@jbrowse/core 5.0.0-beta.1 → 5.0.0-beta.11

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "5.0.0-beta.1",
+  "version": "5.0.0-beta.11",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -32,8 +32,13 @@
     "./PluginLoader": "./esm/PluginLoader.js",
     "./PluginManager": "./esm/PluginManager.js",
     "./ReExports/list": "./esm/ReExports/list.js",
+    "./ReExports/modules": "./esm/ReExports/modules.js",
+    "./ReExports/registry": "./esm/ReExports/registry.js",
+    "./ReExports/uiStub": "./esm/ReExports/uiStub.js",
+    "./ReExports/workerModules": "./esm/ReExports/workerModules.js",
     "./TextSearch/BaseResults": "./esm/TextSearch/BaseResults.js",
     "./TextSearch/TextSearchManager": "./esm/TextSearch/TextSearchManager.js",
+    "./TextSearch/places": "./esm/TextSearch/places.js",
     "./assemblyManager": "./esm/assemblyManager/index.js",
     "./assemblyManager/assembly": "./esm/assemblyManager/assembly.js",
     "./assemblyManager/assemblyConfigSchema": "./esm/assemblyManager/assemblyConfigSchema.js",
@@ -42,8 +47,11 @@
     "./configuration/configurationSchema": "./esm/configuration/configurationSchema.js",
     "./data_adapters/BaseAdapter": "./esm/data_adapters/BaseAdapter/index.js",
     "./data_adapters/BaseAdapter/getAdapterId": "./esm/data_adapters/BaseAdapter/getAdapterId.js",
+    "./data_adapters/BaseAdapter/rowSources": "./esm/data_adapters/BaseAdapter/rowSources.js",
     "./data_adapters/BaseAdapter/stats": "./esm/data_adapters/BaseAdapter/stats.js",
     "./data_adapters/BaseAdapter/types": "./esm/data_adapters/BaseAdapter/types.js",
+    "./data_adapters/BaseAdapter/zoomRange": "./esm/data_adapters/BaseAdapter/zoomRange.js",
+    "./data_adapters/adapterSessionRefcount": "./esm/data_adapters/adapterSessionRefcount.js",
     "./data_adapters/dataAdapterCache": "./esm/data_adapters/dataAdapterCache.js",
     "./data_adapters/getFeatureAdapter": "./esm/data_adapters/getFeatureAdapter.js",
     "./data_adapters/getSequenceSubAdapter": "./esm/data_adapters/getSequenceSubAdapter.js",
@@ -62,7 +70,6 @@
     "./pluggableElementTypes/WidgetType": "./esm/pluggableElementTypes/WidgetType.js",
     "./pluggableElementTypes/models": "./esm/pluggableElementTypes/models/index.js",
     "./pluggableElementTypes/models/BaseViewModel": "./esm/pluggableElementTypes/models/BaseViewModel.js",
-    "./pluggableElementTypes/models/HighlightsMixin": "./esm/pluggableElementTypes/models/HighlightsMixin.js",
     "./pluggableElementTypes/models/assertDisplayContract": "./esm/pluggableElementTypes/models/assertDisplayContract.js",
     "./pluggableElementTypes/models/baseConnectionConfig": "./esm/pluggableElementTypes/models/baseConnectionConfig.js",
     "./pluggableElementTypes/renderers/util/serializableFilterChain": "./esm/pluggableElementTypes/renderers/util/serializableFilterChain.js",
@@ -72,8 +79,11 @@
     "./rpc/WebWorkerRpcDriver": "./esm/rpc/WebWorkerRpcDriver.js",
     "./rpc/byteBudget": "./esm/rpc/byteBudget.js",
     "./svg/SvgExport": "./esm/svg/SvgExport.js",
+    "./svg/SvgThemeProviders": "./esm/svg/SvgThemeProviders.js",
     "./svg/constants": "./esm/svg/constants.js",
+    "./svg/exportViewSvg": "./esm/svg/exportViewSvg.js",
     "./svg/saveSvgAsImage": "./esm/svg/saveSvgAsImage.js",
+    "./svg/serializeSvg": "./esm/svg/serializeSvg.js",
     "./svg/svgId": "./esm/svg/svgId.js",
     "./svg/svgReady": "./esm/svg/svgReady.js",
     "./svg/trackNames": "./esm/svg/trackNames.js",
@@ -82,6 +92,7 @@
     "./ui/AddCustomPluginDialog": "./esm/ui/AddCustomPluginDialog.js",
     "./ui/AddGenomePane": "./esm/ui/AddGenomePane.js",
     "./ui/AppLogo": "./esm/ui/AppLogo.js",
+    "./ui/AppReadyMarker": "./esm/ui/AppReadyMarker.js",
