@jbrowse/core 1.7.11 → 2.1.0

package/ui/theme.test.js

@@ -1,111 +0,0 @@
-"use strict";
-
-var _theme = require("./theme");
-
-describe('theme utils', function () {
-  it('can create a default theme', function () {
-    var theme = (0, _theme.createJBrowseTheme)();
-    expect(theme.palette.primary.main).toEqual('#0D233F');
-    expect(theme.palette.secondary.main).toEqual('#721E63');
-    expect(theme.palette.tertiary.main).toEqual('#135560');
-    expect(theme.palette.quaternary.main).toEqual('#FFB11D');
-  });
-  it('allows overriding primary and secondary colors', function () {
-    var theme = (0, _theme.createJBrowseTheme)({
-      palette: {
-        primary: {
-          main: '#888888'
-        },
-        secondary: {
-          main: 'rgb(137,137,137)'
-        }
-      }
-    });
-    expect(theme.palette.primary.main).toEqual('#888888');
-    expect(theme.palette.secondary.main).toEqual('rgb(137,137,137)');
-  });
-  it('allows overriding tertiary and quaternary colors', function () {
-    var theme = (0, _theme.createJBrowseTheme)({
-      palette: {
-        tertiary: {
-          main: '#888'
-        },
-        quaternary: {
-          main: 'hsl(0,0,54)'
-        }
-      }
-    });
-    expect(theme.palette.tertiary.main).toEqual('#888');
-    expect(theme.palette.tertiary.light).toBeTruthy();
-    expect(theme.palette.quaternary.main).toEqual('hsl(0,0,54)');
-    expect(theme.palette.quaternary.dark).toBeTruthy();
-  });
-  it('allows customizing spacing', function () {
-    var defaultTheme = (0, _theme.createJBrowseTheme)();
-    expect(defaultTheme.spacing(1)).toBe(4);
-    var biggerSpacingTheme = (0, _theme.createJBrowseTheme)({
-      spacing: 16
-    });
-    expect(biggerSpacingTheme.spacing(1)).toBe(16);
-  });
-  it('allows adding a custom override', function () {
-    var _theme$overrides;
-
-    var muiPaperStyle = {
-      root: {
-        backgroundColor: 'green'
-      }
-    };
-    var theme = (0, _theme.createJBrowseTheme)({
-      overrides: {
-        MuiPaper: muiPaperStyle
-      }
-    });
-    expect((_theme$overrides = theme.overrides) === null || _theme$overrides === void 0 ? void 0 : _theme$overrides.MuiPaper).toEqual(muiPaperStyle);
-    expect(Object.keys(theme.overrides || {}).length).toBe(10);
-  });
-  it('allows modifying a default override', function () {
-    var _theme$overrides2;
-
-    var muiButtonStyle = {
-      textSecondary: {
-        color: 'orange'
-      }
-    };
-    var theme = (0, _theme.createJBrowseTheme)({
-      overrides: {
-        MuiButton: muiButtonStyle
-      }
-    });
-    expect((_theme$overrides2 = theme.overrides) === null || _theme$overrides2 === void 0 ? void 0 : _theme$overrides2.MuiButton).toEqual(muiButtonStyle);
-    expect(Object.keys(theme.overrides || {}).length).toBe(9);
-  });
-  it('allows adding a custom prop', function () {
-    var _theme$props;
-
-    var muiPaperProps = {
-      variant: 'outlined'
-    };
-    var theme = (0, _theme.createJBrowseTheme)({
-      props: {
-        MuiPaper: muiPaperProps
-      }
-    });
-    expect((_theme$props = theme.props) === null || _theme$props === void 0 ? void 0 : _theme$props.MuiPaper).toEqual(muiPaperProps);
-    expect(Object.keys(theme.props || {}).length).toBe(18);
-  });
-  it('allows modifying a prop override', function () {
-    var _theme$props2;
-
-    var muiButtonProps = {
-      size: 'medium'
-    };
-    var theme = (0, _theme.createJBrowseTheme)({
-      props: {
-        MuiButton: muiButtonProps
-      }
-    });
-    expect((_theme$props2 = theme.props) === null || _theme$props2 === void 0 ? void 0 : _theme$props2.MuiButton).toEqual(muiButtonProps);
-    expect(Object.keys(theme.props || {}).length).toBe(17);
-  });
-});

