@jbrowse/plugin-wiggle 2.4.2 → 2.6.1

package/esm/MultiDensityRenderer/configSchema.d.ts

@@ -1,2 +1,34 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

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

package/esm/MultiLineRenderer/MultiLineRenderer.js.map

@@ -1 +1 @@
-{"version":3,"file":"MultiLineRenderer.js","sourceRoot":"","sources":["../../src/MultiLineRenderer/MultiLineRenderer.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAA;AACpC,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAEjC,OAAO,kBAEN,MAAM,uBAAuB,CAAA;AAE9B,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,kBAAkB;IAC/D,mBAAmB;IACnB,KAAK,CAAC,IAAI,CAAC,GAA6B,EAAE,KAAgB;QACxD,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QACnC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;QACpE,IAAI,KAAK,GAAG,EAAe,CAAA;QAC3B,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;YACvB,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YACpC,IAAI,CAAC,QAAQ,EAAE;gBACb,OAAM;aACP;YACD,MAAM,EAAE,eAAe,EAAE,GAAG,QAAQ,CAAC,GAAG,EAAE;gBACxC,GAAG,KAAK;gBACR,QAAQ;gBACR,aAAa,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,IAAI,MAAM;aAC5C,CAAC,CAAA;YACF,KAAK,GAAG,CAAC,GAAG,KAAK,EAAE,GAAG,eAAe,CAAC,CAAA;QACxC,CAAC,CAAC,CAAA;QACF,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,CAAA;IACnC,CAAC;CACF"}
+{"version":3,"file":"MultiLineRenderer.js","sourceRoot":"","sources":["../../src/MultiLineRenderer/MultiLineRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAW,MAAM,oBAAoB,CAAA;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAA;AAEpC,OAAO,kBAEN,MAAM,uBAAuB,CAAA;AAE9B,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,kBAAkB;IAC/D,mBAAmB;IACnB,KAAK,CAAC,IAAI,CAAC,GAA6B,EAAE,KAAgB;QACxD,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QACnC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;QACpE,IAAI,KAAK,GAAG,EAAe,CAAA;QAC3B,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;YACvB,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YACpC,IAAI,CAAC,QAAQ,EAAE;gBACb,OAAM;aACP;YACD,MAAM,EAAE,eAAe,EAAE,GAAG,QAAQ,CAAC,GAAG,EAAE;gBACxC,GAAG,KAAK;gBACR,QAAQ;gBACR,aAAa,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,IAAI,MAAM;aAC5C,CAAC,CAAA;YACF,KAAK,GAAG,CAAC,GAAG,KAAK,EAAE,GAAG,eAAe,CAAC,CAAA;QACxC,CAAC,CAAC,CAAA;QACF,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,CAAA;IACnC,CAAC;CACF"}

package/esm/MultiLineRenderer/configSchema.d.ts

@@ -1,2 +1,52 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    displayCrossHatches: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    summaryScoreMode: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

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

@@ -1,7 +1,7 @@
-/// <reference types="react" />
+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/SetColorDialog.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { Source } from '../../util';
 export default function SetColorDialog({ model, handleClose, }: {
     model: {
@@ -7,4 +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,
@@ -58,43 +58,11 @@ function SourcesGrid({ rows, onChange, showTips, }) {
     const [selected, setSelected] = useState([]);
     // @ts-expect-error
     const { name: _name, color: _color, baseUri: _baseUri, ...rest } = rows[0];
-    // similar to BaseFeatureDetail data-grid for auto-measuring columns
-    const columns = [
-        {
-            field: 'color',
-            headerName: 'Color',
-            renderCell: (params) => {
-                const { value, id } = params;
-                return (React.createElement(ColorPicker, { color: value || 'blue', onChange: c => {
-                        const elt = rows.find(f => f.name === id);
-                        if (elt) {
-                            elt.color = c;
-                        }
-                        onChange([...rows]);
-                    } }));
-            },
-        },
-        {
-            field: 'name',
-            sortingOrder: [null],
-            headerName: 'Name',
-            width: measureGridWidth(rows.map(r => r.name)),
-        },
-        ...Object.keys(rest).map(val => ({
-            field: val,
-            sortingOrder: [null],
-            renderCell: (params) => {
-                const { value } = params;
-                return isUriLocation(value) ? React.createElement(UriLink, { value: value }) : getStr(value);
-            },
-            // @ts-expect-error
-            width: measureGridWidth(rows.map(r => r[val])),
-        })),
-    ];
-    // this helps keep track of the selection, even though it is not used
-    // anywhere except inside the picker
     const [widgetColor, setWidgetColor] = useState('blue');
-    const [currSort, setCurrSort] = useState({ idx: 0, field: null });
+    const [currSort, setCurrSort] = useState({
+        idx: 0,
+        field: null,
+    });
     return (React.createElement("div", null,
         React.createElement(Button, { disabled: !selected.length, onClick: event => setAnchorEl(event.currentTarget) }, "Change color of selected items"),
         React.createElement(Button, { onClick: () => onChange(moveUp([...rows], selected)), disabled: !selected.length },
@@ -120,7 +88,38 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                 onChange([...rows]);
             }, onClose: () => setAnchorEl(null) }),
         React.createElement("div", { style: { height: 400, width: '100%' } },
-            React.createElement(DataGrid, { getRowId: row => row.name, checkboxSelection: true, disableSelectionOnClick: true, onSelectionModelChange: arg => setSelected(arg), rows: rows, rowHeight: 25, headerHeight: 33, columns: columns, sortModel: [
+            React.createElement(DataGrid, { getRowId: row => row.name, checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => setSelected(arg), rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
+                    {
+                        field: 'color',
+                        headerName: 'Color',
+                        renderCell: params => {
+                            const { value, id } = params;
+                            return (React.createElement(ColorPicker, { color: value || 'blue', onChange: c => {
+                                    const elt = rows.find(f => f.name === id);
+                                    if (elt) {
+                                        elt.color = c;
+                                    }
+                                    onChange([...rows]);
+                                } }));
+                        },
+                    },
+                    {
+                        field: 'name',
+                        sortingOrder: [null],
+                        headerName: 'Name',
+                        width: measureGridWidth(rows.map(r => r.name)),
+                    },
+                    ...Object.keys(rest).map(val => ({
+                        field: val,
+                        sortingOrder: [null],
+                        renderCell: (params) => {
+                            const { value } = params;
+                            return isUriLocation(value) ? (React.createElement(UriLink, { value: value })) : (getStr(value));
+                        },
+                        // @ts-ignore
+                        width: measureGridWidth(rows.map(r => r[val])),
+                    })),
+                ], sortModel: [
                 /* we control the sort as a controlled component using onSortModelChange */
                 ], onSortModelChange: args => {
                     const sort = args[0];

