircularView(pluginManager) {
             ], this.centerXY, this.radiusPx);
         },
         get circumferencePx() {
-            var e_1, _a;
-            var elidedBp = 0;
-            try {
-                for (var _b = __values(this.elidedRegions), _c = _b.next(); !_c.done; _c = _b.next()) {
-                    var r = _c.value;
-                    elidedBp += r.widthBp;
-                }
-            }
-            catch (e_1_1) { e_1 = { error: e_1_1 }; }
-            finally {
-                try {
-                    if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
-                }
-                finally { if (e_1) throw e_1.error; }
+            let elidedBp = 0;
+            for (const r of this.elidedRegions) {
+                elidedBp += r.widthBp;
             }
             return (elidedBp / self.bpPerPx + self.spacingPx * this.elidedRegions.length);
         },
@@ -108,20 +75,9 @@ function CircularView(pluginManager) {
             ];
         },
         get totalBp() {
-            var e_2, _a;
-            var total = 0;
-            try {
-                for (var _b = __values(self.displayedRegions), _c = _b.next(); !_c.done; _c = _b.next()) {
-                    var region = _c.value;
-                    total += region.end - region.start;
-                }
-            }
-            catch (e_2_1) { e_2 = { error: e_2_1 }; }
-            finally {
-                try {
-                    if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
-                }
-                finally { if (e_2) throw e_2.error; }
+            let total = 0;
+            for (const region of self.displayedRegions) {
+                total += region.end - region.start;
             }
             return total;
         },
@@ -131,12 +87,12 @@ function CircularView(pluginManager) {
                 : 1000000;
         },
         get maxBpPerPx() {
-            var minCircumferencePx = 2 * Math.PI * self.minimumRadiusPx;
+            const minCircumferencePx = 2 * Math.PI * self.minimumRadiusPx;
             return this.totalBp / minCircumferencePx;
         },
         get minBpPerPx() {
             // min depends on window dimensions, clamp between old min(0.01) and max
-            var maxCircumferencePx = 2 * Math.PI * this.maximumRadiusPx;
+            const maxCircumferencePx = 2 * Math.PI * this.maximumRadiusPx;
             return (0, util_1.clamp)(this.totalBp / maxCircumferencePx, 0.0000000001, this.maxBpPerPx);
         },
         get atMaxBpPerPx() {
@@ -164,43 +120,43 @@ function CircularView(pluginManager) {
         // elide regions that are too small to see reasonably
         get elidedRegions() {
             // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            var visible = [];
-            self.displayedRegions.forEach(function (region) {
-                var widthBp = region.end - region.start;
-                var widthPx = widthBp / self.bpPerPx;
+            const visible = [];
+            self.displayedRegions.forEach(region => {
+                const widthBp = region.end - region.start;
+                const widthPx = widthBp / self.bpPerPx;
                 if (widthPx < self.minVisibleWidth) {
                     // too small to see, collapse into a single elision region
-                    var lastVisible = visible[visible.length - 1];
+                    const lastVisible = visible[visible.length - 1];
                     if (lastVisible && lastVisible.elided) {
-                        lastVisible.regions.push(__assign({}, region));
+                        lastVisible.regions.push({ ...region });
                         lastVisible.widthBp += widthBp;
                     }
                     else {
                         visible.push({
                             elided: true,
-                            widthBp: widthBp,
-                            regions: [__assign({}, region)],
+                            widthBp,
+                            regions: [{ ...region }],
                         });
                     }
                 }
                 else {
                     // big enough to see, display it
-                    visible.push(__assign(__assign({}, region), { widthBp: widthBp }));
+                    visible.push({ ...region, widthBp });
                 }
             });
             // remove any single-region elisions
-            for (var i = 0; i < visible.length; i += 1) {
-                var v = visible[i];
+            for (let i = 0; i < visible.length; i += 1) {
+                const v = visible[i];
                 if (v.elided && v.regions.length === 1) {
                     delete v.elided;
-                    visible[i] = __assign(__assign({}, v), v.regions[0]);
+                    visible[i] = { ...v, ...v.regions[0] };
                 }
             }
             return visible;