     "./ui/BaseTooltip": "./esm/ui/BaseTooltip.js",
     "./ui/CascadingMenuButton": "./esm/ui/CascadingMenuButton.js",
     "./ui/ColorPicker": "./esm/ui/ColorPicker.js",
@@ -114,17 +125,21 @@
     "./ui/ReturnToImportFormDialog": "./esm/ui/ReturnToImportFormDialog.js",
     "./ui/SanitizedHTML": "./esm/ui/SanitizedHTML.js",
     "./ui/ScrollZoomToggle": "./esm/ui/ScrollZoomToggle.js",
+    "./ui/SessionJsonPanel": "./esm/ui/SessionJsonPanel.js",
     "./ui/ShareLinkField": "./esm/ui/ShareLinkField.js",
     "./ui/Snackbar": "./esm/ui/Snackbar.js",
     "./ui/SnackbarModel": "./esm/ui/SnackbarModel.js",
     "./ui/StackTraceButton": "./esm/ui/StackTraceButton.js",
+    "./ui/SvgColorLegend": "./esm/ui/SvgColorLegend.js",
     "./ui/VerticalScrollbar": "./esm/ui/VerticalScrollbar.js",
     "./ui/buildExtraTrackMenuItems": "./esm/ui/buildExtraTrackMenuItems.js",
+    "./ui/colorScale": "./esm/ui/colorScale.js",
     "./ui/colors": "./esm/ui/colors.js",
     "./ui/filterMenuItems": "./esm/ui/filterMenuItems.js",
     "./ui/gpuFallback": "./esm/ui/gpuFallback.js",
-    "./ui/highlightChipReveal": "./esm/ui/highlightChipReveal.js",
+    "./ui/hoverBoxStyle": "./esm/ui/hoverBoxStyle.js",
     "./ui/legendSpec": "./esm/ui/legendSpec.js",
+    "./ui/measureLegendText": "./esm/ui/measureLegendText.js",
     "./ui/menuItems": "./esm/ui/menuItems.js",
     "./ui/multiTrackMenuItems": "./esm/ui/multiTrackMenuItems.js",
     "./ui/palette": "./esm/ui/palette.js",
@@ -140,37 +155,48 @@
     "./util/Base1DUtils": "./esm/util/Base1DUtils.js",
     "./util/Base1DViewModel": "./esm/util/Base1DViewModel.js",
     "./util/FileSaver": "./esm/util/FileSaver/index.js",
-    "./util/QuickLRU": "./esm/util/QuickLRU/index.js",
     "./util/SvgCanvas": "./esm/util/SvgCanvas.js",
     "./util/TimeTraveller": "./esm/util/TimeTraveller.js",
     "./util/aborting": "./esm/util/aborting.js",
     "./util/adapterMetadata": "./esm/util/adapterMetadata.js",
     "./util/addRelativeUris": "./esm/util/addRelativeUris.js",
+    "./util/aggregateFieldName": "./esm/util/aggregateFieldName.js",
     "./util/analytics": "./esm/util/analytics.js",
-    "./util/applyInitSettings": "./esm/util/applyInitSettings.js",
+    "./util/animationAllowed": "./esm/util/animationAllowed.js",
     "./util/assemblyConfigUtils": "./esm/util/assemblyConfigUtils.js",
     "./util/bandHeight": "./esm/util/bandHeight.js",
     "./util/bandLayout": "./esm/util/bandLayout.js",
+    "./util/baseDisplayConfig": "./esm/util/baseDisplayConfig.js",
     "./util/bgzfWorkerPool": "./esm/util/bgzfWorkerPool.js",
     "./util/blockTypes": "./esm/util/blockTypes.js",
     "./util/cacheBudgets": "./esm/util/cacheBudgets.js",
     "./util/calculateDynamicBlocks": "./esm/util/calculateDynamicBlocks.js",
     "./util/calculateStaticBlocks": "./esm/util/calculateStaticBlocks.js",
+    "./util/categoricalField": "./esm/util/categoricalField.js",
     "./util/chooseGridPitch": "./esm/util/chooseGridPitch.js",
     "./util/color": "./esm/util/color/index.js",
+    "./util/color/cssColorsLevel4": "./esm/util/color/cssColorsLevel4.js",
     "./util/colorBits": "./esm/util/colorBits.js",
     "./util/colorRamp": "./esm/util/colorRamp.js",
+    "./util/colorScale": "./esm/util/colorScale.js",
+    "./util/colorSchemes": "./esm/util/colorSchemes.js",
     "./util/colord": "./esm/util/colord.js",
     "./util/convertCodingSequenceToPeptides": "./esm/util/convertCodingSequenceToPeptides.js",
     "./util/copyText": "./esm/util/copyText.js",
-    "./util/createStopTokenRotation": "./esm/util/createStopTokenRotation.js",
+    "./util/createAbortRotation": "./esm/util/createAbortRotation.js",
+    "./util/createSvgRasterCanvas": "./esm/util/createSvgRasterCanvas.js",
