@apollo-annotation/jbrowse-plugin-apollo 0.3.5 → 0.3.7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.esm.js +6964 -4598
- package/dist/index.esm.js.map +1 -1
- package/dist/jbrowse-plugin-apollo.cjs.development.js +6610 -4261
- package/dist/jbrowse-plugin-apollo.cjs.development.js.map +1 -1
- package/dist/jbrowse-plugin-apollo.cjs.production.min.js +1 -1
- package/dist/jbrowse-plugin-apollo.cjs.production.min.js.map +1 -1
- package/dist/jbrowse-plugin-apollo.umd.development.js +11563 -7493
- package/dist/jbrowse-plugin-apollo.umd.development.js.map +1 -1
- package/dist/jbrowse-plugin-apollo.umd.production.min.js +1 -1
- package/dist/jbrowse-plugin-apollo.umd.production.min.js.map +1 -1
- package/package.json +4 -4
- package/src/ApolloInternetAccount/addMenuItems.ts +23 -2
- package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +1 -0
- package/src/ApolloInternetAccount/components/LoginButtons.tsx +1 -1
- package/src/ApolloInternetAccount/components/LoginIcons.tsx +1 -1
- package/src/ApolloInternetAccount/configSchema.ts +1 -1
- package/src/ApolloInternetAccount/model.ts +11 -10
- package/src/ApolloJobModel.ts +1 -1
- package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts +8 -6
- package/src/ApolloRefNameAliasAdapter/index.ts +2 -2
- package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts +4 -4
- package/src/ApolloSequenceAdapter/index.ts +1 -1
- package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts +8 -7
- package/src/ApolloTextSearchAdapter/index.ts +1 -1
- package/src/BackendDrivers/BackendDriver.ts +7 -7
- package/src/BackendDrivers/CollaborationServerDriver.ts +14 -10
- package/src/BackendDrivers/DesktopFileDriver.ts +11 -10
- package/src/BackendDrivers/InMemoryFileDriver.ts +10 -6
- package/src/ChangeManager.ts +15 -11
- package/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx +8 -7
- package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +35 -14
- package/src/FeatureDetailsWidget/AttributeKey.tsx +50 -0
- package/src/FeatureDetailsWidget/AttributeKeySelector.tsx +104 -0
- package/src/FeatureDetailsWidget/Attributes.tsx +215 -367
- package/src/FeatureDetailsWidget/BasicInformation.tsx +6 -5
- package/src/FeatureDetailsWidget/DefaultAttributeEditor.tsx +104 -0
- package/src/FeatureDetailsWidget/DefaultAttributeViewer.tsx +22 -0
- package/src/FeatureDetailsWidget/FeatureDetailsNavigation.tsx +4 -4
- package/src/FeatureDetailsWidget/NumberTextField.tsx +1 -1
- package/src/FeatureDetailsWidget/Sequence.tsx +2 -2
- package/src/FeatureDetailsWidget/StringTextField.tsx +1 -1
- package/src/FeatureDetailsWidget/TranscriptSequence.tsx +15 -23
- package/src/FeatureDetailsWidget/TranscriptWidgetEditLocation.tsx +950 -196
- package/src/FeatureDetailsWidget/TranscriptWidgetSummary.tsx +8 -4
- package/src/FeatureDetailsWidget/model.ts +8 -3
- package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +7 -7
- package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +59 -72
- package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +253 -60
- package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +52 -6
- package/src/LinearApolloDisplay/glyphs/Glyph.ts +16 -8
- package/src/LinearApolloDisplay/stateModel/base.ts +81 -10
- package/src/LinearApolloDisplay/stateModel/index.ts +4 -3
- package/src/LinearApolloDisplay/stateModel/layouts.ts +8 -39
- package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +63 -46
- package/src/LinearApolloDisplay/stateModel/rendering.ts +60 -31
- package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx +226 -0
- package/src/LinearApolloSixFrameDisplay/components/TrackLines.tsx +32 -0
- package/src/LinearApolloSixFrameDisplay/components/index.ts +2 -0
- package/src/LinearApolloSixFrameDisplay/configSchema.ts +7 -0
- package/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts +940 -0
- package/src/LinearApolloSixFrameDisplay/glyphs/Glyph.ts +63 -0
- package/src/LinearApolloSixFrameDisplay/glyphs/index.ts +1 -0
- package/src/LinearApolloSixFrameDisplay/index.ts +2 -0
- package/src/LinearApolloSixFrameDisplay/stateModel/base.ts +302 -0
- package/src/LinearApolloSixFrameDisplay/stateModel/index.ts +27 -0
- package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts +252 -0
- package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts +368 -0
- package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts +201 -0
- package/src/LinearApolloSixFrameDisplay/types.ts +1 -0
- package/src/OntologyManager/OntologyStore/fulltext.test.ts +1 -1
- package/src/OntologyManager/OntologyStore/fulltext.ts +8 -3
- package/src/OntologyManager/OntologyStore/index.test.ts +3 -1
- package/src/OntologyManager/OntologyStore/index.ts +19 -14
- package/src/OntologyManager/OntologyStore/indexeddb-schema.ts +6 -5
- package/src/OntologyManager/OntologyStore/indexeddb-storage.ts +11 -5
- package/src/OntologyManager/index.ts +12 -7
- package/src/OntologyManager/util.ts +3 -2
- package/src/TabularEditor/HybridGrid/ChangeHandling.ts +2 -2
- package/src/TabularEditor/HybridGrid/Feature.tsx +13 -7
- package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx +1 -1
- package/src/TabularEditor/HybridGrid/HybridGrid.tsx +3 -2
