@jbrowse/plugin-linear-genome-view 1.7.11 → 2.0.0

package/dist/LinearGenomeView/index.test.js

@@ -1,1187 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-
-var _models = require("@jbrowse/core/pluggableElementTypes/models");
-
-var _TrackType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _ = require(".");
-
-var _2 = require("..");
-
-var _LinearBareDisplay = require("../LinearBareDisplay");
-
-var _hg38DisplayedRegions = _interopRequireDefault(require("./hg38DisplayedRegions.json"));
-
-var _volvoxDisplayedRegions = _interopRequireDefault(require("./volvoxDisplayedRegions.json"));
-
-// use initializer function to avoid having console.warn jest.fn in a global
-function initialize() {
-  console.warn = jest.fn(); // a stub linear genome view state model that only accepts base track types.
-  // used in unit tests.
-
-  var stubManager = new _PluginManager.default();
-  stubManager.addTrackType(function () {
-    var configSchema = (0, _configuration.ConfigurationSchema)('BasicTrack', {}, {
-      baseConfiguration: (0, _models.createBaseTrackConfig)(stubManager),
-      explicitIdentifier: 'trackId'
-    });
-    return new _TrackType.default({
-      name: 'BasicTrack',
-      configSchema: configSchema,
-      stateModel: (0, _models.createBaseTrackModel)(stubManager, 'BasicTrack', configSchema)
-    });
-  });
-  stubManager.addDisplayType(function () {
-    var configSchema = (0, _configuration.ConfigurationSchema)('LinearBareDisplay', {}, {
-      explicitlyTyped: true
-    });
-    return new _DisplayType.default({
-      name: 'LinearBareDisplay',
-      configSchema: configSchema,
-      stateModel: (0, _LinearBareDisplay.stateModelFactory)(configSchema),
-      trackType: 'BasicTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: _2.BaseLinearDisplayComponent
-    });
-  });
-  stubManager.createPluggableElements();
-  stubManager.configure();
-
-  var Assembly = _mobxStateTree.types.model({}).volatile(function () {
-    return {
-      regions: _volvoxDisplayedRegions.default
-    };
-  }).views(function () {
-    return {
-      getCanonicalRefName: function getCanonicalRefName(refName) {
-        if (refName === 'contigA') {
-          return 'ctgA';
-        }
-
-        return refName;
-      }
-    };
-  });
-
-  var AssemblyManager = _mobxStateTree.types.model({
-    assemblies: _mobxStateTree.types.map(Assembly)
-  }).actions(function (self) {
-    return {
-      isValidRefName: function isValidRefName(str) {
-        return str === 'ctgA' || str === 'ctgB';
-      },
-      get: function get(str) {
-        return self.assemblies.get(str);
-      }
-    };
-  });
-
-  var LinearGenomeModel = (0, _.stateModelFactory)(stubManager);
-
-  var Session = _mobxStateTree.types.model({
-    name: 'testSession',
-    rpcManager: 'rpcManagerExists',
-    view: _mobxStateTree.types.maybe(LinearGenomeModel),
-    configuration: _mobxStateTree.types.map(_mobxStateTree.types.string),
-    assemblyManager: _mobxStateTree.types.optional(AssemblyManager, {
-      assemblies: {
-        volvox: {
-          regions: _volvoxDisplayedRegions.default
-        }
-      }
-    })
-  }).actions(function (self) {
-    return {
-      setView: function setView(view) {
-        self.view = view;
-        return view;
-      }
-    };
-  });
-
-  return {
-    Session: Session,
-    LinearGenomeModel: LinearGenomeModel,
-    Assembly: Assembly
-  };
-}
-
-test('can instantiate a mostly empty model and read a default configuration value', function () {
-  var _initialize = initialize(),
-      Session = _initialize.Session,
-      LinearGenomeModel = _initialize.LinearGenomeModel;
-
-  var model = Session.create({
-    configuration: {}
-  }).setView(LinearGenomeModel.create({
-    type: 'LinearGenomeView',
-    tracks: [{
-      name: 'foo track',
-      type: 'BasicTrack'
-    }]
-  }));
-  expect(model.tracks[0]).toBeTruthy();
-  expect(model.trackSelectorType).toBe('hierarchical');
-});
-test('can instantiate a model that lets you navigate', function () {
-  var _initialize2 = initialize(),
-      Session = _initialize2.Session,
-      LinearGenomeModel = _initialize2.LinearGenomeModel;
-
-  var session = Session.create({
