@jbrowse/plugin-wiggle 1.7.11 → 2.1.0

package/dist/WiggleRendering.test.js

@@ -1,52 +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");
-
-var _WiggleRendering = _interopRequireDefault(require("./WiggleRendering"));
-
-// these tests do very little, let's try to expand them at some point
-test('one', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var _render, container, getByTestId, test;
-
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_WiggleRendering.default, {
-            width: 500,
-            height: 500,
-            features: new Map(),
-            highResolutionScaling: 1,
-            regions: [{
-              refName: 'chr1',
-              start: 1,
-              end: 3
-            }],
-            bpPerPx: 3,
-            config: {
-              type: 'DummyRenderer'
-            }
-          })), container = _render.container, getByTestId = _render.getByTestId;
-          _context.next = 3;
-          return getByTestId('wiggle-rendering-test');
-
-        case 3:
-          test = _context.sent;
-          expect(_react2.fireEvent.click(test)).toBeTruthy();
-          expect(container.firstChild).toMatchSnapshot();
-
-        case 6:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/XYPlotRenderer/XYPlotRenderer.test.js

@@ -1,87 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _offscreenCanvasUtils = require("@jbrowse/core/util/offscreenCanvasUtils");
-
-var _ = _interopRequireWildcard(require("."));
-
-var _canvas = require("canvas");
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-global.nodeImage = _canvas.Image;
-global.nodeCreateCanvas = _canvas.createCanvas;
-test('several features', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var pluginManager, renderer, renderProps, res;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          pluginManager = {};
-          renderer = new _.default({
-            name: 'XYPlotRenderer',
-            ReactComponent: _.ReactComponent,
-            configSchema: _.configSchema,
-            pluginManager: pluginManager
-          });
-          renderProps = {
-            features: [new _simpleFeature.default({
-              id: 't1',
-              data: {
-                start: 1,
-                end: 100,
-                score: 1
-              }
-            }), new _simpleFeature.default({
-              id: 't2',
-              data: {
-                start: 101,
-                end: 200,
-                score: 2
-              }
-            })],
-            regions: [{
-              end: 100,
-              start: 1
-            }],
-            scaleOpts: {
-              domain: [0, 100],
-              scaleType: 'linear'
-            },
-            config: {},
-            bpPerPx: 3,
-            highResolutionScaling: 1,
-            height: 100,
-            ticks: {
-              values: [0, 100]
-            }
-          };
-          _context.next = 5;
-          return (0, _offscreenCanvasUtils.renderToAbstractCanvas)(1000, 200, renderProps, function (ctx) {
-            return renderer.draw(ctx, renderProps);
-          });
-
-        case 5:
-          res = _context.sent;
-          expect(res).toMatchSnapshot({
-            imageData: expect.any(Object)
-          });
-
-        case 7:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/declare.d.js

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

package/dist/index.test.js

@@ -1,24 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _ = _interopRequireDefault(require("."));
-
-test('plugin in a stock JBrowse', function () {
-  console.warn = jest.fn();
-  var pluginManager = new _PluginManager.default([new _.default()]);
-  pluginManager.createPluggableElements();
-  pluginManager.configure();
-  expect(function () {
-    return pluginManager.addPlugin(new _.default());
-  }).toThrow(/JBrowse already configured, cannot add plugins/);
-  var BigWigAdapter = pluginManager.getAdapterType('BigWigAdapter');
-  var config = BigWigAdapter.configSchema.create({
-    type: 'BigWigAdapter'
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-});

package/dist/util.test.js

@@ -1,66 +0,0 @@
-"use strict";
-
-var _util = require("./util");
-
-test('linear scale', function () {
-  var scaleType = 'linear';
-  var domain = [0, 100];
-  var range = [0, 100];
-  var scale = (0, _util.getScale)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range
-  });
-  expect(scale.domain()).toEqual(domain);
-});
-test('log scale', function () {
-  var scaleType = 'log';
-  var domain = [1, 100];
-  var range = [0, 100];
-  var scale = (0, _util.getScale)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range
-  });
-  expect(scale.domain()).toEqual([1, 128]);
-});
-test('test inverted', function () {
-  var scaleType = 'log';
-  var inverted = true;
-  var domain = [1, 100];
-  var range = [0, 100];
-  var scale = (0, _util.getScale)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range,
-    inverted: inverted
-  });
-  expect(scale.domain()).toEqual([1, 128]);
-  expect(scale.range()).toEqual(range.reverse());
-});
-test('test minScore', function () {
-  var scaleType = 'linear';
-  var domain = [0, 100];
-  var range = [0, 100];
-  var bounds = [50, undefined];
-  var ret = (0, _util.getNiceDomain)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range,
-    bounds: bounds
-  });
-  expect(ret).toEqual([50, 100]);
-});
-test('test min and max score', function () {
-  var scaleType = 'linear';
-  var domain = [1, 100];
-  var range = [0, 100];
-  var bounds = [undefined, 70];
-  var ret = (0, _util.getNiceDomain)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range,
-    bounds: bounds
-  });
-  expect(ret).toEqual([0, 70]);
-});

