@jbrowse/core 1.7.11 → 2.1.0

package/util/Base1DViewModel.d.ts

@@ -1,13 +1,7 @@
 import { Instance } from 'mobx-state-tree';
 import { Feature } from './simpleFeature';
 import { Region as IRegion } from './types';
-export interface BpOffset {
-    refName?: string;
-    index: number;
-    offset: number;
-    start?: number;
-    end?: number;
-}
+import { BpOffset } from './Base1DUtils';
 declare const Base1DView: import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -38,37 +32,22 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
     readonly maxOffset: number;
     readonly minOffset: number;
     readonly totalBp: number;
+} & {
+    readonly dynamicBlocks: import("./blockTypes").BlockSet;
+    readonly staticBlocks: import("./blockTypes").BlockSet;
+    readonly currBp: number;
+} & {
     pxToBp(px: number): {
-        oob: boolean;
         coord: number;
-        offset: number;
         index: number;
         refName: string;
-        start: number;
-        end: number;
-        reversed: boolean;
-        assemblyName: string;
-    } | {
-        coord: number;
-        index: number;
-        start: number;
-        refName: string;
         oob: boolean;
         assemblyName: string;
         offset: number;
+        start: number;
+        end: number;
         reversed: boolean;
     };
-} & {
-    readonly dynamicBlocks: import("./blockTypes").BlockSet;
-    readonly staticBlocks: import("./blockTypes").BlockSet;
-    readonly currBp: number;
-    /**
-     * calculates the Px at which coord is found.
-     *
-     * @param refName - string, refName of region
-     * @param coord - number, bp to be translated to Px
-     * @param regionNumber - number, index of displayedRegion in displayedRegions array
-     */
     bpToPx({ refName, coord, regionNumber, }: {
         refName: string;
         coord: number;
@@ -76,8 +55,14 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
     }): number | undefined;
 } & {
     setFeatures(features: Feature[]): void;
-    zoomToDisplayedRegions(leftPx: BpOffset | undefined, rightPx: BpOffset | undefined): void;
     showAllRegions(): void;
+    zoomOut(): void;
+    zoomIn(): void;
+    zoomTo(newBpPerPx: number, offset?: number): number;
+    scrollTo(offsetPx: number): number;
+    centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+    scroll(distance: number): number;
+} & {
     /**
      * offset is the base-pair-offset in the displayed region, index is the index of the
      * displayed region in the linear genome view
@@ -85,13 +70,7 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
      * @param start - object as `{start, end, offset, index}`
      * @param end - object as `{start, end, offset, index}`
      */
-    moveTo(start: BpOffset, end: BpOffset): void;
-    zoomOut(): void;
-    zoomIn(): void;
-    zoomTo(newBpPerPx: number, offset?: number): void;
-    scrollTo(offsetPx: number): number;
-    centerAt(bp: number, refName: string, regionIndex: number): void;
-    scroll(distance: number): number;
+    moveTo(start?: BpOffset, end?: BpOffset): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export declare type Base1DViewStateModel = typeof Base1DView;
 export declare type Base1DViewModel = Instance<Base1DViewStateModel>;

package/util/Base1DViewModel.js

@@ -1,244 +1,142 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _index = require("./index");
-
-var _mst = require("./types/mst");
-
-var _calculateDynamicBlocks = _interopRequireDefault(require("./calculateDynamicBlocks"));
-
-var _calculateStaticBlocks = _interopRequireDefault(require("./calculateStaticBlocks"));
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
-var Base1DView = _mobxStateTree.types.model('Base1DView', {
-  id: _mst.ElementId,
-  displayedRegions: _mobxStateTree.types.array(_mst.Region),
-  bpPerPx: 0,
-  offsetPx: 0,
-  interRegionPaddingWidth: _mobxStateTree.types.optional(_mobxStateTree.types.number, 0),
-  minimumBlockWidth: _mobxStateTree.types.optional(_mobxStateTree.types.number, 0)
-}).volatile(function () {
-  return {
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const mobx_state_tree_1 = require("mobx-state-tree");
+const index_1 = require("./index");
+const mst_1 = require("./types/mst");
+const calculateDynamicBlocks_1 = __importDefault(require("./calculateDynamicBlocks"));
+const calculateStaticBlocks_1 = __importDefault(require("./calculateStaticBlocks"));
+const Base1DUtils_1 = require("./Base1DUtils");
+const Base1DView = mobx_state_tree_1.types
+    .model('Base1DView', {
+    id: mst_1.ElementId,
+    displayedRegions: mobx_state_tree_1.types.array(mst_1.Region),
+    bpPerPx: 0,
+    offsetPx: 0,
+    interRegionPaddingWidth: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
+    minimumBlockWidth: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
+})
+    .volatile(() => ({
     features: undefined,
-    volatileWidth: 0
-  };
-}).actions(function (self) {
-  return {
-    setDisplayedRegions: function setDisplayedRegions(regions) {
-      self.displayedRegions = (0, _mobxStateTree.cast)(regions);
+    volatileWidth: 0,
+}))
+    .actions(self => ({