-    configuration: {}
-  });
-  var model = session.setView(LinearGenomeModel.create({
-    id: 'test1',
-    type: 'LinearGenomeView',
-    tracks: [{
-      name: 'foo track',
-      type: 'BasicTrack'
-    }]
-  }));
-  model.setWidth(800);
-  model.setDisplayedRegions([{
-    assemblyName: 'volvox',
-    start: 0,
-    end: 10000,
-    refName: 'ctgA'
-  }]);
-  expect(model.maxBpPerPx).toBeCloseTo(13.888);
-  model.setNewView(0.02, 0);
-  expect(model.scaleBarHeight).toEqual(20); // header height 20 + area where polygons get drawn has height of 48
-
-  expect(model.headerHeight).toEqual(68); // TODO: figure out how to better test height
-  // expect(model.height).toBe(191)
-  // test some sanity values from zooming around
-
-  model.setNewView(0.02, 0);
-  expect(model.pxToBp(10).offset).toEqual(0.2);
-  model.setNewView(0.1, 0);
-  expect(model.pxToBp(100).offset).toEqual(10);
-  model.setNewView(1, 0);
-  expect(model.pxToBp(100).offset).toEqual(100);
-  model.setNewView(10, 0);
-  expect(model.pxToBp(100).offset).toEqual(1000);
-  model.horizontallyFlip(); // this is actually the same in reverse mode, the offset is a representation of linear bp offset not actual bp
-
-  model.setNewView(0.02, 0);
-  expect(model.pxToBp(10).offset).toEqual(0.2);
-  model.setNewView(0.1, 0);
-  expect(model.pxToBp(100).offset).toEqual(10);
-  model.setNewView(1, 0);
-  expect(model.pxToBp(100).offset).toEqual(100);
-  model.setNewView(10, 0);
-  expect(model.pxToBp(100).offset).toEqual(1000);
-});
-test('can instantiate a model that has multiple displayed regions', function () {
-  var _initialize3 = initialize(),
-      Session = _initialize3.Session,
-      LinearGenomeModel = _initialize3.LinearGenomeModel;
-
-  var session = Session.create({
-    configuration: {}
-  });
-  var model = session.setView(LinearGenomeModel.create({
-    id: 'test2',
-    type: 'LinearGenomeView',
-    tracks: [{
-      name: 'foo track',
-      type: 'BasicTrack'
-    }]
-  }));
-  model.setWidth(800);
-  model.setDisplayedRegions([{
-    assemblyName: 'volvox',
-    start: 0,
-    end: 10000,
-    refName: 'ctgA'
-  }, {
-    assemblyName: 'volvox',
-    start: 0,
-    end: 10000,
-    refName: 'ctgB'
-  }]);
-  expect(model.maxBpPerPx).toBeCloseTo(27.777);
-  model.setNewView(0.02, 0);
-  expect(model.offsetPx).toEqual(0);
-  model.moveTo({
-    index: 0,
-    offset: 100
-  }, {
-    index: 0,
-    offset: 200
-  });
-  expect(model.offsetPx).toEqual(800);
-  model.moveTo({
-    index: 0,
-    offset: 9950
-  }, {
-    index: 1,
-    offset: 50
-  });
-  expect(model.offsetPx).toEqual(79401);
-});
-test('can instantiate a model that tests navTo/moveTo', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var _initialize4, Session, LinearGenomeModel, session, width, model;
-
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          _initialize4 = initialize(), Session = _initialize4.Session, LinearGenomeModel = _initialize4.LinearGenomeModel;
-          session = Session.create({
-            configuration: {}
-          });
-          width = 800;
-          model = session.setView(LinearGenomeModel.create({
-            id: 'test3',
-            type: 'LinearGenomeView',
-            tracks: [{
-              name: 'foo track',
-              type: 'BasicTrack'
-            }]
-          }));
-          model.setWidth(width);
-          model.setDisplayedRegions([{
-            assemblyName: 'volvox',
-            start: 0,
-            end: 10000,
-            refName: 'ctgA'
-          }, {
-            assemblyName: 'volvox',
-            start: 0,
-            end: 10000,
-            refName: 'ctgB'
-          }]);
-          expect(model.maxBpPerPx).toBeCloseTo(27.7777);
-          model.navTo({
-            refName: 'ctgA',
-            start: 0,
-            end: 100
-          });
-          expect(model.offsetPx).toBe(0);
-          expect(model.bpPerPx).toBe(0.125);
-          model.navTo({
-            refName: 'ctgA'
-          });
-          expect(model.offsetPx).toBe(0);
-          expect(model.bpPerPx).toBe(12.5);
-          model.navTo({
-            refName: 'contigA',
-            start: 0,
-            end: 100