package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js.map

@@ -1 +1 @@
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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/WiggleDisplayComponent.d.ts

@@ -1,12 +1,12 @@
-/// <reference types="react" />
+import React from 'react';
 import { WiggleDisplayModel } from '../models/model';
 export declare const StatBars: (props: {
     model: WiggleDisplayModel;
     orientation?: string;
     exportSVG?: boolean;
-}) => JSX.Element | null;
+}) => React.JSX.Element | null;
 declare const _default: (props: {
     model: WiggleDisplayModel;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;
 export { default as YScaleBar } from '../../shared/YScaleBar';

package/esm/MultiLinearWiggleDisplay/index.js

@@ -1,7 +1,7 @@
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import configSchemaFactory from './models/configSchema';
 import modelFactory from './models/model';
-import ReactComponent from './components/WiggleDisplayComponent';
+import { lazy } from 'react';
 export default (pluginManager) => {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
@@ -12,7 +12,7 @@ export default (pluginManager) => {
             stateModel: modelFactory(pluginManager, configSchema),
             trackType: 'MultiQuantitativeTrack',
             viewType: 'LinearGenomeView',
-            ReactComponent,
+            ReactComponent: lazy(() => import('./components/WiggleDisplayComponent')),
         });
     });
 };

package/esm/MultiLinearWiggleDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MultiLinearWiggleDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,cAAc,MAAM,qCAAqC,CAAA;AAEhE,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,WAAW,EAAE,sBAAsB;YACnC,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,wBAAwB;YACnC,QAAQ,EAAE,kBAAkB;YAC5B,cAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MultiLinearWiggleDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,WAAW,EAAE,sBAAsB;YACnC,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,wBAAwB;YACnC,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,qCAAqC,CAAC,CAAC;SAC1E,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/MultiLinearWiggleDisplay/models/configSchema.d.ts

@@ -1,2 +1,88 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    defaultRendering: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        MultiXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        MultiDensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        MultiRowXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        MultiLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        MultiRowLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    autoscale: {
+        type: string;
+        defaultValue: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+    };
+    minimalTicks: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+    minScore: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    maxScore: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    numStdDev: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    scaleType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    inverted: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;

package/esm/MultiLinearWiggleDisplay/models/configSchema.js

@@ -1,6 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
+// locals
+import sharedWiggleConfigFactory from '../../shared/configShared';
 /**
  * #config MultiLinearWiggleDisplay
  */
@@ -12,70 +13,6 @@ export default function WiggleConfigFactory(pluginManager) {
     const MultiLineRendererConfigSchema = pluginManager.getRendererType('MultiLineRenderer').configSchema;
     const MultiRowLineRendererConfigSchema = pluginManager.getRendererType('MultiRowLineRenderer').configSchema;
     return ConfigurationSchema('MultiLinearWiggleDisplay', {
-        /**
-         * #slot
-         */
-        autoscale: {
-            type: 'stringEnum',
-            defaultValue: 'local',
-            model: types.enumeration('Autoscale type', [
-                'global',
-                'local',
-                'globalsd',
-                'localsd',
-                'zscore',
-            ]),
-            description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
-        },
-        /**
-         * #slot
-         */
-        minimalTicks: {
-            type: 'boolean',
-            defaultValue: false,
-            description: 'use the minimal amount of ticks',
-        },
-        /**
-         * #slot
-         */
-        minScore: {
-            type: 'number',
-            defaultValue: Number.MIN_VALUE,
-            description: 'minimum value for the y-scale',
-        },
-        /**
-         * #slot
-         */
-        maxScore: {
-            type: 'number',
-            description: 'maximum value for the y-scale',
-            defaultValue: Number.MAX_VALUE,
-        },
-        /**
-         * #slot
-         */
-        numStdDev: {
-            type: 'number',
-            description: 'number of standard deviations to use for autoscale types globalsd or localsd',
-            defaultValue: 3,
-        },
-        /**
-         * #slot
-         */
-        scaleType: {
-            type: 'stringEnum',
-            model: types.enumeration('Scale type', ['linear', 'log']),
-            description: 'The type of scale to use',
-            defaultValue: 'linear',
-        },
-        /**
-         * #slot
-         */
-        inverted: {
-            type: 'boolean',
-            description: 'draw upside down',
-            defaultValue: false,
-        },
         /**
          * #slot
          */
@@ -111,7 +48,7 @@ export default function WiggleConfigFactory(pluginManager) {
         /**
          * #baseConfiguration
          */
-        baseConfiguration: baseLinearDisplayConfigSchema,
+        baseConfiguration: sharedWiggleConfigFactory(),
         explicitlyTyped: true,
     });
 }

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