@jbrowse/plugin-linear-genome-view 1.7.10 → 2.0.1

package/src/index.ts

@@ -11,7 +11,7 @@ import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
-import LineStyleIcon from '@material-ui/icons/LineStyle'
+import LineStyleIcon from '@mui/icons-material/LineStyle'
 import {
   BaseLinearDisplay,
   BaseLinearDisplayComponent,

package/dist/LinearBareDisplay/index.test.js

@@ -1,33 +0,0 @@
-"use strict";
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _ = require(".");
-
-test('config schema renderer type', function () {
-  var stubPluginManager = {
-    pluggableConfigSchemaType: function pluggableConfigSchemaType(type) {
-      var one = (0, _configuration.ConfigurationSchema)("".concat(type, "_TypeOne"), {}, {
-        explicitlyTyped: true
-      });
-      var two = (0, _configuration.ConfigurationSchema)("".concat(type, "_TypeTwo"), {}, {
-        explicitlyTyped: true
-      });
-      var three = (0, _configuration.ConfigurationSchema)("".concat(type, "_TypeThree"), {}, {
-        explicitlyTyped: true
-      });
-      return _mobxStateTree.types.union(one, two, three);
-    }
-  };
-  var configSchema = (0, _.configSchemaFactory)(stubPluginManager);
-  var instance = configSchema.create({
-    type: 'LinearBareDisplay',
-    displayId: 'displayId0',
-    renderer: {
-      type: 'renderer_TypeTwo'
-    }
-  });
-  expect(instance.renderer.type).toBe('renderer_TypeTwo');
-});