-          });
-          expect(model.offsetPx).toBe(0);
-          expect(model.bpPerPx).toBe(0.125);
-          expect(function () {
-            return model.navTo({
-              refName: 'ctgA',
-              start: 200,
-              end: 100
-            });
-          }).toThrow('start "201" is greater than end "100"');
-          expect(function () {
-            return model.navTo({
-              refName: 'ctgDoesNotExist',
-              start: 0,
-              end: 100
-            });
-          }).toThrow('could not find a region with refName "ctgDoesNotExist"');
-          expect(function () {
-            return model.navTo({
-              refName: 'ctgA',
-              end: 20100
-            });
-          }).toThrow('could not find a region with refName "ctgA" that contained an end position 20100');
-          expect(function () {
-            return model.navTo({
-              refName: 'ctgA',
-              start: 20000
-            });
-          }).toThrow('could not find a region with refName "ctgA" that contained a start position 20001');
-          expect(function () {
-            return model.navTo({
-              refName: 'ctgA',
-              start: 20000,
-              end: 20100
-            });
-          }).toThrow('could not find a region that completely contained "ctgA:20,001..20,100"');
-          expect(function () {
-            return model.navTo({
-              refName: 'ctgA',
-              start: 0,
-              end: 20000
-            });
-          }).toThrow('could not find a region that completely contained "ctgA:1..20,000"');
-
-        case 22:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));
-test('can navToMultiple', function () {
-  var _initialize5 = initialize(),
-      Session = _initialize5.Session,
-      LinearGenomeModel = _initialize5.LinearGenomeModel;
-
-  var session = Session.create({
-    configuration: {}
-  });
-  var width = 800;
-  var model = session.setView(LinearGenomeModel.create({
-    id: 'testNavToMultiple',
-    type: 'LinearGenomeView'
-  }));
-  model.setWidth(width);
-  model.setDisplayedRegions([{
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 10000
-  }, {
-    assemblyName: 'volvox',
-    refName: 'ctgB',
-    start: 0,
-    end: 10000
-  }, {
-    assemblyName: 'volvox',
-    refName: 'ctgC',
-    start: 0,
-    end: 10000
-  }, {
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 10000
-  }, {
-    assemblyName: 'volvox',
-    refName: 'ctgC',
-    start: 0,
-    end: 10000
-  }]);
-  model.navToMultiple([{
-    refName: 'ctgA',
-    start: 0,
-    end: 10000
-  }]);
-  expect(model.offsetPx).toBe(0);
-  expect(model.bpPerPx).toBe(12.5);
-  model.navToMultiple([{
-    refName: 'ctgA',
-    start: 5000,
-    end: 10000
-  }, {
-    refName: 'ctgB',
-    start: 0,
-    end: 5000
-  }]);
-  expect(model.offsetPx).toBe(399);
-  expect(model.bpPerPx).toBeCloseTo(12.531);
-  model.navToMultiple([{
-    refName: 'ctgA',
-    start: 5000,
-    end: 10000
-  }, {
-    refName: 'ctgB',
-    start: 0,
-    end: 10000
-  }, {
-    refName: 'ctgC',
-    start: 0,
-    end: 5000
-  }]);
-  expect(model.offsetPx).toBe(199);
-  expect(model.bpPerPx).toBeCloseTo(25.126);
-  model.navToMultiple([{
-    refName: 'ctgA',
-    start: 5000,
-    end: 10000
-  }, {
-    refName: 'ctgC',
-    start: 0,
-    end: 5000
-  }]);
-  expect(model.offsetPx).toBe(2799);
-  expect(model.bpPerPx).toBeCloseTo(12.531);
-});
-describe('Zoom to selected displayed regions', function () {
-  var _initialize6 = initialize(),
-      Session = _initialize6.Session,
-      LinearGenomeModel = _initialize6.LinearGenomeModel;
-
-  var model;
-  var largestBpPerPx;
-  beforeEach(function () {
-    var session = Session.create({
-      configuration: {}
-    });
-    var width = 800;
-    model = session.setView(LinearGenomeModel.create({
-      id: 'testZoomToDisplayed',
-      type: 'LinearGenomeView'
-    }));
-    model.setWidth(width);
-    model.setDisplayedRegions([{
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 5000,
-      end: 20000
-    }, {
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 30000,
-      end: 40000
-    }, {