         },
         get assemblyNames() {
-            var assemblyNames = [];
-            self.displayedRegions.forEach(function (displayedRegion) {
+            const assemblyNames = [];
+            self.displayedRegions.forEach(displayedRegion => {
                 if (!assemblyNames.includes(displayedRegion.assemblyName)) {
                     assemblyNames.push(displayedRegion.assemblyName);
                 }
@@ -208,69 +164,67 @@ function CircularView(pluginManager) {
             return assemblyNames;
         },
         get initialized() {
-            var assemblyManager = (0, util_1.getSession)(self).assemblyManager;
-            return this.assemblyNames.every(function (a) { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.initialized; });
+            const { assemblyManager } = (0, util_1.getSession)(self);
+            return this.assemblyNames.every(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.initialized; });
         },
-    }); })
-        .volatile(function () { return ({
+    }))
+        .volatile(() => ({
         error: undefined,
-    }); })
-        .actions(function (self) { return ({
+    }))
+        .actions(self => ({
         // toggle action with a flag stating which mode it's in
-        setWidth: function (newWidth) {
+        setWidth(newWidth) {
             self.width = Math.max(newWidth, minWidth);
             return self.width;
         },
-        setHeight: function (newHeight) {
+        setHeight(newHeight) {
             self.height = Math.max(newHeight, minHeight);
             return self.height;
         },
-        resizeHeight: function (distance) {
-            var oldHeight = self.height;
-            var newHeight = this.setHeight(self.height + distance);
+        resizeHeight(distance) {
+            const oldHeight = self.height;
+            const newHeight = this.setHeight(self.height + distance);
             this.setModelViewWhenAdjust(!self.tooSmallToLock);
             return newHeight - oldHeight;
         },
-        resizeWidth: function (distance) {
-            var oldWidth = self.width;
-            var newWidth = this.setWidth(self.width + distance);
+        resizeWidth(distance) {
+            const oldWidth = self.width;
+            const newWidth = this.setWidth(self.width + distance);
             this.setModelViewWhenAdjust(!self.tooSmallToLock);
             return newWidth - oldWidth;
         },
-        rotateClockwiseButton: function () {
+        rotateClockwiseButton() {
             this.rotateClockwise(Math.PI / 6);
         },
-        rotateCounterClockwiseButton: function () {
+        rotateCounterClockwiseButton() {
             this.rotateCounterClockwise(Math.PI / 6);
         },
-        rotateClockwise: function (distance) {
-            if (distance === void 0) { distance = 0.17; }
+        rotateClockwise(distance = 0.17) {
             self.offsetRadians += distance;
         },
-        rotateCounterClockwise: function (distance) {
-            if (distance === void 0) { distance = 0.17; }
+        rotateCounterClockwise(distance = 0.17) {
             self.offsetRadians -= distance;
         },
-        zoomInButton: function () {
+        zoomInButton() {
             this.setBpPerPx(self.bpPerPx / 1.4);
         },
-        zoomOutButton: function () {
+        zoomOutButton() {
             this.setBpPerPx(self.bpPerPx * 1.4);
         },
-        setBpPerPx: function (newVal) {
+        setBpPerPx(newVal) {
             self.bpPerPx = (0, util_1.clamp)(newVal, self.minBpPerPx, self.maxBpPerPx);
         },
-        setModelViewWhenAdjust: function (secondCondition) {
+        setModelViewWhenAdjust(secondCondition) {
             if (self.lockedFitToWindow && secondCondition) {
                 this.setBpPerPx(self.minBpPerPx);
             }
         },
-        closeView: function () {
+        closeView() {
             // eslint-disable-next-line @typescript-eslint/no-explicit-any
             (0, mobx_state_tree_1.getParent)(self, 2).removeView(self);
         },
-        setDisplayedRegions: function (regions) {
-            var previouslyEmpty = self.displayedRegions.length === 0;
+        setDisplayedRegions(regions) {
+            const previouslyEmpty = self.displayedRegions.length === 0;
             self.displayedRegions = (0, mobx_state_tree_1.cast)(regions);
             if (previouslyEmpty) {
                 this.setBpPerPx(self.minBpPerPx);
@@ -279,73 +233,80 @@ function CircularView(pluginManager) {
                 this.setBpPerPx(self.bpPerPx);
             }
         },
-        activateTrackSelector: function () {
+        activateTrackSelector() {
             if (self.trackSelectorType === 'hierarchical') {
-                var session = (0, util_1.getSession)(self);
+                const session = (0, util_1.getSession)(self);
