@jbrowse/plugin-wiggle 2.5.0 → 2.6.2

package/esm/LinearWiggleDisplay/models/model.js

@@ -1,14 +1,13 @@
-import React, { lazy } from 'react';
-import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
-import { getEnv, getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
-import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
-import { when } from 'mobx';
+import { lazy } from 'react';
+import { getConf, } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
 import { types } from 'mobx-state-tree';
 import { axisPropsFromTickScale } from 'react-d3-axis-mod';
-import { getNiceDomain, getScale, quantitativeStatsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
+// locals
+import { getScale, quantitativeStatsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
 import Tooltip from '../components/Tooltip';
-import YScaleBar from '../../shared/YScaleBar';
-const SetMinMaxDlg = lazy(() => import('../../shared/SetMinMaxDialog'));
+import SharedWiggleMixin from '../../shared/modelShared';
+// lazies
 const SetColorDlg = lazy(() => import('../components/SetColorDialog'));
 // using a map because it preserves order
 const rendererTypes = new Map([
@@ -18,212 +17,15 @@ const rendererTypes = new Map([
 ]);
 /**
  * #stateModel LinearWiggleDisplay
- * Extends `BaseLinearDisplay`
+ * extends `SharedWiggleMixin`
  */
 function stateModelFactory(pluginManager, configSchema) {
     return types
-        .compose('LinearWiggleDisplay', BaseLinearDisplay, types.model({
+        .compose('LinearWiggleDisplay', SharedWiggleMixin(configSchema), types.model({
         /**
          * #property
          */
         type: types.literal('LinearWiggleDisplay'),
-        /**
-         * #property
-         */
-        configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
-        selectedRendering: types.optional(types.string, ''),
-        /**
-         * #property
-         */
-        resolution: types.optional(types.number, 1),
-        /**
-         * #property
-         */
-        fill: types.maybe(types.boolean),
-        /**
-         * #property
-         */
-        minSize: types.maybe(types.number),
-        /**
-         * #property
-         */
-        color: types.maybe(types.string),
-        /**
-         * #property
-         */
-        posColor: types.maybe(types.string),
-        /**
-         * #property
-         */
-        negColor: types.maybe(types.string),
-        /**
-         * #property
-         */
-        summaryScoreMode: types.maybe(types.string),
-        /**
-         * #property
-         */
-        rendererTypeNameState: types.maybe(types.string),
-        /**
-         * #property
-         */
-        scale: types.maybe(types.string),
-        /**
-         * #property
-         */
-        autoscale: types.maybe(types.string),
-        /**
-         * #property
-         */
-        displayCrossHatches: types.maybe(types.boolean),
-        /**
-         * #property
-         */
-        constraints: types.optional(types.model({
-            max: types.maybe(types.number),
-            min: types.maybe(types.number),
-        }), {}),
-    }))
-        .volatile(() => ({
-        message: undefined,
-        stats: undefined,
-        statsFetchInProgress: undefined,
-    }))
-        .actions(self => ({
-        /**
-         * #action
-         */
-        updateQuantitativeStats(stats) {
-            const { scoreMin, scoreMax } = stats;
-            const EPSILON = 0.000001;
-            if (!self.stats) {
-                self.stats = { scoreMin, scoreMax };
-            }
-            else if (Math.abs(self.stats.scoreMax - scoreMax) > EPSILON ||
-                Math.abs(self.stats.scoreMin - scoreMin) > EPSILON) {
-                self.stats = { scoreMin, scoreMax };
-            }
-        },
-        /**
-         * #action
-         */
-        setColor(color) {
-            self.color = color;
-        },
-        /**
-         * #action
-         */
-        setPosColor(color) {
-            self.posColor = color;
-        },
-        /**
-         * #action
-         */
-        setNegColor(color) {
-            self.negColor = color;
-        },
-        /**
-         * #action
-         */
-        setLoading(aborter) {
-            const { statsFetchInProgress: statsFetch } = self;
-            if (statsFetch !== undefined && !statsFetch.signal.aborted) {
-                statsFetch.abort();
-            }
-            self.statsFetchInProgress = aborter;
-        },
-        /**
-         * #action
-         * this overrides the BaseLinearDisplayModel to avoid popping up a