-      assemblyName: 'volvox',
-      refName: 'ctgB',
-      start: 0,
-      end: 3000
-    }]);
-  });
-  it('can select whole region', function () {
-    // should have no offset and largest bpPerPx
-    expect(model.offsetPx).toBe(0);
-    expect(model.bpPerPx).toEqual(1); // 'ctgA' 15000  bp+ 'ctgA' 10000 bp+ 'ctgB' 3000 bp = 28000 totalbp
-
-    expect(model.totalBp).toEqual(28000);
-    model.zoomToDisplayedRegions({
-      start: 5000,
-      index: 0,
-      end: 20000,
-      coord: 5001,
-      offset: 0,
-      refName: 'ctgA'
-    }, {
-      start: 0,
-      index: 2,
-      coord: 1,
-      end: 3000,
-      offset: 1,
-      refName: 'ctgB'
-    });
-    largestBpPerPx = model.bpPerPx;
-    expect(model.offsetPx).toEqual(0);
-    expect(model.bpPerPx).toBeCloseTo(31.408);
-  });
-  it('can select if start and end object are swapped', function () {
-    // should be same results as above test
-    model.zoomToDisplayedRegions({
-      start: 0,
-      index: 2,
-      coord: 1,
-      end: 3000,
-      offset: 1,
-      refName: 'ctgB'
-    }, {
-      start: 5000,
-      index: 0,
-      end: 20000,
-      coord: 5001,
-      offset: 0,
-      refName: 'ctgA'
-    });
-    expect(model.offsetPx).toEqual(0);
-    expect(model.bpPerPx).toBeCloseTo(31.408);
-  });
-  it('can select over one refSeq', function () {
-    model.zoomToDisplayedRegions({
-      start: 5000,
-      index: 0,
-      end: 20000,
-      coord: 5001,
-      offset: 0,
-      refName: 'ctgA'
-    }, {
-      start: 5000,
-      index: 0,
-      coord: 10000,
-      end: 20000,
-      offset: 5000,
-      refName: 'ctgA'
-    });
-    expect(model.offsetPx).toEqual(0); // 10000 - 5000 = 5000 / 800 = 6.25
-
-    expect(model.bpPerPx).toEqual(6.25);
-    expect(model.bpPerPx).toBeLessThan(largestBpPerPx);
-  });
-  it('can select one region with start or end outside of displayed region', function () {
-    model.zoomToDisplayedRegions({
-      start: 5000,
-      index: 0,
-      end: 20000,
-      coord: 4999,
-      offset: -1,
-      refName: 'ctgA'
-    }, {
-      start: 5000,
-      index: 0,
-      end: 20000,
-      coord: 19000,
-      offset: 19000,
-      refName: 'ctgA'
-    }); // offsetPx is still 0 since we are starting from the first coord
-
-    expect(model.offsetPx).toBe(0); // endOffset 19000 - (-1) = 19001 /  800 = zoomTo(23.75)
-
-    expect(model.bpPerPx).toBeCloseTo(23.75);
-    expect(model.bpPerPx).toBeLessThan(largestBpPerPx);
-  });
-  it('can select over two regions in the same reference sequence', function () {
-    model.setWidth(800);
-    model.showAllRegions();
-    expect(model.bpPerPx).toBeCloseTo(38.8888); // totalBp = 28000 / 1000 = 28 as maxBpPerPx
-
-    model.zoomToDisplayedRegions({
-      start: 5000,
-      index: 0,
-      end: 20000,
-      offset: 5000,
-      refName: 'ctgA'
-    }, {
-      start: 0,
-      index: 2,
-      end: 3000,
-      offset: 2000,
-      refName: 'ctgB'
-    }); // 22000 / 792 (width - interRegionPadding) = 27.78
-
-    expect(model.bpPerPx).toBeCloseTo(27.78, 0); // offset 5000 / bpPerPx (because that is the starting) = 180.5
-
-    expect(model.offsetPx).toBe(181);
-    expect(model.bpPerPx).toBeLessThan(largestBpPerPx);
-  });
-  it('can navigate to overlapping regions with a region between', function () {
-    model.setDisplayedRegions([{
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 5000,
-      end: 20000
-    }, {
-      assemblyName: 'volvox',
-      refName: 'ctgB',
-      start: 0,
-      end: 3000
-    }, {
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 35000
-    }]);
-    model.setWidth(800);
-    model.showAllRegions(); // totalBp 15000 + 3000 + 35000 = 53000
-    // then 53000 / (width*0.9) = 73.6111
-
-    expect(model.bpPerPx).toBeCloseTo(73.61111);
-    model.zoomToDisplayedRegions({
-      start: 5000,
-      coord: 15000,
-      index: 0,
-      end: 20000,
-      offset: 10000,
-      refName: 'ctgA'
-    }, {
-      start: 0,
-      coord: 15000,
-      index: 2,
-      end: 35000,
-      offset: 15000,
-      refName: 'ctgA'
-    });
-    expect(model.offsetPx).toBe(346); // 5000 + 3000 + 15000 / 792
-
-    expect(model.bpPerPx).toBeCloseTo(29.04, 0);