package/dist/LinearGenomeView/components/LinearGenomeView.test.js

@@ -1,234 +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 _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-require("@testing-library/jest-dom/extend-expect");
-
-var _rootModel = require("@jbrowse/web/src/rootModel");
-
-require("requestidlecallback-polyfill");
-
-var _LinearGenomeView = _interopRequireDefault(require("./LinearGenomeView"));
-
-jest.mock('@jbrowse/web/src/makeWorkerInstance', function () {
-  return function () {};
-});
-var assemblyConf = {
-  name: 'volMyt1',
-  sequence: {
-    trackId: 'sequenceConfigId',
-    type: 'ReferenceSequenceTrack',
-    adapter: {
-      type: 'FromConfigSequenceAdapter',
-      features: [{
-        refName: 'ctgA',
-        uniqueId: 'firstId',
-        start: 0,
-        end: 10,
-        seq: 'cattgttgcg'
-      }]
-    }
-  }
-};
-describe('<LinearGenomeView />', function () {
-  it('renders setup wizard', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    var session, model, _render, findByText;
-
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            session = (0, _rootModel.createTestSession)();
-            session.addAssemblyConf(assemblyConf);
-            session.addView('LinearGenomeView', {
-              id: 'lgv'
-            });
-            model = session.views[0];
-            model.setWidth(800);
-            _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_LinearGenomeView.default, {
-              model: model
-            })), findByText = _render.findByText;
-            expect(model.displayedRegions.length).toEqual(0);
-            _context.t0 = _react2.fireEvent;
-            _context.next = 10;
-            return findByText('Open');
-
-          case 10:
-            _context.t1 = _context.sent;
-
-            _context.t0.click.call(_context.t0, _context.t1);
-
-            _context.next = 14;
-            return (0, _react2.waitFor)(function () {
-              expect(model.displayedRegions.length).toEqual(1);
-            });
-
-          case 14:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  })));
-  it('renders one track, one region', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-    var session, model, _render2, container, findByText;
-
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            session = (0, _rootModel.createTestSession)();
-            session.addAssemblyConf(assemblyConf);
-            session.addTrackConf({
-              trackId: 'testConfig',
-              assemblyNames: ['volMyt1'],
-              name: 'Foo Track',
-              type: 'BasicTrack',
-              adapter: {
-                type: 'FromConfigAdapter',
-                features: []
-              }
-            });
-            session.addView('LinearGenomeView', {
-              type: 'LinearGenomeView',
-              id: 'lgv',
-              offsetPx: 0,
-              bpPerPx: 1,
-              tracks: [{
-                id: 'foo',
-                type: 'BasicTrack',
-                height: 20,
-                configuration: 'testConfig',
-                displays: [{
-                  type: 'LinearBareDisplay',
-                  configuration: 'testConfig-LinearBareDisplay'
-                }]
-              }],
-              displayedRegions: [{
-                assemblyName: 'volMyt1',
-                refName: 'ctgA',
-                start: 0,
-                end: 100
-              }]
-            });
-            model = session.views[0];
-            model.setWidth(800);
-            _render2 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_LinearGenomeView.default, {
-              model: model
-            })), container = _render2.container, findByText = _render2.findByText;
-            _context2.next = 9;
-            return findByText('Foo Track');
-
-          case 9:
-            _context2.next = 11;
-            return findByText('100bp');
-
-          case 11:
-            expect(container.firstChild).toMatchSnapshot();
-
-          case 12:
-          case "end":
-            return _context2.stop();
-        }
-      }
-    }, _callee2);
-  })));
-  it('renders two tracks, two regions', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-    var session, model, _render3, container, findByText, findAllByTestId;
-
-    return _regenerator.default.wrap(function _callee3$(_context3) {
-      while (1) {
-        switch (_context3.prev = _context3.next) {
-          case 0:
-            session = (0, _rootModel.createTestSession)();
-            session.addAssemblyConf(assemblyConf);
-            session.addTrackConf({
-              trackId: 'testConfig',
-              name: 'Foo Track',
-              assemblyNames: ['volMyt1'],
-              type: 'BasicTrack',
-              adapter: {
-                type: 'FromConfigAdapter',
-                features: []
-              }
-            });
-            session.addTrackConf({
-              trackId: 'testConfig2',
-              name: 'Bar Track',
-              assemblyNames: ['volMyt1'],
-              type: 'BasicTrack',
-              adapter: {
-                type: 'FromConfigAdapter',
-                features: []
-              }
-            });
-            session.addView('LinearGenomeView', {
-              id: 'lgv',
-              offsetPx: 0,
-              bpPerPx: 1,
-              displayedRegions: [{
-                assemblyName: 'volMyt1',
-                refName: 'ctgA',
-                start: 0,
-                end: 100
-              }, {
-                assemblyName: 'volMyt1',
-                refName: 'ctgB',
-                start: 1000,
-                end: 2000
-              }],
-              tracks: [{
-                id: 'foo',
-                type: 'BasicTrack',
-                height: 20,
-                configuration: 'testConfig',
-                displays: [{
-                  type: 'LinearBareDisplay',
-                  configuration: 'testConfig-LinearBareDisplay'
-                }]
-              }, {
-                id: 'bar',
-                type: 'BasicTrack',
-                height: 20,
-                configuration: 'testConfig2',
-                displays: [{
-                  type: 'LinearBareDisplay',
-                  configuration: 'testConfig2-LinearBareDisplay'
-                }]
-              }]
-            });
-            model = session.views[0];
-            model.setWidth(800);
-            _render3 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_LinearGenomeView.default, {
-              model: model
-            })), container = _render3.container, findByText = _render3.findByText, findAllByTestId = _render3.findAllByTestId;
-            _context3.next = 10;
-            return findByText('Foo Track');
-
-          case 10:
-            _context3.next = 12;
-            return findByText('798bp');
-
-          case 12:
-            _context3.next = 14;
-            return findAllByTestId('svgfeatures');
-
-          case 14:
-            expect(container.firstChild).toMatchSnapshot();
-
-          case 15:
-          case "end":
-            return _context3.stop();
-        }
-      }
-    }, _callee3);
-  })));
-});