-         * feature detail display, but still sets the feature selection on the
-         * model so listeners can detect a click
-         */
-        selectFeature(feature) {
-            const session = getSession(self);
-            if (isSelectionContainer(session)) {
-                session.setSelection(feature);
-            }
-        },
-        /**
-         * #action
-         */
-        setResolution(res) {
-            self.resolution = res;
-        },
-        /**
-         * #action
-         */
-        setFill(fill) {
-            if (fill === 0) {
-                self.fill = true;
-                self.minSize = 0;
-            }
-            else if (fill === 1) {
-                self.fill = false;
-                self.minSize = 1;
-            }
-            else if (fill === 2) {
-                self.fill = false;
-                self.minSize = 2;
-            }
-        },
-        /**
-         * #action
-         */
-        toggleLogScale() {
-            self.scale = self.scale === 'log' ? 'linear' : 'log';
-        },
-        /**
-         * #action
-         */
-        setScaleType(scale) {
-            self.scale = scale;
-        },
-        /**
-         * #action
-         */
-        setSummaryScoreMode(val) {
-            self.summaryScoreMode = val;
-        },
-        /**
-         * #action
-         */
-        setAutoscale(val) {
-            self.autoscale = val;
-        },
-        /**
-         * #action
-         */
-        setMaxScore(val) {
-            self.constraints.max = val;
-        },
-        /**
-         * #action
-         */
-        setRendererType(val) {
-            self.rendererTypeNameState = val;
-        },
-        /**
-         * #action
-         */
-        setMinScore(val) {
-            self.constraints.min = val;
-        },
-        /**
-         * #action
-         */
-        toggleCrossHatches() {
-            self.displayCrossHatches = !self.displayCrossHatches;
-        },
-        /**
-         * #action
-         */
-        setCrossHatches(cross) {
-            self.displayCrossHatches = cross;
-        },
     }))
         .views(self => ({
         /**
@@ -232,157 +34,18 @@ function stateModelFactory(pluginManager, configSchema) {
         get TooltipComponent() {
             return Tooltip;
         },
-        /**
-         * #getter
-         */
-        get adapterTypeName() {
-            return self.adapterConfig.type;
-        },
-        /**
-         * #getter
-         */
-        get rendererTypeNameSimple() {
-            return self.rendererTypeNameState || getConf(self, 'defaultRendering');
-        },
         /**
          * #getter
          */
         get rendererTypeName() {
-            const name = this.rendererTypeNameSimple;
+            const name = self.rendererTypeNameSimple;
             const rendererType = rendererTypes.get(name);
             if (!rendererType) {
                 throw new Error(`unknown renderer ${name}`);
             }
             return rendererType;
         },
-        /**
-         * #getter
-         * subclasses can define these, as snpcoverage track does
-         */
-        get filters() {
-            return undefined;
-        },
-        /**
-         * #getter
-         */
-        get scaleType() {
-            return self.scale || getConf(self, 'scaleType');
-        },
-        /**
-         * #getter
-         */
-        get maxScore() {
-            var _a;
-            return (_a = self.constraints.max) !== null && _a !== void 0 ? _a : getConf(self, 'maxScore');
-        },
-        /**
-         * #getter
-         */
-        get minScore() {
-            var _a;
-            return (_a = self.constraints.min) !== null && _a !== void 0 ? _a : getConf(self, 'minScore');
-        },
     }))
-        .views(self => ({
-        /**
-         * #getter
-         */
-        get rendererConfig() {
-            const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, rendererTypeName, } = self;
-            const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
-            return self.rendererType.configSchema.create({
-                ...configBlob,
-                ...(scaleType ? { scaleType } : {}),
-                ...(fill !== undefined ? { filled: fill } : {}),
-                ...(displayCrossHatches !== undefined
-                    ? { displayCrossHatches }
-                    : {}),
-                ...(summaryScoreMode !== undefined ? { summaryScoreMode } : {}),
-                ...(color !== undefined ? { color } : {}),
-                ...(negColor !== undefined ? { negColor } : {}),