+    "./util/cssColorParse": "./esm/util/cssColorParse.js",
     "./util/deepEqual": "./esm/util/deepEqual.js",
     "./util/deepMerge": "./esm/util/deepMerge.js",
     "./util/diagonalizeRegions": "./esm/util/diagonalizeRegions.js",
     "./util/eventPoint": "./esm/util/eventPoint.js",
+    "./util/expandLooseSearchIndex": "./esm/util/expandLooseSearchIndex.js",
+    "./util/featureTable": "./esm/util/featureTable.js",
+    "./util/featureTransforms": "./esm/util/featureTransforms.js",
     "./util/fetchContext": "./esm/util/fetchContext.js",
     "./util/fetchHub": "./esm/util/fetchHub.js",
     "./util/fetchPhases": "./esm/util/fetchPhases.js",
+    "./util/fieldReader": "./esm/util/fieldReader.js",
     "./util/fileHandleStore": "./esm/util/fileHandleStore.js",
     "./util/flatbush": "./esm/util/flatbush/index.js",
     "./util/formatFastaStrings": "./esm/util/formatFastaStrings.js",
@@ -178,6 +204,7 @@
     "./util/freezeDeep": "./esm/util/freezeDeep.js",
     "./util/geneticCodes": "./esm/util/geneticCodes.js",
     "./util/getRelativeX": "./esm/util/getRelativeX.js",
+    "./util/groupKeys": "./esm/util/groupKeys.js",
     "./util/highlights": "./esm/util/highlights.js",
     "./util/hooks": "./esm/util/hooks.js",
     "./util/htmlText": "./esm/util/htmlText.js",
@@ -185,43 +212,65 @@
     "./util/installClearHoverOnSurfaceMove": "./esm/util/installClearHoverOnSurfaceMove.js",
     "./util/installFetch": "./esm/util/installFetch.js",
     "./util/installInitAutorun": "./esm/util/installInitAutorun.js",
+    "./util/installPrerequisiteFetch": "./esm/util/installPrerequisiteFetch.js",
     "./util/io": "./esm/util/io/index.js",
     "./util/io/RemoteFileWithRangeCache": "./esm/util/io/RemoteFileWithRangeCache.js",
     "./util/isDataCurrent": "./esm/util/isDataCurrent.js",
+    "./util/isTextEntryFocused": "./esm/util/isTextEntryFocused.js",
     "./util/jexl": "./esm/util/jexl.js",
     "./util/jexlFilters": "./esm/util/jexlFilters.js",
     "./util/jexlStrings": "./esm/util/jexlStrings.js",
     "./util/layouts": "./esm/util/layouts/index.js",
     "./util/layouts/GranularRectLayout": "./esm/util/layouts/GranularRectLayout.js",
     "./util/layouts/placeRect": "./esm/util/layouts/placeRect.js",
+    "./util/lazyAfterAttach": "./esm/util/lazyAfterAttach.js",
+    "./util/lazyWithPreload": "./esm/util/lazyWithPreload.js",
     "./util/leadingEdgeAutorun": "./esm/util/leadingEdgeAutorun.js",
+    "./util/legendCandidates": "./esm/util/legendCandidates.js",
     "./util/librpc": "./esm/util/librpc.js",
     "./util/localStorage": "./esm/util/localStorage.js",
     "./util/makeAssembly": "./esm/util/makeAssembly.js",
+    "./util/markEncoding": "./esm/util/markEncoding.js",
+    "./util/measureText": "./esm/util/measureText.js",
+    "./util/mst-reflection": "./esm/util/mst-reflection.js",
     "./util/mstUtils": "./esm/util/mstUtils.js",
     "./util/nanoid": "./esm/util/nanoid.js",
     "./util/numericUtils": "./esm/util/numericUtils.js",
     "./util/offscreenCanvasPonyfill": "./esm/util/offscreenCanvasPonyfill.js",
+    "./util/openViews": "./esm/util/openViews.js",
     "./util/paintLayer": "./esm/util/paintLayer.js",
     "./util/parseLineByLine": "./esm/util/parseLineByLine.js",
+    "./util/preloadComponent": "./esm/util/preloadComponent.js",
     "./util/progress": "./esm/util/progress.js",
+    "./util/quantileExtent": "./esm/util/quantileExtent.js",
     "./util/range": "./esm/util/range.js",
+    "./util/renderToStaticMarkup": "./esm/util/renderToStaticMarkup.js",
     "./util/resolveRowHeight": "./esm/util/resolveRowHeight.js",
     "./util/rowStackGeometry": "./esm/util/rowStackGeometry.js",
     "./util/rxjs": "./esm/util/rxjs.js",
     "./util/sameStrings": "./esm/util/sameStrings.js",