package/dist/LinearGenomeView/components/ScaleBar.test.js

@@ -1,180 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _rootModel = require("@jbrowse/web/src/rootModel");
-
-var _ScaleBar = _interopRequireDefault(require("./ScaleBar"));
-
-/* eslint-disable @typescript-eslint/no-explicit-any */
-jest.mock('@jbrowse/web/src/makeWorkerInstance', function () {
-  return function () {};
-});
-describe('ScaleBar genome view component', function () {
-  it('renders two regions', function () {
-    var session = (0, _rootModel.createTestSession)({
-      views: [{
-        type: 'LinearGenomeView',
-        offsetPx: 0,
-        bpPerPx: 1,
-        displayedRegions: [{
-          assemblyName: 'volvox',
-          refName: 'ctgA',
-          start: 0,
-          end: 100
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgB',
-          start: 100,
-          end: 200
-        }],
-        tracks: [],
-        configuration: {}
-      }]
-    });
-    session.addAssemblyConf({
-      name: 'volMyt1',
-      sequence: {
-        trackId: 'ref0',
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'FromConfigSequenceAdapter',
-          features: [{
-            refName: 'ctgA',
-            uniqueId: 'firstId',
-            start: 0,
-            end: 10,
-            seq: 'cattgttgcg'
-          }]
-        }
-      }
-    });
-    var model = session.views[0];
-
-    var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ScaleBar.default, {
-      model: model
-    })),
-        getByTestId = _render.getByTestId;
-
-    var ret1 = getByTestId('refLabel-ctgA');
-    var ret2 = getByTestId('refLabel-ctgB');
-    expect(ret1.style.left).toBe('-1px');
-    expect(ret2.style.left).toBe('101px');
-  });
-  it('renders two regions when scrolled to the left, the label is ctgA to the actual blocks', function () {
-    var session = (0, _rootModel.createTestSession)({
-      views: [{
-        type: 'LinearGenomeView',
-        offsetPx: -100,
-        bpPerPx: 1,
-        displayedRegions: [{
-          assemblyName: 'volvox',
-          refName: 'ctgA',
-          start: 0,
-          end: 100
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgB',
-          start: 0,
-          end: 100
-        }],
-        tracks: [],
-        configuration: {}
-      }]
-    });
-    session.addAssemblyConf({
-      name: 'volMyt1',
-      sequence: {
-        trackId: 'ref0',
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'FromConfigSequenceAdapter',
-          features: [{
-            refName: 'ctgA',
-            uniqueId: 'firstId',
-            start: 0,
-            end: 10,
-            seq: 'cattgttgcg'
-          }]
-        }
-      }
-    });
-    var model = session.views[0];
-
-    var _render2 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ScaleBar.default, {
-      model: model
-    })),
-        getByTestId = _render2.getByTestId;
-
-    var ret1 = getByTestId('refLabel-ctgA');
-    var ret2 = getByTestId('refLabel-ctgB');
-    expect(ret1.style.left).toBe('99px');
-    expect(ret2.style.left).toBe('201px');
-  });
-  it('renders two regions when scrolled to the left, the label is ctgA to the actual blocks', function () {
-    var session = (0, _rootModel.createTestSession)({
-      views: [{
-        type: 'LinearGenomeView',
-        offsetPx: -100,
-        bpPerPx: 1,
-        displayedRegions: [{
-          assemblyName: 'volvox',
-          refName: 'ctgA',
-          start: 0,
-          end: 1000
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgB',
-          start: 0,
-          end: 1
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgC',
-          start: 0,
-          end: 1
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgD',
-          start: 0,
-          end: 1
-        }],
-        tracks: [],
-        configuration: {}
-      }]
-    });
-    session.addAssemblyConf({
-      name: 'volMyt1',
-      sequence: {
-        trackId: 'ref0',
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'FromConfigSequenceAdapter',
-          features: [{
-            refName: 'ctgA',
-            uniqueId: 'firstId',
-            start: 0,
-            end: 10,
-            seq: 'cattgttgcg'
-          }]
-        }
-      }
-    });
-    var model = session.views[0];
-
-    var _render3 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ScaleBar.default, {
-      model: model
-    })),
-        queryByTestId = _render3.queryByTestId;
-
-    var ret2 = queryByTestId('refLabel-ctgB');
-    var ret3 = queryByTestId('refLabel-ctgC');
-    var ret4 = queryByTestId('refLabel-ctgD');
-    expect(ret2).toBe(null);
-    expect(ret3).toBe(null);
-    expect(ret4).toBe(null);
-  });
-});

