@jbrowse/core 1.7.10 → 2.0.1

package/util/Base1DUtils.js

@@ -0,0 +1,213 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.bpToPx = bpToPx;
+exports.moveTo = moveTo;
+exports.pxToBp = pxToBp;
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+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; }
+
+function lengthBetween(self, start, end) {
+  var bpSoFar = 0;
+  var displayedRegions = self.displayedRegions;
+
+  if (start.index === end.index) {
+    bpSoFar += end.offset - start.offset;
+  } else {
+    var s = 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++) {
+        var region = displayedRegions[i];
+        var len = region.end - region.start;
+        bpSoFar += len;
+      }
+    }
+
+    bpSoFar += end.offset;
+  }
+
+  return bpSoFar;
+}
+
+function moveTo(self, start, end) {
+  if (!start || !end) {
+    return;
+  }
+
+  var width = self.width,
+      interRegionPaddingWidth = self.interRegionPaddingWidth;
+  var len = lengthBetween(self, start, end);
+  var numBlocks = end.index - start.index;
+  var targetBpPerPx = len / (width - interRegionPaddingWidth * numBlocks);
+  var newBpPerPx = self.zoomTo(targetBpPerPx); // If our target bpPerPx was smaller than the allowed minBpPerPx, adjust
+  // the scroll so the requested range is in the middle of the screen
+
+  var extraBp = 0;
+
+  if (targetBpPerPx < newBpPerPx) {
+    extraBp = (newBpPerPx - targetBpPerPx) * self.width / 2;
+  }
+
+  var bpToStart = -extraBp;
+
+  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.scrollTo(Math.round(bpToStart / self.bpPerPx));
+} // manual return type since getSnapshot hard to infer here
+
+
+function pxToBp(self, px) {
+  var bpSoFar = 0;
+  var bpPerPx = self.bpPerPx,
+      offsetPx = self.offsetPx,
+      displayedRegions = self.displayedRegions,
+      interRegionPaddingWidth = self.interRegionPaddingWidth,
+      staticBlocks = self.staticBlocks;
+  var blocks = staticBlocks.contentBlocks;
+  var bp = (offsetPx + px) * bpPerPx;
+
+  if (bp < 0) {
+    var region = displayedRegions[0];
+    var snap = (0, _mobxStateTree.getSnapshot)(region); // @ts-ignore
+
+    return _objectSpread(_objectSpread({}, snap), {}, {
+      oob: true,
+      coord: region.reversed ? Math.floor(region.end - bp) + 1 : Math.floor(region.start + bp) + 1,
+      offset: bp,
+      index: 0
+    });
+  }
+
+  var interRegionPaddingBp = interRegionPaddingWidth * bpPerPx;
+  var currBlock = 0;
+
+  for (var i = 0; i < displayedRegions.length; i++) {
+    var _blocks$currBlock;
+
+    var _region = displayedRegions[i];
+    var len = _region.end - _region.start;
+    var offset = bp - bpSoFar;
+
+    if (len + bpSoFar > bp && bpSoFar <= bp) {
+      var _snap = (0, _mobxStateTree.getSnapshot)(_region); // @ts-ignore
+
+
+      return _objectSpread(_objectSpread({}, _snap), {}, {
+        oob: false,
+        offset: offset,
+        coord: _region.reversed ? Math.floor(_region.end - offset) + 1 : Math.floor(_region.start + offset) + 1,
+        index: i
+      });
+    } // add the interRegionPaddingWidth if the boundary is in the screen e.g. in
+    // a static block
+
+
+    if (((_blocks$currBlock = blocks[currBlock]) === null || _blocks$currBlock === void 0 ? void 0 : _blocks$currBlock.regionNumber) === i) {
+      bpSoFar += len + interRegionPaddingBp;
+      currBlock++;
+    } else {
+      bpSoFar += len;
+    }
+  }
+
+  if (bp >= bpSoFar) {
+    var _region2 = displayedRegions[displayedRegions.length - 1];
+
+    var _len = _region2.end - _region2.start;
+
+    var _offset = bp - bpSoFar + _len;
+
+    var _snap2 = (0, _mobxStateTree.getSnapshot)(_region2); // @ts-ignore
+
+
+    return _objectSpread(_objectSpread({}, _snap2), {}, {
+      oob: true,
+      offset: _offset,
+      coord: _region2.reversed ? Math.floor(_region2.end - _offset) + 1 : Math.floor(_region2.start + _offset) + 1,
+      index: displayedRegions.length - 1
+    });
+  }
+
+  return {
+    coord: 0,
+    index: 0,
+    refName: '',
+    oob: true,
+    assemblyName: '',
+    offset: 0,
+    start: 0,
+    end: 0,
+    reversed: false
+  };
+}
+
+function bpToPx(_ref) {
+  var refName = _ref.refName,
+      coord = _ref.coord,
+      regionNumber = _ref.regionNumber,
+      self = _ref.self;
+  var bpSoFar = 0;
+  var interRegionPaddingWidth = self.interRegionPaddingWidth,
+      bpPerPx = self.bpPerPx,
+      displayedRegions = self.displayedRegions,
+      staticBlocks = self.staticBlocks;
+  var blocks = staticBlocks.contentBlocks;
+  var interRegionPaddingBp = interRegionPaddingWidth * bpPerPx;
+  var currBlock = 0;
+  var i = 0;
+
+  for (; i < displayedRegions.length; i++) {
+    var _blocks$currBlock2;
+
+    var region = displayedRegions[i];
+    var len = region.end - region.start;
+
+    if (refName === region.refName && coord >= region.start && coord <= region.end) {
+      if (regionNumber ? regionNumber === i : true) {
+        bpSoFar += region.reversed ? region.end - coord : coord - region.start;
+        break;
+      }
+    } // add the interRegionPaddingWidth if the boundary is in the screen e.g. in
+    // a static block
+
+
+    if (((_blocks$currBlock2 = blocks[currBlock]) === null || _blocks$currBlock2 === void 0 ? void 0 : _blocks$currBlock2.regionNumber) === i) {
+      bpSoFar += len + interRegionPaddingBp;
+      currBlock++;
+    } else {
+      bpSoFar += len;
+    }
+  }
+
+  var found = displayedRegions[i];
+
+  if (found) {
+    return {
+      index: i,
+      offsetPx: Math.round(bpSoFar / bpPerPx)
+    };
+  }
+
+  return undefined;
+}