package/src/LinePlotRenderer/LinePlotRenderer.js

@@ -1,91 +0,0 @@
-import { readConfObject } from '@jbrowse/core/configuration'
-import { featureSpanPx } from '@jbrowse/core/util'
-import { getScale } from '../util'
-import WiggleBaseRenderer from '../WiggleBaseRenderer'
-import { YSCALEBAR_LABEL_OFFSET } from '../LinearWiggleDisplay/models/model'
-
-export default class LinePlotRenderer extends WiggleBaseRenderer {
-  draw(ctx, props) {
-    const {
-      features,
-      regions,
-      bpPerPx,
-      scaleOpts,
-      height: unadjustedHeight,
-      ticks: { values },
-      displayCrossHatches,
-      config,
-    } = props
-    const [region] = regions
-    const width = (region.end - region.start) / bpPerPx
-    const offset = YSCALEBAR_LABEL_OFFSET
-
-    // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
-    // wiggle display, and makes the height of the actual drawn area add
-    // "padding" to the top and bottom of the display
-    const height = unadjustedHeight - offset * 2
-    const clipColor = readConfObject(config, 'clipColor')
-    const highlightColor = readConfObject(config, 'highlightColor')
-    const scale = getScale({ ...scaleOpts, range: [0, height] })
-    const [niceMin, niceMax] = scale.domain()
-    const toY = rawscore => height - scale(rawscore) + offset
-    const colorCallback =
-      readConfObject(config, 'color') === '#f0f'
-        ? () => 'grey'
-        : feature => readConfObject(config, 'color', { feature })
-
-    let lastVal
-    for (const feature of features.values()) {
-      const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)
-      const score = feature.get('score')
-      const lowClipping = score < niceMin
-      const highClipping = score > niceMax
-      const w = rightPx - leftPx + 0.3 // fudge factor for subpixel rendering
-
-      const c = colorCallback(feature)
-
-      ctx.strokeStyle = c
-      ctx.beginPath()
-      if (!region.reversed) {
-        ctx.moveTo(
-          leftPx,
-          toY(typeof lastVal !== 'undefined' ? lastVal : score),
-        )
-        ctx.lineTo(leftPx, toY(score))
-        ctx.lineTo(rightPx, toY(score))
-      } else {
-        ctx.moveTo(
-          rightPx,
-          toY(typeof lastVal !== 'undefined' ? lastVal : score),
-        )
-        ctx.lineTo(rightPx, toY(score))
-        ctx.lineTo(leftPx, toY(score))
-      }
-      ctx.stroke()
-      lastVal = score
-
-      if (highClipping) {
-        ctx.fillStyle = clipColor
-        ctx.fillRect(leftPx, 0, w, 4)
-      } else if (lowClipping && scaleOpts.scaleType !== 'log') {
-        ctx.fillStyle = clipColor
-        ctx.fillRect(leftPx, height - 4, w, height)
-      }
-      if (feature.get('highlighted')) {
-        ctx.fillStyle = highlightColor
-        ctx.fillRect(leftPx, 0, w, height)
-      }
-    }
-
-    if (displayCrossHatches) {
-      ctx.lineWidth = 1
-      ctx.strokeStyle = 'rgba(200,200,200,0.8)'
-      values.forEach(tick => {
-        ctx.beginPath()
-        ctx.moveTo(0, Math.round(toY(tick)))
-        ctx.lineTo(width, Math.round(toY(tick)))
-        ctx.stroke()
-      })
-    }
-  }
-}

package/src/LinePlotRenderer/configSchema.js

@@ -1,68 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
-
-export default ConfigurationSchema(
-  'WiggleRenderer',
-  {
-    color: {
-      type: 'color',
-      description: 'the color of track, overrides posColor and negColor',
-      defaultValue: '#f0f',
-    },
-    posColor: {
-      type: 'color',
-      description: 'the color to use when the score is positive',
-      defaultValue: 'blue',
-    },
-    negColor: {
-      type: 'color',
-      description: 'the color to use when the score is negative',
-      defaultValue: 'red',
-    },
-    highlightColor: {
-      type: 'color',
-      description: 'the color of highlights over the wiggle track',
-      defaultValue: 'rgba(255,255,0,0.5)',
-    },
-    clipColor: {
-      type: 'color',
-      description: 'the color of the clipping marker',
-      defaultValue: 'red',
-    },
-    renderType: {
-      type: 'stringEnum',
-      model: types.enumeration('Rendering type', ['xyplot', 'density', 'line']),
-      description: 'The type of rendering for wiggle data to use',
-      defaultValue: 'xyplot',
-    },
-    filled: {
-      type: 'boolean',
-      description: 'fill in histogram',
-      defaultValue: true,
-    },
-    bicolorPivot: {
-      type: 'stringEnum',
-      model: types.enumeration('Scale type', [
-        'numeric',
-        'mean',
-        'z_score',
-        'none',
-      ]),
-      description: 'type of bicolor pivot',
-      defaultValue: 'numeric',
-    },
-    bicolorPivotValue: {
-      type: 'number',
-      defaultValue: 0,
-      description: 'value to use for bicolor pivot',
-    },
-    summaryScoreMode: {
-      type: 'stringEnum',
-      model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
-      description:
-        'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
-      defaultValue: 'whiskers',
-    },
-  },
-  { explicitlyTyped: true },
-)