package/dist/LinearGenomeView/components/VerticalGuides.js

@@ -1,116 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _blockTypes = require("@jbrowse/core/util/blockTypes");
-
-var _styles = require("@material-ui/core/styles");
-
-var _clsx = _interopRequireDefault(require("clsx"));
-
-var _mobxReact = require("mobx-react");
-
-var _react = _interopRequireDefault(require("react"));
-
-var _Block = require("../../BaseLinearDisplay/components/Block");
-
-var _util = require("../util");
-
-var useStyles = (0, _styles.makeStyles)(function (theme) {
-  return {
-    verticalGuidesZoomContainer: {
-      position: 'absolute',
-      height: '100%',
-      width: '100%',
-      zIndex: 1,
-      pointerEvents: 'none'
-    },
-    verticalGuidesContainer: {
-      position: 'absolute',
-      height: '100%',
-      zIndex: 1,
-      pointerEvents: 'none',
-      display: 'flex'
-    },
-    tick: {
-      position: 'absolute',
-      height: '100%',
-      width: 1
-    },
-    majorTick: {
-      background: theme.palette.text.hint
-    },
-    minorTick: {
-      background: theme.palette.divider
-    }
-  };
-});
-var RenderedVerticalGuides = (0, _mobxReact.observer)(function (_ref) {
-  var model = _ref.model;
-  var classes = useStyles();
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, model.staticBlocks.map(function (block, index) {
-    if (block instanceof _blockTypes.ContentBlock) {
-      var ticks = (0, _util.makeTicks)(block.start, block.end, model.bpPerPx);
-      return /*#__PURE__*/_react.default.createElement(_Block.ContentBlock, {
-        key: "".concat(block.key, "-").concat(index),
-        block: block
-      }, ticks.map(function (tick) {
-        var x = (block.reversed ? block.end - tick.base : tick.base - block.start) / model.bpPerPx;
-        return /*#__PURE__*/_react.default.createElement("div", {
-          key: tick.base,
-          className: (0, _clsx.default)(classes.tick, tick.type === 'major' || tick.type === 'labeledMajor' ? classes.majorTick : classes.minorTick),
-          style: {
-            left: x
-          }
-        });
-      }));
-    }
-
-    if (block instanceof _blockTypes.ElidedBlock) {
-      return /*#__PURE__*/_react.default.createElement(_Block.ElidedBlock, {
-        key: block.key,
-        width: block.widthPx
-      });
-    }
-
-    if (block instanceof _blockTypes.InterRegionPaddingBlock) {
-      return /*#__PURE__*/_react.default.createElement(_Block.InterRegionPaddingBlock, {
-        key: block.key,
-        width: block.widthPx,
-        boundary: block.variant === 'boundary'
-      });
-    }
-
-    return null;
-  }));
-});
-
-function VerticalGuides(_ref2) {
-  var model = _ref2.model;
-  var classes = useStyles(); // find the block that needs pinning to the left side for context
-
-  var offsetLeft = model.staticBlocks.offsetPx - model.offsetPx;
-  return /*#__PURE__*/_react.default.createElement("div", {
-    className: classes.verticalGuidesZoomContainer,
-    style: {
-      transform: model.scaleFactor !== 1 ? "scaleX(".concat(model.scaleFactor, ")") : undefined
-    }
-  }, /*#__PURE__*/_react.default.createElement("div", {
-    className: classes.verticalGuidesContainer,
-    style: {
-      left: offsetLeft,
-      width: model.staticBlocks.totalWidthPx
-    }
-  }, /*#__PURE__*/_react.default.createElement(RenderedVerticalGuides, {
-    model: model
-  })));
-}
-
-var _default = (0, _mobxReact.observer)(VerticalGuides);
-
-exports.default = _default;