package/util/Base1DViewModel.test.js

@@ -1,130 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _Base1DViewModel = _interopRequireDefault(require("./Base1DViewModel"));
-
-test('create Base1DView and set displayedRegions', function () {
-  var model = _Base1DViewModel.default.create({
-    bpPerPx: 1,
-    offsetPx: 0
-  });
-
-  model.setDisplayedRegions([{
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 40000
-  }, {
-    assemblyName: 'volvox',
-    refName: 'ctgB',
-    start: 0,
-    end: 3000
-  }]);
-  model.setVolatileWidth(800);
-  expect(model.width).toBe(800);
-  model.setBpPerPx(2);
-  expect(model.bpPerPx).toBe(2);
-  expect(model.displayedRegions).toBeTruthy();
-});
-test('Able to set bpPerPx, width and calculate widths', function () {
-  var model = _Base1DViewModel.default.create({
-    bpPerPx: 0,
-    offsetPx: 0
-  });
-
-  model.setDisplayedRegions([{
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 40000
-  }, {
-    assemblyName: 'volvox',
-    refName: 'ctgB',
-    start: 600,
-    end: 3000
-  }]);
-  model.setVolatileWidth(800);
-  expect(model.width).toBe(800);
-  model.setBpPerPx(1);
-  expect(model.bpPerPx).toBe(1); // 40000 + (3000 - 600 = 2400) = 42400
-
-  expect(model.totalBp).toEqual(42400); // 40000 + (3000 - 600 = 2400) = 42400 / 1 (bpPerPx) = 42400
-
-  expect(model.displayedRegionsTotalPx).toEqual(42400);
-  expect(model.interRegionPaddingWidth).toEqual(0);
-  expect(model.minimumBlockWidth).toEqual(0);
-});
-test('Able to set and showAll Regions', function () {
-  var model = _Base1DViewModel.default.create({
-    bpPerPx: 0,
-    offsetPx: 0
-  });
-
-  model.setDisplayedRegions([{
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 40000
-  }, {
-    assemblyName: 'volvox',
-    refName: 'ctgB',
-    start: 600,
-    end: 3000
-  }]);
-  model.setVolatileWidth(800);
-  expect(model.width).toBe(800);
-  model.setBpPerPx(1);
-  expect(model.bpPerPx).toBe(1); // 400 is expected because the bpPerPx is set to 1
-
-  expect(model.pxToBp(400).offset).toEqual(400);
-  model.showAllRegions(); // offset is equal to zero after making a call to showAllRegions
-
-  expect(model.offsetPx).toEqual(0); // bpPerPx should now equal totalbp 42400 / width 800
-
-  expect(model.bpPerPx).toEqual(53);
-});
-test('Navigate to displayedRegions', function () {
-  var model = _Base1DViewModel.default.create({
-    bpPerPx: 0,
-    offsetPx: 0
-  });
-
-  model.setDisplayedRegions([{
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 40000
-  }]);
-  model.setVolatileWidth(800);
-  expect(model.width).toBe(800);
-  model.showAllRegions(); // totalBp 40000 / 800 = 50
-
-  expect(model.bpPerPx).toBe(50);
-  model.moveTo({
-    start: 0,
-    end: 40000,
-    offset: 5000,
-    index: 0
-  }, {
-    start: 0,
-    end: 40000,
-    offset: 15000,
-    index: 0
-  }); // 15000 - 5000 = 1000 / 800
-  // zooming To newBpPerPx 12.5
-  // the offset is now 5000 start / bpPerPx = 400
-
-  expect(model.offsetPx).toEqual(400); // previous bpPerPx was calculated to be 12.5 ...
-  // zooming in should be 12.5 / 2 = 6.25
-
-  model.zoomIn();
-  expect(model.bpPerPx).toEqual(6.25);
-  model.zoomOut();
-  expect(model.bpPerPx).toEqual(12.5); // lets scroll back to zero since we moved to bp 5000
-
-  model.scroll(-400); // offsetPx should be 0 because we have old offsetPx of 400
-  // clamp takes 400 + -400 then clamping returns 0
-
-  expect(model.offsetPx).toEqual(0);
-});