                 if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                    var selector = session.addWidget('HierarchicalTrackSelectorWidget', 'hierarchicalTrackSelector', { view: self });
+                    const selector = session.addWidget('HierarchicalTrackSelectorWidget', 'hierarchicalTrackSelector', { view: self });
                     session.showWidget(selector);
                     return selector;
                 }
             }
-            throw new Error("invalid track selector type ".concat(self.trackSelectorType));
+            throw new Error(`invalid track selector type ${self.trackSelectorType}`);
         },
-        toggleTrack: function (trackId) {
+        toggleTrack(trackId) {
             // if we have any tracks with that configuration, turn them off
-            var hiddenCount = this.hideTrack(trackId);
+            const hiddenCount = this.hideTrack(trackId);
             // if none had that configuration, turn one on
             if (!hiddenCount) {
                 this.showTrack(trackId);
             }
         },
-        setError: function (error) {
+        setError(error) {
             console.error(error);
             self.error = error;
         },
-        showTrack: function (trackId, initialSnapshot) {
-            if (initialSnapshot === void 0) { initialSnapshot = {}; }
-            var schema = pluginManager.pluggableConfigSchemaType('track');
-            var conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
-            var trackType = pluginManager.getTrackType(conf.type);
+        showTrack(trackId, initialSnapshot = {}) {
+            const schema = pluginManager.pluggableConfigSchemaType('track');
+            const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
+            const trackType = pluginManager.getTrackType(conf.type);
             if (!trackType) {
-                throw new Error("unknown track type ".concat(conf.type));
+                throw new Error(`unknown track type ${conf.type}`);
             }
-            var viewType = pluginManager.getViewType(self.type);
-            var supportedDisplays = viewType.displayTypes.map(function (d) { return d.name; });
-            var displayConf = conf.displays.find(function (d) {
-                return supportedDisplays.includes(d.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 track = trackType.stateModel.create({
+                ...initialSnapshot,
+                type: conf.type,
+                configuration: conf,
+                displays: [{ type: displayConf.type, configuration: displayConf }],
             });
-            var track = trackType.stateModel.create(__assign(__assign({}, initialSnapshot), { type: conf.type, configuration: conf, displays: [{ type: displayConf.type, configuration: displayConf }] }));
             self.tracks.push(track);
         },
-        addTrackConf: function (configuration, initialSnapshot) {
-            if (initialSnapshot === void 0) { initialSnapshot = {}; }
-            var type = configuration.type;
-            var name = (0, configuration_1.readConfObject)(configuration, 'name');
-            var trackType = pluginManager.getTrackType(type);
+        addTrackConf(configuration, initialSnapshot = {}) {
+            const { type } = configuration;
+            const name = (0, configuration_1.readConfObject)(configuration, 'name');
+            const trackType = pluginManager.getTrackType(type);
             if (!trackType) {
-                throw new Error("unknown track type ".concat(configuration.type));
+                throw new Error(`unknown track type ${configuration.type}`);
             }
-            var viewType = pluginManager.getViewType(self.type);
-            var supportedDisplays = viewType.displayTypes.map(function (d) { return d.name; });
-            var displayConf = configuration.displays.find(function (d) { return supportedDisplays.includes(d.type); });
-            var track = trackType.stateModel.create(__assign(__assign({}, initialSnapshot), { name: name, type: type, configuration: configuration, displays: [{ type: displayConf.type, configuration: displayConf }] }));
+            const viewType = pluginManager.getViewType(self.type);
+            const supportedDisplays = viewType.displayTypes.map(d => d.name);
+            const displayConf = configuration.displays.find((d) => supportedDisplays.includes(d.type));
+            const track = trackType.stateModel.create({
+                ...initialSnapshot,
+                name,
+                type,
+                configuration,
+                displays: [{ type: displayConf.type, configuration: displayConf }],
+            });
             self.tracks.push(track);
         },
-        hideTrack: function (trackId) {
-            var schema = pluginManager.pluggableConfigSchemaType('track');
-            var conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
