@jbrowse/plugin-wiggle 1.6.4 → 1.6.7

package/dist/BigWigAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 export default _default;

package/dist/DensityRenderer/index.d.ts

@@ -3,4 +3,4 @@ export { default as ReactComponent } from '../WiggleRendering';
 export default class DensityRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): void;
 }
-export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/LinePlotRenderer/LinePlotRenderer.d.ts

@@ -2,7 +2,7 @@ export default class LinePlotRenderer extends WiggleBaseRenderer {
     constructor(stuff: {
         name: string;
         ReactComponent: import("react").ComponentType<any>;
-        configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+        configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         pluginManager: import("@jbrowse/core/PluginManager").default;
     });
 }

package/dist/LinePlotRenderer/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare var _default: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+declare var _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 export default _default;

package/dist/LinePlotRenderer/index.d.ts

@@ -1,3 +1,3 @@
 export { default as ReactComponent } from "../WiggleRendering";
 export { default } from "./LinePlotRenderer";
-export const configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+export const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/LinearWiggleDisplay/components/Tooltip.d.ts

@@ -8,7 +8,7 @@ declare const Tooltip: ({ model, height, clientMouseCoord, offsetMouseCoord, cli
     height: number;
     clientMouseCoord: Coord;
     offsetMouseCoord: Coord;
-    clientRect?: ClientRect | undefined;
+    clientRect?: DOMRect | undefined;
     TooltipContents: React.FC<any>;
 }) => JSX.Element | null;
 declare const WiggleTooltip: (props: {
@@ -18,7 +18,7 @@ declare const WiggleTooltip: (props: {
     height: number;
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;
-    clientRect?: ClientRect;
+    clientRect?: DOMRect;
 }) => JSX.Element;
 export default WiggleTooltip;
 export { Tooltip };

package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts

@@ -1,10 +1,8 @@
 /// <reference types="react" />
 import { WiggleDisplayModel } from '../models/model';
-export declare const YScaleBar: ({ model, orientation, }: {
-    model: WiggleDisplayModel;
-    orientation?: string | undefined;
-}) => JSX.Element;
+import YScaleBar from './YScaleBar';
 declare const LinearWiggleDisplay: (props: {
     model: WiggleDisplayModel;
 }) => JSX.Element;
 export default LinearWiggleDisplay;
+export { YScaleBar };

package/dist/LinearWiggleDisplay/components/YScaleBar.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { WiggleDisplayModel } from '../models/model';
+declare const YScaleBar: ({ model, orientation, }: {
+    model: WiggleDisplayModel;
+    orientation?: string | undefined;
+}) => JSX.Element | null;
+export default YScaleBar;

package/dist/LinearWiggleDisplay/models/configSchema.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/LinearWiggleDisplay/models/model.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 export declare const YSCALEBAR_LABEL_OFFSET = 5;
 declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
@@ -204,10 +204,10 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     stats: {
         scoreMin: number;
         scoreMax: number;
-    } & import("mobx").IObservableObject;
+    };
     statsFetchInProgress: AbortController | undefined;
 } & {
-    updateStats(stats: {
+    updateStats({ scoreMin, scoreMax, }: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -247,7 +247,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         stats: {
             scoreMin: number;
             scoreMax: number;
-        } & import("mobx").IObservableObject;
+        };
         autoscaleType: any;
         scaleType: any;
         inverted: any;

package/dist/WiggleBaseRenderer.d.ts

@@ -38,5 +38,5 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
         reactElement?: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)> | undefined;
         html?: string | undefined;
     }>;
-    abstract draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserialized): void;
+    abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): void;
 }

package/dist/XYPlotRenderer/index.d.ts

@@ -1,3 +1,3 @@
 export { default as ReactComponent } from '../WiggleRendering';
 export { default } from './XYPlotRenderer';
-export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 export default _default;