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

@@ -7,8 +7,6 @@ Object.defineProperty(exports, "__esModule", {
 });
 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");
@@ -21,9 +19,7 @@ var _calculateDynamicBlocks = _interopRequireDefault(require("./calculateDynamic
 
 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 _Base1DUtils = require("./Base1DUtils");
 
 var Base1DView = _mobxStateTree.types.model('Base1DView', {
   id: _mst.ElementId,
@@ -83,77 +79,8 @@ var Base1DView = _mobxStateTree.types.model('Base1DView', {
       }).reduce(function (a, b) {
         return 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 {
@@ -171,27 +98,26 @@ var Base1DView = _mobxStateTree.types.model('Base1DView', {
       }).reduce(function (a, b) {
         return 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
-     */
+  };
+}).views(function (self) {
+  return {
+    pxToBp: function pxToBp(px) {
+      return (0, _Base1DUtils.pxToBp)(self, px);
+    },
     bpToPx: function bpToPx(_ref) {
-      var _viewBpToPx;
+      var _bpToPx2;
 
       var refName = _ref.refName,
           coord = _ref.coord,
           regionNumber = _ref.regionNumber;
-      return (_viewBpToPx = (0, _index.viewBpToPx)({
+      return (_bpToPx2 = (0, _Base1DUtils.bpToPx)({
         refName: refName,
         coord: coord,
         regionNumber: regionNumber,
         self: self
-      })) === null || _viewBpToPx === void 0 ? void 0 : _viewBpToPx.offsetPx;
+      })) === null || _bpToPx2 === void 0 ? void 0 : _bpToPx2.offsetPx;
     }
   };
 }).actions(function (self) {
@@ -199,88 +125,12 @@ var Base1DView = _mobxStateTree.types.model('Base1DView', {
     setFeatures: function setFeatures(features) {
       self.features = features;
     },
-    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');
-      }
-    },
     // 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;
     },
-
-    /**
-     * offset is the base-pair-offset in the displayed region, index is the index of the
-     * displayed region in the linear genome view
-     *
-     * @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);
     },
@@ -292,24 +142,29 @@ var Base1DView = _mobxStateTree.types.model('Base1DView', {
       var bpPerPx = newBpPerPx;
 
       if (bpPerPx === self.bpPerPx) {
-        return;
+        return self.bpPerPx;
       }
 