+    "./util/samplesTsv": "./esm/util/samplesTsv.js",
+    "./util/selectEncodedFeature": "./esm/util/selectEncodedFeature.js",
     "./util/setStackTraceLimit": "./esm/util/setStackTraceLimit.js",
+    "./util/shapeNameList": "./esm/util/shapeNameList.js",
+    "./util/shapeNames": "./esm/util/shapeNames.js",
     "./util/simpleFeature": "./esm/util/simpleFeature.js",
+    "./util/starFusion": "./esm/util/starFusion.js",
     "./util/stats": "./esm/util/stats.js",
-    "./util/stopToken": "./esm/util/stopToken.js",
+    "./util/svAlt": "./esm/util/svAlt.js",
+    "./util/svgColorProps": "./esm/util/svgColorProps.js",
+    "./util/systemColorScheme": "./esm/util/systemColorScheme.js",
     "./util/tabix": "./esm/util/tabix.js",
+    "./util/thresholdScale": "./esm/util/thresholdScale.js",
     "./util/tickLabels": "./esm/util/tickLabels.js",
     "./util/tracks": "./esm/util/tracks.js",
+    "./util/translateTranscript": "./esm/util/translateTranscript.js",
     "./util/tss-react": "./esm/util/tss-react/index.js",
     "./util/tss-react/types": "./esm/util/tss-react/types.js",
     "./util/types": "./esm/util/types/index.js",
     "./util/types/data": "./esm/util/types/data.js",
     "./util/types/mst": "./esm/util/types/mst.js",
+    "./util/unknownSnapshotKeys": "./esm/util/unknownSnapshotKeys.js",
     "./util/unzip": "./esm/util/unzip.js",
     "./util/useEventCallback": "./esm/util/useEventCallback.js",
     "./util/useFetch": "./esm/util/useFetch.js",
@@ -232,10 +281,12 @@
     "./util/usePointerDrag": "./esm/util/usePointerDrag.js",
     "./util/useResizeDrag": "./esm/util/useResizeDrag.js",
     "./util/useRowVirtualScroll": "./esm/util/useRowVirtualScroll.js",
+    "./util/viewHighlights": "./esm/util/viewHighlights.js",
     "./util/viewStatus": "./esm/util/viewStatus.js",
     "./util/virtualRange": "./esm/util/virtualRange.js",
     "./util/wheelZoom": "./esm/util/wheelZoom.js",
-    "./util/whenViewSettled": "./esm/util/whenViewSettled.js"
+    "./util/whenViewSettled": "./esm/util/whenViewSettled.js",
+    "./util/withLaunchInput": "./esm/util/withLaunchInput.js"
   },
   "files": [
     "esm"
@@ -246,29 +297,29 @@
     "@emotion/serialize": "^1.3.3",
     "@emotion/utils": "^1.4.2",
     "@floating-ui/react": "^0.27.20",
-    "@gmod/bgzf-filehandle": "^6.6.0",
-    "@gmod/range-cache-filehandle": "^1.4.0",
+    "@gmod/bgzf-filehandle": "^6.7.0",
+    "@gmod/range-cache-filehandle": "^1.5.0",
     "@gmod/shared-read-cache": "^1.7.2",
-    "@jbrowse/jexl": "^4.0.1",
-    "@jbrowse/mobx-state-tree": "^6.5.1",
-    "@jbrowse/quick-lru": "^7.3.5",
+    "@gmod/vcf": "^7.2.0",
+    "@jbrowse/jexl": "^6.0.0",
+    "@jbrowse/mobx-state-tree": "^6.7.0",
+    "@jbrowse/quick-lru": "^8.0.0",
     "@leeoniya/ufuzzy": "^1.0.19",
-    "@mui/icons-material": "^9.3.1",
-    "@mui/material": "^9.3.1",
-    "@mui/system": "^9.3.0",
-    "@mui/x-data-grid": "^9.12.0",
+    "@mui/icons-material": "^9.4.0",
+    "@mui/material": "^9.4.0",
+    "@mui/system": "^9.4.0",
+    "@mui/x-data-grid": "^9.14.0",
     "canvas-sequencer-ts": "^3.1.3",
     "compare-versions": "^6.1.1",
-    "dompurify": "^3.4.14",
-    "generic-filehandle2": "^2.4.0",
+    "dompurify": "^3.4.16",
+    "generic-filehandle2": "^2.5.0",
     "idb": "^8.0.3",
-    "mobx": "^7.0.3",
+    "mobx": "^7.0.5",
     "mobx-react": "^10.0.2",
-    "pako-esm2": "^2.0.2",
     "rxjs": "^7.8.2",
-    "source-map-js": "^1.2.1",
-    "@jbrowse/add-track-core": "^5.0.0-beta.1",
-    "@jbrowse/render-core": "^5.0.0-beta.1"
+    "source-map-js": "^1.2.2",
+    "@jbrowse/add-track-core": "^5.0.0-beta.11",
+    "@jbrowse/render-core": "^5.0.0-beta.11"
   },
   "peerDependencies": {
     "react": ">=19.0.0",