-    expect(model.bpPerPx).toBeLessThan(53);
-  });
-});
-test('can instantiate a model that >2 regions', function () {
-  var _initialize7 = initialize(),
-      Session = _initialize7.Session,
-      LinearGenomeModel = _initialize7.LinearGenomeModel;
-
-  var session = Session.create({
-    configuration: {}
-  });
-  var width = 800;
-  var model = session.setView(LinearGenomeModel.create({
-    id: 'test4',
-    type: 'LinearGenomeView',
-    tracks: [{
-      name: 'foo track',
-      type: 'BasicTrack'
-    }]
-  }));
-  model.setWidth(width);
-  model.setDisplayedRegions([{
-    assemblyName: 'volvox',
-    start: 0,
-    end: 10000,
-    refName: 'ctgA'
-  }, {
-    assemblyName: 'volvox',
-    start: 0,
-    end: 10000,
-    refName: 'ctgB'
-  }, {
-    assemblyName: 'volvox',
-    start: 0,
-    end: 10000,
-    refName: 'ctgC'
-  }]);
-  model.moveTo({
-    index: 0,
-    offset: 100
-  }, {
-    index: 2,
-    offset: 100
-  });
-  model.setNewView(1, 0); // extending in the minus gives us first displayed region
-
-  expect(model.pxToBp(-5000).refName).toEqual('ctgA');
-  expect(model.pxToBp(5000).refName).toEqual('ctgA');
-  expect(model.pxToBp(15000).refName).toEqual('ctgB');
-  expect(model.pxToBp(25000).refName).toEqual('ctgC'); // extending past gives us the last displayed region
-
-  expect(model.pxToBp(35000).refName).toEqual('ctgC');
-  model.setDisplayName('Volvox view');
-  expect(model.displayName).toBe('Volvox view');
-  model.moveTo({
-    refName: 'ctgA',
-    index: 0,
-    offset: 0,
-    start: 0,
-    end: 10000
-  }, {
-    refName: 'ctgC',
-    index: 2,
-    offset: 0,
-    start: 0,
-    end: 10000
-  });
-  model.moveTo({
-    refName: 'ctgB',
-    index: 1,
-    offset: 0,
-    start: 0,
-    end: 10000
-  }, {
-    refName: 'ctgC',
-    index: 2,
-    offset: 0,
-    start: 0,
-    end: 10000
-  });
-  expect(model.offsetPx).toEqual(10000 / model.bpPerPx + 2);
-  expect(model.displayedRegionsTotalPx).toEqual(30000 / model.bpPerPx);
-  model.showAllRegions();
-  expect(model.offsetPx).toEqual(-40);
-  expect(model.bpToPx({
-    refName: 'ctgA',
-    coord: 100
-  })).toEqual({
-    index: 0,
-    offsetPx: Math.round(100 / model.bpPerPx)
-  });
-  expect(model.bpToPx({
-    refName: 'ctgB',
-    coord: 100
-  })).toEqual({
-    index: 1,
-    offsetPx: Math.round(10100 / model.bpPerPx) + model.interRegionPaddingWidth
-  });
-});
-test('can perform bpToPx in a way that makes sense on things that happen outside', function () {
-  var _initialize8 = initialize(),
-      Session = _initialize8.Session,
-      LinearGenomeModel = _initialize8.LinearGenomeModel;
-
-  var session = Session.create({
-    configuration: {}
-  });
-  var width = 800;
-  var model = session.setView(LinearGenomeModel.create({
-    id: 'test5',
-    type: 'LinearGenomeView',
-    tracks: [{
-      name: 'foo track',
-      type: 'BasicTrack'
-    }]
-  }));
-  model.setWidth(width);
-  model.setDisplayedRegions([{
-    assemblyName: 'volvox',
-    start: 1000,
-    end: 2000,
-    refName: 'ctgA',
-    reversed: true
-  }]);
-  expect(model.bpToPx({
-    refName: 'ctgA',
-    coord: 500
-  })).toBe(undefined);
-  expect(model.pxToBp(-1).coord).toEqual(2002);
-  expect(model.pxToBp(100).offset).toEqual(100);
-  expect(model.pxToBp(100).coord).toEqual(1901); // testing bpToPx and pxToBp when region is reversed
-  // coordinate is out of bounds
-
-  expect(model.bpToPx({
-    refName: 'ctgA',
-    coord: 0
-  })).toEqual(undefined);
-  expect(model.bpToPx({
-    refName: 'ctgA',
-    coord: 2001
-  })).toEqual(undefined); // offset here should be 500 because coord 1500 - 1000 start = 500
-
-  expect(model.bpToPx({
-    refName: 'ctgA',
-    coord: 1500
-  })).toEqual({
-    index: 0,
-    offsetPx: 500
-  });
-  expect(model.pxToBp(-1).oob).toEqual(true);
-  model.centerAt(1500, 'ctgA', 0);
-  expect(model.bpPerPx).toEqual(1);
-  expect(model.offsetPx).toEqual(100);
-  model.toggleHeader();
-  expect(model.hideHeader).toEqual(true);
-  model.toggleHeader();
-  model.toggleHeaderOverview();
-  expect(model.hideHeaderOverview).toEqual(true);
-  model.toggleHeaderOverview();