+    setDisplayedRegions(regions) {
+        self.displayedRegions = (0, mobx_state_tree_1.cast)(regions);
     },
-    setBpPerPx: function setBpPerPx(val) {
-      self.bpPerPx = val;
+    setBpPerPx(val) {
+        self.bpPerPx = val;
     },
-    setVolatileWidth: function setVolatileWidth(width) {
-      self.volatileWidth = width;
-    }
-  };
-}).views(function (self) {
-  return {
+    setVolatileWidth(width) {
+        self.volatileWidth = width;
+    },
+}))
+    .views(self => ({
     get width() {
-      return self.volatileWidth;
+        return self.volatileWidth;
     },
-
     get assemblyNames() {
-      return (0, _toConsumableArray2.default)(new Set(self.displayedRegions.map(function (region) {
-        return region.assemblyName;
-      })));
+        return [
+            ...new Set(self.displayedRegions.map(region => region.assemblyName)),
+        ];
     },
-
     get displayedRegionsTotalPx() {
-      return this.totalBp / self.bpPerPx;
+        return this.totalBp / self.bpPerPx;
     },
-
     get maxOffset() {
-      // objectively determined to keep the linear genome on the main screen
-      var leftPadding = 10;
-      return this.displayedRegionsTotalPx - leftPadding;
+        // objectively determined to keep the linear genome on the main screen
+        const leftPadding = 10;
+        return this.displayedRegionsTotalPx - leftPadding;
     },
-
     get minOffset() {
-      // objectively determined to keep the linear genome on the main screen
-      var rightPadding = 30;
-      return -this.width + rightPadding;
+        // objectively determined to keep the linear genome on the main screen
+        const rightPadding = 30;
+        return -this.width + rightPadding;
     },
-
     get totalBp() {
-      return self.displayedRegions.map(function (a) {
-        return a.end - a.start;
-      }).reduce(function (a, b) {
-        return a + b;
-      }, 0);
+        return self.displayedRegions
+            .map(a => a.end - a.start)
+            .reduce((a, b) => a + b, 0);
     },
-
-    pxToBp: function pxToBp(px) {
-      var bpSoFar = 0;
-      var bp = (self.offsetPx + px) * self.bpPerPx;
-      var n = self.displayedRegions.length;
-
-      if (bp < 0) {
-        var region = self.displayedRegions[0];
-        var offset = bp;
-        return _objectSpread(_objectSpread({}, (0, _mobxStateTree.getSnapshot)(region)), {}, {
-          oob: true,
-          coord: region.reversed ? Math.floor(region.end - offset) + 1 : Math.floor(region.start + offset) + 1,
-          offset: offset,
-          index: 0
-        });
-      }
-
-      var interRegionPaddingBp = self.interRegionPaddingWidth * self.bpPerPx;
-      var minimumBlockBp = self.minimumBlockWidth * self.bpPerPx;
-
-      for (var index = 0; index < self.displayedRegions.length; index += 1) {
-        var _region = self.displayedRegions[index];
-        var len = _region.end - _region.start;
-
-        var _offset = bp - bpSoFar;
-
-        if (len + bpSoFar > bp && bpSoFar <= bp) {
-          return _objectSpread(_objectSpread({}, (0, _mobxStateTree.getSnapshot)(_region)), {}, {
-            oob: false,
-            offset: _offset,
-            coord: _region.reversed ? Math.floor(_region.end - _offset) + 1 : Math.floor(_region.start + _offset) + 1,
-            index: index
-          });
-        } // add the interRegionPaddingWidth if the boundary is in the screen
-        // e.g. offset>0 && offset<width
-
-
-        if (_region.end - _region.start > minimumBlockBp && _offset / self.bpPerPx > 0 && _offset / self.bpPerPx < this.width) {
-          bpSoFar += len + interRegionPaddingBp;
-        } else {
-          bpSoFar += len;
-        }
-      }
-
-      if (bp >= bpSoFar) {
-        var _region2 = self.displayedRegions[n - 1];
-
-        var _len = _region2.end - _region2.start;
-
-        var _offset2 = bp - bpSoFar + _len;
-
-        return _objectSpread(_objectSpread({}, (0, _mobxStateTree.getSnapshot)(_region2)), {}, {
-          oob: true,
-          offset: _offset2,
-          coord: _region2.reversed ? Math.floor(_region2.end - _offset2) + 1 : Math.floor(_region2.start + _offset2) + 1,
-          index: n - 1
-        });
-      }
-
-      return {
-        coord: 0,
-        index: 0,
-        start: 0,
-        refName: '',
-        oob: true,
-        assemblyName: '',
-        offset: 0,
-        reversed: false
-      };
-    }
-  };
-}).views(function (self) {
-  return {
+}))
+    .views(self => ({
     get dynamicBlocks() {
-      return (0, _calculateDynamicBlocks.default)(self);
+        return (0, calculateDynamicBlocks_1.default)(self);
     },
-
     get staticBlocks() {
-      return (0, _calculateStaticBlocks.default)(self);
+        return (0, calculateStaticBlocks_1.default)(self);
     },
-
     get currBp() {
-      return this.dynamicBlocks.map(function (a) {
-        return a.end - a.start;
-      }).reduce(function (a, b) {
-        return a + b;
-      }, 0);
+        return this.dynamicBlocks
+            .map(a => a.end - a.start)
+            .reduce((a, b) => a + b, 0);
     },
-
-    /**
-     * calculates the Px at which coord is found.