-            var t = self.tracks.filter(function (t) { return t.configuration === conf; });
-            (0, mobx_1.transaction)(function () { return t.forEach(function (t) { return self.tracks.remove(t); }); });
+        hideTrack(trackId) {
+            const schema = pluginManager.pluggableConfigSchemaType('track');
+            const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
+            const t = self.tracks.filter(t => t.configuration === conf);
+            (0, mobx_1.transaction)(() => t.forEach(t => self.tracks.remove(t)));
             return t.length;
         },
-        toggleFitToWindowLock: function () {
+        toggleFitToWindowLock() {
             self.lockedFitToWindow = !self.lockedFitToWindow;
             // when going unlocked -> locked and circle is cut off, set to the locked minBpPerPx
             this.setModelViewWhenAdjust(self.atMinBpPerPx);
             return self.lockedFitToWindow;
         },
-    }); }));
+    })));
 }
 exports.default = CircularView;
 /*

package/dist/CircularView/models/CircularView.js.map

@@ -1 +1 @@
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package/dist/CircularView/models/slices.js

@@ -1,40 +1,13 @@
 "use strict";
-var __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
-        }
-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.sliceIsVisible = exports.calculateStaticSlices = exports.Slice = void 0;
-var util_1 = require("@jbrowse/core/util");
-var viewportVisibleRegion_1 = require("./viewportVisibleRegion");
-var Slice = /** @class */ (function () {
-    function Slice(view, region, currentRadianOffset, radianWidth) {
+const util_1 = require("@jbrowse/core/util");
+const viewportVisibleRegion_1 = require("./viewportVisibleRegion");
+class Slice {
+    constructor(view, region, currentRadianOffset, radianWidth) {
         this.region = region;
         this.radianWidth = radianWidth;
-        var bpPerRadian = view.bpPerRadian;
+        const { bpPerRadian } = view;
         this.key = (0, util_1.assembleLocString)(region);
         this.offsetRadians = currentRadianOffset;
         this.bpPerRadian = bpPerRadian;
@@ -43,8 +16,8 @@ var Slice = /** @class */ (function () {
         this.endRadians = region.widthBp / this.bpPerRadian + this.offsetRadians;
         Object.freeze(this);
     }
-    Slice.prototype.bpToXY = function (bp, radiusPx) {
-        var offsetBp;
+    bpToXY(bp, radiusPx) {
+        let offsetBp;
         if (this.region.elided) {
             offsetBp = this.region.widthBp / 2;
         }
@@ -54,43 +27,31 @@ var Slice = /** @class */ (function () {
         else {
             offsetBp = bp - this.region.start;
         }
-        var totalRadians = offsetBp / this.bpPerRadian + this.offsetRadians;
+        const totalRadians = offsetBp / this.bpPerRadian + this.offsetRadians;
         return (0, util_1.polarToCartesian)(radiusPx, totalRadians);
-    };
-    Slice.prototype.toJSON = function () {
+    }
+    toJSON() {
         return Object.fromEntries(Object.entries(this));
-    };
-    return Slice;
-}());
+    }
+}
 exports.Slice = Slice;
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function calculateStaticSlices(self) {
-    var e_1, _a;
-    var slices = [];
-    var currentRadianOffset = 0;
-    try {
-        for (var _b = __values(self.elidedRegions), _c = _b.next(); !_c.done; _c = _b.next()) {
-            var region = _c.value;
-            var radianWidth = region.widthBp / self.bpPerRadian + self.spacingPx / self.pxPerRadian;
-            slices.push(new Slice(self, region, currentRadianOffset, radianWidth));
-            currentRadianOffset += radianWidth;
-        }
-    }
-    catch (e_1_1) { e_1 = { error: e_1_1 }; }
-    finally {
-        try {
-            if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
-        }
-        finally { if (e_1) throw e_1.error; }
+    const slices = [];
+    let currentRadianOffset = 0;
+    for (const region of self.elidedRegions) {
+        const radianWidth = region.widthBp / self.bpPerRadian + self.spacingPx / self.pxPerRadian;
+        slices.push(new Slice(self, region, currentRadianOffset, radianWidth));
+        currentRadianOffset += radianWidth;
     }
     return slices;
 }
 exports.calculateStaticSlices = calculateStaticSlices;
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function sliceIsVisible(self, slice) {
-    var 
+    const { 
     // rho: visibleRhoRange,
-    _a = __read(self.visibleSection.theta, 2), visibleThetaMin = _a[0], visibleThetaMax = _a[1];
+    theta: [visibleThetaMin, visibleThetaMax], } = self.visibleSection;
     return (0, viewportVisibleRegion_1.thetaRangesOverlap)(slice.offsetRadians + self.offsetRadians, slice.radianWidth, visibleThetaMin, visibleThetaMax - visibleThetaMin);
 }
 exports.sliceIsVisible = sliceIsVisible;

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