@jbrowse/core 5.0.0-beta.10 → 5.0.0-beta.11

package/README.md

@@ -99,6 +99,19 @@ historically drifted.
 
 [Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/bandLayout.ts)
 
+### baseDisplayConfig
+
+The base's entry for this display, hydrated, which a reset returns to and "is
+this the reader's" compares against: the config.json's, or the one a track the
+session owns was added with; empty in a session that keeps no base.
+
+```js
+// type signature
+(self: object) => Record<string, unknown>
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/baseDisplayConfig.ts)
+
 ### BinStep
 
 Place every feature in a genome-aligned bin of `step` bp, writing the bin's
@@ -1057,6 +1070,22 @@ steps that follow it read the rows already in section order.
 
 [Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/featureTransforms.ts)
 
+### liftPlot
+
+A draft as the display's config would hold it, through the schema's own lift and
+checks: a shorthand becomes its object, a default falls off, and what a config
+file is refused for throws, a key outside the plot included. The node is never
+attached, so nothing on the display is touched; a display reads its typed
+members off it. The draft is copied first, since MST freezes what it creates
+from.
+
+```js
+// type signature
+(conf: AnyConfigurationModel, draft: Plot) => AnyConfigurationModel
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/plot.ts)
+
 ### ListColumn
 
 A list of rows per row: row `i`'s entries are the rows of `entries` from
@@ -1123,14 +1152,15 @@ the worker.
 ### matedBy
 
 How a record states its other end, or undefined where it states none: the `mate`
-a paired adapter fills (BEDPE, STAR-Fusion), or an `ALT` the breakend and
-symbolic-SV readers resolve. The `mate` step admits exactly the features this
-names one for, so a caller deciding whether links are the picture a track wants
-asks here rather than re-reading the fields.
+a paired adapter fills (BEDPE, STAR-Fusion), an `ALT` the breakend and
+symbolic-SV readers resolve, or a read's `next_ref` and `next_pos`. The `mate`
+step admits exactly the features this names one for, so a caller deciding
+whether links are the picture a track wants asks here rather than re-reading the
+fields.
 
 ```js
 // type signature
-(f: Feature) => "alt" | "mate" | undefined
+(f: Feature) => "alt" | "mate" | "pair" | undefined
 ```
 
 [Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/featureTransforms.ts)
@@ -1228,6 +1258,18 @@ every comparison against it declines.
 
 [Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/thresholdScale.ts)
 
+### parsePlot
+
+The text as a plot, refusing a key the display's plot does not hold. The schema
+is the parser past this point.
+
+```js
+// type signature
+(text: string, keys: readonly string[]) => Plot
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/plot.ts)
+
 ### parseSvAlt
 
 Parse raw (non-assembly-resolved) mate coordinates from a VCF SV feature+alt.
@@ -1253,6 +1295,72 @@ packs each section on its own.
 
 [Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/markEncodingTypes.ts)
 
+### Plot
+
+A display's plot settings as written: a key left out is left alone, and `null`
+resets that setting. Untyped, since a value may be a shorthand the schema lifts,
+and the schema is what judges it.
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/plot.ts)
+
+### PLOT_VOCABULARY
+
+The grammar's settings, by the slot name every display that has one gives it,
+and what each holds: what "Edit plot..." shows and an agent reads as a display's
+`plot`. A display's plot is the ones its config declares (`plotKeysOf`).
+
+```js
+// type signature
+Readonly<Record<string, string>>
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/plot.ts)
+
+### PlotExample
+
+A worked example of a display's plot: the text it fills the editor with, and
+what it does.
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/plot.ts)
+
+### plotKeysOf
+
+The plot keys a display config declares.
+
+```js
+// type signature
+(conf: AnyConfigurationModel) => string[]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/plot.ts)
+
+### plotOf
+
+A display's plot as declared, defaults left off. A list sitting at a default it
+shares with no other display, a default plot's marks, shows its entries, since
+they are what is drawn.
+
+```js
+// type signature
+(conf: AnyConfigurationModel) => Plot
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/plot.ts)
+
+### plotWrites
+
+What applying a draft writes: each setting whose lifted value differs from the
+plot, as the lifted value, and `null` for one it resets. A value spelled another
+way but lifting to the same setting writes nothing. Throws a refusal before
+anything is written.
+
+```js
+// type signature
+(conf: AnyConfigurationModel, draft: Plot) => Record<string, unknown>
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/plot.ts)
+
 ### preProcessConfigSnapshot
 