package/dist/index.d.ts

@@ -211,10 +211,10 @@ export default class WigglePlugin extends Plugin {
                 stats: {
                     scoreMin: number;
                     scoreMax: number;
-                } & import("mobx").IObservableObject;
+                };
                 statsFetchInProgress: AbortController | undefined;
             } & {
-                updateStats(stats: {
+                updateStats({ scoreMin, scoreMax, }: {
                     scoreMin: number;
                     scoreMax: number;
                 }): void;
@@ -254,7 +254,7 @@ export default class WigglePlugin extends Plugin {
                     stats: {
                         scoreMin: number;
                         scoreMax: number;
-                    } & import("mobx").IObservableObject;
+                    };
                     autoscaleType: any;
                     scaleType: any;
                     inverted: any;
@@ -482,10 +482,10 @@ export default class WigglePlugin extends Plugin {
                 stats: {
                     scoreMin: number;
                     scoreMax: number;
-                } & import("mobx").IObservableObject;
+                };
                 statsFetchInProgress: AbortController | undefined;
             } & {
-                updateStats(stats: {
+                updateStats({ scoreMin, scoreMax, }: {
                     scoreMin: number;
                     scoreMax: number;
                 }): void;
@@ -525,7 +525,7 @@ export default class WigglePlugin extends Plugin {
                     stats: {
                         scoreMin: number;
                         scoreMax: number;
-                    } & import("mobx").IObservableObject;
+                    };
                     autoscaleType: any;
                     scaleType: any;
                     inverted: any;
@@ -574,10 +574,10 @@ export default class WigglePlugin extends Plugin {
             blockKey: string;
         }) => JSX.Element;
         XYPlotRenderer: typeof XYPlotRenderer;
-        xyPlotRendererConfigSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+        xyPlotRendererConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         utils: typeof utils;
         WiggleBaseRenderer: typeof WiggleBaseRenderer;
-        linearWiggleDisplayModelFactory: (pluginManager: PluginManager, configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
+        linearWiggleDisplayModelFactory: (pluginManager: PluginManager, configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -777,10 +777,10 @@ export default class WigglePlugin extends Plugin {
             stats: {
                 scoreMin: number;
                 scoreMax: number;
-            } & import("mobx").IObservableObject;
+            };
             statsFetchInProgress: AbortController | undefined;
         } & {
-            updateStats(stats: {
+            updateStats({ scoreMin, scoreMax, }: {
                 scoreMin: number;
                 scoreMax: number;
             }): void;
@@ -820,7 +820,7 @@ export default class WigglePlugin extends Plugin {
                 stats: {
                     scoreMin: number;
                     scoreMax: number;
-                } & import("mobx").IObservableObject;
+                };
                 autoscaleType: any;
                 scaleType: any;
                 inverted: any;

package/dist/plugin-wiggle.cjs.development.js

@@ -22,7 +22,7 @@ var mobxStateTree = require('mobx-state-tree');
 var pluginLinearGenomeView = require('@jbrowse/plugin-linear-genome-view');
 var tracks = require('@jbrowse/core/util/tracks');
 var mobx = require('mobx');
-var reactD3Axis = require('react-d3-axis');
+var reactD3AxisMod = require('react-d3-axis-mod');
 var core = require('@material-ui/core');
 var reactPopper = require('react-popper');
 var Color = _interopDefault(require('color'));
@@ -1621,6 +1621,11 @@ function WiggleConfigFactory(pluginManager) {
       model: mobxStateTree.types.enumeration('Autoscale type', ['global', 'local', 'globalsd', 'localsd', 'zscore']),
       description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)'
     },
+    minimalTicks: {
+      type: 'boolean',
+      defaultValue: false,
+      description: 'use the minimal amount of ticks'
+    },
     minScore: {
       type: 'number',
       defaultValue: Number.MIN_VALUE,
@@ -1688,7 +1693,7 @@ var useStyles = /*#__PURE__*/core.makeStyles(function (theme) {
       color: theme.palette.common.white,
       fontFamily: theme.typography.fontFamily,
       padding: '4px 8px',
-      fontSize: theme.typography.pxToRem(10),
+      fontSize: theme.typography.pxToRem(12),
       lineHeight: "".concat(round(14 / 10), "em"),
       maxWidth: 300,
       wordWrap: 'break-word'
@@ -1794,25 +1799,32 @@ var YScaleBar = /*#__PURE__*/mobxReact.observer(function (_ref) {
   var model = _ref.model,
       orientation = _ref.orientation;
   var ticks = model.ticks;
-  return React__default.createElement(reactD3Axis.Axis, Object.assign({}, ticks, {
+  return ticks ? React__default.createElement(reactD3AxisMod.Axis, Object.assign({}, ticks, {
+    shadow: 2,
     format: function format(n) {
       return n;
     },
     style: {
-      orient: orientation === 'left' ? reactD3Axis.LEFT : reactD3Axis.RIGHT
+      orient: orientation === 'left' ? reactD3AxisMod.LEFT : reactD3AxisMod.RIGHT
     }
-  }));
+  })) : null;
 });
+
 var LinearWiggleDisplay = /*#__PURE__*/mobxReact.observer(function (props) {
   var model = props.model;
   var stats = model.stats,
       height = model.height,
-      needsScalebar = model.needsScalebar;
+      needsScalebar = model.needsScalebar; // @ts-ignore
+
+  var _getContainingView = util.getContainingView(model),
+      trackLabels = _getContainingView.trackLabels;
+
+  var left = trackLabels === 'overlapping' ? util.measureText(configuration.getConf(util.getContainingTrack(model), 'name'), 12.8) + 100 : 50;
   return React__default.createElement("div", null, React__default.createElement(pluginLinearGenomeView.BaseLinearDisplayComponent, Object.assign({}, props)), stats && needsScalebar ? React__default.createElement("svg", {
     style: {
       position: 'absolute',
       top: 0,
-      left: 300,
+      left: left,
       pointerEvents: 'none',
       height: height,
       width: 50
@@ -1833,15 +1845,6 @@ var YSCALEBAR_LABEL_OFFSET = 5; // using a map because it preserves order
 