-  model.setError(Error('pxToBp failed to map to a region'));
-  expect("".concat(model.error)).toEqual('Error: pxToBp failed to map to a region');
-}); // determined objectively by looking at
-// http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-Se2K5q_Jog&password=qT9on
-//
-// this test is important because interregionpadding blocks outside the current
-// view should not be taken into account
-
-test('can perform pxToBp on human genome things with ellided blocks (zoomed in)', function () {
-  var _initialize9 = initialize(),
-      Session = _initialize9.Session,
-      LinearGenomeModel = _initialize9.LinearGenomeModel;
-
-  var session = Session.create({
-    configuration: {}
-  });
-  var model = session.setView(LinearGenomeModel.create({
-    id: 'test6',
-    type: 'LinearGenomeView',
-    tracks: [{
-      name: 'foo track',
-      type: 'BasicTrack'
-    }]
-  }));
-  var width = 800;
-  model.setWidth(width);
-  model.setDisplayedRegions(_hg38DisplayedRegions.default);
-  model.setNewView(6359.273152497633, 503862);
-  expect(model.pxToBp(0).refName).toBe('Y');
-  expect(model.pxToBp(400).refName).toBe('Y');
-  expect(model.pxToBp(800).refName).toBe('Y_KI270740v1_random');
-}); // determined objectively from looking at http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-TUJdqKI2c9&password=01tan
-//
-// this tests some places on hg38 when zoomed to whole genome, so inter-region
-// padding blocks and elided blocks matter
-
-test('can perform pxToBp on human genome things with ellided blocks (zoomed out)', function () {
-  var _initialize10 = initialize(),
-      Session = _initialize10.Session,
-      LinearGenomeModel = _initialize10.LinearGenomeModel;
-
-  var session = Session.create({
-    configuration: {}
-  });
-  var model = session.setView(LinearGenomeModel.create({
-    id: 'test6',
-    type: 'LinearGenomeView',
-    tracks: [{
-      name: 'foo track',
-      type: 'BasicTrack'
-    }]
-  }));
-  var width = 800;
-  model.setWidth(width);
-  model.setDisplayedRegions(_hg38DisplayedRegions.default);
-  model.setNewView(3209286.105, -225.5083315372467); // chr1 to the left
-
-  expect(model.pxToBp(0).refName).toBe('1');
-  expect(model.pxToBp(0).oob).toBeTruthy(); // chr10 in the middle, tests a specific coord but should just be probably
-  // somewhat around here
-
-  expect(model.pxToBp(800).coord).toBe(111057351);
-  expect(model.pxToBp(800).refName).toBe('10'); // chrX after an ellided block, this tests a specific coord but should just be
-  // probably somewhat around here
-
-  expect(model.pxToBp(1228).coord).toBe(99349155);
-  expect(model.pxToBp(1228).refName).toBe('X'); // chrY_random at the end
-
-  expect(model.pxToBp(1500).refName).toBe('Y_KI270740v1_random');
-  expect(model.pxToBp(1500).oob).toBeTruthy();
-});
-test('can showAllRegionsInAssembly', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var _initialize11, Session, LinearGenomeModel, session, width, model;
-
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          _initialize11 = initialize(), Session = _initialize11.Session, LinearGenomeModel = _initialize11.LinearGenomeModel;
-          session = Session.create({
-            configuration: {}
-          });
-          width = 800;
-          model = session.setView(LinearGenomeModel.create({
-            id: 'test4',
-            type: 'LinearGenomeView',
-            tracks: [{
-              name: 'foo track',
-              type: 'BasicTrack'
-            }]
-          }));
-          model.setWidth(width);
-          model.showAllRegionsInAssembly('volvox');
-          expect(model.displayedRegions.map(function (reg) {
-            return reg.refName;
-          })).toEqual(['ctgA', 'ctgB']);
-
-        case 7:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));
-describe('Get Sequence for selected displayed regions', function () {
-  var _initialize12 = initialize(),
-      Session = _initialize12.Session,
-      LinearGenomeModel = _initialize12.LinearGenomeModel;
-  /* the start of all the results should be +1
-  the sequence dialog then handles converting from 1-based closed to interbase
-  */
-
-
-  var model;
-  beforeEach(function () {
-    var session = Session.create({