-                ...(posColor !== undefined ? { posColor } : {}),
-                ...(minSize !== undefined ? { minSize } : {}),
-            }, getEnv(self));
-        },
-    }))
-        .views(self => {
-        let oldDomain = [0, 0];
-        return {
-            /**
-             * #getter
-             */
-            get filled() {
-                return readConfObject(self.rendererConfig, 'filled');
-            },
-            /**
-             * #getter
-             */
-            get summaryScoreModeSetting() {
-                return readConfObject(self.rendererConfig, 'summaryScoreMode');
-            },
-            /**
-             * #getter
-             */
-            get domain() {
-                const { stats, scaleType, minScore, maxScore } = self;
-                if (!stats) {
-                    return undefined;
-                }
-                const ret = getNiceDomain({
-                    domain: [stats.scoreMin, stats.scoreMax],
-                    bounds: [minScore, maxScore],
-                    scaleType,
-                });
-                // avoid weird scalebar if log value and empty region displayed
-                if (scaleType === 'log' && ret[1] === Number.MIN_VALUE) {
-                    return [0, Number.MIN_VALUE];
-                }
-                // avoid returning a new object if it matches the old value
-                if (JSON.stringify(oldDomain) !== JSON.stringify(ret)) {
-                    oldDomain = ret;
-                }
-                return oldDomain;
-            },
-            /**
-             * #getter
-             */
-            get needsScalebar() {
-                return (self.rendererTypeName === 'XYPlotRenderer' ||
-                    self.rendererTypeName === 'LinePlotRenderer');
-            },
-            /**
-             * #getter
-             */
-            get scaleOpts() {
-                return {
-                    domain: this.domain,
-                    stats: self.stats,
-                    autoscaleType: this.autoscaleType,
-                    scaleType: self.scaleType,
-                    inverted: getConf(self, 'inverted'),
-                };
-            },
-            /**
-             * #getter
-             */
-            get canHaveFill() {
-                return self.rendererTypeName === 'XYPlotRenderer';
-            },
-            /**
-             * #getter
-             */
-            get autoscaleType() {
-                var _a;
-                return (_a = self.autoscale) !== null && _a !== void 0 ? _a : getConf(self, 'autoscale');
-            },
-            /**
-             * #getter
-             */
-            get displayCrossHatchesSetting() {
-                return readConfObject(self.rendererConfig, 'displayCrossHatches');
-            },
-        };
-    })
         .views(self => ({
         /**
          * #getter
@@ -406,13 +69,6 @@ function stateModelFactory(pluginManager, configSchema) {
                 ? { ...ticks, values: domain }
                 : ticks;
         },
-        /**
-         * #getter
-         */
-        get adapterCapabilities() {
-            const type = self.adapterTypeName;
-            return pluginManager.getAdapterType(type).adapterCapabilities;
-        },
     }))
         .views(self => {
         const { renderProps: superRenderProps } = self;
@@ -440,14 +96,9 @@ function stateModelFactory(pluginManager, configSchema) {
             /**
              * #getter
              */
-            get hasResolution() {
-                return self.adapterCapabilities.includes('hasResolution');
-            },
-            /**
-             * #getter
-             */
-            get hasGlobalStats() {
-                return self.adapterCapabilities.includes('hasGlobalStats');
+            get needsScalebar() {
+                const { rendererTypeName: type } = self;
+                return type === 'XYPlotRenderer' || type === 'LinePlotRenderer';
             },
             /**
              * #getter
@@ -475,32 +126,10 @@ function stateModelFactory(pluginManager, configSchema) {
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
-                    ...(self.hasResolution
-                        ? [
-                            {
-                                label: 'Resolution',
-                                subMenu: [
-                                    {
-                                        label: 'Finer resolution',
-                                        onClick: () => self.setResolution(self.resolution * 5),
-                                    },
-                                    {