 var rendererTypes = /*#__PURE__*/new Map([['xyplot', 'XYPlotRenderer'], ['density', 'DensityRenderer'], ['line', 'LinePlotRenderer']]);
 
-function logb(x, y) {
-  return Math.log(y) / Math.log(x);
-}
-
-function round$1(v) {
-  var b = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 1.5;
-  return (v >= 0 ? 1 : -1) * Math.pow(b, 1 + Math.floor(logb(b, Math.abs(v))));
-}
-
 var stateModelFactory = function stateModelFactory(pluginManager, configSchema) {
   return mobxStateTree.types.compose('LinearWiggleDisplay', pluginLinearGenomeView.BaseLinearDisplay, mobxStateTree.types.model({
     type: mobxStateTree.types.literal('LinearWiggleDisplay'),
@@ -1865,17 +1868,25 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
     return {
       statsReady: false,
       message: undefined,
-      stats: mobx.observable({
+      stats: {
         scoreMin: 0,
         scoreMax: 50
-      }),
+      },
       statsFetchInProgress: undefined
     };
   }).actions(function (self) {
     return {
-      updateStats: function updateStats(stats) {
-        self.stats.scoreMin = stats.scoreMin;
-        self.stats.scoreMax = stats.scoreMax;
+      updateStats: function updateStats(_ref) {
+        var scoreMin = _ref.scoreMin,
+            scoreMax = _ref.scoreMax;
+
+        if (self.stats.scoreMin !== scoreMin || self.stats.scoreMax !== scoreMax) {
+          self.stats = {
+            scoreMin: scoreMin,
+            scoreMax: scoreMax
+          };
+        }
+
         self.statsReady = true;
       },
       setColor: function setColor(color) {
@@ -2020,25 +2031,16 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
             scaleType = self.scaleType,
             minScore = self.minScore,
             maxScore = self.maxScore;
+        var scoreMin = stats.scoreMin,
+            scoreMax = stats.scoreMax;
         var ret = getNiceDomain({
-          domain: [stats.scoreMin, stats.scoreMax],
+          domain: [scoreMin, scoreMax],
           bounds: [minScore, maxScore],
           scaleType: scaleType
-        });
-        var headroom = configuration.getConf(self, 'headroom') || 0; // avoid weird scalebar if log value and empty region displayed
+        }); // avoid weird scalebar if log value and empty region displayed
 
         if (scaleType === 'log' && ret[1] === Number.MIN_VALUE) {
           return [0, Number.MIN_VALUE];
-        } // heuristic to just give some extra headroom on bigwig scores if no
-        // maxScore/minScore specified (they have MAX_VALUE/MIN_VALUE if so)
-
-
-        if (maxScore === Number.MAX_VALUE && ret[1] > 1.0) {
-          ret[1] = round$1(ret[1] + headroom);
-        }
-
-        if (minScore === Number.MIN_VALUE && ret[0] < -1.0) {
-          ret[0] = round$1(ret[0] - headroom);
         } // avoid returning a new object if it matches the old value
 