-      configuration: {}
-    });
-    var width = 800;
-    model = session.setView(LinearGenomeModel.create({
-      id: 'testGetSequenceSelectedRegions',
-      type: 'LinearGenomeView'
-    }));
-    model.setWidth(width);
-    model.setDisplayedRegions([{
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 50001
-    }, {
-      assemblyName: 'volvox',
-      refName: 'ctgB',
-      start: 0,
-      end: 6079
-    }]);
-  });
-  it('can select whole region and handles both offsets being oob', function () {
-    model.setDisplayedRegions([{
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 800
-    }]);
-    model.setOffsets({
-      refName: 'ctgA',
-      index: 0,
-      offset: -10,
-      start: 0,
-      end: 800,
-      coord: -10,
-      reversed: false,
-      assemblyName: 'volvox',
-      oob: true
-    }, {
-      refName: 'ctgA',
-      index: 0,
-      offset: 810,
-      start: 0,
-      end: 800,
-      coord: 810,
-      reversed: false,
-      assemblyName: 'volvox',
-      oob: true
-    });
-    var singleRegion = model.getSelectedRegions(model.leftOffset, model.rightOffset);
-    expect(singleRegion.length).toEqual(1);
-    expect(singleRegion[0].start).toEqual(0);
-    expect(singleRegion[0].end).toEqual(800);
-  });
-  it('handles when start or end offsets are out of bounds of displayed regions', function () {
-    model.setOffsets({
-      refName: 'ctgA',
-      start: 0,
-      end: 50001,
-      reversed: false,
-      assemblyName: 'volvox',
-      oob: true,
-      coord: -8,
-      offset: -8.77999706864357,
-      index: 0
-    }, {
-      refName: 'ctgA',
-      start: 0,
-      end: 50001,
-      reversed: false,
-      assemblyName: 'volvox',
-      oob: true,
-      coord: -4,
-      offset: -4.12999706864357,
-      index: 0
-    });
-    var outOfBounds = model.getSelectedRegions(model.leftOffset, model.rightOffset);
-    expect(outOfBounds.length).toEqual(0);
-  });
-  it('selects multiple regions with a region in between', function () {
-    model.setDisplayedRegions([{
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 500
-    }, {
-      assemblyName: 'volvox',
-      refName: 'ctgB',
-      start: 0,
-      end: 3000
-    }, {
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 200
-    }]);
-    model.setWidth(800);
-    model.showAllRegions(); // created by console logging getSelectedRegion's arguments after manually
-    // setting up this test case in the browser
-
-    model.setOffsets({
-      refName: 'ctgA',
-      start: 0,
-      end: 500,
-      reversed: false,
-      assemblyName: 'volvox',
-      oob: false,
-      offset: 200,
-      coord: 200,
-      index: 0
-    }, {
-      refName: 'ctgA',
-      start: 0,
-      end: 200,
-      reversed: false,
-      assemblyName: 'volvox',
-      oob: false,
-      offset: 100,
-      coord: 100,
-      index: 2
-    });
-    var overlapping = model.getSelectedRegions(model.leftOffset, model.rightOffset);
-    expect(overlapping.length).toEqual(3);
-    expect(overlapping[0].start).toEqual(200);
-    expect(overlapping[0].end).toEqual(500);
-    expect(overlapping[1].start).toEqual(0);
-    expect(overlapping[1].end).toEqual(3000);
-    expect(overlapping[2].start).toEqual(0);
-    expect(overlapping[2].end).toEqual(110);
-  });
-  it('can select over two regions in diff reference sequence', function () {
-    model.setDisplayedRegions([{
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 50001
-    }, {
-      assemblyName: 'volvox',
-      refName: 'ctgB',
-      start: 0,
-      end: 6079
-    }]);
-    model.setOffsets({
-      refName: 'ctgA',
-      index: 0,
-      offset: 49998,
-      start: 0,
-      end: 50001,
-      coord: 49999,
-      reversed: false,
-      assemblyName: 'volvox',
-      oob: false
-    }, {
-      refName: 'ctgB',
-      index: 1,
-      offset: 9,
-      start: 0,
-      end: 6079,
-      coord: 10,
-      reversed: false,
-      assemblyName: 'volvox',
-      oob: false
-    });
-    var multipleRegions = model.getSelectedRegions(model.leftOffset, model.rightOffset);
-    expect(multipleRegions.length).toEqual(2);
-    expect(multipleRegions[0].start).toEqual(49998);