 A snapshot as `type` admits it: the same lift and checks `type.create` applies,

package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js

@@ -18,11 +18,9 @@ const useStyles = makeStyles()(theme => ({
     },
     fieldSubvalue: {
         wordBreak: 'break-word',
-        maxHeight: 300,
         padding: theme.spacing(0.5),
         border: `1px solid ${theme.palette.action.selected}`,
         boxSizing: 'border-box',
-        overflow: 'auto',
     },
 }));
 /**

package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js

@@ -1,16 +1,27 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import { isValidElement } from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { isValidElement, useState } from 'react';
 import { Link } from '@mui/material';
 import { SanitizedHTML } from '../../ui/index.js';
 import { isObject } from '../../util/index.js';
 import { makeStyles } from '../../util/tss-react/index.js';
+import useMeasure from '../../util/useMeasure.js';
+const CLAMP_HEIGHT = 300;
 const useStyles = makeStyles()(theme => ({
     fieldValue: {
         wordBreak: 'break-word',
-        maxHeight: 300,
         fontSize: 12,
         padding: theme.spacing(0.5),
-        overflow: 'auto',
+        minWidth: 0,
+    },
+    clip: {
+        overflowX: 'auto',
+        overflowY: 'hidden',
+    },
+    clamped: {
+        maxHeight: CLAMP_HEIGHT,
+    },
+    faded: {
+        maskImage: 'linear-gradient(to bottom, black 75%, transparent)',
     },
 }));
 export function isBareUrl(text) {
@@ -29,6 +40,11 @@ export function ValueText({ text }) {
     return isBareUrl(text) ? (_jsx(Link, { href: text, target: "_blank", rel: "noopener noreferrer", children: text })) : (_jsx(SanitizedHTML, { html: text }));
 }
 export default function BasicValue({ value }) {
-    const { classes } = useStyles();
-    return (_jsx("div", { className: classes.fieldValue, children: isValidElement(value) ? value : _jsx(ValueText, { text: valueText(value) }) }));
+    const { classes, cx } = useStyles();
+    const [expanded, setExpanded] = useState(false);
+    const [ref, { height }] = useMeasure('height');
+    const overflows = height !== undefined && height > CLAMP_HEIGHT;
+    return (_jsxs("div", { className: classes.fieldValue, children: [_jsx("div", { className: cx(classes.clip, !expanded && classes.clamped, !expanded && overflows && classes.faded), children: _jsx("div", { ref: ref, children: isValidElement(value) ? (value) : (_jsx(ValueText, { text: valueText(value) })) }) }), overflows ? (_jsx(Link, { component: "button", variant: "caption", onClick: () => {
+                    setExpanded(v => !v);
+                }, children: expanded ? 'Show less' : 'Show more' })) : null] }));
 }

package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js

@@ -1,5 +1,4 @@
 import { pathSubject, printCondition } from '@jbrowse/jexl';
-import { activeJexlFilters } from '../../util/jexlFilters.js';
 import { ensureJexlPrefix } from '../../util/jexlStrings.js';
 import { getNotificationSink } from '../../util/sessionServices.js';
 const MAX_LABEL_VALUE = 30;
@@ -26,17 +25,17 @@ export function filterByValueItems(display, path, value) {
     const text = String(value);
     const shown = text.length > MAX_LABEL_VALUE ? `${text.slice(0, MAX_LABEL_VALUE)}…` : text;
     const add = (op) => () => {
-        const previous = display.filterSetting;
+        const previous = display.configuredFilters();
         const line = printCondition({
             subject: pathSubject('feature', path),
             op,
             value,
         });
-        display.setFilter([...activeJexlFilters(display), ensureJexlPrefix(line)]);
+        display.setFilter([...previous, ensureJexlPrefix(line)]);
         getNotificationSink(display).notify('Filter added', 'info', {
             name: 'Undo',
             onClick: () => {
-                display.setFilter(previous && [...previous]);
+                display.setFilter(previous);
             },
         });
     };