-                                        label: 'Coarser resolution',
-                                        onClick: () => self.setResolution(self.resolution / 5),
-                                    },
-                                ],
-                            },
-                            {
-                                label: 'Summary score mode',
-                                subMenu: ['min', 'max', 'avg', 'whiskers'].map(elt => ({
-                                    label: elt,
-                                    type: 'radio',
-                                    checked: self.summaryScoreModeSetting === elt,
-                                    onClick: () => self.setSummaryScoreMode(elt),
-                                })),
-                            },
-                        ]
-                        : []),
+                    {
+                        label: 'Score',
+                        subMenu: self.scoreTrackMenuItems(),
+                    },
                     ...(self.canHaveFill
                         ? [
                             {
@@ -514,10 +143,6 @@ function stateModelFactory(pluginManager, configSchema) {
                             },
                         ]
                         : []),
-                    {
-                        label: self.scaleType === 'log' ? 'Set linear scale' : 'Set log scale',
-                        onClick: () => self.toggleLogScale(),
-                    },
                     ...(self.needsScalebar
                         ? [
                             {
@@ -541,33 +166,6 @@ function stateModelFactory(pluginManager, configSchema) {
                             },
                         ]
                         : []),
-                    {
-                        label: 'Autoscale type',
-                        subMenu: [
-                            ['local', 'Local'],
-                            ...(self.hasGlobalStats
-                                ? [
-                                    ['global', 'Global'],
-                                    ['globalsd', 'Global ± 3σ'],
-                                ]
-                                : []),
-                            ['localsd', 'Local ± 3σ'],
-                        ].map(([val, label]) => ({
-                            label,
-                            type: 'radio',
-                            checked: self.autoscaleType === val,
-                            onClick: () => self.setAutoscale(val),
-                        })),
-                    },
-                    {
-                        label: 'Set min/max score',
-                        onClick: () => {
-                            getSession(self).queueDialog(handleClose => [
-                                SetMinMaxDlg,
-                                { model: self, handleClose },
-                            ]);
-                        },
-                    },
                     {
                         label: 'Set color',
                         onClick: () => {
@@ -582,16 +180,8 @@ function stateModelFactory(pluginManager, configSchema) {
         };
     })
         .actions(self => {
-        const { reload: superReload, renderSvg: superRenderSvg } = self;
+        const { renderSvg: superRenderSvg } = self;
         return {
-            /**
-             * #action
-             * re-runs stats and refresh whole display on reload
-             */
-            async reload() {
-                self.setError();
-                superReload();
-            },
             afterAttach() {
                 quantitativeStatsAutorun(self);
             },
@@ -599,16 +189,10 @@ function stateModelFactory(pluginManager, configSchema) {
              * #action
              */
             async renderSvg(opts) {
-                await when(() => !!self.stats && !!self.regionCannotBeRenderedText);
-                const { needsScalebar, stats } = self;
-                const { offsetPx } = getContainingView(self);
-                return (React.createElement(React.Fragment, null,
-                    React.createElement("g", { id: "snpcov" }, await superRenderSvg(opts)),
-                    needsScalebar && stats ? (React.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
-                        React.createElement(YScaleBar, { model: self, orientation: "left" }))) : null));
+                const { renderSvg } = await import('./renderSvg');
+                return renderSvg(self, opts, superRenderSvg);
             },
         };
     });
 }
 export default stateModelFactory;
-//# sourceMappingURL=model.js.map