-     *
-     * @param refName - string, refName of region
-     * @param coord - number, bp to be translated to Px
-     * @param regionNumber - number, index of displayedRegion in displayedRegions array
-     */
-    bpToPx: function bpToPx(_ref) {
-      var _viewBpToPx;
-
-      var refName = _ref.refName,
-          coord = _ref.coord,
-          regionNumber = _ref.regionNumber;
-      return (_viewBpToPx = (0, _index.viewBpToPx)({
-        refName: refName,
-        coord: coord,
-        regionNumber: regionNumber,
-        self: self
-      })) === null || _viewBpToPx === void 0 ? void 0 : _viewBpToPx.offsetPx;
-    }
-  };
-}).actions(function (self) {
-  return {
-    setFeatures: function setFeatures(features) {
-      self.features = features;
+}))
+    .views(self => ({
+    pxToBp(px) {
+        return (0, Base1DUtils_1.pxToBp)(self, px);
+    },
+    bpToPx({ refName, coord, regionNumber, }) {
+        var _a;
+        return (_a = (0, Base1DUtils_1.bpToPx)({ refName, coord, regionNumber, self })) === null || _a === void 0 ? void 0 : _a.offsetPx;
     },
-    zoomToDisplayedRegions: function zoomToDisplayedRegions(leftPx, rightPx) {
-      if (leftPx === undefined || rightPx === undefined) {
-        return;
-      }
-
-      var singleRefSeq = leftPx.refName === rightPx.refName && leftPx.index === rightPx.index; // zooming into one displayed Region
-
-      if (singleRefSeq && rightPx.offset < leftPx.offset || leftPx.index > rightPx.index) {
-        ;
-        var _ref2 = [rightPx, leftPx];
-        leftPx = _ref2[0];
-        rightPx = _ref2[1];
-      }
-
-      var startOffset = {
-        start: leftPx.start,
-        end: leftPx.end,
-        index: leftPx.index,
-        offset: leftPx.offset
-      };
-      var endOffset = {
-        start: rightPx.start,
-        end: rightPx.end,
-        index: rightPx.index,
-        offset: rightPx.offset
-      };
-
-      if (startOffset && endOffset) {
-        this.moveTo(startOffset, endOffset);
-      } else {
-        throw new Error('regions not found');
-      }
+}))
+    .actions(self => ({
+    setFeatures(features) {
+        self.features = features;
     },
     // this makes a zoomed out view that shows all displayedRegions
     // that makes the overview bar square with the scale bar
-    showAllRegions: function showAllRegions() {
-      self.bpPerPx = self.totalBp / self.width;
-      self.offsetPx = 0;
+    showAllRegions() {
+        self.bpPerPx = self.totalBp / self.width;
+        self.offsetPx = 0;
+    },
+    zoomOut() {
+        this.zoomTo(self.bpPerPx * 2);
     },
-
+    zoomIn() {
+        this.zoomTo(self.bpPerPx / 2);
+    },
+    zoomTo(newBpPerPx, offset = self.width / 2) {
+        const bpPerPx = newBpPerPx;
+        if (bpPerPx === self.bpPerPx) {
+            return self.bpPerPx;
+        }
+        const oldBpPerPx = self.bpPerPx;
+        self.bpPerPx = bpPerPx;
+        // tweak the offset so that the center of the view remains at the same coordinate
+        self.offsetPx = (0, index_1.clamp)(Math.round(((self.offsetPx + offset) * oldBpPerPx) / bpPerPx - offset), self.minOffset, self.maxOffset);
+        return self.bpPerPx;
+    },
+    scrollTo(offsetPx) {
+        const newOffsetPx = (0, index_1.clamp)(offsetPx, self.minOffset, self.maxOffset);
+        self.offsetPx = newOffsetPx;
+        return newOffsetPx;
+    },
+    centerAt(coord, refName, regionNumber) {
+        if (!refName) {
+            return;
+        }
+        const centerPx = self.bpToPx({
+            refName,
+            coord,
+            regionNumber,
+        });
+        if (centerPx) {