 
@@ -2082,6 +2084,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
         var scaleType = self.scaleType,
             domain = self.domain,
             height = self.height;
+        var minimalTicks = configuration.getConf(self, 'minimalTicks');
         var range = [height - YSCALEBAR_LABEL_OFFSET, YSCALEBAR_LABEL_OFFSET];
         var scale = getScale({
           scaleType: scaleType,
@@ -2089,8 +2092,10 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
           range: range,
           inverted: configuration.getConf(self, 'inverted')
         });
-        var ticks = height < 50 ? 2 : 4;
-        return reactD3Axis.axisPropsFromTickScale(scale, ticks);
+        var ticks = reactD3AxisMod.axisPropsFromTickScale(scale, 4);
+        return height < 100 || minimalTicks ? _objectSpread2(_objectSpread2({}, ticks), {}, {
+          values: domain
+        }) : ticks;
       }
 
     };
@@ -2182,10 +2187,10 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
           })
         }] : []), [{
           label: 'Autoscale type',
-          subMenu: [['local', 'Local']].concat(_toConsumableArray(self.hasGlobalStats ? [['global', 'Global'], ['globalsd', 'Global ± 3σ']] : []), [['localsd', 'Local ± 3σ']]).map(function (_ref) {
-            var _ref2 = _slicedToArray(_ref, 2),
-                val = _ref2[0],
-                label = _ref2[1];
+          subMenu: [['local', 'Local']].concat(_toConsumableArray(self.hasGlobalStats ? [['global', 'Global'], ['globalsd', 'Global ± 3σ']] : []), [['localsd', 'Local ± 3σ']]).map(function (_ref2) {
+            var _ref3 = _slicedToArray(_ref2, 2),
+                val = _ref3[0],
+                label = _ref3[1];
 
             return {
               label: label,
@@ -2499,7 +2504,7 @@ var XYPlotRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
           scaleOpts = props.scaleOpts,
           unadjustedHeight = props.height,
           config = props.config,
-          values = props.ticks.values,
+          ticks = props.ticks,
           displayCrossHatches = props.displayCrossHatches;
 
       var _regions = _slicedToArray(regions, 1),
@@ -2543,10 +2548,6 @@ var XYPlotRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
           feature: feature
         });
       };
-      ctx.strokeStyle = 'grey';
-      ctx.moveTo(0, toY(0));
-      ctx.lineTo(width, toY(0));
-      ctx.stroke();
       var crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
 
       var _iterator = _createForOfIteratorHelper(features.values()),
@@ -2621,7 +2622,7 @@ var XYPlotRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
       if (displayCrossHatches) {
         ctx.lineWidth = 1;
         ctx.strokeStyle = 'rgba(200,200,200,0.8)';
-        values.forEach(function (tick) {
+        ticks.values.forEach(function (tick) {
           ctx.beginPath();
           ctx.moveTo(0, Math.round(toY(tick)));
           ctx.lineTo(width, Math.round(toY(tick)));
@@ -2693,10 +2694,6 @@ var LinePlotRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
           feature: feature
         });
       };
-      ctx.strokeStyle = 'grey';
-      ctx.moveTo(0, toY(0));
-      ctx.lineTo(width, toY(0));
-      ctx.stroke();
       var lastVal;
 
       var _iterator = _createForOfIteratorHelper(features.values()),
@@ -2845,26 +2842,9 @@ var WiggleGetGlobalStats = /*#__PURE__*/function (_RpcMethodType) {
               case 6:
                 _yield$getAdapter = _context2.sent;
                 dataAdapter = _yield$getAdapter.dataAdapter;
-
-                if (!(dataAdapter instanceof BaseAdapter.BaseFeatureDataAdapter)) {
-                  _context2.next = 12;
-                  break;
-                }
-
-                if (!dataAdapter.capabilities.includes('hasGlobalStats')) {
-                  _context2.next = 11;
-                  break;
-                }
-
                 return _context2.abrupt("return", dataAdapter.getGlobalStats(deserializedArgs));
 
-              case 11:
-                throw new Error('Data adapter does not support global stats');
-
-              case 12:
-                throw new Error('Data adapter not found');
-
-              case 13:
+              case 9:
               case "end":
                 return _context2.stop();
             }