package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts

@@ -1,2 +0,0 @@
-import type { BaseProps } from '../types.tsx';
-export default function Position(props: BaseProps): import("react").JSX.Element;

package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js

@@ -1,8 +0,0 @@
-import { Fragment as _Fragment, jsx as _jsx } from "react/jsx-runtime";
-import { assembleLocString } from '../../util/index.js';
-import { getStrandStr } from '../util.js';
-export default function Position(props) {
-    const { feature } = props;
-    const loc = assembleLocString(feature);
-    return _jsx(_Fragment, { children: `${loc} ${getStrandStr(feature.strand)}` });
-}

package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts

@@ -1,8 +0,0 @@
-import type { BaseFeatureWidgetModel } from '../stateModelFactory.ts';
-import type { BaseCardProps, Descriptors, FeatureFormatter } from '../types.tsx';
-export interface BaseInputProps extends BaseCardProps {
-    omit?: string[];
-    model: BaseFeatureWidgetModel;
-    descriptions?: Descriptors;
-    formatter?: FeatureFormatter;
-}

package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts

@@ -1,80 +0,0 @@
-declare const _default: {
-    source: string;
-    type: string;
-    start: number;
-    end: number;
-    strand: number;
-    phase: number;
-    refName: string;
-    id: string;
-    dbxref: string[];
-    name: string;
-    description: string;
-    gbkey: string;
-    gene: string;
-    gene_biotype: string;
-    gene_synonym: string[];
-    subfeatures: {
-        source: string;
-        type: string;
-        start: number;
-        end: number;
-        strand: number;
-        phase: number;
-        refName: string;
-        id: string;
-        parent: string;
-        dbxref: string[];
-        name: string;
-        gbkey: string;
-        gene: string;
-        product: string;
-        tag: string;
-        transcript_id: string;
-        subfeatures: ({
-            source: string;
-            type: string;
-            start: number;
-            end: number;
-            strand: number;
-            phase: number;
-            refName: string;
-            parent: string;
-            dbxref: string[];
-            gbkey: string;
-            gene: string;
-            product: string;
-            tag: string;
-            transcript_id: string;
-            uniqueId: string;
-            parentId: string;
-            id?: undefined;
-            name?: undefined;
-            protein_id?: undefined;
-        } | {
-            transcript_id?: undefined;
-            source: string;
-            type: string;
-            start: number;
-            end: number;
-            strand: number;
-            phase: number;
-            refName: string;
-            id: string;
-            parent: string;
-            dbxref: string[];
-            name: string;
-            gbkey: string;
-            gene: string;
-            product: string;
-            protein_id: string;
-            tag: string;
-            uniqueId: string;
-            parentId: string;
-        })[];
-        uniqueId: string;
-        parentId: string;
-    }[];
-    uniqueId: string;
-};
-export default _default;