package/util/calculateDynamicBlocks.test.js

@@ -1,74 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _calculateDynamicBlocks = _interopRequireDefault(require("./calculateDynamicBlocks"));
-
-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 ctgA = {
-  assemblyName: 'test',
-  refName: 'ctgA',
-  start: 0,
-  end: 50000
-};
-test('one', function () {
-  expect((0, _calculateDynamicBlocks.default)({
-    offsetPx: 0,
-    width: 200,
-    displayedRegions: [ctgA],
-    bpPerPx: 1,
-    minimumBlockWidth: 20,
-    interRegionPaddingWidth: 2
-  }).getBlocks()).toMatchSnapshot();
-});
-test('two', function () {
-  expect((0, _calculateDynamicBlocks.default)({
-    offsetPx: 0,
-    width: 200,
-    displayedRegions: [_objectSpread(_objectSpread({}, ctgA), {}, {
-      reversed: true
-    })],
-    bpPerPx: 1,
-    minimumBlockWidth: 20,
-    interRegionPaddingWidth: 2
-  }).getBlocks()).toMatchSnapshot();
-});
-test('three', function () {
-  expect((0, _calculateDynamicBlocks.default)({
-    offsetPx: -100,
-    width: 200,
-    displayedRegions: [_objectSpread(_objectSpread({}, ctgA), {}, {
-      reversed: true
-    })],
-    bpPerPx: 1,
-    minimumBlockWidth: 20,
-    interRegionPaddingWidth: 2
-  }).getBlocks()).toMatchSnapshot();
-});
-test('four', function () {
-  expect((0, _calculateDynamicBlocks.default)({
-    offsetPx: -100,
-    width: 350,
-    displayedRegions: [ctgA],
-    bpPerPx: 1,
-    minimumBlockWidth: 20,
-    interRegionPaddingWidth: 2
-  }).getBlocks()).toMatchSnapshot();
-});
-test('five', function () {
-  expect((0, _calculateDynamicBlocks.default)({
-    offsetPx: 521,
-    width: 927,
-    displayedRegions: [_objectSpread(_objectSpread({}, ctgA), {}, {
-      reversed: false
-    })],
-    bpPerPx: 0.05,
-    minimumBlockWidth: 20,
-    interRegionPaddingWidth: 2
-  }).getBlocks()).toMatchSnapshot();
-});