-    expect(multipleRegions[0].end).toEqual(50001);
-    expect(multipleRegions[1].start).toEqual(0);
-    expect(multipleRegions[1].end).toEqual(9);
-  });
-  it('can handle horizontally flipped regions', function () {
-    model.setDisplayedRegions([{
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 50001,
-      reversed: true
-    }]);
-    var hfRegion = model.getSelectedRegions({
-      refName: 'ctgA',
-      start: 0,
-      end: 50001,
-      reversed: true,
-      assemblyName: 'volvox',
-      oob: false,
-      offset: 1.03696711063385,
-      coord: 50000,
-      index: 0
-    }, {
-      refName: 'ctgA',
-      start: 0,
-      end: 50001,
-      reversed: true,
-      assemblyName: 'volvox',
-      oob: false,
-      offset: 3.93696711063385,
-      coord: 49998,
-      index: 0
-    });
-    expect(hfRegion.length).toEqual(1);
-    expect(hfRegion[0].start).toEqual(49997);
-    expect(hfRegion[0].end).toEqual(50000);
-  });
-});
-test('navToLocString with human assembly', function () {
-  var _initialize13 = initialize(),
-      LinearGenomeModel = _initialize13.LinearGenomeModel;
-
-  var HumanAssembly = _mobxStateTree.types.model({}).volatile(function () {
-    return {
-      regions: _hg38DisplayedRegions.default
-    };
-  }).views(function () {
-    return {
-      getCanonicalRefName: function getCanonicalRefName(refName) {
-        return refName.replace('chr', '');
-      }
-    };
-  });
-
-  var AssemblyManager = _mobxStateTree.types.model({
-    assemblies: _mobxStateTree.types.map(HumanAssembly)
-  }).actions(function (self) {
-    return {
-      isValidRefName: function isValidRefName(str) {
-        return !str.includes(':');
-      },
-      get: function get(str) {
-        return self.assemblies.get(str);
-      }
-    };
-  });
-
-  var HumanSession = _mobxStateTree.types.model({
-    name: 'testSession',
-    rpcManager: 'rpcManagerExists',
-    configuration: _mobxStateTree.types.map(_mobxStateTree.types.string),
-    assemblyManager: AssemblyManager,
-    view: LinearGenomeModel
-  });
-
-  var model = HumanSession.create({
-    configuration: {},
-    assemblyManager: {
-      assemblies: {
-        hg38: {
-          regions: _hg38DisplayedRegions.default
-        }
-      }
-    },
-    view: {
-      type: 'LinearGenomeView'
-    }
-  });
-  model.view.setWidth(800);
-  model.view.setDisplayedRegions(_hg38DisplayedRegions.default.slice(0, 1));
-  model.view.navToLocString('2');
-  expect(model.view.bpPerPx).toBe(_hg38DisplayedRegions.default[1].end / model.view.width);
-  model.view.navToLocString('chr3');
-  expect(model.view.bpPerPx).toBe(_hg38DisplayedRegions.default[2].end / model.view.width);
-  model.view.navToLocString('chr3:1,000,000,000-1,100,000,000');
-  expect(model.view.bpPerPx).toBe(0.02);
-  expect(model.view.offsetPx).toBe(9914777550);
-  model.view.navToLocString('chr3:-1,100,000,000..-1,000,000,000');
-});
-test('multi region', function () {
-  var _initialize14 = initialize(),
-      Session = _initialize14.Session,
-      LinearGenomeModel = _initialize14.LinearGenomeModel;
-
-  var model = Session.create({
-    configuration: {}
-  }).setView(LinearGenomeModel.create({
-    type: 'LinearGenomeView',
-    tracks: [{
-      name: 'foo track',
-      type: 'BasicTrack'
-    }]
-  }));
-  model.setWidth(800);
-  model.setDisplayedRegions(_volvoxDisplayedRegions.default.slice(0, 1));
-  model.navToLocString('ctgA ctgB');
-  expect(model.displayedRegions[0].refName).toBe('ctgA');
-  expect(model.displayedRegions[1].refName).toBe('ctgB');
-});
-test('space separated locstring', function () {
-  var _initialize15 = initialize(),
-      Session = _initialize15.Session,
-      LinearGenomeModel = _initialize15.LinearGenomeModel;
-
-  var model = Session.create({
-    configuration: {}
-  }).setView(LinearGenomeModel.create({
-    type: 'LinearGenomeView',
-    tracks: [{
-      name: 'foo track',
-      type: 'BasicTrack'
-    }]
-  }));
-  model.setWidth(800);
-  model.setDisplayedRegions(_volvoxDisplayedRegions.default.slice(0, 1));
-  model.navToLocString('ctgA 0 100');
-  expect(model.offsetPx).toBe(0);
-  expect(model.bpPerPx).toBe(0.125);
-});