+            this.scrollTo(Math.round(centerPx - self.width / 2));
+        }
+    },
+    scroll(distance) {
+        const oldOffsetPx = self.offsetPx;
+        // the scroll is clamped to keep the linear genome on the main screen
+        const newOffsetPx = (0, index_1.clamp)(self.offsetPx + distance, self.minOffset, self.maxOffset);
+        self.offsetPx = newOffsetPx;
+        return newOffsetPx - oldOffsetPx;
+    },
+}))
+    .actions(self => ({
     /**
      * offset is the base-pair-offset in the displayed region, index is the index of the
      * displayed region in the linear genome view
@@ -246,85 +144,8 @@ var Base1DView = _mobxStateTree.types.model('Base1DView', {
      * @param start - object as `{start, end, offset, index}`
      * @param end - object as `{start, end, offset, index}`
      */
-    moveTo: function moveTo(start, end) {
-      // find locations in the modellist
-      var bpSoFar = 0;
-
-      if (start.index === end.index) {
-        bpSoFar += end.offset - start.offset;
-      } else {
-        var s = self.displayedRegions[start.index];
-        bpSoFar += s.end - s.start - start.offset;
-
-        if (end.index - start.index >= 2) {
-          for (var i = start.index + 1; i < end.index; i += 1) {
-            bpSoFar += self.displayedRegions[i].end - self.displayedRegions[i].start;
-          }
-        }
-
-        bpSoFar += end.offset;
-      }
-
-      this.zoomTo(bpSoFar / (self.width - self.interRegionPaddingWidth * (end.index - start.index)));
-      var bpToStart = 0;
-
-      for (var _i = 0; _i < self.displayedRegions.length; _i += 1) {
-        var region = self.displayedRegions[_i];
-
-        if (start.index === _i) {
-          bpToStart += start.offset;
-          break;
-        } else {
-          bpToStart += region.end - region.start;
-        }
-      }
-
-      self.offsetPx = Math.round(bpToStart / self.bpPerPx) + self.interRegionPaddingWidth * start.index;
-    },
-    zoomOut: function zoomOut() {
-      this.zoomTo(self.bpPerPx * 2);
-    },
-    zoomIn: function zoomIn() {
-      this.zoomTo(self.bpPerPx / 2);
-    },
-    zoomTo: function zoomTo(newBpPerPx) {
-      var offset = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : self.width / 2;
-      var bpPerPx = newBpPerPx;
-
-      if (bpPerPx === self.bpPerPx) {
-        return;
-      }
-
-      var oldBpPerPx = self.bpPerPx;
-      self.bpPerPx = bpPerPx; // tweak the offset so that the center of the view remains at the same coordinate
-
-      self.offsetPx = (0, _index.clamp)(Math.round((self.offsetPx + offset) * oldBpPerPx / bpPerPx - offset), self.minOffset, self.maxOffset);
-    },
-    scrollTo: function scrollTo(offsetPx) {
-      var newOffsetPx = (0, _index.clamp)(offsetPx, self.minOffset, self.maxOffset);
-      self.offsetPx = newOffsetPx;
-      return newOffsetPx;
-    },
-    centerAt: function centerAt(bp, refName, regionIndex) {
-      var centerPx = self.bpToPx({
-        refName: refName,
-        coord: bp,
-        regionNumber: regionIndex
-      });
-
-      if (centerPx) {
-        this.scrollTo(Math.round(centerPx - self.width / 2));
-      }
+    moveTo(start, end) {
+        (0, Base1DUtils_1.moveTo)(self, start, end);
     },
-    scroll: function scroll(distance) {
-      var oldOffsetPx = self.offsetPx; // the scroll is clamped to keep the linear genome on the main screen
-
-      var newOffsetPx = (0, _index.clamp)(self.offsetPx + distance, self.minOffset, self.maxOffset);
-      self.offsetPx = newOffsetPx;
-      return newOffsetPx - oldOffsetPx;
-    }
-  };
-});
-
-var _default = Base1DView;
-exports.default = _default;
+}));
+exports.default = Base1DView;