package/util/calculateStaticBlocks.test.js

@@ -1,297 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _calculateStaticBlocks = _interopRequireDefault(require("./calculateStaticBlocks"));
-
-describe('block calculation', function () {
-  it('can calculate some blocks 1', function () {
-    var blocks1 = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 0,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 10000
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    var blocks2 = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 0,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 10000
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blocks1).toMatchSnapshot();
-    expect(blocks1).toEqual(blocks2);
-  });
-  it('can calculate some blocks 2', function () {
-    var blocks = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 30,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 100
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgB',
-        start: 100,
-        end: 200
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blocks).toMatchSnapshot();
-  });
-  it('can calculate some blocks (should be empty because offscreen to the right)', function () {
-    var blockSet = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 2000,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 100
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgB',
-        start: 100,
-        end: 200
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blockSet.getBlocks()).toEqual([]);
-  });
-  it('can calculate some blocks (should be empty because offscreen to the left)', function () {
-    var blockSet = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: -2000,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 100
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgB',
-        start: 100,
-        end: 200
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blockSet.getBlocks()).toEqual([]);
-  });
-  it('can calculate some blocks 5', function () {
-    var blocks = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 5000,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 10000
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgB',
-        start: 100,
-        end: 10000
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blocks).toMatchSnapshot();
-  });
-  it('can calculate some blocks 6', function () {
-    var blockSet = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 0,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 200
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgB',
-        start: 0,
-        end: 1000
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blockSet).toMatchSnapshot();
-    expect(blockSet.blocks[1].offsetPx).toBe(0);
-  });
-  it('can calculate some blocks 7', function () {
-    var blocks = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 801,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 200
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgB',
-        start: 0,
-        end: 1000
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blocks).toMatchSnapshot();
-  });
-  it('can calculate some blocks 8', function () {
-    var blocks = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 1600,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 200
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgB',
-        start: 0,
-        end: 10000000
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blocks).toMatchSnapshot();
-  });
-  it('can calculate some blocks 9', function () {
-    var blockSet = (0, _calculateStaticBlocks.default)({
-      width: 800,
-      offsetPx: 1069,
-      bpPerPx: 2,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 50000
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgB',
-        start: 0,
-        end: 300
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blockSet).toMatchSnapshot();
-  });
-  it('can calculate some blocks 10', function () {
-    var blockSet = (0, _calculateStaticBlocks.default)({
-      width: 800,
-      offsetPx: 0,
-      bpPerPx: 0.05,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 100,
-        end: 200
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 300,
-        end: 400
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    }); // console.log(JSON.stringify(blockSet.blocks, null, '  '))
-
-    expect(blockSet.blocks[1].offsetPx).toBe(0);
-    expect(blockSet.blocks).toMatchSnapshot();
-  });
-});
-describe('reverse block calculation', function () {
-  test('1', function () {
-    var blocks = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 0,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 10000,
-        reversed: true
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blocks).toMatchSnapshot();
-  });
-});
-describe('reversed displayed regions', function () {
-  test('without elided region', function () {
-    var blocks = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 0,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 100,
-        end: 200,
-        reversed: true
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 500,
-        end: 600,
-        reversed: true
-      }],
-      minimumBlockWidth: 20,
-      interRegionPaddingWidth: 2
-    });
-    expect(blocks).toMatchSnapshot();
-  });
-  test('with elided region', function () {
-    var blocks = (0, _calculateStaticBlocks.default)({
-      bpPerPx: 1,
-      width: 800,
-      offsetPx: 0,
-      minimumBlockWidth: 2,
-      displayedRegions: [{
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 1,
-        reversed: true
-      }, {
-        assemblyName: 'test',
-        refName: 'ctgA',
-        start: 0,
-        end: 10000,
-        reversed: true
-      }],
-      interRegionPaddingWidth: 2
-    }, true, true, 1, 800);
-    expect(blocks).toMatchSnapshot();
-  });
-});

package/util/declare.d.js

@@ -1 +0,0 @@
-"use strict";

package/util/formatFastaStrings.test.js

@@ -1,40 +0,0 @@
-"use strict";
-
-var _formatFastaStrings = require("./formatFastaStrings");
-
-describe('formatting seqChunks and strings into Fasta format', function () {
-  var small = 'cattgttgcg';
-  var medium = 'cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgattatgattggttctttagcct';
-  var large = 'cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgattatgattggttctttagcctt';
-  it('sequence length is less than 80 characters', function () {
-    var formattedSmallFasta = (0, _formatFastaStrings.formatFastaLines)(small);
-    expect(formattedSmallFasta).toMatchSnapshot();
-  });
-  it('sequence length is 80 characters', function () {
-    var formattedMediumFasta = (0, _formatFastaStrings.formatFastaLines)(medium);
-    expect(formattedMediumFasta).toMatchSnapshot();
-  });
-  it('sequence length is more than 80 characters', function () {
-    var formattedLargeFasta = (0, _formatFastaStrings.formatFastaLines)(large);
-    expect(formattedLargeFasta).toMatchSnapshot();
-  });
-  it('formats headers and sequence', function () {
-    var chunks = [{
-      header: 'ctgA:1-10',
-      seq: small
-    }, {
-      header: 'ctgB:1-81',
-      seq: large
-    }];
-    var formattedFastaFile = (0, _formatFastaStrings.formatSeqFasta)(chunks);
-    /*
-    >ctgA:1-10
-    cattgttgcg
-    >ctgB:1-81
-    cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgattatgattggttctttagcct
-    t
-    */
-
-    expect(formattedFastaFile).toMatchSnapshot();
-  });
-});