package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js

@@ -18,13 +18,16 @@ function processFeatureData(children, feature) {
     // translations if included)
     const featureType = feature.type?.toLowerCase();
     const isMatureProteinRegion = featureType === 'mature_protein_region_of_cds';
+    const ofType = (type) => children.filter(sub => sub.type?.toLowerCase() === type);
+    // A frameshift polyprotein's CDS carries its reading frames as CDS rows beside
+    // its cleavage products; a single-frame one has only the products.
+    const codingRows = ofType('cds');
     const cds = isMatureProteinRegion
         ? [{ start: 0, end: feature.end - feature.start, type: 'CDS' }]
-        : filterSuccessiveElementsWithSameStartAndEndCoord(children.filter(sub => {
-            const type = sub.type?.toLowerCase();
-            return type === 'cds' || type === 'mature_protein_region_of_cds';
-        }));
-    const exons = filterSuccessiveElementsWithSameStartAndEndCoord(children.filter(sub => sub.type?.toLowerCase() === 'exon'));
+        : filterSuccessiveElementsWithSameStartAndEndCoord(codingRows.length > 0
+            ? codingRows
+            : ofType('mature_protein_region_of_cds'));
+    const exons = filterSuccessiveElementsWithSameStartAndEndCoord(ofType('exon'));
     // annotated UTRs are deliberately not read: a UTR is just the exonic sequence
     // outside the CDS, so the renderer derives the split from cds+exons. Trusting
     // the annotation meant a transcript that named only one of its UTRs lost the

package/esm/CorePlugin.js

@@ -1,10 +1,40 @@
+import { trackTypeForAdapter } from '@jbrowse/add-track-core';
 import { configSchema, stateModelFactory } from './BaseFeatureWidget/index.js';
 import Plugin from './Plugin.js';
 import CytobandAdapterF from './data_adapters/CytobandAdapter/index.js';
 import WidgetType from './pluggableElementTypes/WidgetType.js';
 import * as coreRpcMethods from './rpc/coreRpcMethods.js';
-import { installFormatGuessers } from './util/formatGuessers.js';
+import { guessTrackConfFromTable } from './util/formatGuessers.js';
+import { getFileName } from './util/getFileName.js';
 import { lazyWithPreload } from './util/lazyWithPreload.js';
+import { addAdapterGuesser, addTrackTypeGuesser } from './util/tracks.js';
+/**
+ * Guess every format `@jbrowse/add-track-core`'s table describes — the same
+ * table `@jbrowse/cli`'s `add-track` reads, so a file resolves to the same
+ * adapter config in the app and on the command line.
+ *
+ * Whether a build can open a format is decided by `hasAdapterType`, not by the
+ * table: guessing `BamAdapter` in a build with no alignments plugin writes a
+ * track config that fails at render. A plugin therefore registers its adapters
+ * and nothing else — there is no format list to keep in step. ADR-077.
+ *
+ * `CorePlugin` installs this first, so any `addAdapterGuesser` a plugin
+ * registers is later in the chain and wins over the table. That is how a format
+ * the table cannot express is added, and how a third-party plugin claims one.
+ */
+// #region installFormatGuessers
+function installFormatGuessers(pluginManager) {
+    addAdapterGuesser(pluginManager, (file, index, adapterHint) => {
+        const adapter = guessTrackConfFromTable(file, index, adapterHint)?.adapter;
+        return adapter && pluginManager.hasAdapterType(adapter.type)
+            ? adapter
+            : undefined;
+    });
+    addTrackTypeGuesser(pluginManager, (adapterName, file) => pluginManager.hasAdapterType(adapterName)
+        ? trackTypeForAdapter(adapterName, file && getFileName(file))
+        : undefined);
+}
+// #endregion
 // the core plugin, which registers types that ALL JBrowse applications are
 // expected to need.
 export default class CorePlugin extends Plugin {
@@ -19,6 +49,7 @@ export default class CorePlugin extends Plugin {
         pluginManager.addWidgetType(() => {
             return new WidgetType({
                 name: 'BaseFeatureWidget',
+                discardOnClose: true,
                 heading: 'Feature details',
                 configSchema,
                 stateModel: stateModelFactory(pluginManager),