package/esm/LinearWiggleDisplay/models/renderSvg.d.ts

@@ -0,0 +1,4 @@
+import React from 'react';
+import { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+import { WiggleDisplayModel } from './model';
+export declare function renderSvg(self: WiggleDisplayModel, opts: ExportSvgDisplayOptions, superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>): Promise<React.JSX.Element>;

package/esm/LinearWiggleDisplay/models/renderSvg.js

@@ -0,0 +1,13 @@
+import React from 'react';
+import { getContainingView } from '@jbrowse/core/util';
+import { when } from 'mobx';
+import YScaleBar from '../../shared/YScaleBar';
+export async function renderSvg(self, opts, superRenderSvg) {
+    await when(() => !!self.stats && !!self.regionCannotBeRenderedText);
+    const { needsScalebar, stats } = self;
+    const { offsetPx } = getContainingView(self);
+    return (React.createElement(React.Fragment, null,
+        React.createElement("g", { id: "snpcov" }, await superRenderSvg(opts)),
+        needsScalebar && stats ? (React.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
+            React.createElement(YScaleBar, { model: self, orientation: "left" }))) : null));
+}

package/esm/MultiDensityRenderer/MultiDensityRenderer.js

@@ -1,4 +1,4 @@
-import { groupBy } from '../util';
+import { groupBy } from '@jbrowse/core/util';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 import { drawDensity } from '../drawxy';
 export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
@@ -33,4 +33,3 @@ export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
         return { reducedFeatures: feats };
     }
 }
-//# sourceMappingURL=MultiDensityRenderer.js.map

package/esm/MultiDensityRenderer/configSchema.js

@@ -12,4 +12,3 @@ const configSchema = ConfigurationSchema('MultiDensityRenderer', {}, {
     explicitlyTyped: true,
 });
 export default configSchema;
-//# sourceMappingURL=configSchema.js.map

package/esm/MultiDensityRenderer/index.js

@@ -9,4 +9,3 @@ export default (pluginManager) => {
         pluginManager,
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/MultiLineRenderer/MultiLineRenderer.js

@@ -1,5 +1,5 @@
+import { groupBy } from '@jbrowse/core/util';
 import { drawLine } from '../drawxy';
-import { groupBy } from '../util';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 export default class MultiLineRenderer extends WiggleBaseRenderer {
     // @ts-expect-error
@@ -22,4 +22,3 @@ export default class MultiLineRenderer extends WiggleBaseRenderer {
         return { reducedFeatures: feats };
     }
 }
-//# sourceMappingURL=MultiLineRenderer.js.map

package/esm/MultiLineRenderer/configSchema.js

@@ -31,4 +31,3 @@ const configSchema = ConfigurationSchema('MultiLineRenderer', {
     explicitlyTyped: true,
 });
 export default configSchema;
-//# sourceMappingURL=configSchema.js.map

package/esm/MultiLineRenderer/index.js

@@ -9,4 +9,3 @@ export default (pluginManager) => {
         pluginManager,
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts

@@ -1,6 +1,7 @@
+import React from 'react';
 import { DialogProps } from '@mui/material';
 declare function DraggableDialog(props: DialogProps & {
     title: string;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof DraggableDialog;
 export default _default;

package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.js

@@ -35,4 +35,3 @@ function DraggableDialog(props) {
             children)));
 }
 export default observer(DraggableDialog);
-//# sourceMappingURL=DraggableDialog.js.map

package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts

@@ -1,3 +1,4 @@
+import React from 'react';
 import { Source } from '../../util';
 export default function SetColorDialog({ model, handleClose, }: {
     model: {
@@ -6,4 +7,4 @@ export default function SetColorDialog({ model, handleClose, }: {
         clearLayout: () => void;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;

package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js

@@ -7,13 +7,13 @@ import clone from 'clone';
 // locals
 import DraggableDialog from './DraggableDialog';
 import ColorPicker, { ColorPopover } from '@jbrowse/core/ui/ColorPicker';
-import { UriLink } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import { moveUp, moveDown } from './util';
 // icons
 import KeyboardDoubleArrowUpIcon from '@mui/icons-material/KeyboardDoubleArrowUp';
 import KeyboardDoubleArrowDownIcon from '@mui/icons-material/KeyboardDoubleArrowDown';
 import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
 import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp';
+import UriLink from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/UriLink';
 const useStyles = makeStyles()({
     content: {
         minWidth: 800,
@@ -139,4 +139,3 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                         : rows);
                 } }))));
 }
-//# sourceMappingURL=SetColorDialog.js.map

package/esm/MultiLinearWiggleDisplay/components/Tooltip.d.ts

@@ -20,6 +20,6 @@ declare const WiggleTooltip: (props: {
     clientMouseCoord: Coord;
     clientRect?: DOMRect;
     TooltipContents?: TooltipContentsComponent;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default WiggleTooltip;
 export { default as Tooltip } from '../../Tooltip';

package/esm/MultiLinearWiggleDisplay/components/Tooltip.js

@@ -40,4 +40,3 @@ const WiggleTooltip = observer((props) => {
 });
 export default WiggleTooltip;
 export { default as Tooltip } from '../../Tooltip';
-//# sourceMappingURL=Tooltip.js.map