- package/src/TabularEditor/HybridGrid/ToolBar.tsx +1 -1
- package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts +114 -22
- package/src/TabularEditor/TabularEditorPane.tsx +1 -1
- package/src/TabularEditor/model.ts +2 -2
- package/src/TabularEditor/types.ts +5 -2
- package/src/components/AddAssembly.tsx +182 -179
- package/src/components/AddAssemblyAliases.tsx +114 -0
- package/src/components/AddChildFeature.tsx +8 -10
- package/src/components/AddFeature.tsx +216 -44
- package/src/components/AddRefSeqAliases.tsx +14 -12
- package/src/components/CopyFeature.tsx +10 -11
- package/src/components/CreateApolloAnnotation.tsx +342 -158
- package/src/components/DeleteAssembly.tsx +9 -8
- package/src/components/DeleteFeature.tsx +362 -14
- package/src/components/Dialog.tsx +1 -1
- package/src/components/DownloadGFF3.tsx +31 -11
- package/src/components/FilterFeatures.tsx +6 -4
- package/src/components/FilterTranscripts.tsx +86 -0
- package/src/components/ImportFeatures.tsx +7 -6
- package/src/components/LogOut.tsx +5 -4
- package/src/components/ManageChecks.tsx +9 -8
- package/src/components/ManageUsers.tsx +11 -10
- package/src/components/MergeExons.tsx +193 -0
- package/src/components/MergeTranscripts.tsx +185 -0
- package/src/components/OntologyTermAutocomplete.tsx +5 -5
- package/src/components/OntologyTermMultiSelect.tsx +6 -6
- package/src/components/OpenLocalFile.tsx +4 -3
- package/src/components/SplitExon.tsx +134 -0
- package/src/components/ViewChangeLog.tsx +7 -6
- package/src/components/ViewCheckResults.tsx +8 -7
- package/src/components/index.ts +3 -0
- package/src/config.ts +5 -0
- package/src/extensions/annotationFromJBrowseFeature.test.ts +1 -0
- package/src/extensions/annotationFromJBrowseFeature.ts +13 -10
- package/src/extensions/annotationFromPileup.ts +104 -94
- package/src/index.ts +33 -50
- package/src/makeDisplayComponent.tsx +90 -37
- package/src/session/ClientDataStore.ts +21 -17
- package/src/session/session.ts +46 -39
- package/src/types.ts +4 -4
- package/src/util/annotationFeatureUtils.ts +66 -1
- package/src/util/copyToClipboard.ts +21 -0
- package/src/util/glyphUtils.ts +49 -0
- package/src/util/index.ts +5 -3
- package/src/util/loadAssemblyIntoClient.ts +10 -3
- package/src/util/mouseEventsUtils.ts +113 -0
- package/src/ApolloSixFrameRenderer/ApolloSixFrameRenderer.tsx +0 -13
- package/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx +0 -707
- package/src/ApolloSixFrameRenderer/configSchema.ts +0 -7
- package/src/ApolloSixFrameRenderer/index.ts +0 -3
- package/src/SixFrameFeatureDisplay/components/TrackLines.tsx +0 -19
- package/src/SixFrameFeatureDisplay/components/index.ts +0 -1
- package/src/SixFrameFeatureDisplay/configSchema.ts +0 -21
- package/src/SixFrameFeatureDisplay/index.ts +0 -2
- package/src/SixFrameFeatureDisplay/stateModel.ts +0 -443
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import { gffColumnToInternal, gffToInternal } from '@apollo-annotation/shared'
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import { getEnv } from '@jbrowse/core/util'
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import {
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Button,
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DialogActions,
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FormControl,
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InputLabel,
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MenuItem,
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Select,
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TextField,
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} from '@mui/material'
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import { observer } from 'mobx-react'
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import React, { useState } from 'react'
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import { type ApolloSessionModel } from '../session'
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const customKeyName = 'Custom'
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const gffKeys: Record<string, string | undefined> = {
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[customKeyName]: 'custom',
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}
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for (const [value, key] of Object.entries(gffToInternal)) {
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gffKeys[`GFF ${key}`] = value
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}
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for (const [value, key] of Object.entries(gffColumnToInternal)) {
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gffKeys[`GFF ${key}`] = value
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}
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export const AttributeKeySelector = observer(function AttributeKeySelector({
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setKey,
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session,
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}: {
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setKey: (newKey?: string) => void