       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);
+      return self.bpPerPx;
     },
     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) {
+    centerAt: function centerAt(coord, refName, regionNumber) {
+      if (!refName) {
+        return;
+      }
+
       var centerPx = self.bpToPx({
         refName: refName,
-        coord: bp,
-        regionNumber: regionIndex
+        coord: coord,
+        regionNumber: regionNumber
       });
 
       if (centerPx) {
@@ -324,6 +179,19 @@ var Base1DView = _mobxStateTree.types.model('Base1DView', {
       return newOffsetPx - oldOffsetPx;
     }
   };
+}).actions(function (self) {
+  return {
+    /**
+     * offset is the base-pair-offset in the displayed region, index is the index of the
+     * displayed region in the linear genome view
+     *
+     * @param start - object as `{start, end, offset, index}`
+     * @param end - object as `{start, end, offset, index}`
+     */
+    moveTo: function moveTo(start, end) {
+      (0, _Base1DUtils.moveTo)(self, start, end);
+    }
+  };
 });
 
 var _default = Base1DView;

package/util/color/index.js

@@ -19,7 +19,7 @@ Object.defineProperty(exports, "namedColorToHex", {
   }
 });
 
-var _colorManipulator = require("@material-ui/core/styles/colorManipulator");
+var _styles = require("@mui/material/styles");
 
 var _cssColorsLevel = require("./cssColorsLevel4");
 
@@ -51,7 +51,7 @@ function contrastingTextColor(color) {
 
 function getLuminance(color) {
   var convertedColor = (0, _cssColorsLevel.namedColorToHex)(color);
-  return (0, _colorManipulator.getLuminance)(convertedColor || color);
+  return (0, _styles.getLuminance)(convertedColor || color);
 }
 /**
  * Darken or lighten a color, depending on its luminance.
@@ -68,7 +68,7 @@ function getLuminance(color) {
 function emphasize(color) {
   var coefficient = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0.15;
   var convertedColor = (0, _cssColorsLevel.namedColorToHex)(color);
-  return (0, _colorManipulator.emphasize)(convertedColor || color, coefficient);
+  return (0, _styles.emphasize)(convertedColor || color, coefficient);
 }
 
 function makeContrasting(foreground) {
@@ -77,14 +77,14 @@ function makeContrasting(foreground) {
   var convertedForeground = (0, _cssColorsLevel.namedColorToHex)(foreground) || foreground;
   var convertedBackground = (0, _cssColorsLevel.namedColorToHex)(background) || background;
   var backgroundLuminance = getLuminance(convertedBackground);
-  var contrastRatio = (0, _colorManipulator.getContrastRatio)(convertedForeground, convertedBackground);
+  var contrastRatio = (0, _styles.getContrastRatio)(convertedForeground, convertedBackground);
   var originalColor = convertedForeground;
   var coefficient = 0.05;
 
   while (contrastRatio < minContrastRatio) {
-    convertedForeground = backgroundLuminance > 0.5 ? (0, _colorManipulator.darken)(originalColor, coefficient) : (0, _colorManipulator.lighten)(originalColor, coefficient);
+    convertedForeground = backgroundLuminance > 0.5 ? (0, _styles.darken)(originalColor, coefficient) : (0, _styles.lighten)(originalColor, coefficient);
     coefficient += 0.05;
-    contrastRatio = (0, _colorManipulator.getContrastRatio)(convertedForeground, convertedBackground);
+    contrastRatio = (0, _styles.getContrastRatio)(convertedForeground, convertedBackground);
   }
 
   return convertedForeground;