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session: ApolloSessionModel
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}) {
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const { pluginManager } = getEnv(session)
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const reservedKeys = pluginManager.evaluateExtensionPoint(
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'Apollo-ReservedAttributeKeys',
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gffKeys,
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) as Record<string, string | undefined>
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const firstKey = Object.keys(reservedKeys).at(0) ?? customKeyName
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const [selectedKey, setSelectedKey] = useState<string>(firstKey)
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const [customKey, setCustomKey] = useState<string>()
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const isCustom = selectedKey === customKeyName
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function handleSubmit(event: React.FormEvent<HTMLFormElement>) {
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event.preventDefault()
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if (isCustom) {
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setKey(customKey)
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return
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}
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setKey(reservedKeys[selectedKey])
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}
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function handleCancel() {
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setKey()
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}
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return (
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<form onSubmit={handleSubmit}>
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<div style={{ display: 'flex', flexDirection: 'column', margin: 8 }}>
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<FormControl variant="outlined">
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<InputLabel id="attribute-key-select-label">Key</InputLabel>
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<Select
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labelId="attribute-key-select-label"
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value={selectedKey}
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label="Key"
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onChange={(event) => {
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setSelectedKey(event.target.value)
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}}
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>
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{Object.keys(reservedKeys).map((val) => (
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<MenuItem key={val} value={val}>
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{val}
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</MenuItem>
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))}
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</Select>
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</FormControl>
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{isCustom ? (
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<TextField
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label="Attribute key"
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variant="outlined"
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id="attributeKey"
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onChange={(event) => {
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setCustomKey(event.target.value)
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}}
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/>
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) : null}
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</div>
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<DialogActions>
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<Button
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color="primary"
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variant="contained"
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type="submit"
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disabled={isCustom && !customKey}
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>
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Add
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</Button>
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<Button variant="outlined" onClick={handleCancel}>
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Cancel
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</Button>
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</DialogActions>
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</form>
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)
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})
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